Method of determining viral or bacterial properties of infection

Abstract

The present invention relates to in vitro or ex vivo methods and kits for determining viral or bacterial properties of infection based on a biological sample of a patient by identifying changes in expression levels of multiple biomarkers. In particular, the method comprises the steps of: (a) measuring the expression of at least one viral target gene and at least one bacterial target gene selected from the group consisting of OLAH, FAM20A, ILIR2, MMP8, RETN and SLCIA2; (b) comparing the expression measured in step (a) with reference expression values for these target genes; and (c) determining whether the infection is a viral or bacterial property based on the result of the comparison.

Description

Technical Field

[0001] The present invention relates to the technical field of methods and kits for in vitro diagnosis. In particular, the subject of the present invention is a method and kit for determining the nature of an infection (i.e., a viral infection or a bacterial infection) from a biological sample from a subject by identifying changes in the expression levels of multiple biomarkers. Background Art

[0002] Viruses and bacteria interact with different recognition receptors present on the surface of leukocytes in the circulating blood. This interaction leads to host-specific transcriptional events that modulate the immune response (Takeuchi et al., 2010). Thus, differential activation of host transcriptional programs generates unique transcriptomic signatures, making it possible to distinguish between viral and bacterial causes.

[0003] In this context, analysis of the host transcriptome profile could provide an indirect method of detecting the nature of the infection, thus complementing direct methods such as culture or nucleic acid amplification (Ramilo et al., 2009). This also represents a special interest, as viral infections are frequently responsible for fever of unknown cause, especially in young children.

[0004] Furthermore, given that it is common hospital practice to routinely administer antibiotics as a preventive measure to febrile patients until the results of culture tests are available, this unfortunately means that many viral infections are mistakenly treated with antimicrobial drugs.

[0005] Furthermore, it has been shown that over-administration of antibiotics has led to increased bacterial resistance not only at an individual level, but also at a broader global level. Thus, the misuse and over-use of existing antibiotics actively contributes to the development of antibiotic resistance (Fauci et al., 2014). Furthermore, a certain number of patients are inappropriately treated with high levels of antibiotics due to the difficulty in distinguishing between viral, bacterial or non-infectious etiologies.

[0006] Therefore, early differentiation between patients with viral infections and those with bacterial infections may allow for more precise and sophisticated management of said patients while significantly reducing unnecessary antibiotic use.

[0007] In recent years, there has been increasing interest in discovering biomarkers that can distinguish viral and bacterial infections with similar initial clinical phenotypes based on whole blood gene expression. For example, the authors described that the transcriptional profiles of febrile virus-positive children and children with febrile acute bacterial infections were different from those of febrile virus-positive and -negative children (Hu et al., 2013).

[0008] Therefore, there are increasing efforts to develop host biomarkers to distinguish viral from bacterial infections, especially in the setting of febrile children (D. Brown et al., 2016).

[0009] This interest stems not only from the need to differentiate between life-threatening bacterial and viral infections, but also to avoid unnecessary prescription of empirical antibiotic therapy, regardless of the severity of the infection. As mentioned earlier, the overconsumption of antibiotics worldwide is accelerating antibiotic resistance (AMR), which is considered by the World Health Organization to be one of the greatest threats to human health in the coming years.

[0010] For example, WO 2018 / 011316 describes a method for identifying a subject presenting a bacterial infection. In particular, the method is to detect the expression regulation of two to ten genes selected from the following gene markers in an mRNA sample: IFI44L, FAM89A, IFI27L, IFTI1, RSAD2, IFIT3, OTOF, IFIT2, EPSTI1, SERPING1, OAS1, IFI6, HLA-DRB6, HBZ, HS.386275, EIF2AK2, IFIT1L, FCER1A, C21ORF7, GYPE, GYPB, HBM, EIF1AY, LOC649143, HBD, FBX07, KCNMA1, MERTK, EBI3, UPB1, EMR1, PTPN20, TMEM119, SLPI, S100P and PI3.

[0011] Other authors have also described differentiating viral and bacterial infections based on transcriptome signatures. In particular, 45 mRNA signatures were identified to distinguish viral or bacterial infections from an independent cohort of 623 patients presenting with bacterial, viral, mixed, or non-infectious diseases (ELTsalik et al., 2021).

[0012] However, further efforts are needed to evaluate the accuracy and diagnostic utility of biomarkers, especially transcriptomic biomarkers, before they can be translated into clinically applicable tests to determine the viral or bacterial source of infection.

[0013] Therefore, while solutions exist, there is a need to develop new transcriptomic markers that can identify the nature of the infection and thus distinguish between viral and bacterial etiologies. This is particularly important to improve patient management (especially in the case of febrile children), reduce the inappropriate use of antibiotics and help combat the development of antibiotic resistance. Summary of the invention

[0014] The present invention is based on the identification of transcriptome markers associated with viral and bacterial infections. The method according to the invention allows the identification of the nature of the infection in a subject diagnosed with or suspected of having an infection in order to select the most appropriate treatment. Fully advantageously, the method according to the invention makes it possible to exclude the presence of bacterial infections and to limit the inappropriate use of antibiotics.

[0015] Thus, a first aspect of the invention relates to an in vitro or ex vivo method for determining the nature of an infection in a subject by measuring changes in the expression levels of at least one target viral gene and at least one target bacterial gene selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2 from a biological sample of the subject.

[0016] Therefore, the method according to the present invention uses a biological sample from a subject who is or may be infected, thus comprising the following steps:

[0017] (a) measuring the expression of at least one target viral gene and at least one target bacterial gene selected from the group consisting of target bacterial genes OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2,

[0018] (b) comparing the expression measured in step (a) with a predetermined reference expression value of the target gene, and

[0019] (c) draw conclusions about the viral or bacterial nature of the infection based on the comparison.

[0020] The advantages of the method according to the invention are numerous, in particular:

[0021] (i) accurately distinguished the viral or bacterial nature of the infection with a high level of performance, with most biomarker combinations having an area under the curve (AUC) performance of at least 0.85, or sometimes even at least 0.90,

[0022] (ii) exclude the presence of bacterial infection,

[0023] (iii) rapidly identifying significant changes in gene expression levels, in particular by using an automated system or detection kit according to the invention,

[0024] (iv) avoiding false positive identifications corresponding to the presence of non-pathogenic bacteria or viruses naturally present in the subject,

[0025] (v) Allows identification of the nature of an infection when the pathogen is unidentifiable or unavailable. Specifically, the method does not require direct contact with the pathogen, only a biological sample from the subject.

[0026] After extensive research, the inventors, to their credit, identified a transcriptome signature whose expression was characteristic of the viral or bacterial nature of the infection and used the measurement of this expression change to identify the source of the infection. This is highly noteworthy because it is particularly difficult to identify effective target bacterial genes that, when combined with target viral genes, specifically allow for the exclusion of the presence of a bacterial infection.

[0027] Identification of the nature of the infection has certain benefits, in particular it can support clinicians in more appropriate and personalized treatment, especially when the infection is viral or when the presence of a bacterial infection has been excluded, avoiding unnecessary prescription of antibiotics.

[0028] Preferably, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from host viral genes involved in a proinflammatory cytokine pathway, an interferon pathway, a Toll-like receptor (TLR) signaling pathway, a RIG-I-like receptor (RLR) signaling pathway, and a class II major histocompatibility complex (MHC)-mediated antigen presentation pathway, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN, and SLC1A2.

[0029] Preferably, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from host viral genes involved in the interferon pathway and the class II MHC-mediated antigen presentation pathway, and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0030] Preferably, the measuring step (a) comprises or consists of measuring at least one target viral gene, the target viral gene being selected from host viral genes involved in the interferon pathway, and in particular, the gene being selected from target viral genes IFI27, IFN-α, IFN-β, IFN-ε, IFN-κ, IFN-ω, IFN-γ, IFNL1, IFNL2, IFNL3, ADAR1, IFIT1, IFIT2, IFIT3, IFIT5, IFI44L, ISG15, ISG20, MDA5, OAS1, OAS 2. OAS3, OASL, PARP12, PKR, RIG-I, RNaseL, TRIM25, ZAP, ZCCHC3, ZNFX1, RBBP6, SHFL, TRIM22, TRIM25, TRIM32, TRIM69, Viperin, HERC1, HERC2, HERC3, HERC4, HERC5, HERC6, and combinations thereof, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN, and SLC1A2.

[0031] Preferably, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from RSAD2, IFI27, OAS1, IFIT1, IFI44L, SIGLEC1, ISG15 and HERC6, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0032] Preferably, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from RSAD2, IFI27, OAS1, IFIT1, IFI44L, SIGLEC1, ISG15 and HERC6, and measuring the target bacterial gene FAM20A and optionally at least one other target bacterial gene selected from OLAH, IL1R2, MMP8, RETN and SLC1A2.

[0033] Preferably, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from ISG15 and OAS1, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0034] Preferably, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from SIGLEC1, ISG15 and HERC6, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2. More preferably, the measuring step (a) comprises or consists of measuring the target viral genes SIGLEC1, ISG15 and HERC6, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0035] Preferably, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from RSAD2, IFI27, OAS1, IFIT1, IFI44L, SIGLEC1, ISG15 and HERC6, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0036] Preferably, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from SIGLEC1, ISG15 and HERC6, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0037] Preferably, step (a) comprises or consists of measuring at least one target viral gene selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0038] Preferably, step (a) comprises measuring the expression of the target viral gene IFI27 and the target bacterial gene OLAH, and more preferably also measuring the expression of the target bacterial gene FAM20A.

[0039] Preferably, the measuring step (a) comprises or consists of measuring the expression of two target viral genes selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, and measuring the expression of two target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from OLAH, FAM20A, IL1R2 and MMP8.

[0040] Preferably, the measuring step (a) comprises or consists of measuring the expression of two to five target viral genes selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and measuring the expression of three or four target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from OLAH, FAM20A, IL1R2 and MMP8.

[0041] Preferably, the measuring step (a) comprises or consists of measuring the expression of the target viral gene IFI27 and optionally at least one other viral gene selected from SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, and the expression of at least two target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from OLAH, FAM20A, IL1R2 and MMP8.

[0042] Preferably, step (a) comprises or consists of measuring at least one target viral gene selected from SIGLEC1, ISG15 and HERC6, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from IL1R2, OLAH and FAM20A.

[0043] Preferably, step (a) comprises or consists of measuring at least one target viral gene selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, and measuring the target bacterial gene OLAH and at least one other target bacterial gene selected from FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from FAM20A, IL1R2 and MMP8.

[0044] Preferably, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, and the target bacterial gene FAM20A and at least one other target bacterial gene selected from OLAH, IL1R2, MMP8, RETN and SLC1A2, preferably OLAH, IL1R2 and MMP8.

[0045] Preferably, step (a) comprises or consists of measuring the expression of the target viral gene IFI27, another target viral gene selected from HERC6, SIGLEC1, IFI44L and ISG15, the target bacterial gene FAM20A and another target bacterial gene selected from OLAH and IL1R2.

[0046] Preferably, step (a) comprises or consists of measuring the expression of the target viral gene IFI27, two other target viral genes selected from SIGLEC1, HERC6, OAS1 and IFIT1, the target bacterial gene FAM20A and another target bacterial gene selected from OLAH, IL1R2 and MMP8.

[0047] Preferably, step (a) comprises or consists of measuring the expression of target viral genes IFI27 and SIGLEC1, another target viral gene selected from IFIT1, HERC6, ISG15 and ISG15, target bacterial genes FAM20A and MMP8 and another target bacterial gene selected from OLAH and IL1R2.

[0048] Preferably, step (a) comprises or consists of measuring the expression of target viral genes IFI27 and SIGLEC1, two other target viral genes selected from IFIT1, OAS1, HERC6 and ISG15, target bacterial genes FAM20A and MMP8 and another target bacterial gene selected from OLAH and IL1R2.

[0049] Preferably, step (a) consists in measuring a combination of target viral and bacterial genes selected from the target gene combinations listed in Tables 6 to 12 and whose AUC for the model for determining the viral or bacterial nature of the infection is at least 0.90.

[0050] Preferably, in the method according to the invention, the reference expression value of the target gene corresponds to the corresponding expression of said target gene in a reference biological sample obtained from a subject suffering from a bacterial infection. Thus, it can be judged that the infection is of a viral nature when the expression level of the target gene at the mRNA transcript level is compared relative to the corresponding reference value, highlighting at least one expression change selected from the group consisting of:

[0051] - Overexpression of SIGLEC1,

[0052] - Overexpression of ISG15,

[0053] - Overexpression of HERC6,

[0054] - Overexpression of RSAD2,

[0055] - Overexpression of IFI27,

[0056] - Overexpression of OAS1,

[0057] - Overexpression of IFIT1, and

[0058] - Overexpression of IFI44L,

[0059] and at least one other expression change selected from the group consisting of:

[0060] - Low expression of SLC1A2,

[0061] - Low expression of IL1R2,

[0062] - Low expression of FAM20A,

[0063] - Low expression of OLAH,

[0064] -low expression of RETN, and

[0065] -Low expression of MMP8.

[0066] More preferably, in the method according to the present invention, the reference expression value of the target gene corresponds to the corresponding expression of the target gene in a reference biological sample obtained from a subject suffering from a viral infection. Thus, it can be judged that the infection is of a bacterial nature when the result of the comparison of the target gene expression shows at least two changes selected from the following:

[0067] - Low expression of SIGLEC1,

[0068] - Low expression of ISG15,

[0069] - Low expression of HERC6,

[0070] - Low expression of RSAD2,

[0071] - Low expression of IFI27,

[0072] - Low expression of OAS1,

[0073] - Low expression of IFIT1, and

[0074] - Low expression of IFI44L,

[0075] and at least one other expression change selected from the group consisting of:

[0076] - Overexpression of SLC1A2,

[0077] - Overexpression of IL1R2,

[0078] - Overexpression of FAM20A,

[0079] - Overexpression of OLAH,

[0080] -Overexpression of RETN, and

[0081] - Overexpression of MMP8.

[0082] Preferably, the method according to the present invention further comprises a step (a') of measuring the expression of at least one additional target gene selected from PI3, EBI3, ADGRE1 and S100P, a step (b') of comparing the expression measured in step (a') with a reference expression value of the additional target gene, and a step (c') of determining whether the infection is viral or bacterial based on the comparison result.

[0083] Preferably, in the method according to the invention, the target gene expression is measured at the mRNA level.

[0084] Preferably, in the method according to the invention, the expression changes are measured by amplification by RT-PCR, preferably quantitative RT-PCR or nested PCR.

[0085] Preferably, in the method according to the invention, said expression is normalized to the expression of one or more housekeeping genes selected from the group consisting of DECR1, HPRT1, PPIB, GAPDH and ACTB.

[0086] Preferably, in the method according to the present invention, the subject is a child, preferably a child under 4 years old, more preferably a child under 4 years old.

[0087] Preferably, in the method according to the present invention, the biological sample is a blood sample, preferably a whole blood sample.

[0088] The present invention also relates to a kit for measuring in vitro or ex vivo the expression of at least one target viral gene selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, the kit comprising a reagent specific for the expression product of the target gene, the reagent being preferably a primer or a probe. The kit is particularly suitable for implementing the method according to the present invention and is therefore able to determine the viral or bacterial nature of the infection from a biological sample of a subject. BRIEF DESCRIPTION OF THE DRAWINGS

[0089] Figure 1 Box plots representing the expression of target genes SIGLEC1, ISG15, HERC6, SLC1A2, IL1R2, FAM20A, OLAH, RETN, and MMP8, obtained from raw RT-PCR values ​​normalized with housekeeping genes DECR1, HPRT1, and PPIB; A: bacterial infection (n=68); B: viral infection (n=123).

[0090] Figure 2 Box plots representing the expression of target genes RSAD2, IFI27, OAS1, IFIT1 and IFI44L obtained from raw RT-PCR values ​​normalized with housekeeping genes DECR1, HPRT1 and PPIB; A: bacterial infection (n=68); B: viral infection (n=123). DETAILED DESCRIPTION

[0091] The transcriptome is the set of RNAs produced by transcription of the genome. Transcriptome analysis allows characterization of the entire or partial transcriptome of a specific tissue or cell type, or comparison of transcriptomes under different experimental or clinical conditions. Pathogens such as viruses and bacteria interact in the host with different recognition receptors present on the surface of leukocytes in the circulating blood. As mentioned earlier, this interaction ensures specific transcriptional events that regulate the immune response, resulting in a specific transcriptome signature.

[0092] Therefore, transcriptome signatures can be a decision support tool based on the analysis of previously selected gene transcripts.

[0093] The first subject of the present invention relates to an in vitro or ex vivo method for determining the viral or bacterial nature of a subject's infection. More specifically, the inventors have determined that demonstrating changes in the expression levels of multiple target genes in a biological sample from a subject that is infected or susceptible to infection can characterize the viral or bacterial nature of the infection. In other words, the method according to the present invention can exclude the presence of a bacterial infection.

[0094] Therefore, the method according to the present invention comprises the following steps:

[0095] (a) measuring the expression of at least one target viral gene and at least one target bacterial gene selected from the group consisting of target bacterial genes OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2 from a biological sample of an infected subject,

[0096] (b) comparing the expression measured in step (a) with a predetermined reference expression value of the target gene, and

[0097] (c) drawing conclusions about the nature of the virus or bacteria with which the subject is infected based on the comparison results.

[0098] The term "target viral gene" refers to a host gene whose expression is deregulated in the presence of a viral infection, ie, a gene whose expression is significantly increased or decreased in the presence of said infection.

[0099] The term "target bacterial gene" refers to a host gene whose expression is deregulated in the presence of a bacterial infection, ie a gene whose expression is significantly increased or decreased in the presence of said infection.

[0100] For the purpose of this specification, the expression "target gene" refers indiscriminately to a target viral gene or a target bacterial gene, unless the context allows it to be clearly identified as a target viral gene or a target bacterial gene.

[0101] The terms "biomarker" and "marker" refer to a biological characteristic that can be objectively measured and that indicates a normal or pathological biological process following the presence of an infection. Thus, for the purposes of the present invention, biomarkers are target viral genes and target bacterial genes, most particularly, transcripts of said target genes.

[0102] In this specification, when referring to measuring the expression of "at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2", this includes the possibility of measuring the expression of multiple target genes, thus in fact comprising all possible combinations of 2-6 target bacterial genes, without having to give an exhaustive list. This applies to all target gene lists introduced by the term "at least" in this specification, thus also involving the measurement of target viral gene expression.

[0103] The term "infected subject" refers to a subject suffering from an infection, in other words, a subject that has been diagnosed as suffering from an infection. The presence of an infection can be diagnosed by any method known to those skilled in the art for reaching such a conclusion. Thus, diagnosis can be made by molecular methods, such as procalcitonin (PCT) protein assay, or by a clinician directly making a diagnosis based on clinical symptoms or signs of the subject.

[0104] Clinical symptoms or signs associated with the presence of infection are also well known to those skilled in the art, for example, headache, pain in a specific part of the body (e.g., abdomen), fever (>38°C) with or without chills, body temperature below 35.5°C, respiratory symptoms selected from the group consisting of cough, sputum, dyspnea, shortness of breath and pleuritic pain; auscultatory findings, nausea with or without vomiting, systolic blood pressure greater than 90 mmHg, heart rate greater than 120 beats / min, symptoms of infection in an organ or organ system selected from the group consisting of respiratory tract infection, digestive tract infection, vaginal infection, meningitis, sepsis, erysipelas, peritonitis, cholangitis, cholecystitis and osteomyelitis.

[0105] Thus, the method according to the invention enables the nature of the infection in said subject to be identified.

[0106] The expression "nature of the infection" refers only to the etiology of the infection, i.e. viral infection or bacterial infection. Thus, the method according to the invention is able to distinguish viral infection from bacterial infection and vice versa. In other words, the method according to the invention is able to exclude the presence of bacterial infection.

[0107] For the purpose of this specification, the term "subject" means a human being, and the subject is preferably a patient. By definition, a patient is a person who has come into contact with a health care professional, particularly a physician, or a medical institution or health care facility.

[0108] The target genes involved in the method of the present invention are well known to those skilled in the art, but it is commendable that the inventors have identified that transcriptome signatures based on changes in the expression of the genes can effectively determine the viral or bacterial nature of the infection.

[0109] Specifically, a person skilled in the art is able to identify a target viral gene for implementing the method of the invention. Similarly, the chromosomal location of the target gene is available in public databases, such as the Ensembl database (GRCh38 / hg38 component).

[0110] Therefore, any target viral gene whose expression is significantly increased or decreased in the presence of infection can be used in the method according to the invention. These genes are known to those skilled in the art.

[0111] Thus, the target viral gene can be selected from genes of the interferon pathway, the proinflammatory cytokine pathway, the Toll-like receptor (TLR) signaling pathway, the RIG-I-like receptor (RLR) signaling pathway, or the class II MHC-mediated antigen presentation pathway.

[0112] Target viral genes of the interferon pathway, in particular interferon-stimulated genes, called ISG genes, are well known to those skilled in the art (Schneider et al., 2014; Yang et al., 2020). As examples of these genes, mention may be made of IFN-α, IFN-β, IFN-ε, IFN-κ, IFN-ω, IFN-γ, IFNL1, IFNL2, IFNL3, ADAR1, IFIT1, IFIT2, IFIT3, IFIT5, IFI27, IFI44L, ISG15, ISG20, MDA5, OAS1, OAS2, OAS3, OASL, PARP12, PKR, RIG-I, RNaseL, RSAD2, RBBP6, SIGLEC1, SHFL, TRIM22, TRIM25, TRIM32, TRIM69, Viperin, ZAP, ZCCHC3 and ZNFX1.

[0113] Target viral genes of the proinflammatory cytokine pathway are also well known to those skilled in the art (Mogensen et al., 2001). As examples of these genes, mention may be made of IFN-α, L-1β, IL-6, IL-1Ra, IL-8, GM-CSF, MIP-1α, MIP-1β, IL-10, IL-1α, TGF-β, TGF-β1, IL-2, IL-4, IL-13, IL-15, IL-3, IL-5, IP10 and SCM-1.

[0114] Therefore, according to a specific embodiment, the measuring step (a) comprises or consists of measuring at least one target viral gene, wherein the target viral gene is selected from host viral genes involved in proinflammatory cytokine pathways, in particular selected from target viral genes TNFα, IL-1β, IL-6, IL-1Ra, IL-8, GM-CSF, MIP-1α, MIP-1β, IL-10, IL-1α, TGF-β, TGF-β1, IL-2, IL-4, IL-13, IL-15, IL-3, IL-5, IP10, SCM-1 and combinations thereof, and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0115] Target viral genes of the Toll-like receptor pathway are also well known to those skilled in the art (Kawasaki et al., 2014), and specifically include native TLR genes, TLR coreceptor genes, TLR regulator genes, TLR signaling inhibitor genes, TLR adaptor genes, and TLR signaling genes.

[0116] As examples of natural TLR genes, mention may in particular be made of the genes TLR3, TLR7, TLR8 and TLR9.

[0117] As examples of TLR coreceptor genes, mention may in particular be made of the genes CD14, LBP, MD1 and MD2.

[0118] As examples of TLR modulator genes, mention may in particular be made of the genes CD300LF, GRP94, PRAT4A, PRAT4B and UNC93B1.

[0119] As examples of TLR signaling inhibitor genes, particular mention may be made of the genes ATF3, AXL, BAMBI, BCL3, BPI, CENTB1, DAK, FLII, HSP10, IRAKM (IRAK3), LGP2 (DHX58), MSK1, MSK2, NLRP12 (NALP12), NFKBIA, NFKBIB, NFKBIE, PECAM1, PIN1, PPP3CA, PPP3CB, PPP3R1, PTPN6, RNF125, RP105, SHIP1, SIGIRR, SIKE, TNFAIP3, TNIP1, TNIP2, TNIP3, TOLLIP, TRAFD1, TRIAD3, TYRO3 and ZCCHC11.

[0120] As examples of TLR adaptor genes, mention may in particular be made of the genes MyD88, RAC1, SARM1, TANK, TIRAP, TRAM (TICAM2) and TRIF (TICAM1).

[0121] As examples of TLR signaling genes, mention may be made in particular of the genes AAMP, ACT1 (TRAF3IP2), AGER, AKT1, BECN1, BTK, CARD6, CARD11, DDX3X, FADD, IKKα, IKKβ, IKKε, IPS1, IRAK1, IRAK4, IRF1, IRF3, IRF5, IRF7, IRF8, IRF9, ITCH, LRRC59, LRRFIP2, MAP2K2, MAP3K7 (TAK1), MAPK1, MDA5 (IFIH1), NAIP5, NAP1, NEMO, NIBP, OTUD5, PKR, PRKRA, RIG-1, RIPK1, RIPK2, RIPK3, STAP2, SUGT1, SYK, TAB1, TAB2, TAB3, TBK1, TBKBP1, TIFA, TRADD, TRAF3, TRAF6, TRIL and WDFY1.

[0122] Therefore, according to a specific embodiment, the measuring step (a) comprises or consists of measuring at least one target viral gene, the target viral gene being selected from host viral genes involved in the TLR receptor signaling pathway, and in particular selected from TLR3, TLR7, TLR8, TLR9, CD14, LBP, MD1, MD2, CD300LF, GRP94, PRAT4A, PRAT4B, UNC93B1 ATF3, AXL, BAMBI, BCL3, BPI, CENTB1, DAK, FLII, HSP10, IRAKM(IRAK3), LGP2(DHX58), MSK1, MSK2, NLR P12(NALP12), NFKBIA, NFKBIB, NFKBIE, PECAM1, PIN1, PPP3CA, PPP3CB, PPP3R1, PTPN6, RNF125, RP105, SHIP1, SIGIRR, SIKE, TNFAIP3, TNIP1, TNIP2, TNIP3, TOLLIP, TRAFD1, TRIAD3, TYRO3, ZCCHC11, MyD88, RAC1, SARM1, TANK, TIRAP, TRAM(TICAM2), TRIF(TICAM1), AAMP, ACT1(TRAF3IP2), AGER, AKT1, BECN1, B TK, CARD6, CARD11, DDX3X, FADD, IKKα, IKKβ, IKKε, IPS1, IRAK1, IRAK4, IRF1, IRF3, IRF5, IRF7, IRF8, IRF9, ITCH, LRRC59, LRRFIP2, MAP2K2, MAP3K7 (TAK1), MAPK1, MDA5 (IFIH1), NAIP5, NAP1, NEMO, NIBP, OTUD5, PKR, PRKRA, RIG-1, RIPK1, RIPK2, RIPK3, STAP2, SUGT1, SYK, TAB1, TAB2, TAB3, TBK1, TBKBP1, TIFA, TRADD, TRAF3, TRAF6, TRIL, WDFY1, and combinations thereof, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN, and SLC1A2.

[0123] Target viral genes of the RIG-I-like receptor signaling pathway are also known to those skilled in the art. Examples that may be mentioned include genes LGP2 (DHX58), MDA5 (IFIH1), RIG-I (DDX58), TRAFD1, CYLD, DAK, DDX60, MFN2, MUL1, OTUD5, PIN1, RNF125, SIKE, TNFAIP3, IPS1, IPS1-HA, PARP13, STING, TOMM70A, TRIM13, TRIM26, TRIM32, and ZDHHC1.

[0124] Therefore, according to a specific embodiment, the measuring step (a) comprises or consists of: measuring at least one target viral gene, wherein the target viral gene is selected from the host viral genes involved in the RLR receptor signaling pathway, and in particular the gene is selected from the target viral genes LGP2 (DHX58), MDA5 (IFIH1), RIG-I (DDX58), TRAFD1, CYLD, DAK, DDX60, MFN2, MUL1, OTUD5, PIN1, RNF125, SIKE, TNFAIP3, IPS1, IPS1-HA, PARP13, STING, TOMM70A, TRIM13, TRIM26, TRIM32, ZDHHC1 and combinations thereof, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0125] Finally, target viral genes of the class II MHC-mediated antigen presentation pathway are also well known to those skilled in the art. By way of example, the target genes of the ubiquitin ligase family may be mentioned, in particular HERC1, HERC2, HERC3, HERC4, HERC5 and HERC6 (Hochrainer et al., 2005).

[0126] Therefore, according to a specific embodiment, the target viral gene whose expression is measured in step (a) is selected from the target viral gene of the proinflammatory cytokine pathway, the interferon pathway, the Toll-like receptor (TLR) signaling pathway, the RIG-I-like receptor (RLR) signaling pathway and the class II MHC-mediated antigen presentation pathway.

[0127] According to a specific embodiment, the target viral gene whose expression is measured in step (a) is selected from TNFα, IL-1β, IL-6, IL-1Ra, IL-8, GM-CSF, MIP-1α, MIP-1β, IL-10, IL-1α, TGF-β, TGF-β1, IL-2, IL-4, IL-13, IL-15, IL-3, IL-5, IP10, SCM-1, IFN-α, IFN-β, IFN-ε, IFN-κ, IFN-ω, IFN-γ, IFNL1, IFNL2, IFNL3, ADAR1, IFIT1, IFIT2, IFIT3, IFIT5, IFI27, IFI44L, IS G15, ISG20, MDA5, OAS1, OAS2, OAS3, OASL, PARP12, PKR, RIG-I, RNaseL, ZAP, ZCCHC3, ZNFX1, RBBP6, SHFL, TRIM22, TRIM25, TRIM32, TRIM69, Viperin, T LR3, TLR7, TLR8, TLR9, CD14, LBP, MD1, MD2, CD300LF, GRP94, PRAT4A, PRAT4B, UNC93B1ATF3, AXL, BAMBI, BCL3, BPI, CENTB1, DAK, FLII, HSP10, IRAKM (IR AK3), LGP2(DHX58), MSK1, MSK2, NLRP12(NALP12), NFKBIA, NFKBIB, NFKBIE, PECAM1, PIN1, PPP3CA, PPP3CB, PPP3R1, PTPN6, RNF125, RP105, SHIP1, SIG IRR, SIKE, TNFAIP3, TNIP1, TNIP2, TNIP3, TOLLIP, TRAFD1, TRIAD3, TYRO3, ZCCHC11, MyD88, RAC1, SARM1, TANK, TIRAP, TRAM(TICAM2), TRIF(TICAM1), A AMP, ACT1(TRAF3IP2), AGER, AKT1, BECN1, BTK, CARD6, CARD11, DDX3X, FADD, IKKα, IKKβ, IKKε, IPS1, IRAK1, IRAK4, IRF1, IRF3, IRF5, IRF7, IRF8, IRF9, ITCH, LRRC59, LRRFIP2, MAP2K2, MAP3K7(TAK1), MAPK1, MDA5(IFIH1), NAIP5, NAP1, NEMO, NIBP, OTUD5, PKR, PRKRA, RIG-1, RIPK1, RIPK2, RIPK3, STAP2,SUGT1, SYK, TAB1, TAB2, TAB3, TBK1, TBKBP1, TIFA, TRADD, TRAF3, TRAF6, TRIL, WDFY1, LGP2(DHX58), MDA5(IFIH1), RIG-I(DDX58), TRAFD1, CYLD, DAK, DDX60, MFN2, M UL1, OTUD5, PIN1, RNF125, SIKE, TNFAIP3, IPS1, IPS1-HA, PARP13, STING, TOMM70A, TRIM13, TRIM26, TRIM32, ZDHHC1, HERC1, HERC2, HERC3, HERC4, HERC5, HERC6 and their combinations. ,

[0128] According to a preferred embodiment, the target viral genes whose expression is measured in step (a) are selected from the group consisting of target viral genes of the interferon pathway and the MHC class II-mediated antigen presentation pathway.

[0129] According to another preferred embodiment, the measuring step (a) comprises or consists of measuring at least one selected from IFN-α, IFN-β, IFN-ε, IFN-κ, IFN-ω, IFN-γ, IFNL1, IFNL2, IFNL3, ADAR1, IFIT1, IFIT2, IFIT3, IFIT5, IFI27, IFI44L, ISG15, ISG20, MDA5, OAS1, OAS2, OAS3, OASL, PARP12, PKR, RI Target viral genes of G-I, RNaseL, RSAD2, RBBP6, SIGLEC1, SHFL, TRIM22, TRIM25, TRIM32, TRIM69, Viperin, ZAP, ZCCHC3, ZNFX1, HERC1, HERC2, HERC3, HERC4, HERC5, HERC6 and combinations thereof, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0130] According to another preferred embodiment, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from IFI27, IFN-γ, IFIT1, IFIT2, IFI44L, ISG15, OAS1, OAS2, OAS3, RSAD2, TRIM25, SIGLEC1, TRIM22, TRIM32, HERC5, HERC6 and combinations thereof, and measuring at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0131] According to another particularly preferred embodiment, the measuring step (a) comprises or consists of measuring at least one target viral gene selected from SIGLEC1, RSAD2, IFI27, OAS1, IFIT1, IFI44L, ISG15 and HERC6, and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0132] The chromosomal locations of the target genes according to this preferred embodiment are given in particular in the following Table 1:

[0133] [Table 1]

[0134]

[0135]

[0136] The SIGLEC1 gene encodes a member of the immunoglobulin superfamily. The encoded protein is a lectin-like adhesion molecule that binds glycoconjugate ligands on the cell surface in a sialic acid-dependent manner. It is a type I transmembrane protein expressed only by a subset of macrophages and is involved in regulating cell-cell interactions.

[0137] The ISG15 gene encodes a ubiquitin-like protein that conjugates to intracellular target proteins upon activation by interferon-α and interferon-β. The encoded protein leads to a variety of functions, in particular, chemotactic activity for neutrophils, direction of target proteins conjugated to intermediate filaments, intercellular signaling, and antiviral activity during viral infection.

[0138] The HERC6 gene belongs to the HERC family of ubiquitin ligases, all of which contain at least one 350-amino-acid HECT domain that catalyzes the formation of thioesters from ubiquitin and then transfers it to the substrate.

[0139] The SLC1A2 gene encodes a member of the solute transporter family. This membrane-bound protein is the major transporter that removes the excitatory neurotransmitter glutamate from the extracellular space at central nervous system synapses. Glutamate clearance is essential for proper synaptic activation and to prevent neuronal damage due to overactivation of glutamate receptors.

[0140] The IL1R2 gene encodes a cytokine receptor protein that belongs to the interleukin-1 receptor family. This protein binds interleukin alpha (IL1(A), interleukin beta (IL1B), and type I interleukin 1 receptor (IL1R1 / IL1R(A)) and acts as a decoy receptor to inhibit the activity of their ligands. Interleukin 4 (IL4) antagonizes the activity of interleukin 1 by inducing the expression and release of interleukin 1. This gene and three others form a cluster of cytokine receptor genes on chromosome 2q12. Alternative splicing generates multiple transcript variants and isoforms of both membrane and soluble proteins.

[0141] The FAM20A gene encodes a secreted protein that may play a role in hematopoiesis. Mutations at this site are associated with amelogenesis imperfecta and gingival hyperplasia syndrome.

[0142] The OLAH gene allows for dodecanoyl hydrolase activity [with acyl protein]; myristoyl hydrolase activity [with acyl protein]; and palmitoyl hydrolase activity [with acyl protein]. It is involved in the biosynthesis of medium-chain fatty acids.

[0143] The RETN gene encodes a protein that has an antibacterial effect in the skin through antibacterial activity against Gram-positive and Gram-negative bacteria.

[0144] The MMP8 gene encodes a member of the matrix metalloproteinase (MMP) protein family. These proteins are involved in the degradation of the extracellular matrix during embryonic development, reproduction, and tissue remodeling, and are also involved in pathological processes such as arthritis and metastasis. Proteolysis at different sites on this protein produces multiple enzymatically active forms with different N-termini. This protein plays a role in the degradation of type I, type II, and type III collagen.

[0145] The RASAD2 gene encodes an interferon-inducible antiviral protein that belongs to the S-adenosyl-L-methionine (SAM) enzyme superfamily and plays a role in cellular antiviral responses and innate immune signaling. The antiviral effect mainly comes from inhibiting viral RNA replication, interfering with secretory pathways, binding to viral proteins, and dysregulating cellular lipid metabolism.

[0146] The IFI27 gene is mainly involved in the metabolic process of cellular proteins, defense responses to other organisms, and extrinsic apoptosis signaling pathways. The gene also plays a role in the upstream or downregulation of RNA polymerase II transcription and regulates protein export from the cell nucleus.

[0147] The OAS1 gene encodes a protein that synthesizes 2',5'-oligoadenylic acid (2-5A) and plays a key role in the innate cellular antiviral response.

[0148] The IFIT1 gene encodes a protein containing a tetratricopeptide repeat sequence that was originally identified as induced by interferon treatment. The encoded protein can inhibit viral replication and translation initiation.

[0149] The IFI44L gene is associated with GTP-binding activity and is involved in viral defense responses.

[0150] According to the present specification, identifying or measuring the expression level of a gene consists in highlighting changes in the transcriptome expression of said gene, said changes being highlighted relative to a reference expression of said gene. For this reason, the term "transcriptome signature" will be used in particular.

[0151] Transcripts of various target genes used to implement the methods of the present specification are also known to those skilled in the art, and their sequences can be obtained in the NCBI or Ensembl databases.

[0152] Table 2 below shows examples of transcripts of certain preferred target viral and bacterial genes:

[0153] [Table 2]

[0154]

[0155]

[0156] According to a specific embodiment, the expression of target viral and bacterial genes is measured at the mRNA transcript level, preferably at the transcript level selected from the transcripts in Table 2.

[0157] According to a preferred embodiment, at the mRNA transcript level, preferably at the transcript level selected from the group consisting of (NCBI database) NM_023068.4, NM_001367089.1, NM_005101.4, NM_017912.4, NM_001165136.2, NM_017565.4, NM_001243746.2, NM_002424.3, NM_001304442.2, NM_001304441.2, NM_00103970 The expression of the target genes was measured at the transcript level of 2.3, NM_018324.3, NM_004633.4, NM_001261419.2, NM_003256.4, NM_004171.4, NM_001195728.3, NM_001252652.2, NM_020415.4, NM_001385725.1, NM_001385726.1, NM_001385727.1, NM_001193374.2 and combinations thereof.

[0158] Any method known to the person skilled in the art for measuring gene expression levels or changes in gene expression at the transcriptional level can be used in the method according to the invention.

[0159] Thus, the measurement can be performed by direct methods for determining the presence of said transcript in a biological sample, or by indirect detection of the transcript after conversion of the latter into DNA.

[0160] The techniques commonly used to simultaneously measure the concentration of a large number of different types of messenger RNA are known to those skilled in the art and need not be described in detail herein. For example, DNA chips, CAGE, SAGE and the more recent high-throughput RNA sequencing, known as RNA-Seq, are particularly mentioned.

[0161] According to the present description, gene expression at the transcriptional level can be measured by any known molecular detection method. Thus, changes in gene expression can be detected by amplification, in particular by reverse transcription-polymerase chain reaction or RT-PCR, by sequencing (preferably by high-throughput sequencing) or by hybridization techniques (for example using hybridization microarrays or by All these methods are also well known to those skilled in the art and there is no need to describe them in detail in this article.

[0162] According to a specific embodiment, the determination of gene expression can be performed in the following manner:

[0163] (1) extracting total RNA from a blood sample or PBMC and performing a reverse transcription step to obtain various complementary DNAs (or cDNAs) of various messenger RNAs originally present in the sample or PBMC,

[0164] (2) Specific amplification of cDNA. In this case, the specific reagent used includes at least one specific amplification primer for the gene. This step can be performed by a PCR-type amplification reaction or any other suitable amplification technique.

[0165] (3) Determine gene expression by quantifying cDNA.

[0166] According to a preferred embodiment, gene expression is measured by RT-PCR, preferably quantitative or semi-quantitative RT-PCR, or nested PCR, e.g. using Technology (Poritz et al., 2011) or Fluidigm's BiomarkTM platform. According to this embodiment, expression is measured at the level of mRNA transcripts of the target gene.

[0167] Those skilled in the art are fully capable of determining the sequences of primers or primer pairs required for amplifying the target gene, and optionally the transcripts of other target genes defined later in the specification, to determine their respective expression levels. Specifically, many tools are available, such as Geneious or Primer 3, and the sequences can then be adjusted according to the needs of those skilled in the art.

[0168] The measurement of expression levels makes it possible to determine the amount of a transcript in a biological sample, or to derive a value derived therefrom.

[0169] According to a specific embodiment, the expression level of a marker target gene is a derived or normalized value of the amount of transcript (particularly mRNA) of said target gene.

[0170] According to a specific embodiment, gene expression is normalized relative to the expression of one or more housekeeping genes (or reference genes) according to methods known to those skilled in the art. Thus, expression is normalized using one or more of the following housekeeping genes: DECR1 (chromosome location: chr8, 90001352-90053633), HPRT1 (chromosome location: chrX, 134452842-134520513) and PPIB (chromosome location: chr15: 64155812-64163205), RPLP0 (chromosome location: chr12, 120196699-120201111), PPIA (chromosome location: chr7, 44795960-44803117), G LYR1 (chromosome location: chr16, 4803203-4847288), RANBP3 (chromosome location: chr19, 5916139-5978140), B2M (chromosome location: chr15, 44711492-44718145), TBP (chromosome location: chr6, 170554369-170572859), GAPDH (chromosome location: chr12, 6534517-6538371) and ACTB (chromosome location: chr14, 5527148-5530601). Chromosome locations are given according to GRCh38 / hg38. Preferably, expression is normalized using one or more housekeeping genes selected from the following: DECR1, HPRT1, PPIB, GAPDH, ACTB and combinations thereof, more preferably selected from DECR1, HPRT1, PPIB and combinations thereof.

[0171] In this case, the reference level used is also pre-standardized in the same manner. Standardization of both the reference level and the transcript level of the biological sample to be tested is performed before the comparison, in particular before calculating the relationship between the transcript level of the sample to be tested and the reference level. When a threshold value different from the reference level is used to draw a conclusion, this standardization can be taken into account for the choice of the threshold value.

[0172] Where the level of gene transcripts is normalised to the level of transcripts of one or more housekeeping genes, this of course means that the method comprises determining the transcript levels of the housekeeping genes used for normalisation.

[0173] In general, according to the method of the present invention, no matter how its embodiment is, the expression level (preferably standardized expression) of the target gene in the biological sample from the subject is compared with the predetermined expression value (preferably standardized expression) of the same gene in the reference biological sample. This comparison makes it possible to obtain the change of the expression of the target gene measured according to the method of the present invention.

[0174] For a given target gene, the reference expression value corresponds to the expression level of the transcript of the gene obtained from a reference biological sample, the reference biological sample being obtained from a subject with an infection of a given nature. The reference biological sample has the same properties as the biological sample to be tested, or at least has compatible properties, thereby constituting a reference for determining the expression level of the target gene. Advantageously, in particular for the embodiments below, the reference value of a given gene corresponds to the average level of the mRNA transcript of the gene obtained from a reference biological sample of a population of subjects exhibiting an infection.

[0175] For the purpose of the present invention, the expression "reference value" or "predetermined reference value" is synonymous with the expression "control value" or "threshold value", and is used as a comparison point for determining whether the expression level of the target gene is decreased or increased.

[0176] According to a specific embodiment, the target gene reference value corresponds to the expression level of an mRNA transcript of said gene obtained from a reference biological sample from a subject suffering from a bacterial infection.

[0177] According to a specific embodiment, the target gene reference value corresponds to the expression level of an mRNA transcript of said gene obtained from a reference biological sample from a subject suffering from a viral infection.

[0178] The comparison can be performed by any method known to those skilled in the art, and can, for example, include calculating a ratio or a difference. Advantageously, in the context of the present method, the comparison and the issuance of a conclusion about the nature of the infection of the subject from which the biological sample was obtained are performed by automated, computer-operated or computer-assisted techniques.

[0179] Thus, when the expression levels of the target genes are compared to their respective reference values, statistically significant differences can be identified, in other words, changes in the expression levels can determine the nature of the virus or bacteria with which the subject is infected. Thus, when a significantly increased expression is detected, the term "overexpression" is used, whereas, when a significantly decreased expression is detected, "underexpression" is used.

[0180] A person skilled in the art is able to determine a statistical test for determining a reference value to compare with the expression level of a target gene. The exemplary embodiment gives one possible method.

[0181] According to a first embodiment variant of the invention, the reference expression value of each target gene is determined based on a reference biological sample from a pool of biological samples of subjects suffering from bacterial infections. Preferably, in the method according to the invention, the reference expression value of the target gene corresponds to the corresponding expression of the target gene in a reference biological sample obtained from a subject suffering from a bacterial infection. Thus, it can be judged that the infection is of a viral nature when the expression level of the target gene is compared at the mRNA transcript level relative to the corresponding reference value, highlighting at least one expression change selected from the following:

[0182] - Overexpression of SIGLEC1,

[0183] - Overexpression of ISG15,

[0184] - Overexpression of HERC6,

[0185] - Overexpression of RSAD2,

[0186] - Overexpression of IFI27,

[0187] - Overexpression of OAS1,

[0188] - Overexpression of IFIT1, and

[0189] - Overexpression of IFI44L,

[0190] and at least one other expression change selected from the group consisting of:

[0191] - Low expression of SLC1A2,

[0192] - Low expression of IL1R2,

[0193] - Low expression of FAM20A,

[0194] - Low expression of OLAH,

[0195] -low expression of RETN, and

[0196] -Low expression of MMP8.

[0197] According to a second embodiment variant of the present invention, the reference value of each target gene is determined based on a reference biological sample from a pool of biological samples of subjects suffering from viral infection. Thus, it can be judged that the infection is of bacterial nature when the target gene expression comparison result shows at least two changes selected from the following:

[0198] - Low expression of SIGLEC1,

[0199] - Low expression of ISG15,

[0200] - Low expression of HERC6,

[0201] - Low expression of RSAD2,

[0202] - Low expression of IFI27,

[0203] - Low expression of OAS1,

[0204] - Low expression of IFIT1, and

[0205] - Low expression of IFI44L,

[0206] and at least one other expression change selected from the group consisting of:

[0207] - Overexpression of SLC1A2,

[0208] - Overexpression of IL1R2,

[0209] - Overexpression of FAM20A,

[0210] - Overexpression of OLAH,

[0211] -Overexpression of RETN, and

[0212] - Overexpression of MMP8.

[0213] The skilled person will be able to select one or other variant depending on available reference biological samples.The reference biological sample is advantageously a pool of biological samples from subjects suffering from bacterial infections or a pool of biological samples from subjects suffering from viral infections.

[0214] In all specific embodiments described below, conclusions about the nature of the infection are drawn by taking into account the overexpression / underexpression of various target genes detected in the subject's biological sample, as previously defined in one or other of the two embodiment variants.

[0215] According to a specific embodiment, step (a) comprises or consists of measuring the expression of at least one target viral gene selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and the expression of at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0216] According to another specific embodiment, step (a) comprises or consists of measuring the expression of a single target viral gene selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and the expression of two, three, four, five or six target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably the expression of two or three target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0217] According to another specific embodiment, step (a) comprises or consists of measuring the expression of two target viral genes selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and the expression of two, three, four, five or six target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably the expression of two or three target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2,

[0218] According to another specific embodiment, step (a) comprises or consists of measuring the expression of three target viral genes selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and the expression of two, three, four, five or six target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0219] According to another specific embodiment, step (a) comprises or consists of measuring the expression of four target viral genes selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and the expression of two, three, four, five or six target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0220] According to another specific embodiment, step (a) comprises or consists of measuring the expression of five target viral genes selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and the expression of two, three, four, five or six target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0221] According to another specific embodiment, step (a) comprises or consists of measuring the expression of six target viral genes selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and the expression of two, three, four, five or six target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0222] According to another specific embodiment, step (a) comprises or consists of measuring the expression of seven target viral genes selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and the expression of two, three, four, five or six target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0223] According to another specific embodiment, step (a) comprises or consists of measuring the expression of eight target viral genes SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and the expression of two, three, four, five or six target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0224] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene SIGLEC1 and the expression of one or more target bacterial genes, wherein the target bacterial genes are selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from SLC1A2, IL1R2, OLAH, FAM20A and RETN, and even more preferably selected from SLC1A2, IL1R2, OLAH and FAM20A.

[0225] According to a preferred variant of this embodiment, step (a) comprises or consists of measuring the expression of the target viral gene SIGLEC1 and the expression of at least three target bacterial genes selected from the group consisting of SLC1A2, IL1R2, OLAH, FAM20A and RETN.

[0226] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene ISG15 and the expression of one or more target bacterial genes, wherein the target bacterial genes are selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from SLC1A2, IL1R2, OLAH, FAM20A and RETN, and even more preferably selected from SLC1A2, IL1R2, OLAH and FAM20A.

[0227] According to another specific embodiment, the measuring step comprises or consists of measuring the expression of the viral gene HERC6 and the expression of one or more target bacterial genes, wherein the target bacterial genes are selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from SLC1A2, IL1R2, OLAH, FAM20A and RETN, and more preferably selected from SLC1A2, IL1R2, OLAH and FAM20A.

[0228] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene IFIT1 and the expression of one or more target bacterial genes selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0229] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene IFI44L and the expression of one or more target bacterial genes selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0230] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene RSAD2 and the expression of one or more target bacterial genes selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0231] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene OAS1 and the expression of one or more target bacterial genes selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0232] According to a preferred embodiment, step (a) comprises or consists of measuring the expression of the target viral gene IFI27 and the expression of one or more target bacterial genes, wherein the target bacterial genes are selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, and preferably selected from IL1R2, OLAH, FAM20 and RETN.

[0233] According to another preferred embodiment, the measuring step (a) comprises or consists of measuring the expression of the target viral gene IFI27 and optionally at least one other viral gene selected from SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1, IFI44L, and two target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, and preferably selected from OLAH, FAM20A, IL1R2 and MMP8.

[0234] According to another preferred embodiment, step (a) comprises or consists of measuring the expression of the target viral gene IFI27, the target bacterial gene OLAH and at least one other target bacterial gene selected from SLC1A2, IL1R2, FAM20A, RETN and MMP8.

[0235] According to another specific embodiment, step (a) comprises or consists of measuring the expression of a combination of two target genes selected from the combinations in Table 6, preferably those whose area under the ROC curve of the model exhibits a value of at least 0.86, most particularly at least 0.88.

[0236] According to a preferred variant of this specific embodiment, step (a) comprises or consists of measuring the expression of a combination of target viral genes and target bacterial genes selected from the group consisting of: SIGLEC1_IL1R2, IFI44L_OLAH and IFI27_1L1R2.

[0237] According to another embodiment, step (a) comprises or consists of measuring the expression of a combination of two target genes selected from the following combination: SIGLEC1_IL1R2; SIGLEC1_FAM20A; HERC6_IL1R2; SIGLEC1_OLAH; HERC6_OLAH; ISG15_IL1R2; SIGLEC1_RETN; HERC6_FAM20A; SLC1A2_OLAH; HERC6_RETN; SIGLEC1_SLC1A2; ISG15_OLAH; SIGLEC1_MMP8; HERC6_ MMP8; IL1R2_OLAH; IL1R2_FAM20A; SIGLEC1_HERC6; HERC6_SLC1A2; SIGLEC1_ISG15; FAM20A_OLAH; ISG15_FAM20A; SLC1A2_IL1R2; ISG15_RETN; ISG15_MMP8 and ISG15_SLC1A2, preferably selected from the following gene combination: SIGLEC1_IL1R2; SIGLEC1_FAM20A; HERC6_IL1R2; SIGLEC1_OLAH and HERC6_OLAH.

[0238] According to another specific embodiment, step (a) comprises or consists of measuring at least one target viral gene selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, the target bacterial gene OLAH, and at least one other target bacterial gene selected from FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from FAM20A, IL1R2 and MMP8.

[0239] According to another specific embodiment, step (a) comprises or consists of measuring at least one target viral gene selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, the target bacterial gene FAM20A, and at least one other target bacterial gene selected from OLAH, IL1R2, MMP8, RETN and SLC1A2, preferably selected from OLAH, IL1R2 and MMP8.

[0240] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1 and ISG15 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0241] According to a specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1 and HERC6 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0242] According to a specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1 and RSAD2 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0243] According to a preferred embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0244] According to a variant of this preferred embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1 and IFI27, and the expression of two to four target bacterial genes selected from OLAH, FAM20A, IL1R2 and MMP8.

[0245] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1 and OAS1 and the expression of one or more target bacterial genes selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0246] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1 and IFIT1 and one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from OLAH and FAM20A.

[0247] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1 and IFI44L and one or more target bacterial genes selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0248] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15 and HERC6 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0249] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15 and RSAD2 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0250] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from OLAH and FAM20A.

[0251] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes ISG15 and OAS1 and the expression of one or more target bacterial genes selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0252] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15 and IFIT1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0253] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0254] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6 and RSAD2 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0255] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from OLAH and FAM20A.

[0256] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6 and OAS1 and one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0257] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes HERC6 and IFIT1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0258] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0259] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes RSAD2 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0260] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes RSAD2 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0261] According to a specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes RSAD2 and IFIT1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0262] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes RSAD2 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0263] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes IFI27 and OAS1 and the expression of one or more target bacterial genes selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0264] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes IFI27 and IFIT1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0265] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes IFI27 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0266] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes OAS1 and IFIT1 and the expression of one or more target bacterial genes selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0267] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes OAS1 and IFI44L and the expression of one or more target bacterial genes selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0268] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes IFI44L and IFIT1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0269] According to another specific embodiment, the measuring step comprises or consists of measuring at least one target viral gene selected from SIGLEC1, ISG15 and HERC6, and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2. Preferably, according to this embodiment, the measuring step comprises or consists of measuring at least one target viral gene selected from SIGLEC1, ISG15 and HERC6, and at least one target gene selected from IL1R2, OLAH and FAM20A.

[0270] According to another specific embodiment, the measuring step comprises or consists of measuring at least one target viral gene selected from RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2. Preferably, according to this embodiment, the measuring step comprises or consists of measuring at least one target viral gene selected from RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and at least one target bacterial gene selected from IL1R2, OLAH and FAM20A.

[0271] According to another preferred embodiment, the measuring step comprises or consists of measuring at least one target viral gene selected from SIGLEC1, ISG15 and HERC6, and at least two target bacterial genes selected from SLC1A2, IL1R2, OLAH, FAM20A and RETN and MMP8, and preferably IL1R2, OLAH and FAM20A.

[0272] According to a variant of this specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene SIGLEC1 and the expression of at least two target bacterial genes selected from the group consisting of OLAH, SLC1A2, IL1R2, FAM20A, RETN and MMP8.

[0273] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene HERC6, and the expression of at least two target bacterial genes selected from the group consisting of OLAH, SLC1A2, IL1R2, FAM20A, RETN and MMP8.

[0274] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene ISG15, and the expression of at least two target bacterial genes selected from the group consisting of OLAH, SLC1A2, IL1R2, FAM20A, RETN and MMP8.

[0275] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene SIGLEC1, the target bacterial gene OLAH and at least one other target gene selected from the group consisting of ISG15, HERC6, SLC1A2, IL1R2, FAM20A, RETN and MMP8.

[0276] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of the target viral gene SIGLEC1, the target bacterial gene IL1R2 and at least one other target gene selected from ISG15, HERC6, SLC1A2, OLAH, FAM20A, RETN and MMP8, preferably selected from SLC1A2, OLAH, FAM20A, RETN and MMP8.

[0277] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, ISG15 and HERC6 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0278] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, ISG15 and RSAD2 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0279] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, ISG15 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0280] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1, ISG15 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0281] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1, ISG15 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0282] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, ISG15 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0283] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, HERC6 and RSAD2 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0284] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, HERC6 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0285] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, HERC6 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0286] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1, HERC6 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0287] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, HERC6 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0288] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, RSAD2 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0289] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, RSAD2 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0290] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1, HRSAD2 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0291] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, RSAD2 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0292] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1, IFI27 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0293] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1, IFI27 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0294] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, IFI27 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0295] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1, IFIT1 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0296] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes SIGLEC1, OAS1 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0297] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes SIGLEC1, IFI27 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0298] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, HERC6 and RSAD2 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0299] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, HERC6 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0300] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, HERC6 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0301] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, HERC6 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0302] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, HERC6 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0303] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, RSAD2 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0304] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, RSAD2 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0305] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, RSAD2 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0306] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, RSAD2 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0307] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, IFI27 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0308] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, IFI27 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0309] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, IFI27 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0310] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, OAS1 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0311] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, OAS1 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0312] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes ISG15, IFIT1 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0313] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6, RSAD2 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0314] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6, RSAD2 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0315] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6, RSAD2 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0316] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6, RSAD2 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0317] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6, IFI27 and OAS1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0318] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6, IFI27 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0319] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6, IFI27 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0320] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes HERC6, OAS1 and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0321] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes HERC6, OAS1 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0322] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes HERC6, IFI44L and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0323] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes RSAD2, OAS1 and IFI27 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0324] According to another specific embodiment, step (a) comprises or consists of: measuring the expression of the target viral genes RSAD2, IFI27, and IFIT1 and the expression of one or more bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN, and SLC1A2.

[0325] According to another specific embodiment, step (a) comprises or consists of: measuring the expression of the target viral genes RSAD2, IFI27, and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN, and SLC1A2.

[0326] According to another specific embodiment, step (a) comprises or consists of: measuring the expression of the target viral genes RSAD2, OAS1, and IFIT1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN, and SLC1A2.

[0327] According to another specific embodiment, step (a) comprises or consists of: measuring the expression of the target viral genes RSAD2, OAS1, and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN, and SLC1A2.

[0328] According to another specific embodiment, step (a) comprises or consists of: measuring the expression of the target viral genes RSAD2, IFIT1, and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN, and SLC1A2.

[0329] According to another specific embodiment, step (a) comprises or consists of: measuring the expression of the target viral genes IFI27, OAS1, and IFIT1 and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN, and SLC1A2.

[0330] According to another specific embodiment, step (a) comprises or consists of: measuring the expression of the target viral genes IFI27, OAS1, and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN, and SLC1A2.

[0331] According to another specific embodiment, step (a) comprises or consists of measuring the expression of target viral genes IFI27, IFIT1 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0332] According to another specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes OAS1, IFIT1 and IFI44L and the expression of one or more target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0333] According to another specific embodiment, step (a) comprises or consists of measuring the expression of a combination of three target genes selected from those listed in Table 7, preferably those whose area under the ROC curve of the model exhibits a value of at least 0.86, at least 0.88, and most particularly at least 0.90.

[0334] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of a combination of three target genes selected from the following combination: SIGLEC1_IL1R2_FAM20A, HERC6_IL1R2_FAM20A, SIGLEC1_SLC1A2_OLAH, SIGLEC1_HERC6_IL1R2, SIGLEC1_FAM20A_OLAH, SIGLEC1_IL1R2_MMP8, SIGLEC1_ISG15_IL1R2, SIGLEC1_SLC1A2_IL1R2, SIGLEC1_SLC1A2_OLAH, SIGLEC1_HERC6_IL1R2, SIGLEC1_FAM20A_OLAH, SIGLEC1_IL1R2_MMP8, SIGLEC1_ISG15_IL1R2, SIGLEC1_SLC1A2_IL1R2, SIGLEC1_SLC1A2_OLAH, SIGLEC1_HERC6_IL1R2 AM20A, HERC6_FAM20A_OLAH, SIGLEC1_FAM20A_RETN, SIGLEC1_HERC6_FAM20A, SIGLEC1_FAM20A_MMP8, SIGLEC1_IL1R2_RETN, ISG15_IL1R2_FAM20A, S IGLEC1_ISG15_FAM20A, ISG15_HERC6_IL1R2, HERC6_IL1R2_OLAH, SIGLEC1_HERC6_OLAH, HERC6_SLC1A2_OLAH, HERC6_IL1R2_RETN, HERC6_IL1R2_MMP 8. SIGLEC1_OLAH_MMP8, SIGLEC1_ISG15_OLAH, SIGLEC1_OLAH_RETN, HERC6_SLC1A2_IL1R2, ISG15_SLC1A2_OLAH, HERC6_FAM20A_RETN, HERC6_OLAH_ RETN, ISG15_SLC1A2_IL1R2, HERC6_OLAH_MMP8, SIGLEC1_HERC6_RETN, ISG15_IL1R2_OLAH, ISG15_HERC6_OLAH, SIGLEC1_SLC1A2_RETN, ISG15_IL1R2 _RETN, ISG15_FAM20A_OLAH, ISG15_IL1R2_MMP8, SIGLEC1_SLC1A2_MMP8, ISG15_HERC6_RETN, SIGLEC1_ISG15_RETN, HERC6_SLC1A2_FAM20A, ISG15_H ERC6_FAM20A, HERC6_FAM20A_MMP8, SLC1A2_FAM20A_OLAH, SIGLEC1_RETN_MMP8, HERC6_SLC1A2_RETN, SIGLEC1_HERC6_SLC1A2, SLC1A2_IL1R2_OLAH,SIGLEC1_HERC6_MMP8, ISG15_OLAH_RETN, SIGLEC1_ISG15_SLC1A2, ISG15_OLAH_MMP8, SLC1A2_OLAH_MMP8, SLC1A2_OLAH_RETN, HERC6_RETN_MMP8, HERC6_SLC1A2_MMP8, SIGLEC1_IS G15_MMP8, IL1R2_FAM20A_OLAH, ISG15_HERC6_MMP8, ISG15_SLC1A2_FAM20A, ISG15_FAM20 A_RETN, IL1R2_OLAH_MMP8, SLC1A2_IL1R2_FAM20A, IL1R2_OLAH_RETN, SIGLEC1_ISG15_HER C6, FAM20A_OLAH_MMP8, ISG15_SLC1A2_RETN, IL1R2_FAM20A_MMP8, ISG15_HERC6_SLC1A2, ISG15_SLC1A2_MMP8, ISG15_FAM20A_MMP8, IL1R2_FAM20A_RETN, SLC1A2_IL1R2_RETN, FAM 20A_OLAH_RETN, OLAH_RETN_MMP8, SLC1A2_IL1R2_MMP8, ISG15_RETN_MMP8, IL1R2_RETN_M MP8, SLC1A2_FAM20A_RETN, SLC1A2_FAM20A_MMP8, SLC1A2_RETN_MMP8 and FAM20A_RETN_MMP8. Preferably, according to this variant, the measuring step comprises or consists of measuring the expression of a combination of three target genes selected from the following combination: SIGLEC1_IL1R2_FAM20A, HERC6_IL1R2_FAM20A, SIGLEC1_SLC1A2_OLAH, SIGLEC1_HERC6_IL1R2, SIGLEC1_FAM20A_OLAH, SIGLEC1_IL1R2_MMP8, SIGLEC1_ISG15_IL1R2, SIGLEC1_SLC1A2_IL1R2, SIGLEC1_IL1R2_OLAH, SIGLEC1_SLC1A2_FAM20A and HERC6_FAM20A_OLAH, and more preferably selected from SIGLEC1_IL1R2_FAM20A, HERC6_IL1R2_FAM20A and SIGLEC1_SLC1A2_OLAH.

[0335] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of a combination of three target genes selected from the following combination: IFI27_OLAH_FAM20A, IFI27_IL1R2_FAM20A, IFI27_OLAH_MMP8, IFI27_HERC6_OLAH, IFI27_IL1R2_OLAH, IFI27_ISG15_OLAH, IFI27_OLAH_RETN, IFI27_SLC1A2_OLAH, IFI27_SIGLEC 1_OLAH, IFI27_SIGLEC1_IL1R2, IFI27_IFI44L_OLAH, IFI27_IFIT1_OLAH, IFI27_OAS1_OLAH, IFI27_HERC6_IL1R2, RSAD2 _IFI27_OLAH, IFI27_IL1R2_RETN, IFI27_IFI44L_IL1R2, IFI27_IFIT1_IL1R2, IFI27_ISG15_IL1R2 and RSAD2_IFI27_IL1R2.

[0336] According to another specific embodiment, step (a) comprises or consists of measuring the expression of at least four target genes.

[0337] According to a variant of this embodiment, the measuring step comprises or consists of measuring at least two target genes selected from SIGLEC1, ISG15 and HERC6, and at least two target genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, and preferably IL1R2, OLAH and FAM20A.

[0338] According to another variant of this embodiment, the measuring step comprises or consists of measuring SIGLEC1 and at least three target genes selected from the group consisting of SLC1A2, IL1R2, OLAH, FAM20A and RETN.

[0339] According to another variant of this embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1 and IL1R2, and at least two other target genes selected from ISG15, HERC6, SLC1A2, OLAH, FAM20A, RETN and MMP8, and preferably SLC1A2, OLAH and FAM20A.

[0340] According to another variant of this embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1 and HERC6, and at least two other target genes selected from ISG15, IL1R2, SLC1A2, OLAH, FAM20A, RETN and MMP8. According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1, IL1R2 and FAM20A, and at least one other target gene selected from ISG15, HERC6, SLC1A2, OLAH, RETN and MMP8.

[0341] According to another variant of this embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1 and SLC1A2, and at least two other target genes selected from ISG15, IL1R2, HERC6, OLAH, FAM20A, RETN and MMP8, and preferably IL1R2, OLAH, FAM20A and MMP8.

[0342] According to another preferred embodiment, step (a) comprises or consists of measuring the expression of the target viral gene IFI27, another target viral gene selected from HERC6, SIGLEC1, IFI44L and ISG15, the target bacterial gene FAM20A and another target bacterial gene selected from OLAH and IL1R2.

[0343] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of a combination of four target genes selected from those listed in Table 8, and preferably those for which the area under the ROC curve of the model in this table exhibits an area of ​​at least 0.86, at least 0.88, and most particularly at least 0.90.

[0344] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of a combination of four target genes selected from the combinations shown in Table 3 below:

[0345] [Table 3]

[0346]

[0347]

[0348]

[0349] Preferably, according to this variant, the measuring step comprises or consists of measuring the expression of a combination of four target genes selected from the following combination: SIGLEC1_IL1R2_FAM20A_MMP8, SIGLEC1_HERC6_IL1R2_FAM20A, SIGLEC1_ISG15_IL1R2_FAM20A, SIGLEC1_IL1R2_FAM20A_OLAH, SIGLEC1_IL1R2_FAM20A_RETN, SIGLEC1_SLC1A2_IL1R2_FAM20A, SIGLEC1_SLC1A2_FAM20A_OLAH, ISG15_HERC6_IL1R2_FAM20A, SIGLEC1_FAM20A_OLAH_MMP8 and HERC6_IL1R2_FAM20A_OLAH.

[0350] According to another specific embodiment, step (a) comprises or consists of measuring the expression of at least five target genes.

[0351] According to a variant of this embodiment, the measuring step comprises or consists of measuring at least two target genes selected from SIGLEC1, ISG15 and HERC6, and at least three other target genes selected from IL1R2, SLC1A2, OLAH, FAM20A, RETN and MMP8.

[0352] According to another variant of this embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1, ISG15 and HERC6, and at least two other target genes selected from IL1R2, SLC1A2, OLAH, FAM20A, RETN and MMP8, and preferably IL1R2, OLAH and FAM20A.

[0353] According to a variant of this embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1 and ISG15, and at least three other target genes selected from HERC6, IL1R2, SLC1A2, OLAH, FAM20A, RETN and MMP8, and preferably selected from IL1R2, OLAH, FAM20A and MMP8.

[0354] According to a variant of this embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1 and IL1R2, and at least three other target genes selected from HERC6, ISG15, SLC1A2, OLAH, FAM20A, RETN and MMP8, preferably selected from OLAH, SLC1A2, FAM20A and MMP8.

[0355] According to a variant of this embodiment, the measuring step comprises or consists of: measuring the target genes SIGLEC1 and MMP8, and the expression of at least three other target genes selected from HERC6, ISG15, SLC1A2, OLAH, FAM20A, RETN and IL1R2, preferably OLAH, SLC1A2, FAM20A and IL1R2.

[0356] According to a variant of this embodiment, the measuring step comprises or consists of: measuring the target genes SIGLEC1 and HERC6, and the expression of at least three other target genes selected from ISG15, IL1R2, SLC1A2, OLAH, FAM20A, RETN and MMP8, and preferably selected from IL1R2, OLAH, FAM20A and MMP8.

[0357] According to another variant of this embodiment, the measuring step comprises or consists of: measuring the target genes SIGLEC1, FAM20A and MMP8, and the expression of at least two other target genes selected from IL1R2, ISG15, HERC6, SLC1A2, OLAH and RETN, and preferably IL1R2, ISG15, SLC1A2 and OLAH.

[0358] According to a variant of this embodiment, the measuring step comprises or consists of: measuring the target genes SIGLEC1, IL1R2 and HERC6, and the expression of at least two other target genes selected from ISG15, SLC1A2, OLAH, FAM20A, RETN and MMP8.

[0359] According to another variant of this embodiment, the measuring step comprises or consists of: measuring the target genes SIGLEC1, IL1R2 and ISG15, and the expression of at least two other target genes selected from HERC6, SLC1A2, OLAH, FAM20A, RETN and MMP8.

[0360] According to another variant of this embodiment, the measuring step comprises or consists of: measuring the expression of a combination of five target genes selected from the combinations shown in Table 4 below:

[0361] [Table 4]

[0362]

[0363]

[0364]

[0365]

[0366] Preferably, according to this variant, the measuring step comprises or consists of measuring the expression of a combination of five target genes selected from the following combinations:

[0367] SIGLEC1_HERC6_IL1R2_FAM20A_MMP8, SIGLEC1_IL1R2_FAM20A_OLAH_MMP8; SIGLEC1_ISG15_IL1R2_FAM20A_MMP8; SIGLEC1_IL1R2_FAM20A_RETN_MMP8; SIGLEC1_SLC1A2_IL1 R2_FAM20A_MMP8; SIGLEC1_ISG15_HERC6_IL1R2_FAM20A; SIGLEC1_HERC6_IL1R2_FAM20A_OLAH; SIGLEC1_SLC1A2_FAM20A_OLAH_MMP8 and SIGLEC1_ISG15_IL1R2_FAM20A_OLAH.

[0368] According to a preferred variant of this embodiment, step (a) comprises or consists of measuring the expression of the target viral gene IFI27, two other target viral genes selected from SIGLEC1, HERC6, OAS1 and IFIT1, the target bacterial gene FAM20A and another target bacterial gene selected from OLAH, IL1R2 and MMP8.

[0369] According to another preferred variation of this embodiment, step (a) comprises or consists of measuring the expression of a combination of five target genes selected from those listed in Table 9, and preferably those whose area under the ROC curve of the model in this table exhibits an area of ​​at least 0.86, at least 0.88, and most particularly at least 0.90.

[0370] According to another preferred variant of this embodiment, step (a) comprises or consists of measuring the expression of the target viral genes IFI27 and SIGLEC1, and the target bacterial genes FAM20A, IL1R2 and MMP8.

[0371] According to another specific embodiment, step (a) comprises or consists of measuring the expression of at least six target genes.

[0372] According to a variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1, ISG15 and HERC6, and at least three other target genes selected from IL1R2, SLC1A2, OLAH, FAM20A, RETN and MMP8.

[0373] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1, FAM20A and MMP8, and at least three other target genes selected from ISG15, HERC6, IL1R2, SLC1A2, OLAH and RETN.

[0374] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1, ISG15 and SLC1A2, and at least three other target genes selected from HERC6, IL1R2, OLAH, FAM20A, MMP8 and RETN.

[0375] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1 and IL1R2, and at least four other target genes selected from HERC6, SLC1A2, OLAH, FAM20A, RETN and MMP8.

[0376] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1 and HERC6, and at least four other target genes selected from ISG15, IL1R2, SLC1A2, OLAH, FAM20A, RETN and MMP8.

[0377] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1 and MMP8, and at least four other target genes selected from HERC6, ISG15, IL1R2, SLC1A2, OLAH, FAM20A and RETN.

[0378] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC and OLAH, and at least four other target genes selected from HERC6, ISG15, IL1R2, SLC1A2, MMP8, FAM20A and RETN.

[0379] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of a combination of six target genes selected from the following combinations:

[0380] SIGLEC1_ISG15_IL1R2_FAM20A_OLAH_MMP8;

[0381] SIGLEC1_HERC6_IL1R2_FAM20A_OLAH_MMP8;

[0382] SIGLEC1_ISG15_HERC6_IL1R2_FAM20A_MMP8;

[0383] SIGLEC1_SLC1A2_IL1R2_FAM20A_OLAH_MMP8;

[0384] SIGLEC1_HERC6_IL1R2_FAM20A_RETN_MMP8;

[0385] SIGLEC1_ISG15_IL1R2_FAM20A_RETN_MMP8;

[0386] SIGLEC1_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0387] SIGLEC1_ISG15_SLC1A2_IL1R2_FAM20A_MMP8;

[0388] SIGLEC1_HERC6_SLC1A2_IL1R2_FAM20A_MMP8;

[0389] SIGLEC1_SLC1A2_IL1R2_FAM20A_RETN_MMP8;

[0390] SIGLEC1_ISG15_SLC1A2_FAM20A_OLAH_MMP8;

[0391] SIGLEC1_ISG15_HERC6_IL1R2_FAM20A_OLAH;

[0392] SIGLEC1_HERC6_SLC1A2_FAM20A_OLAH_MMP8;

[0393] SIGLEC1_ISG15_IL1R2_FAM20A_OLAH_RETN;

[0394] SIGLEC1_HERC6_SLC1A2_IL1R2_FAM20A_OLAH;

[0395] SIGLEC1_SLC1A2_IL1R2_FAM20A_OLAH_RETN;

[0396] SIGLEC1_SLC1A2_FAM20A_OLAH_RETN_MMP8;

[0397] SIGLEC1_ISG15_SLC1A2_IL1R2_FAM20A_OLAH;

[0398] SIGLEC1_ISG15_HERC6_IL1R2_FAM20A_RETN;

[0399] SIGLEC1_HERC6_IL1R2_FAM20A_OLAH_RETN;

[0400] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_FAM20A;

[0401] SIGLEC1_ISG15_SLC1A2_IL1R2_FAM20A_RETN;

[0402] SIGLEC1_HERC6_FAM20A_OLAH_RETN_MMP8;

[0403] SIGLEC1_ISG15_HERC6_FAM20A_OLAH_MMP8;

[0404] SIGLEC1_ISG15_HERC6_SLC1A2_FAM20A_OLAH;

[0405] SIGLEC1_HERC6_SLC1A2_IL1R2_FAM20A_RETN;

[0406] SIGLEC1_ISG15_FAM20A_OLAH_RETN_MMP8;

[0407] SIGLEC1_ISG15_SLC1A2_FAM20A_OLAH_RETN;

[0408] ISG15_HERC6_IL1R2_FAM20A_OLAH_MMP8;

[0409] SIGLEC1_ISG15_HERC6_FAM20A_RETN_MMP8;

[0410] ISG15_HERC6_IL1R2_FAM20A_RETN_MMP8;

[0411] SIGLEC1_HERC6_SLC1A2_FAM20A_OLAH_RETN;

[0412] ISG15_HERC6_IL1R2_FAM20A_OLAH_RETN;

[0413] SIGLEC1_ISG15_HERC6_FAM20A_OLAH_RETN;

[0414] SIGLEC1_ISG15_SLC1A2_IL1R2_OLAH_MMP8;

[0415] SIGLEC1_HERC6_SLC1A2_IL1R2_OLAH_MMP8;

[0416] SIGLEC1_ISG15_HERC6_SLC1A2_OLAH_MMP8;

[0417] HERC6_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0418] SIGLEC1_HERC6_SLC1A2_FAM20A_RETN_MMP8;

[0419] ISG15_HERC6_SLC1A2_IL1R2_FAM20A_OLAH;

[0420] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_OLAH;

[0421] SIGLEC1_SLC1A2_IL1R2_OLAH_RETN_MMP8;

[0422] SIGLEC1_ISG15_SLC1A2_FAM20A_RETN_MMP8;

[0423] SIGLEC1_ISG15_SLC1A2_IL1R2_OLAH_RETN;

[0424] HERC6_SLC1A2_IL1R2_FAM20A_OLAH_MMP8;

[0425] SIGLEC1_ISG15_HERC6_SLC1A2_FAM20A_RETN;

[0426] ISG15_HERC6_SLC1A2_IL1R2_FAM20A_RETN;

[0427] SIGLEC1_ISG15_HERC6_IL1R2_RETN_MMP8;

[0428] SIGLEC1_ISG15_SLC1A2_OLAH_RETN_MMP8;

[0429] SIGLEC1_HERC6_IL1R2_OLAH_RETN_MMP8;

[0430] SIGLEC1_ISG15_HERC6_IL1R2_OLAH_MMP8;

[0431] SIGLEC1_HERC6_SLC1A2_OLAH_RETN_MMP8;

[0432] HERC6_SLC1A2_IL1R2_FAM20A_OLAH_RETN;

[0433] ISG15_HERC6_SLC1A2_IL1R2_FAM20A_MMP8;

[0434] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_MMP8;

[0435] SIGLEC1_HERC6_SLC1A2_IL1R2_OLAH_RETN;

[0436] ISG15_HERC6_FAM20A_OLAH_RETN_MMP8;

[0437] SIGLEC1_ISG15_HERC6_SLC1A2_OLAH_RETN;

[0438] SIGLEC1_HERC6_SLC1A2_IL1R2_RETN_MMP8;

[0439] ISG15_HERC6_SLC1A2_FAM20A_OLAH_RETN;

[0440] HERC6_SLC1A2_FAM20A_OLAH_RETN_MMP8;

[0441] SIGLEC1_ISG15_HERC6_SLC1A2_FAM20A_MMP8;

[0442] ISG15_HERC6_SLC1A2_FAM20A_OLAH_MMP8;

[0443] SIGLEC1_ISG15_SLC1A2_IL1R2_RETN_MMP8;

[0444] HERC6_SLC1A2_IL1R2_FAM20A_RETN_MMP8;

[0445] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_RETN;

[0446] SIGLEC1_ISG15_IL1R2_OLAH_RETN_MMP8;

[0447] ISG15_SLC1A2_IL1R2_FAM20A_OLAH_MMP8;

[0448] SIGLEC1_ISG15_HERC6_IL1R2_OLAH_RETN;

[0449] ISG15_SLC1A2_IL1R2_FAM20A_OLAH_RETN;

[0450] SIGLEC1_ISG15_HERC6_OLAH_RETN_MMP8;

[0451] ISG15_HERC6_IL1R2_OLAH_RETN_MMP8;

[0452] ISG15_HERC6_SLC1A2_IL1R2_OLAH_RETN;

[0453] ISG15_HERC6_SLC1A2_OLAH_RETN_MMP8;

[0454] ISG15_HERC6_SLC1A2_IL1R2_OLAH_MMP8;

[0455] HERC6_SLC1A2_IL1R2_OLAH_RETN_MMP8;

[0456] ISG15_SLC1A2_IL1R2_FAM20A_RETN_MMP8;

[0457] ISG15_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0458] ISG15_HERC6_SLC1A2_FAM20A_RETN_MMP8;

[0459] ISG15_HERC6_SLC1A2_IL1R2_RETN_MMP8;

[0460] ISG15_SLC1A2_FAM20A_OLAH_RETN_MMP8;

[0461] SIGLEC1_ISG15_HERC6_SLC1A2_RETN_MMP8;

[0462] ISG15_SLC1A2_IL1R2_OLAH_RETN_MMP8; and

[0463] SLC1A2_IL1R2_FAM20A_OLAH_RETN_MMP8.

[0464] Preferably, according to this variant, the measuring step comprises or consists of: measuring the expression of a combination of six target genes selected from the following combinations:

[0465] SIGLEC1_ISG15_IL1R2_FAM20A_OLAH_MMP8;

[0466] SIGLEC1_HERC6_IL1R2_FAM20A_OLAH_MMP8;

[0467] SIGLEC1_ISG15_HERC6_IL1R2_FAM20A_MMP8;

[0468] SIGLEC1_SLC1A2_IL1R2_FAM20A_OLAH_MMP8;

[0469] SIGLEC1_HERC6_IL1R2_FAM20A_RETN_MMP8;

[0470] SIGLEC1_ISG15_IL1R2_FAM20A_RETN_MMP8; and

[0471] SIGLEC1_IL1R2_FAM20A_OLAH_RETN_MMP8.

[0472] According to a preferred variant of this embodiment, step (a) comprises or consists of: measuring the expression of the target viral genes IFI27 and SIGLEC1, another target viral gene selected from IFIT1, HERC6, ISG15 and ISG15, the target bacterial genes FAM20A and MMP8, and another target bacterial gene selected from OLAH and IL1R2.

[0473] According to another preferred variant of this embodiment, step (a) comprises or consists of: measuring the expression of a combination of six target genes selected from those listed in Table 10, and preferably those for which the area under the ROC curve of the model in this table is at least 0.86, at least 0.88, and most particularly at least 0.90.

[0474] According to another specific embodiment, step (a) comprises or consists of measuring the expression of at least seven target genes.

[0475] According to a variant of this specific embodiment, step (a) comprises or consists of measuring the expression of the target gene SIGLEC1, and six other target genes selected from ISG15, HERC6, OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

[0476] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of the target gene MMP8, and six other target genes selected from ISG15, HERC6, SLC1A2, IL1R2, FAM20A, OLAH, RETN and SIGLEC1.

[0477] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1 and MMP8, and at least four other target genes selected from ISG15, HERC6, IL1R2, SLC1A2, OLAH, FAM20A and RETN, preferably selected from ISG15, HERC6, IL1R2, OLAH, FAM20A and RETN.

[0478] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1 and ISG15, and five other target genes selected from HERC6, SLC1A2, IL1R2, FAM20A, OLAH, RETN and MMP8.

[0479] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1, ISG15 and HERC6, and four other target genes selected from ISLC1A2, IL1R2, FAM20A, OLAH, RETN and MMP8.

[0480] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1, FAM20A and MMP8, and at least three other target genes selected from ISG15, HERC6, IL1R2, SLC1A2, OLAH and RETN, preferably selected from ISG15, HERC6, IL1R2, OLAH and RETN.

[0481] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of the target genes SIGLEC1, FAM20A, IL1R2 and MMP8, and at least two other target genes selected from ISG15, HERC6, SLC1A2, OLAH and RETN, preferably selected from ISG15, HERC6, OLAH and RETN.

[0482] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of seven target genes selected from the following combination:

[0483] SIGLEC1_ISG15_HERC6_IL1R2_FAM20A_OLAH_MMP8;

[0484] SIGLEC1_ISG15_SLC1A2_IL1R2_FAM20A_OLAH_MMP8;

[0485] IGLEC1_HERC6_SLC1A2_IL1R2_FAM20A_OLAH_MMP8;

[0486] SIGLEC1_ISG15_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0487] SIGLEC1_ISG15_HERC6_IL1R2_FAM20A_RETN_MMP8;

[0488] SIGLEC1_HERC6_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0489] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_FAM20A_MMP8;

[0490] SIGLEC1_ISG15_SLC1A2_IL1R2_FAM20A_RETN_MMP8;

[0491] SIGLEC1_SLC1A2_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0492] SIGLEC1_HERC6_SLC1A2_IL1R2_FAM20A_RETN_MMP8;

[0493] SIGLEC1_ISG15_HERC6_SLC1A2_FAM20A_OLAH_MMP8;

[0494] SIGLEC1_ISG15_SLC1A2_FAM20A_OLAH_RETN_MMP8;

[0495] SIGLEC1_ISG15_SLC1A2_IL1R2_FAM20A_OLAH_RETN;

[0496] SIGLEC1_HERC6_SLC1A2_FAM20A_OLAH_RETN_MMP8;

[0497] SIGLEC1_ISG15_HERC6_IL1R2_FAM20A_OLAH_RETN;

[0498] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_FAM20A_OLAH;

[0499] SIGLEC1_ISG15_HERC6_FAM20A_OLAH_RETN_MMP8;

[0500] SIGLEC1_HERC6_SLC1A2_IL1R2_FAM20A_OLAH_RETN;

[0501] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_FAM20A_RETN;

[0502] SIGLEC1_ISG15_HERC6_SLC1A2_FAM20A_OLAH_RETN;

[0503] ISG15_HERC6_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0504] SIGLEC1_ISG15_HERC6_SLC1A2_FAM20A_RETN_MMP8;

[0505] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_OLAH_MMP8;

[0506] SIGLEC1_ISG15_SLC1A2_IL1R2_OLAH_RETN_MMP8;

[0507] ISG15_HERC6_SLC1A2_IL1R2_FAM20A_RETN_MMP8;

[0508] ISG15_HERC6_SLC1A2_IL1R2_FAM20A_OLAH_MMP8;

[0509] SIGLEC1_HERC6_SLC1A2_IL1R2_OLAH_RETN_MMP8;

[0510] ISG15_HERC6_SLC1A2_IL1R2_FAM20A_OLAH_RETN;

[0511] HERC6_SLC1A2_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0512] SIGLEC1_ISG15_HERC6_IL1R2_OLAH_RETN_MMP8;

[0513] SIGLEC1_ISG15_HERC6_SLC1A2_OLAH_RETN_MMP8;

[0514] ISG15_HERC6_SLC1A2_FAM20A_OLAH_RETN_MMP8;

[0515] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_OLAH_RETN;

[0516] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_RETN_MMP8;

[0517] ISG15_SLC1A2_IL1R2_FAM20A_OLAH_RETN_MMP8; and

[0518] ISG15_HERC6_SLC1A2_IL1R2_OLAH_RETN_MMP8.

[0519] Preferably, according to this variant, the measuring step comprises or consists of measuring the expression of seven target genes selected from the following combination:

[0520] SIGLEC1_ISG15_SLC1A2_IL1R2_FAM20A_OLAH_MMP8;

[0521] IGLEC1_HERC6_SLC1A2_IL1R2_FAM20A_OLAH_MMP8;

[0522] SIGLEC1_ISG15_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0523] SIGLEC1_ISG15_HERC6_IL1R2_FAM20A_RETN_MMP8;

[0524] SIGLEC1_HERC6_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0525] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_FAM20A_MMP8; and

[0526] SIGLEC1_ISG15_SLC1A2_IL1R2_FAM20A_RETN_MMP8.

[0527] According to a preferred variant of this specific embodiment, step (a) comprises or consists of measuring the expression of the target viral genes IFI27 and SIGLEC1, two other target viral genes selected from IFIT1, OAS1, HERC6 and ISG15, the target bacterial genes FAM20A and MMP8, and another target bacterial gene selected from OLAH and IL1R2.

[0528] According to another preferred variation of this specific embodiment, step (a) comprises or consists of measuring the expression of a combination of seven target genes selected from those listed in Table 11, and preferably those whose area under the ROC curve of the model in this table shows an area of ​​at least 0.86, at least 0.88, and most particularly at least 0.90.

[0529] According to another specific embodiment, step (a) comprises or consists of measuring the expression of at least eight target genes.

[0530] According to a variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of SIGLEC1 and ISG15, and at least six other target genes selected from HERC6, SLC1A2, IL1R2, FAM20A, OLAH, RETN and MMP8.

[0531] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of SIGLEC1 and MMP8, and at least six other target genes selected from HERC6, ISG15, SLC1A2, IL1R2, FAM20A, OLAH and RETN.

[0532] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of SIGLEC1, MMP8 and ISG15, and at least five other target genes selected from HERC6, SLC1A2, IL1R2, FAM20A, OLAH and RETN.

[0533] According to another variant of this specific embodiment, the measuring step comprises or consists of measuring the expression of a combination of eight target genes selected from the following combinations:

[0534] SIGLEC1_ISG15_HERC6_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0535] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_FAM20A_OLAH_MMP8;

[0536] SIGLEC1_ISG15_SLC1A2_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0537] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_FAM20A_RETN_MMP8;

[0538] SIGLEC1_HERC6_SLC1A2_IL1R2_FAM20A_OLAH_RETN_MMP8;

[0539] SIGLEC1_ISG15_HERC6_SLC1A2_FAM20A_OLAH_RETN_MMP8;

[0540] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_FAM20A_OLAH_RETN;

[0541] ISG15_HERC6_SLC1A2_IL1R2_FAM20A_OLAH_RETN_MMP8 and

[0542] SIGLEC1_ISG15_HERC6_SLC1A2_IL1R2_OLAH_RETN_MMP8.

[0543] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of a combination of eight target genes selected from those listed in Table 12, and preferably those whose area under the ROC curve of the model exhibits a value of at least 0.87, at least 0.88, and most particularly at least 0.89.

[0544] According to another specific embodiment, the method comprises the step of measuring changes in expression of at least nine target genes.

[0545] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of a combination of nine target genes selected from those listed in Table 13, and preferably those whose area under the ROC curve of the model exhibits a value of at least 0.87, at least 0.88, and most particularly at least 0.89.

[0546] According to another specific embodiment, the method comprises the step of measuring changes in expression of ten target genes.

[0547] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of a combination of ten target genes selected from those listed in Table 14, and preferably those whose area under the ROC curve of the model exhibits a value of at least 0.87, at least 0.88, and most particularly at least 0.89.

[0548] According to another specific embodiment, the method comprises the step of measuring changes in expression of at least eleven target genes.

[0549] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of a combination of eleven target genes selected from those listed in Table 15, and preferably those whose area under the ROC curve of the model exhibits at least at least 0.86, and most particularly at least 0.87.

[0550] According to another specific embodiment, the method comprises the step of measuring changes in expression of at least twelve target genes.

[0551] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of a combination of twelve target genes selected from those listed in Table 16, and preferably those whose area under the ROC curve of the model exhibits at least at least 0.86, and most particularly at least 0.87.

[0552] According to another specific embodiment, the method comprises the step of measuring changes in expression of at least thirteen target genes.

[0553] According to another variant of this specific embodiment, step (a) comprises or consists of measuring the expression of a combination of thirteen target genes selected from those listed in Table 17.

[0554] In this specification, the term "biological sample" refers to any sample derived from a subject, which may be of different natures, such as blood or its derivatives, sputum, urine, feces, skin, cerebrospinal fluid, bronchoalveolar lavage fluid, peritoneal puncture fluid, saliva, gastric secretions, sperm, semen, tears, spinal cord, trigeminal ganglion, adipose tissue, lymphatic tissue, placental tissue, gastrointestinal tissue, reproductive tract tissue or central nervous system tissue.

[0555] The expression "reference biological sample" or "control sample" refers to a biological sample used for comparison with the expression level of the target gene and optionally the expression level of additional genes in the biological sample to be tested. The reference biological sample has the same properties as the biological sample to be tested, or at least has compatible properties to constitute a reference for determining the expression level of the target gene. The sample is taken from a subject suffering from a bacterial or viral infection, or from a pool of biological samples all taken from patients suffering from infections of the same nature (i.e., viral or bacterial).

[0556] According to a specific embodiment, the reference biological sample is calibrated to contain the amount of transcripts of at least two target genes, and optionally the amount of transcripts of one or more additional genes, corresponding to an amount or concentration representing the expression level measured in a pool of samples from subjects exhibiting bacterial or viral infections. In other words, the reference biological sample is calibrated to contain the average transcript amount of the target gene obtained from a pool of samples from subjects with bacterial infections or from subjects with viral infections.

[0557] In particular, the biological sample can be a biological fluid, such as a blood sample or a blood-derived sample, which can in particular be selected from whole blood (collected from a vein, i.e. comprising white and red blood cells, platelets and plasma), plasma, serum and any type of cells extracted from blood, such as peripheral blood mononuclear cells (PBMC, comprising B lymphocytes, T lymphocytes, NK cells, dendritic cells and monocytes), B and T cell subsets, purified monocytes or neutrophils.

[0558] According to a preferred embodiment, the biological sample used in the method according to the invention is a blood sample, preferably a whole blood sample.

[0559] According to another specific embodiment, the subject is a patient in a hospital, preferably a patient in the emergency department, resuscitation department, intensive care unit (ICU) or continuous care unit, most particularly a patient in the emergency department.

[0560] According to a preferred embodiment, the subject is a patient less than 6 years old, preferably less than 4 years old, and more preferably less than 2 years old. According to this embodiment, the patient may be in an emergency department, particularly a pediatric emergency department.

[0561] According to a specific embodiment, the method allows identifying the nature of the infection with a sensitivity of at least 80%, 85%, 90% or even 95%. The sensitivity corresponds to the probability of correctly identifying the viral or bacterial nature of the infection when the subject is infected and can be defined by the following formula:

[0562]

[0563] According to a particular embodiment, the method allows identifying the nature of the infection with a specificity of at least 80%, 85%, 90% or even at least 95%.

[0564] Specificity corresponds to the probability of misidentifying the viral or bacterial nature of an infection. In other words, identifying the presence of a viral infection when it is a bacterial infection and vice versa. Specificity can be defined by the following formula:

[0565]

[0566] The sensitivity and specificity of a diagnostic test (such as the method according to the invention) can also be summarized by a ROC (Receiver Operating Characteristic) curve, in particular the area under the ROC curve, which is well known to those skilled in the art.

[0567] Therefore, the method according to the present description allows identification of the viral or bacterial nature of an infection with a performance reflected by the area under the ROC curve of at least 0.85, at least 0.86, at least 0.87, at least 0.88, at least 0.89, and in particular of at least 0.90 for the best performing transcriptomic markers.

[0568] Although the performance of the method according to the invention is entirely satisfactory, in certain cases the measurement of changes in expression of a target gene may be supplemented by measuring changes in expression of additional genes.

[0569] Therefore, the method according to the present invention, in all its embodiments, may further comprise measuring changes in at least one additional gene selected from the group consisting of: PI3, EBI3, ADGRE1 and S100P.

[0570] These additional genes are also known to those skilled in the art and the chromosomal locations are given in Table 5 below:

[0571] [Table 5]:

[0572]

[0573] Similar to the above, for a given additional gene, the reference value corresponds to the expression level of the transcript of said gene, said gene being obtained from a reference biological sample of a subject suffering from an infection. Advantageously, in particular for a variant defined below, the reference value of a given additional gene corresponds to the average mRNA transcript level of said gene obtained from a reference biological sample of a population of subjects exhibiting an infection.

[0574] According to a first variant, the reference value of each additional gene is determined based on a reference biological sample from a subject suffering from a bacterial infection. Thus, when the comparison of the expression level of the additional gene at the mRNA transcript level relative to the corresponding reference value shows at least one expression change selected from the following, it can be judged that a viral infection is present:

[0575] - Low expression of PI3,

[0576] - Low expression of EBI3,

[0577] - low expression of ADGRE1, and

[0578] -Low expression of S100P.

[0579] According to a second variant, the reference value of each additional gene is determined based on a reference biological sample from a subject suffering from a viral infection. Thus, when the comparison of the expression level of the additional gene at the mRNA transcript level relative to the corresponding reference value shows at least one expression change selected from the following, it can be judged that a bacterial infection is present:

[0580] - Overexpression of PI3,

[0581] - Overexpression of EBI3,

[0582] - Overexpression of ADGRE1, and

[0583] - Overexpression of S100P.

[0584] According to a specific embodiment, the method according to the invention comprises measuring changes in the expression of all of the following target genes and additional genes: SIGLEC1, ISG15, HERC6, SLC1A2, IL1R2, FAM20A, OLAH, RETN, MMP8, RSAD2, IFI27, OAS1, IFIT1, IFI44L, PI3, EBI3, ADGRE1 and S100P.

[0585] Conclusions regarding the viral or bacterial nature of the infection are, as previously described, made based on the over- or under-expression of said genes (according to established reference values).

[0586] Therefore, according to a specific embodiment, the method comprises the following steps:

[0587] - obtaining a biological sample of blood, preferably whole blood, from a subject suffering from an infection,

[0588] - contacting the biological sample with an agent that is specific for the expression products of one or more viral genes described herein and for the expression products of at least one target bacterial gene selected from the group consisting of OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, and optionally for the expression products of one or more additional genes selected from the group consisting of PI3, EBI3, ADGRE1 and S100P,

[0589] - measuring the expression of said target gene, and optionally the expression of said additional gene.

[0590] According to a preferred embodiment, the method comprises the following steps:

[0591] - obtaining a biological sample of blood, preferably whole blood, from a subject suffering from an infection,

[0592] - contacting the biological sample with an agent that is specific for the expression product of at least one target viral gene selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1, IFI44L described in the present specification, and for the expression product of at least one target bacterial gene selected from SLC1A2, IL1R2, FAM20A, OLAH, RETN and MMP8, and optionally for the expression product of one or more additional genes selected from PI3, EBI3, ADGRE1 and S100P,

[0593] - measuring the expression of said target gene, and optionally the expression of said additional gene.

[0594] Another subject of the present invention relates to a kit for measuring in vitro or ex vivo the expression of at least one target viral gene selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1, IFI44L and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, the kit comprising a reagent specific for the expression product of the target gene.

[0595] According to a specific embodiment, the kit includes reagents specific for the expression products of at least three target genes, four target genes, five target genes, six target genes, seven target genes, eight target genes, or all target genes.

[0596] Most particularly, said kit allows the implementation of the method according to the invention.Thus, the kit according to the invention can advantageously be used to determine the viral or bacterial nature of an infection.

[0597] Therefore, all specific and preferred embodiments described for the method according to the invention, in particular the combination of target genes whose expression is measured, also apply to the kit.

[0598] Specific reagents for measuring gene expression are known to those skilled in the art and, according to one embodiment, include amplification primers and / or hybridization probes.

[0599] Such reagents allow for quantitative determination of transcript levels of the selected gene in a biological test sample. As previously mentioned, the transcript levels determined may not directly correspond to the amount of transcript present in the biological sample, but may be derived values ​​representing the amount of transcript. Specifically, in a conventional manner, quantitative determinations may include steps such as amplification and / or standardization and / or calculation of ratios.

[0600] The term "kit" refers to a set of products and / or tools used together, in particular for determining the transcript level of a target gene defined in the present invention. The necessary reagents may or may not be integrated in the same kit or device.

[0601] The term "primer" or "amplification primer" refers to a nucleotide fragment, which may consist of 5 to 100 nucleotides, preferably 15 to 30 nucleotides, and has hybridization specificity with a target nucleotide sequence under conditions determined for initiating enzymatic polymerization, such as in an enzymatic amplification reaction of a target nucleotide sequence. Typically, a "primer pair" consisting of two primers is used. When it is desired to amplify a variety of different biomarkers (e.g., a gene or mRNA of the gene), it is preferred to use a variety of different primer pairs, each primer pair preferably having the ability to specifically hybridize with different biomarkers.

[0602] A person skilled in the art is fully capable of determining the nucleotide sequences of primers allowing the amplification of transcripts from gene sequences, and in particular from the sequences of corresponding transcripts, such as those listed in Table 2.

[0603] According to a specific embodiment, the kit contains primers comprising or consisting of nucleotide sequences complementary to at least a portion of the transcript sequences shown in Table 2 above.

[0604] The term "probe" or "hybridization probe" refers to a nucleotide fragment generally consisting of 5 to 100 nucleotides, preferably 15 to 90 nucleotides, and even more preferably 15 to 35 nucleotides, which has hybridization specificity under conditions that determine the formation of a hybridization complex with a target nucleotide sequence. The probe also includes a reporter molecule (such as a fluorophore, an enzyme or any other detection system) that will be able to detect the target nucleotide sequence. In the present invention, the target nucleotide sequence can be a nucleotide sequence contained in a messenger RNA (mRNA) or a nucleotide sequence contained in a complementary DNA (cDNA) obtained by reverse transcription of the mRNA. When it is desired to target a variety of different biomarkers (e.g., a gene or an mRNA of the gene), it is preferred to use a variety of different probes, each of which preferably has the ability to specifically hybridize with different biomarkers.

[0605] The term "hybridization" refers to a process in which two nucleotide fragments with sufficiently complementary sequences, such as a hybridization probe and a target nucleotide fragment, can form a double-stranded chain with stable and specific hydrogen bonds under appropriate conditions.

[0606] A nucleotide fragment "capable of hybridizing to a polynucleotide" is a fragment that is capable of hybridizing to said polynucleotide under hybridization conditions, which can be determined in a known manner in each case. The hybridization conditions are determined by the stringency, i.e. the stringency of the operating conditions. The higher the stringency with which the hybridization is performed, the greater the specificity of the hybridization.

[0607] The definition of stringency is particularly based on the base composition of the probe / target duplex, and also depends on the degree of mismatch between the two nucleic acids. Stringency can also be based on reaction parameters, such as the concentration and type of ionic species present in the hybridization solution, the nature and concentration of denaturing agents, and / or the hybridization temperature. The stringency of the conditions under which hybridization reactions must be performed will depend primarily on the hybridization probe used. All of this information is well known, and those skilled in the art can determine suitable conditions.

[0608] Typically, the temperature of the hybridization reaction is between about 20 and 70° C., depending on the length of the hybridization probe used, and in particular between 35 and 65° C. in a physiological saline solution at a concentration of about 0.5 to 1 M. This is followed by a step of detecting the hybridization reaction.

[0609] According to a preferred embodiment, the kit comprises a control sample calibrated to contain an amount of transcripts of at least two target genes and optionally one or more additional genes, corresponding to an amount or concentration representing the expression levels measured in a pool of samples from subjects exhibiting bacterial infections, and / or a control sample calibrated to contain an amount of transcripts of at least two target genes and optionally one or more additional genes, corresponding to an amount or concentration representing the expression levels measured in a pool of samples from subjects exhibiting viral infections.

[0610] In other words, the control sample is calibrated to contain the average transcript amount of the target gene obtained from a pool of samples from subjects exhibiting bacterial infection or from subjects exhibiting viral infection.

[0611] According to one embodiment, a reagent specific for target gene expression, more precisely, an amplification product and / or a detection product, such as a primer or a probe, can be bound to the same solid support. Therefore, as previously described, the kit may include a solid support comprising one or more oligonucleotides suitable for determining the transcription level of the or each target gene, or even one or more oligonucleotides suitable for determining the transcription level of the or each selected housekeeping gene, or even one or more oligonucleotides suitable for detecting at least one target gene. Such solid supports are well known to those skilled in the art and are particularly described in patent applications WO 2008 / 140568 and WO 2017 / 093672, and further details may refer to these patent applications.

[0612] In all embodiments thereof, the kit may further comprise a reagent specific for the expression product of one or more additional genes selected from the group consisting of PI3, EBI3, ADGRE1 and S100P, and combinations thereof.

[0613] In the same manner as defined above, the kit may also include additional genes and / or threshold values ​​for expression levels of (positive or negative) control samples of said additional genes.

[0614] In all its embodiments, the kit may further comprise a reagent specific for the expression product of one or more housekeeping genes.Herein again, the kit according to the invention may comprise a reagent specific for the expression product of each selected housekeeping gene.

[0615] According to a specific embodiment, the kit is in the form of a consumable product, which integrates nucleic acid purification, multiplex nested PCR and detection in one A single consumable in the form of a box or pouch. This consumable is advantageous for use with V2.0 is used with the Torch system.

[0616] Another subject matter relates to the use of a kit as defined above for determining the nature of a viral or bacterial infection in a subject.

[0617] Another subject of the present description relates to a method comprising quantitatively measuring (in particular by RT-qPCR) the mRNA of at least one target viral gene selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1, IFI44L and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, and optionally one or more additional genes as defined above, in a biological blood sample from a subject presenting with an infection.

[0618] The present description also relates to a method as defined hereinbefore for determining the nature of a viral or bacterial infection in an infected subject, the method further comprising the step of treating the viral or bacterial infection.

[0619] According to a specific embodiment, when a viral infection is identified, the treatment comprises administering at least one antiviral agent. Those skilled in the art will be able to select the most suitable antiviral agent from known agents. For example, the antiviral agent may be selected from the following agents: amantadine; rimantadine; ritonavir; cobicistat; interferon α-2b / ribavirin; ombitasvir / paritaprevir / ritonavir; peginterferon α-2a; peginterferon α-2b; maraviroc; raltegravir; dolute gravir; elvitegravir; sofosbuvir; enfuvirtide; foscarnet; fomivirsen; zanamivir; oseltamivir; peramivir; nevirapine; etravirine; efavirenz; rilpivirine; delavirdine; nevirapine nevirapine, daclatasvir, entecavir, lamivudine, adefovir, didanosine, tenofovir, abacavir, lamivudine, zidovudine, stavudine, emtricitabine, zalcitabine, telbivudine, didanosine, boceprevir boceprevir; simeprevir; telaprevir; lopinavir; fosamprenavir; darunavir; ritonavir; tipranavir; atazanavir; nelfinavir; amprenavir; indinavir; saquinavir; ribavirin;valacyclovir; famciclovir; acyclovir; ganciclovir; valganciclovir; cidofovir. ;

[0620] According to a specific embodiment, when a viral infection is identified, treatment includes administering at least one antibiotic. Those skilled in the art can select the most suitable antibiotic from known antibiotics. For example, the antibiotic can be selected from the following antibiotics: erythromycin, clindamycin, gentamicin, tetracycline, amoxicillin, amikacin, aztreonam, chloramphenicol, ceftazidime, clindamycin, cephalothin, ciprofloxacin, colistin, cefotetan, cefotaxime, erythromycin, fusidic acid, fosfomycin, cefoxitin, furan, gentamicin, imipenem, kanamycin, lincomycin, cefmandol, minocycline, latamoxef, metronidazole, nalidixic acid, netilmicin, oxacillin, benzylpenicillin, pefloxacin, piperacillin, pristinamycin, rifampicin, spiramycin, sulfonamides, streptomycin, trimethoprim, sulfamethoxazole, tetracycline, Teicoplanin, ticarcillin, tobramycin, trimethoprim, vancomycin, meclocycline, sulfacetamide, ceftobiprole, ceftaroline, dalbavancin, daptomycin, linezolid, mupirocin, oritavancin, telavancin, tigecycline, vancomycin, aminoglycosides, carbapenems, ceftazidime, cefepime, ceftobiprole, fluoroquinolones, piperacillin / tazobactam, ticarcillin / clavulanic acid, linezolid, streptogramins, daptomycin, amikacin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, spectinomycin, geldanamycin, herbimycin, and rifaximin.

[0621] The invention is illustrated in a non-limiting manner by the following examples.

[0622] Example

[0623] 1. Materials and Methods

[0624] 1.1 Clinical characteristics of patients and samples

[0625] During the patient's stay in the emergency department (D0), according to the manufacturer's recommendations, Whole blood clinical samples were collected in tubes. A total of 191 samples were collected, broken down as follows: 68 samples from characteristic bacterial infections and 123 samples from characteristic viral infections.

[0626] The sources and distribution of the samples are summarized as follows:

[0627] Patients: Female - 82 (42.9%); Male 109 (57.1%)

[0628] Average age: 3.4 years

[0629] Bacterial infection (Gram-), n (%): 28 (14.6)

[0630] Bacterial infection (Gram+), n (%): 24 (12.6)

[0631] Possible bacterial infection, n (%): 16 (8.4)

[0632] Virus infection, n (%): 123 (64.4)

[0633] 1.2. Identification and validation of biomarkers

[0634] Initial selection of transcriptomic biomarker signatures for viral and bacterial infections was performed using the applicant's in-house database. As a result, hundreds of biomarkers were identified.

[0635] For each biomarker, multiple scores were then assigned to evaluate a variety of criteria, in particular, expression based on RNAseq data from sample libraries, ability to distinguish between viral and bacterial infections based on microarray data from public databases, and the ability to develop assays for use in automated PCR systems (e.g. ) in the ability of the primer pair to amplify.

[0636] Taking into account the different scores obtained for each biomarker, an overall score was calculated to allow for optimal selection and identification of the most promising biomarkers for identifying the nature of the infection.

[0637] Then, in order to finally validate the identified biomarkers, the patient samples were divided into two data sets. The first set, called the "Train" set (n=128), was used to train the learning model based on the data, while the second set, called the "TEST" set (n=63), was used for independent performance validation.

[0638] To evaluate the performance of individual biomarkers, the area under the ROC curve was calculated with 95% confidence interval (CI95%). Regarding the combined performance, the analysis was performed using a sophisticated machine learning based classifier using R version 3.6.1.

[0639] Two methods were used to assess the importance of variables. The first is the "explain" function in the FastShap package, which is derived from game theory. Rewards (weights) are given to the biomarkers that contribute most to the classification of patients and allow identification of the nature of the infection (viral or bacterial) in the machine learning model.

[0640] The second method is the “FeatureImp” function in the iml package, which returns the coefficient by which the model prediction error increases when features are mixed.

[0641] Ultimately, this selection allowed the identification of viral biomarkers, particularly those involved in the interferon pathway and the class II MHC-mediated antigen presentation pathway, as well as bacterial biomarkers, including SLC1A2, IL1R2, FAM20A, OLAH, RETN, and MMP8.

[0642] The performance was also evaluated and confirmed on two other machine learning models, namely, random forest and partial least squares discriminant (PLS) regression.

[0643] 2. Results

[0644] 2.1 Box plot

[0645] Boxplot analysis revealed overexpression / underexpression of different target genes depending on the nature of infection. Thus, when comparing target gene expression between viral and bacterial infection, SLC1A2, IL1R2, FAM20A, OLAH, RETN, and MMP genes were found to be overexpressed during bacterial infection, whereas SIGLEC1, ISG15, HERC6, IFI44L, RSAD2, IFI27, OAS1, and IFIT1 genes were overexpressed during viral infection.

[0646] 2.2 Performance analysis of biomarkers according to the present invention

[0647] The following table shows the performance of target genes for determining the viral or bacterial nature of an infection in the method according to the invention. For each model, the performance was evaluated multiple times, so the AUC of the model corresponds to the average of the different AUCs obtained.

[0648] Performance obtained based on double gene combination to identify the viral or bacterial nature of infection:

[0649] [Table 6]

[0650]

[0651]

[0652]

[0653] Performance obtained by identifying the viral or bacterial nature of infection based on a three-gene panel:

[0654] [Table 7]

[0655]

[0656]

[0657]

[0658]

[0659]

[0660]

[0661]

[0662]

[0663]

[0664] Performance obtained based on identification of the viral or bacterial nature of infection based on a four-gene panel:

[0665] [Table 8]

[0666]

[0667]

[0668]

[0669]

[0670]

[0671]

[0672]

[0673]

[0674]

[0675]

[0676]

[0677]

[0678]

[0679]

[0680]

[0681]

[0682]

[0683]

[0684]

[0685]

[0686]

[0687]

[0688]

[0689]

[0690]

[0691]

[0692]

[0693]

[0694]

[0695]

[0696] Performance obtained by identifying the viral or bacterial nature of infection based on a five-gene panel:

[0697] [Table 9]

[0698]

[0699]

[0700]

[0701]

[0702]

[0703]

[0704]

[0705]

[0706]

[0707]

[0708]

[0709]

[0710]

[0711]

[0712]

[0713]

[0714]

[0715]

[0716]

[0717]

[0718]

[0719]

[0720]

[0721]

[0722]

[0723]

[0724]

[0725]

[0726]

[0727]

[0728]

[0729]

[0730]

[0731]

[0732]

[0733]

[0734]

[0735]

[0736]

[0737]

[0738]

[0739]

[0740]

[0741]

[0742]

[0743]

[0744]

[0745]

[0746]

[0747]

[0748]

[0749]

[0750]

[0751]

[0752]

[0753]

[0754]

[0755]

[0756]

[0757]

[0758]

[0759]

[0760]

[0761]

[0762]

[0763]

[0764] Performance obtained by identifying the viral or bacterial nature of infection based on a six-gene panel:

[0765] [Table 10]

[0766]

[0767]

[0768]

[0769]

[0770]

[0771]

[0772]

[0773]

[0774]

[0775]

[0776]

[0777]

[0778]

[0779]

[0780]

[0781]

[0782]

[0783]

[0784]

[0785]

[0786]

[0787]

[0788]

[0789]

[0790]

[0791]

[0792]

[0793]

[0794]

[0795]

[0796]

[0797]

[0798]

[0799]

[0800]

[0801]

[0802]

[0803]

[0804]

[0805]

[0806]

[0807]

[0808]

[0809]

[0810]

[0811]

[0812]

[0813]

[0814]

[0815]

[0816]

[0817]

[0818]

[0819]

[0820]

[0821]

[0822]

[0823]

[0824]

[0825]

[0826]

[0827]

[0828]

[0829]

[0830]

[0831]

[0832]

[0833]

[0834]

[0835]

[0836]

[0837]

[0838]

[0839]

[0840]

[0841]

[0842]

[0843]

[0844]

[0845]

[0846]

[0847]

[0848]

[0849]

[0850]

[0851]

[0852]

[0853]

[0854]

[0855]

[0856]

[0857]

[0858]

[0859]

[0860]

[0861]

[0862]

[0863]

[0864]

[0865]

[0866]

[0867]

[0868]

[0869] Performance obtained based on seven-gene panel to identify the viral or bacterial nature of infection:

[0870] [Table 11]

[0871]

[0872]

[0873]

[0874]

[0875]

[0876]

[0877]

[0878]

[0879]

[0880]

[0881]

[0882]

[0883]

[0884]

[0885]

[0886]

[0887]

[0888]

[0889]

[0890]

[0891]

[0892]

[0893]

[0894]

[0895]

[0896]

[0897]

[0898]

[0899]

[0900]

[0901]

[0902]

[0903]

[0904]

[0905]

[0906]

[0907]

[0908]

[0909]

[0910]

[0911]

[0912]

[0913]

[0914]

[0915]

[0916]

[0917]

[0918]

[0919]

[0920]

[0921]

[0922]

[0923]

[0924]

[0925]

[0926]

[0927]

[0928]

[0929]

[0930]

[0931]

[0932]

[0933]

[0934]

[0935]

[0936]

[0937]

[0938]

[0939]

[0940]

[0941]

[0942]

[0943]

[0944]

[0945]

[0946]

[0947]

[0948]

[0949]

[0950]

[0951]

[0952]

[0953]

[0954]

[0955]

[0956]

[0957]

[0958]

[0959]

[0960]

[0961]

[0962]

[0963]

[0964]

[0965]

[0966]

[0967]

[0968]

[0969]

[0970]

[0971]

[0972]

[0973]

[0974]

[0975]

[0976]

[0977]

[0978]

[0979]

[0980]

[0981]

[0982]

[0983]

[0984]

[0985]

[0986]

[0987]

[0988]

[0989]

[0990]

[0991] Performance obtained based on eight-gene panel to identify the viral or bacterial nature of infection:

[0992] [Table 12]

[0993]

[0994]

[0995]

[0996]

[0997]

[0998]

[0999]

[1000]

[1001]

[1002]

[1003]

[1004]

[1005]

[1006]

[1007]

[1008]

[1009]

[1010]

[1011]

[1012]

[1013]

[1014]

[1015]

[1016]

[1017]

[1018]

[1019]

[1020]

[1021]

[1022]

[1023]

[1024]

[1025]

[1026]

[1027]

[1028]

[1029]

[1030]

[1031]

[1032]

[1033]

[1034]

[1035]

[1036]

[1037]

[1038]

[1039]

[1040]

[1041]

[1042]

[1043]

[1044]

[1045]

[1046]

[1047]

[1048]

[1049]

[1050]

[1051]

[1052]

[1053]

[1054]

[1055]

[1056]

[1057]

[1058]

[1059]

[1060]

[1061]

[1062]

[1063]

[1064]

[1065]

[1066]

[1067]

[1068]

[1069]

[1070]

[1071]

[1072]

[1073]

[1074]

[1075]

[1076]

[1077]

[1078]

[1079]

[1080]

[1081]

[1082]

[1083]

[1084]

[1085]

[1086]

[1087]

[1088]

[1089]

[1090]

[1091]

[1092]

[1093]

[1094]

[1095]

[1096]

[1097] Performance obtained based on a nine-gene panel to identify the viral or bacterial nature of the infection:

[1098] [Table 13]

[1099]

[1100]

[1101]

[1102]

[1103]

[1104]

[1105]

[1106]

[1107]

[1108]

[1109]

[1110]

[1111]

[1112]

[1113]

[1114]

[1115]

[1116]

[1117]

[1118]

[1119]

[1120]

[1121]

[1122]

[1123]

[1124]

[1125]

[1126]

[1127]

[1128]

[1129]

[1130]

[1131]

[1132]

[1133]

[1134]

[1135]

[1136]

[1137]

[1138]

[1139]

[1140]

[1141]

[1142]

[1143]

[1144]

[1145]

[1146]

[1147]

[1148]

[1149]

[1150]

[1151]

[1152]

[1153]

[1154]

[1155]

[1156]

[1157]

[1158]

[1159]

[1160]

[1161]

[1162]

[1163]

[1164]

[1165]

[1166]

[1167]

[1168]

[1169] Performance obtained by identifying the viral or bacterial nature of infection based on a target 10-gene panel:

[1170] [Table 14]

[1171]

[1172]

[1173]

[1174]

[1175]

[1176]

[1177]

[1178]

[1179]

[1180]

[1181]

[1182]

[1183]

[1184]

[1185]

[1186]

[1187]

[1188]

[1189]

[1190]

[1191]

[1192]

[1193]

[1194]

[1195]

[1196]

[1197]

[1198]

[1199]

[1200]

[1201]

[1202]

[1203]

[1204]

[1205]

[1206]

[1207]

[1208]

[1209]

[1210]

[1211]

[1212]

[1213]

[1214]

[1215]

[1216]

[1217]

[1218]

[1219]

[1220]

[1221]

[1222]

[1223]

[1224]

[1225]

[1226]

[1227]

[1228]

[1229]

[1230]

[1231]

[1232]

[1233]

[1234]

[1235]

[1236] Performance obtained by identifying the viral or bacterial nature of infection based on a target 11-gene panel:

[1237] [Table 15]

[1238]

[1239]

[1240]

[1241]

[1242]

[1243]

[1244]

[1245]

[1246]

[1247]

[1248]

[1249]

[1250]

[1251]

[1252]

[1253]

[1254]

[1255]

[1256]

[1257]

[1258]

[1259]

[1260]

[1261]

[1262]

[1263] Performance obtained by identifying the viral or bacterial nature of infection based on a target 12-gene panel:

[1264] [Table 16]

[1265]

[1266]

[1267]

[1268]

[1269]

[1270]

[1271]

[1272] Performance obtained by identifying the viral or bacterial nature of infection based on a target 13-gene panel:

[1273] [Table 17]

[1274]

[1275] Performance obtained by identifying the viral or bacterial nature of infection based on a target 14-gene panel:

[1276] [Table 18]

[1277]

[1278]

[1279] Performance obtained for identifying the viral or bacterial nature of infection based on a combination of 14 target genes and 4 additional genes:

[1280] [Table 19]

[1281]

[1282] Thus, the transcriptomic signature according to the invention allows determining the viral or bacterial nature of the infection in infected patients with a robust performance level, since the AUC obtained on the test set is generally greater than or equal to the AUC obtained on the training set.

[1283] References

[1284] Takeuchi O, Akira S(2010), "Pattern recognition receptors andinflammation"; Cell 140(6):805–820. Ramilo O, Mejías A. (2009), "Shifting the paradigm: Host gene signatures for diagnosis of infectious diseases"; Cell HostMicrobe 6(3):199–200.

[1285] Fauci, AS et al. (2014), "The perpetual challenge of antimicrobialresistance"; JAMA 311, 1853–1854.

[1286] Hu et al.(2013),“Gene expression profiles in febrile children withdefined viral and bacterial infection”;PNAS12792-12797,vol.110,No.31.

[1287] Eric D.Brown et al.(2016),“Antibacterial drug discovery in theresistance era”-Review–doi:10.1038 / nature17042.

[1288] Ephraim L.Tsalik et al.(2021),“Discriminating bacterial and viralinfection using a rapid host gene expression test”;Critical Care Medicine–Vol.49,No.10.

[1289] Mark A.Poritz et al.(2011),“FilmArray,an automated Nested MultiplexPCR System for Multi-Pathogen Detection:development and application torespiratory tract infection”,PLoS ONE 6(10):e26047.

[1290] William M.Schneider et al.(2014),“Interferon-stimulated genes:acomplex web of host response”Annu.Rev.Immunol.2014;32:513–545.doi:10.1146 / annurev-immunol-032713-120231.

[1291] Emily Yang et al.(2020),“All about the RNA:interferon-stimulatedgenes that interfere with viral RNA processes”;Front.Immunol.11:605024.

[1292] Trine H.Mogensen et al.(2001),“Molecular pathways in virus-inducedcytokine production”;Microbiology and Molecular Biology Review,Mar.2001,pp.131-150.

[1293] Kawasaki et al.(2014),“Toll-like receptor signaling pathway”;Front.Immunol.,Sec.CancerImmunity and Immunotherapy.

[1294] Hochrainer et al.(2005),“The human HERC family of ubiquitin ligases:novel members,genomicorganization,expression profiling,and evolutionaryaspects”;Genomics 85 153-164

Claims

1. An in vitro or ex vivo method for determining the viral or bacterial nature of an infection from a biological sample of an infected or susceptible subject, wherein The following steps are involved: (a) measuring the expression of at least one target viral gene and at least one target bacterial gene selected from the group consisting of target bacterial genes OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, (b) comparing the expression measured in step (a) with a predetermined reference expression value of the target gene, and (c) drawing conclusions about the viral or bacterial nature of the infection based on the comparison.

2. The method according to claim 1, It is characterized in that The target viral genes are selected from target viral genes of the interferon pathway, the proinflammatory cytokine pathway, the Toll-like receptor signaling pathway, the RIG-I-like receptor signaling pathway, and the class II MHC-mediated antigen presentation pathway.

3. The method according to claim 1 or 2, It is characterized in that The target viral genes are selected from target viral genes involved in the interferon pathway and the class II MHC-mediated antigen presentation pathway.

4. The method according to claim 3, It is characterized in that The target viral gene is selected from IFI27, SIGLEC1, IFN-α, IFN-β, IFN-ε, IFN-κ, IFN-ω, IFN-γ, IFNL1, IFNL2, IFNL3, ADAR1, IFIT1, IFIT2, IFIT3, IFIT5, IFI44L, ISG15, ISG20, MDA5, OAS1, OAS2, OAS3, OASL, PARP12, PKR, RIG-I, RNaseL, RSAD2, RBBP6, SHFL, TRIM22, TRIM25, TRIM32, TRIM69, Viperin, ZAP, ZCCHC3, ZNFX1, HERC1, HERC2, HERC3, HERC4, HERC5, HERC6 and a combination thereof.

5. The method according to any one of claims 1 to 4, It is characterized in that Step (a) comprises or consists of measuring at least one target viral gene selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2.

6. The method according to claim 5, Features Step (a) includes measuring the expression of the target viral gene IFI27 and the expression of the target bacterial gene OLAH.

7. The method according to claim 6, Features Step (a) further comprises measuring the expression of the target bacterial gene FAM20A.

8. The method according to any one of claims 1 to 5, It is characterized in that The measuring step (a) comprises or consists of measuring the expression of two target viral genes selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, and the expression of two target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from OLAH, FAM20A, IL1R2 and MMP8.

9. The method according to any one of claims 1 to 5, It is characterized in that The measuring step (a) comprises or consists of: The expression of two to five target viral genes selected from SIGLEC1, ISG15, HERC6, RSAD2, IFI27, OAS1, IFIT1 and IFI44L, and the expression of three or four target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from OLAH, FAM20A, IL1R2 and MMP8, are measured.

10. The method according to claim 5, It is characterized in that The measuring step (a) comprises or consists of measuring the expression of the target viral gene IFI27 and optionally at least one other viral gene selected from SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, and the expression of at least two target bacterial genes selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from OLAH, FAM20A, IL1R2 and MMP8.

11. The method according to claim 5, It is characterized in that Step (a) comprises or consists of measuring at least one target viral gene selected from SIGLEC1, ISG15 and HERC6, and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from IL1R2, OLAH and FAM20A.

12. The method according to claim 5, It is characterized in that Step (a) comprises or consists of measuring at least one target viral gene selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, and the target bacterial gene OLAH and at least one other target bacterial gene selected from FAM20A, IL1R2, MMP8, RETN and SLC1A2, preferably selected from FAM20A, IL1R2 and MMP8.

13. The method according to claim 5, It is characterized in that The measuring step (a) comprises or consists of measuring at least one target viral gene selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1 and IFI44L, and the target bacterial gene FAM20A and at least one other target bacterial gene selected from OLAH, IL1R2, MMP8, RETN and SLC1A2, preferably OLAH, IL1R2 and MMP8.

14. The method according to claim 5, It is characterized in that Step (a) comprises or consists of measuring the expression of the target viral gene IFI27, the expression of another target viral gene selected from HERC6, SIGLEC1, IFI44L and ISG15, the expression of the target bacterial gene FAM20A and the expression of another target bacterial gene selected from OLAH and IL1R2.

15. The method according to claim 9, It is characterized in that Step (a) comprises or consists of measuring the expression of the target viral gene IFI27, the expression of two other target viral genes selected from SIGLEC1, HERC6, OAS1 and IFIT1, the expression of the target bacterial gene FAM20A and the expression of another target bacterial gene selected from OLAH, IL1R2 and MMP8.

16. The method according to claim 5, It is characterized in that Step (a) comprises or consists of measuring the expression of target viral genes IFI27 and SIGLEC1, the expression of another target viral gene selected from IFIT1, HERC6, ISG15 and ISG15, the expression of target bacterial genes FAM20A and MMP8 and the expression of another target bacterial gene selected from OLAH and IL1R2.

17. The method according to claim 5, It is characterized in that Step (a) comprises or consists of measuring the expression of target viral genes IFI27 and SIGLEC1, the expression of two other target viral genes selected from IFIT1, OAS1, HERC6 and ISG15, the expression of target bacterial genes FAM20A and MMP8 and the expression of another target bacterial gene selected from OLAH and IL1R2.

18. The method according to claim 1, It is characterized in that Step (a) consists of measuring a target viral and bacterial gene combination selected from the target gene combinations listed in Tables 6 to 12 and having an AUC of at least 0.90 for a model for determining the viral or bacterial nature of an infection.

19. The method according to any one of claims 5 to 18, It is characterized in that The predetermined reference expression value of the target gene corresponds to the corresponding expression of the target gene in a reference biological sample obtained from a subject suffering from a bacterial infection, and is characterized in that the infection is judged to be viral in nature when the comparison result of the target gene expression shows at least one expression change selected from the following: - Overexpression of SIGLEC1, - Overexpression of ISG15, - Overexpression of HERC6, - Overexpression of RSAD2, - Overexpression of IFI27, - Overexpression of OAS1, - Overexpression of IFIT1, and - Overexpression of IFI44L, and at least one other expression change selected from: - Low expression of SLC1A2, - Low expression of IL1R2, - Low expression of FAM20A, - Low expression of OLAH, -low expression of RETN, and -Low expression of MMP8.

20. The method according to any one of claims 5 to 18, It is characterized in that The predetermined reference expression value of the target gene corresponds to the corresponding expression of the target gene in a reference biological sample obtained from a subject suffering from a viral infection, and is characterized in that the infection is judged to be bacterial in nature when the comparison result of the target gene expression shows at least one expression change selected from the group consisting of: - Low expression of SIGLEC1, - Low expression of ISG15, - Low expression of HERC6, - Low expression of RSAD2, - Low expression of IFI27, - Low expression of OAS1, - Low expression of IFIT1, and - Low expression of IFI44L, and at least one other expression change selected from: - Overexpression of SLC1A2, - Overexpression of IL1R2, - Overexpression of FAM20A, - Overexpression of OLAH, -Overexpression of RETN, and - Overexpression of MMP8.

21. The method according to any one of claims 1 to 20, It is characterized in that It further comprises the step (a') of measuring the expression of at least one additional target gene selected from PI3, EBI3, ADGRE1 and S100P, and the step (b') of comparing the expression measured in step (a') with a reference expression value of the additional target gene.

22. The method according to any one of claims 1 to 21, It is characterized in that The expression of the target gene was measured at the mRNA level.

23. The method according to any one of claims 1 to 22, It is characterized in that The expression changes are measured by amplification by RT-PCR, preferably quantitative RT-PCR or nested PCR.

24. The method according to any one of claims 1 to 23, It is characterized in that The expression is normalized to the expression of one or more housekeeping genes, preferably selected from the group consisting of DECR1, HPRT1, PPIB, GAPDH and ACTB.

25. The method according to any one of claims 1 to 24, It is characterized in that The biological sample is taken from a pediatric subject, preferably a child under 4 years old, more preferably a child under 2 years old.

26. The method according to any one of claims 1 to 25, It is characterized in that The biological sample is a blood sample, preferably a whole blood sample.

27. A kit for measuring gene expression in a biological sample in vitro or ex vivo, the kit comprising a tool for determining changes in the expression levels of at least one target viral gene selected from IFI27, SIGLEC1, ISG15, HERC6, RSAD2, OAS1, IFIT1, IFI44L and at least one target bacterial gene selected from OLAH, FAM20A, IL1R2, MMP8, RETN and SLC1A2, the tool preferably being a primer or a probe.

28. Use of a kit according to claim 27 for determining the viral or bacterial nature of an infection from a biological sample of a subject.

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