Compositions and methods for detecting gastrointestinal pathogens

Abstract

Compositions, methods, kits, and uses are provided for detecting the presence of Salmonella, Shigella, Campylobacter, and Shigatoxigenic Escherichia coli (STEC) in a sample. In some embodiments, the compositions, methods, kits, and uses include one or more oligonucleotides, or the use of one or more oligonucleotides. In some embodiments, the methods are performed as a multiplex assay with separate primers / probes for C. jejuni and C. coli. Some of the oligonucleotides contain inosine and / or contain 5-methylcytosine substituted nucleotides. The use of cyclodextrin and / or polysorbate 20 in the amplification reaction is described.

Description

[Technical field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit under priority of U.S. Provisional Application No. 63 / 226,079, filed July 27, 2021, the disclosure of which is incorporated herein by reference in its entirety. [Background technology]

[0002] Introduction and Summary Bacterial gastroenteritis is a gastrointestinal inflammation that causes acute diarrhea (three or more episodes per day) lasting less than 14 days and may also include symptoms such as nausea, vomiting, and abdominal cramps. See Thielman and Guerrant, The New England Journal of Medicine, 350:38-47, 2004. It is estimated that there are more than 200 million cases of diarrheal disease per year in the United States, resulting in 73 million physician visits, 1.8 million hospitalizations, and up to 6,000 deaths. See Guerrant et al., Clinical Infectious Diseases, 32:331-350, 2001. According to Centers for Disease Control Food Net data (a compilation of data from 10 state health departments), in 2010, the number of reported infections and incidence rates per 100,000 population included: Salmonella (8256, 17.6), Campylobacter (6365, 13.6), and Shigella (1780, 3.8). See Centers for Disease Control and Prevention, “Vital Signs: Incidence and Trends of Infection with Pathogens Transmitted Commonly Through Food-Foodborne Diseases Active Surveillance Network, 10 US Sites, 1996-2010,” MMWR 60(22):749-755, 2011. These three bacteria, along with Shigatoxigenic Escherichia coli (STEC), are common causes of bacterial gastroenteritis. Populations at highest risk from bacterial gastroenteritis infections are children (≤5), the elderly, and immunocompromised individuals. However, infection can occur in all age groups. The mode of infection is typically via the fecal-oral route, from ingesting contaminated food or water, or as a result of poor hygiene (hand washing).

[0003] Salmonella are gram-negative, aerobic, rod-shaped bacilli. There are two species of Salmonella, including Salmonella enterica and Salmonella bongori. Salmonella enterica is further classified into six subspecies, with only a small proportion of Salmonella enterica subspecies I causing human disease. See Sabbagh et al., FEMS Microbiol Lett 305:1-13, 2010. In the United States, Salmonella serovars Typhimurium, Enteritidis, and Newport account for approximately half of culture-confirmed Salmonella isolates. Salmonella serovar Typhi, the strain that causes typhoid fever, is not common in the United States, but Salmonella serovars Mississippi and Javiana are increasingly being identified as causes of disease. See Centers for Disease Control and Prevention, "Summary of Notifiable Diseases-United States, 2008," MMWR 57(54):15-16, 2008.

[0004] Campylobacter are curved, motile, microaerophilic, gram-negative rods. They exhibit rapid, darting motility in a corkscrew fashion using one or two flagella and also possess lipopolysaccharide endotoxins. Two species of Campylobacter, C. jejuni and C. coli, are responsible for the majority of human infections. See Klena et al., Journal of Clinical Microbiology, 42:5549-5557, 2004; Poly and Guerry, Current Opinion in Gastroenterology 24:27-31, 2008; Granato et al., Journal of Clinical Microbiology, 48:4022-4027, 2010.

[0005] E. coli is a gram-negative rod-shaped bacterium commonly found in the lower intestine of warm-blooded organisms. Most strains of E. coli are non-pathogenic and part of the normal intestinal flora. However, some strains, such as STEC, can cause life-threatening infections in humans. There are two main types of Shiga toxins produced by STEC, Shiga toxin type 1 and Shiga toxin type 2, carried by two different genes, stx1 and stx2, respectively. Some strains of STEC contain the stx1 gene and others contain the stx2 gene. There are also certain STEC strains that contain both the stx1 and stx2 genes.

[0006] Shigella are gram-negative, aerobic, rod-shaped bacteria closely related to E. coli. See Liu et al., FEMS Microbiol. Rev. 32:627-653, 2008. There are four species of Shigella, all of which can cause disease in humans and include S. sonnei (subgroup D), S. flexneri (subgroup B), S. boydii (subgroup B), and S. dysenteriae (subgroup A). ​​According to the 2006 Shigella Annual Summary published by the CDC, S. sonnei is the most common cause of infections at 76%, followed by S. flexneri (14%), S. boydii (1.1%), and S. dysenteriae (0.5%). See Centers for Disease Control and Prevention, "Shigella Surveillance: Annual Summary, 2006," Atlanta, GA: US Department of Health and Human Services, November 2008. There is a need to efficiently and sensitively detect the presence of Salmonella, Shigella, Campylobacter, and STEC in samples, including biological specimens, to provide diagnostic and prognostic information to physicians treating patients suffering from or suspected of suffering from bacterial gastroenteritis or related diseases. [Prior art documents] [Non-patent literature]

[0007] [Non-Patent Document 1] Thielman and Guerrant, The New England Journal of Medicine, 350:38-47, 2004 [Non-Patent Document 2] Guerrant et al.,Clinical Infectious Diseases,32:331-350,2001 [Non-Patent Document 3] Centers for Disease Control and Prevention, “Vital Signs: Incidence and Trends of Infection with Pathogens Transmitted Commonly Through Food-Foodborne Diseases Active Surveillance Network, 10 USSites, 1996-2010,” MMWR 60(22):749-755, 2011 [Non-Patent Document 4] Sabbagh et al.,FEMS Microbiol Lett 305:1-13,2010 [Non-Patent Document 5] Centers for Disease Control and Prevention, “Summary of Notifiable Diseases-United States, 2008,” MMWR 57(54):15-16, 2008 [Non-Patent Document 6] Klena et al., Journal of Clinical Microbiology, 42:5549-5557, 2004 [Non-Patent Document 7] Poly and Guerry,Current Opinion in Gastroenterology 24:27-31,2008 [Non-Patent Document 8] Granato et al.,Journal of Clinical Microbiology,48:4022-4027,2010 [Non-Patent Document 9] Liu et al.,FEMS Microbiol.Rev.32:627-653,2008 [Non-Patent Document 10] Centers for Disease Control and Prevention, “Shigella Surveillance: Annual Summary, 2006,” Atlanta, GA: US Department of Health and Human Services, November 2008 Summary of the Invention

[0008] Thus, the present specification provides a set of oligonucleotides for determining the presence or absence of at least one enteric pathogen, the set comprising: (a) to (e): (a) a Salmonella-specific amplification oligomer set comprising first and second oligomers, respectively, comprising target hybridization sequences substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:12 and SEQ ID NO:14; (ii) SEQ ID NO:21 and SEQ ID NO:47; (iii) SEQ ID NO:38 and SEQ ID NO:36; (iv) SEQ ID NO:35 and SEQ ID NO:40; (v) SEQ ID NO:12 and SEQ ID NO:28; (vi) SEQ ID NO:42 and SEQ ID NO:31; or (vii) SEQ ID NO:41 and SEQ ID NO:27; (b)(i) a C. jejuni-specific amplification oligomer set comprising first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:11 and SEQ ID NO:19, respectively; (c)(i) a C. coli specific amplification oligomer set comprising first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:8 and SEQ ID NO:10, respectively; (d) a Shigella-specific amplification oligomer set comprising first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:15 and SEQ ID NO:17, (ii) SEQ ID NO:34 and SEQ ID NO:22, or (iii) SEQ ID NO:32 and SEQ ID NO:33, respectively; and (e) A set of oligonucleotides is provided, comprising at least one of a Shigatoxigenic E. coli (STEC)-specific amplification oligomer set, comprising first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:20 and SEQ ID NO:3, (ii) SEQ ID NO:49 and SEQ ID NO:3, or (iii) SEQ ID NO:4 and SEQ ID NO:7, respectively.

[0009] In some embodiments, the set of oligonucleotides comprises a Salmonella-specific amplification oligomer set. In some embodiments, the Salmonella-specific amplification oligomer set comprises a first and a second oligomer comprising a target hybridization sequence substantially corresponding to the nucleotide sequences of SEQ ID NO:21 and SEQ ID NO:47, respectively. In some embodiments, the Salmonella-specific amplification oligomer set comprises a first and a second oligomer comprising a target hybridization sequence substantially corresponding to the nucleotide sequences of SEQ ID NO:38 and SEQ ID NO:36, respectively. In some embodiments, the Salmonella-specific amplification oligomer set comprises a first and a second oligomer comprising a target hybridization sequence substantially corresponding to the nucleotide sequences of SEQ ID NO:35 and SEQ ID NO:40, respectively. In some embodiments, the Salmonella-specific amplification oligomer set comprises a first and a second oligomer comprising a target hybridization sequence substantially corresponding to the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:28, respectively. In some embodiments, a Salmonella-specific amplification oligomer set comprises a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO: 42 and SEQ ID NO: 31, respectively. In some embodiments, a Salmonella-specific amplification oligomer set comprises a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO: 41 and SEQ ID NO: 27, respectively.

[0010] In some embodiments, the set of oligonucleotides comprises a C. jejuni specific amplification oligomer set.

[0011] In some embodiments, the set of oligonucleotides comprises a C. coli specific amplification oligomer set.

[0012] In some embodiments, the set of oligonucleotides comprises a Shigella-specific amplification oligomer set. In some embodiments, the Shigella-specific amplification oligomer set comprises a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:15 and SEQ ID NO:17, respectively. In some embodiments, the Shigella-specific amplification oligomer set comprises a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:34 and SEQ ID NO:22, respectively. In some embodiments, the Shigella-specific amplification oligomer set comprises a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:32 and SEQ ID NO:33, respectively.

[0013] In some embodiments, the set of oligonucleotides comprises a STEC-specific amplification oligomer set.

[0014] In some embodiments, the set of oligonucleotides comprises at least two of a Salmonella-specific amplification oligomer set, a C. jejuni-specific amplification oligomer set, a C. coli-specific amplification oligomer set, a Shigella-specific amplification oligomer set, and a STEC-specific amplification oligomer set.

[0015] In some embodiments, the set of oligonucleotides comprises at least three of a Salmonella-specific amplification oligomer set, a C. jejuni-specific amplification oligomer set, a C. coli-specific amplification oligomer set, a Shigella-specific amplification oligomer set, and a STEC-specific amplification oligomer set.

[0016] In some embodiments, the set of oligonucleotides comprises at least four of a Salmonella-specific amplification oligomer set, a C. jejuni-specific amplification oligomer set, a C. coli-specific amplification oligomer set, a Shigella-specific amplification oligomer set, and a STEC-specific amplification oligomer set.

[0017] In some embodiments, the sets of oligonucleotides include a Salmonella-specific amplification oligomer set, a C. jejuni-specific amplification oligomer set, a C. coli-specific amplification oligomer set, a Shigella-specific amplification oligomer set, and a STEC-specific amplification oligomer set.

[0018] In some embodiments, the Salmonella-specific amplification oligomer set comprises a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:14, respectively; the C. jejuni specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:11 and SEQ ID NO:19, respectively; the C. coli specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:8 and SEQ ID NO:10, respectively; the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:15 and SEQ ID NO:17, respectively; The STEC-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:20 and SEQ ID NO:3, and (ii) SEQ ID NO:4 and SEQ ID NO:7, respectively.

[0019] In some embodiments, the set of oligonucleotides comprises: When a Salmonella-specific amplification oligomer set includes first and second oligomers that contain target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:14, respectively, SEQ ID NO:13 When a Salmonella-specific amplification oligomer set includes first and second oligomers that contain target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:28, respectively, SEQ ID NO:13 When the Salmonella-specific amplification oligomer set includes first and second oligomers that contain target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:21 and SEQ ID NO:47, respectively, the set of SEQ ID NO:45 When the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:38 and SEQ ID NO:36, respectively, the set of oligomers may further comprise any of SEQ ID NO:44, SEQ ID NO:26, or SEQ ID NO:25, Where the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:35 and SEQ ID NO:40, respectively, SEQ ID NO:30, SEQ ID NO:23, or when the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:42 and SEQ ID NO:31, respectively. When the Salmonella-specific amplification oligomer set comprises a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequence of SEQ ID NO:41 and SEQ ID NO:27, respectively, it further comprises a Salmonella detection probe comprising a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:43.

[0020] In some embodiments, in SEQ ID NO:23, one or more, or each of nucleotides 2, 5, 7, and 14 are 5-methylcytosine. In some embodiments, in SEQ ID NO:25, one or more, or each of nucleotides 7, 9, 13, and 15 are 5-methylcytosine. In some embodiments, in SEQ ID NO:26, one or more, or each of nucleotides 9, 18, and 23 are 5-methylcytosine. In some embodiments, in SEQ ID NO:27, one or more, or each of nucleotides 6, 10, and 18 are 5-methylcytosine. In some embodiments, in SEQ ID NO:30, one or more, or each of nucleotides 2, 4, 18, 19, and 20 are 5-methylcytosine. In some embodiments, in SEQ ID NO:43, one or more, or each of nucleotides 2, 9, 12, 16, 17, 22, 23, and 26 are 5-methylcytosine. In some embodiments, in SEQ ID NO: 44, one or more, or each of nucleotides 7, 9, 13, and 15 is a 5-methylcytosine. In some embodiments, in SEQ ID NO: 45, one or more, or each of nucleotides 3, 6, 8, and 17 is a 5-methylcytosine.

[0021] In some embodiments, the set of oligonucleotides further comprises a C. jejuni detection probe, the C. jejuni detection probe comprising a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:18.

[0022] In some embodiments, in SEQ ID NO: 18, one or more of nucleotides 7, 12, and 25, or each of nucleotides 7 and 12, or each of nucleotides 7, 12, and 25, is a 5-methylcytosine.

[0023] In some embodiments, the set of oligonucleotides further comprises a C. coli detection probe, wherein the C. coli detection probe comprises a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:9, SEQ ID NO:37, or SEQ ID NO:39.

[0024] In some embodiments, in SEQ ID NO: 9, one or more, or each of nucleotides 2, 6, 13, 16, 23, 26, 28, and 29 are 5-methylcytosine. In some embodiments, in SEQ ID NO: 37, one or more, or each of nucleotides 17, 22, 23, and 27 are 5-methylcytosine. In some embodiments, in SEQ ID NO: 39, one or more, or each of nucleotides 2, 9, 12, 19, 22, 24, and 25 are 5-methylcytosine.

[0025] In some embodiments, the set of oligonucleotides comprises: The Shigella detection probe further comprises: When a Shigella-specific amplification oligomer set includes first and second oligomers that contain target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:15 and SEQ ID NO:17, respectively, SEQ ID NO:16, SEQ ID NO:46 or SEQ ID NO:29, when the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:34 and SEQ ID NO:22, respectively; When the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequence of SEQ ID NO:32 and SEQ ID NO:33, respectively, it comprises a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:24.

[0026] In some embodiments, in SEQ ID NO:46, each of nucleotides 5, 11, and 12 is a 5-methylcytosine.

[0027] In some embodiments, the set of oligonucleotides comprises: The method further comprises the steps of: Where the STEC-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:20 and SEQ ID NO:3, respectively, SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:48, SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:48, where the STEC-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:49 and SEQ ID NO:3, respectively. When the STEC-specific amplification oligomer set includes a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:4 and SEQ ID NO:7, respectively, it includes a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:5 or SEQ ID NO:6.

[0028] In some embodiments, in SEQ ID NO:1, one or more, or each of nucleotides 6, 7, 9, 14, 17, and 24 are 5-methylcytosine. In some embodiments, in SEQ ID NO:2, one or more, or each of nucleotides 5, 8, 11, 13, 18, and 21 are 5-methylcytosine. In some embodiments, in SEQ ID NO:6, one or more, or each of nucleotides 3, 7, 8, 15, 20, 24, and 27 are 5-methylcytosine. In some embodiments, in SEQ ID NO:15, one or more, or each of nucleotides 7 and 15 are 5-methylcytosine. In some embodiments, in SEQ ID NO:19, one or more, or each of nucleotides 1, 2, 7, 14, 15, 19, and 20 are 5-methylcytosine. In some embodiments, in SEQ ID NO:21, one or more, or each of nucleotides 13, 17, and 24 are 5-methylcytosine. In some embodiments, in SEQ ID NO:28, one or more, or each of nucleotides 2, 4, 12, 14, 15, and 17 are 5-methylcytosine. In some embodiments, in SEQ ID NO:31, one or more, or each of nucleotides 6, 7, 8, 13, 23, 24, and 26 are 5-methylcytosine. In some embodiments, in SEQ ID NO:32, one or more, or each of nucleotides 5, 11, 12, and 15 are 5-methylcytosine. In some embodiments, in SEQ ID NO:36, one or more, or each of nucleotides 2, 3, 4, 16, 18, 19, and 22 are 5-methylcytosine. In some embodiments, in SEQ ID NO:38, one or more, or each of nucleotides 4, 6, 7, and 8 are 5-methylcytosine. In some embodiments, in SEQ ID NO:40, one or more, or each of nucleotides 4, 13, 18, and 22 are 5-methylcytosine. In some embodiments, in SEQ ID NO: 47, one or more, or each, of nucleotides 11, 16, and 17 is a 5-methylcytosine. In some embodiments, in SEQ ID NO: 7, one or more, or each, of nucleotides 3, 4, 18, and 19 is a 5-methylcytosine.In some embodiments, in SEQ ID NO: 12, one or more, or each of nucleotides 4, 11, 12, and 16 is a 5-methylcytosine. In some embodiments, in SEQ ID NO: 22, each of nucleotides 5 and 16 is a 5-methylcytosine.

[0029] In some embodiments, one or more, or each, of the detection probes comprises a fluorescent dye compound. In some embodiments, each of the detection probes further comprises a non-fluorescent quenching dye compound.

[0030] Provided herein is an oligonucleotide for determining the presence or absence of at least one enteric pathogen, the oligonucleotide comprising: SEQ ID NO:15 (nucleotides 7 and 15 are each 5-methylcytosine); SEQ ID NO:16, SEQ ID NO:19 (each of nucleotides 1, 2, 7, 14, 15, 19, and 20 is a 5-methylcytosine); SEQ ID NO:21 (nucleotides 13, 17, and 24 are each 5-methylcytosine); SEQ ID NO:23 (nucleotides 2, 5, 7, and 14 are each 5-methylcytosine); SEQ ID NO:25 (nucleotides 7, 9, 13, and 15 are each 5-methylcytosine); SEQ ID NO:26 (nucleotides 9, 18, and 23 are each 5-methylcytosine); SEQ ID NO:27 (nucleotides 6, 10, and 18 each contain a 5-methylcytosine); SEQ ID NO:28 (nucleotides 2, 4, 12, 14, 15, and 17 are each 5-methylcytosine); SEQ ID NO:30 (wherein each of nucleotides 2, 4, 18, 19, and 20 is a 5-methylcytosine); SEQ ID NO:31 (each of nucleotides 6, 7, 8, 13, 23, 24, and 26 is a 5-methylcytosine); SEQ ID NO:32 (nucleotides 5, 11, 12, and 15 are each 5-methylcytosine); SEQ ID NO:36 (nucleotides 2, 3, 4, 16, 18, 19, and 22 are each 5-methylcytosine); SEQ ID NO:38 (nucleotides 4, 6, 7, and 8 are each 5-methylcytosine); SEQ ID NO:39 (wherein each of nucleotides 2, 9, 12, 19, 22, 24, and 25 is a 5-methylcytosine); SEQ ID NO:40 (nucleotides 4, 13, 18, and 22 are each 5-methylcytosine); SEQ ID NO:42, SEQ ID NO:43 (each of nucleotides 2, 9, 12, 16, 17, 22, 23, and 26 is a 5-methylcytosine); SEQ ID NO:44 (nucleotides 7, 9, 13, and 15 are each 5-methylcytosine); SEQ ID NO:45 (nucleotides 3, 6, 8, and 17 are each 5-methylcytosine); SEQ ID NO:47 (nucleotides 11, 16, and 17 are each 5-methylcytosine); SEQ ID NO:1 (nucleotides 6, 7, 9, 14, 17, and 24 are each 5-methylcytosine); SEQ ID NO:2 (nucleotides 5, 8, 11, 13, 18, and 21 are each 5-methylcytosine); SEQ ID NO:6 (nucleotides 3, 7, 8, 15, 20, 24, and 27 are each 5-methylcytosine); SEQ ID NO:7 (nucleotides 3, 4, 18, and 19 are each 5-methylcytosine); SEQ ID NO:9 (wherein each of nucleotides 2, 6, 13, 16, 23, 26, 28, and 29 is a 5-methylcytosine); SEQ ID NO:12 (nucleotides 4, 11, 12, and 16 are each 5-methylcytosine); SEQ ID NO:18 (each of nucleotides 7 and 12 or each of nucleotides 7, 12, and 25 is a 5-methylcytosine); SEQ ID NO:22 (nucleotides 5 and 16 are each 5-methylcytosine); SEQ ID NO:37 (nucleotides 17, 22, 23, and 27 are each 5-methylcytosine), and Also provided is an oligonucleotide comprising the sequence of any one of SEQ ID NO:46 (in which each of nucleotides 5, 11, and 12 is a 5-methylcytosine).

[0031] In some embodiments, the oligonucleotide comprises: SEQ ID NO:15 (nucleotides 7 and 15 are each 5-methylcytosine); SEQ ID NO:16, SEQ ID NO:19 (each of nucleotides 1, 2, 7, 14, 15, 19, and 20 is a 5-methylcytosine); SEQ ID NO:21 (nucleotides 13, 17, and 24 are each 5-methylcytosine); SEQ ID NO:23 (nucleotides 2, 5, 7, and 14 are each 5-methylcytosine); SEQ ID NO:25 (nucleotides 7, 9, 13, and 15 are each 5-methylcytosine); SEQ ID NO:26 (nucleotides 9, 18, and 23 are each 5-methylcytosine); SEQ ID NO:27 (nucleotides 6, 10, and 18 each contain a 5-methylcytosine); SEQ ID NO:28 (nucleotides 2, 4, 12, 14, 15, and 17 are each 5-methylcytosine); SEQ ID NO:30 (wherein each of nucleotides 2, 4, 18, 19, and 20 is a 5-methylcytosine); SEQ ID NO:31 (each of nucleotides 6, 7, 8, 13, 23, 24, and 26 is a 5-methylcytosine); SEQ ID NO:32 (nucleotides 5, 11, 12, and 15 are each 5-methylcytosine); SEQ ID NO:36 (each of nucleotides 2, 3, 4, 16, 18, 19, and 22 is a 5-methylcytosine); SEQ ID NO:38 (nucleotides 4, 6, 7, and 8 are each 5-methylcytosine); SEQ ID NO:39 (wherein each of nucleotides 2, 9, 12, 19, 22, 24, and 25 is a 5-methylcytosine); SEQ ID NO:40 (nucleotides 4, 13, 18, and 22 are each 5-methylcytosine); SEQ ID NO:42, SEQ ID NO:43 (each of nucleotides 2, 9, 12, 16, 17, 22, 23, and 26 is a 5-methylcytosine); SEQ ID NO:44 (nucleotides 7, 9, 13, and 15 are each 5-methylcytosine); SEQ ID NO:45 (wherein each of nucleotides 3, 6, 8, and 17 is a 5-methylcytosine), and It comprises any one of the sequences of SEQ ID NO:47 (wherein each of nucleotides 11, 16, and 17 is 5-methylcytosine).

[0032] Also provided herein is a set of oligonucleotides according to any one of the above embodiments, or a kit comprising the oligonucleotides according to any one of the above embodiments.

[0033] Also provided herein is a set of oligonucleotides according to any one of the above embodiments, or a reaction mixture comprising the oligonucleotides according to any one of the above embodiments.

[0034] Provided herein is a multiplexing method, comprising: (1) contacting a sample suspected of containing at least one enteric pathogen with the set of oligonucleotides of any one of the preceding embodiments; (2) performing an in vitro nucleic acid amplification reaction in which any Salmonella, C. jejuni, C. coli, Shigella, and STEC target nucleic acids, if present in the sample, are used as templates to generate one or more amplification products corresponding to Salmonella, C. jejuni, C. coli, Shigella, and STEC target regions; (3) detecting the presence or absence of one or more amplification products; and determining the presence or absence of at least one of Salmonella, C. jejuni, C. coli, Shigella, and STEC in the sample.

[0035] In some embodiments, step (3) of the multiplexing method comprises: contacting the sample with at least one of a Salmonella detection probe, a C. jejuni detection probe, a C. coli detection probe, a Shigella detection probe, and a STEC detection probe; performing electrophoresis on the sample; or Determining the sequence of one or more amplification products, if present.

[0036] Provided herein is a method for synthesizing an oligonucleotide, comprising: (a) obtaining a solid support comprising at least one nucleobase residue, wherein the at least one nucleobase residue is covalently attached to the solid support at a 3′ position; (b) linking the 5'-position of the nucleobase residue furthest from the solid support to the 3'-position of another nucleobase residue; (c) repeating step (b) at least 13 additional times, thereby generating at least 15 consecutive nucleobase residues bound to the solid support; (d) cleaving at least 15 consecutive nucleobase residues produced in step (c), thereby obtaining an oligonucleotide; The oligonucleotide is SEQ ID NO:15 (nucleotides 7 and 15 are each 5-methylcytosine); SEQ ID NO:16, SEQ ID NO:19 (each of nucleotides 1, 2, 7, 14, 15, 19, and 20 is a 5-methylcytosine); SEQ ID NO:21 (nucleotides 13, 17, and 24 are each 5-methylcytosine); SEQ ID NO:23 (nucleotides 2, 5, 7, and 14 are each 5-methylcytosine); SEQ ID NO:25 (nucleotides 7, 9, 13, and 15 are each 5-methylcytosine); SEQ ID NO:26 (nucleotides 9, 18, and 23 are each 5-methylcytosine); SEQ ID NO:27 (nucleotides 6, 10, and 18 each contain a 5-methylcytosine); SEQ ID NO:28 (nucleotides 2, 4, 12, 14, 15, and 17 are each 5-methylcytosine); SEQ ID NO:30 (wherein each of nucleotides 2, 4, 18, 19, and 20 is a 5-methylcytosine); SEQ ID NO:31 (each of nucleotides 6, 7, 8, 13, 23, 24, and 26 is a 5-methylcytosine); SEQ ID NO:32 (nucleotides 5, 11, 12, and 15 are each 5-methylcytosine); SEQ ID NO:36 (each of nucleotides 2, 3, 4, 16, 18, 19, and 22 is a 5-methylcytosine); SEQ ID NO:38 (nucleotides 4, 6, 7, and 8 are each 5-methylcytosine); SEQ ID NO:39 (wherein each of nucleotides 2, 9, 12, 19, 22, 24, and 25 is a 5-methylcytosine); SEQ ID NO:40 (nucleotides 4, 13, 18, and 22 are each 5-methylcytosine); SEQ ID NO:42, SEQ ID NO:43 (each of nucleotides 2, 9, 12, 16, 17, 22, 23, and 26 is a 5-methylcytosine); SEQ ID NO:44 (nucleotides 7, 9, 13, and 15 are each 5-methylcytosine); SEQ ID NO:45 (nucleotides 3, 6, 8, and 17 are each 5-methylcytosine); SEQ ID NO:47 (nucleotides 11, 16, and 17 are each 5-methylcytosine); SEQ ID NO:1 (nucleotides 6, 7, 9, 14, 17, and 24 are each 5-methylcytosine); SEQ ID NO:2 (nucleotides 5, 8, 11, 13, 18, and 21 are each 5-methylcytosine); SEQ ID NO:6 (nucleotides 3, 7, 8, 15, 20, 24, and 27 are each 5-methylcytosine); SEQ ID NO:7 (nucleotides 3, 4, 18, and 19 are each 5-methylcytosine); SEQ ID NO:9 (wherein each of nucleotides 2, 6, 13, 16, 23, 26, 28, and 29 is a 5-methylcytosine); SEQ ID NO:12 (nucleotides 4, 11, 12, and 16 are each 5-methylcytosine); SEQ ID NO:18 (each of nucleotides 7 and 12 or each of nucleotides 7, 12, and 25 is a 5-methylcytosine); SEQ ID NO:22 (nucleotides 5 and 16 are each 5-methylcytosine); SEQ ID NO:37 (nucleotides 17, 22, 23, and 27 are each 5-methylcytosine), and Also provided is a method comprising the sequence of any one of SEQ ID NO:46 (wherein each of nucleotides 5, 11, and 12 is a 5-methylcytosine).

[0037] In some embodiments, the oligonucleotide has a length of 18 to 32 contiguous nucleobase residues, hi some embodiments, the oligonucleotide has a length of 20 to 30 contiguous nucleobase residues.

[0038] Provided herein is a method for synthesizing a pair of oligonucleotides, comprising synthesizing a first oligonucleotide and synthesizing a second oligonucleotide, Each of synthesizing a first oligonucleotide and synthesizing a second oligonucleotide comprises: (a) obtaining a solid support comprising at least one nucleobase residue, wherein the at least one nucleobase residue is covalently attached to the solid support at a 3′ position; (b) linking the 5'-position of the nucleobase residue furthest from the solid support to the 3'-position of another nucleobase residue; (c) repeating step (b) at least 13 additional times, thereby generating at least 15 consecutive nucleobase residues bound to the solid support; (d) cleaving at least 15 consecutive nucleobase residues produced in step (c), thereby obtaining an oligonucleotide; The first oligonucleotide and the second oligonucleotide each comprise: SEQ ID NO:12 and SEQ ID NO:14, SEQ ID NO: 21 and SEQ ID NO: 47, SEQ ID NO:38 and SEQ ID NO:36, SEQ ID NO: 35 and SEQ ID NO: 40, SEQ ID NO: 12 and SEQ ID NO: 28, SEQ ID NO: 42 and SEQ ID NO: 31, SEQ ID NO: 41 and SEQ ID NO: 27, SEQ ID NO:11 and SEQ ID NO:19, SEQ ID NO: 8 and SEQ ID NO: 10, SEQ ID NO: 15 and SEQ ID NO: 17, SEQ ID NO:34 and SEQ ID NO:22, SEQ ID NO: 32 and SEQ ID NO: 33, SEQ ID NO: 49 and SEQ ID NO: 3, SEQ ID NO: 20 and SEQ ID NO: 3, and Methods are also provided that include any one of the sequences of SEQ ID NO:4 and SEQ ID NO:7.

[0039] In some embodiments, the first oligonucleotide and the second oligonucleotide each have a length of 18 to 32 contiguous nucleobase residues.In some embodiments, the first oligonucleotide and the second oligonucleotide each have a length of 20 to 30 contiguous nucleobase residues.

[0040] Thus, the following embodiments are among those provided by this disclosure.

[0041] Embodiment 1 is a set of oligonucleotides for determining the presence or absence of at least one enteric pathogen, comprising: (a) to (e): (a) a Salmonella-specific amplification oligomer set comprising first and second oligomers, respectively, comprising target hybridization sequences substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:12 and SEQ ID NO:14; (ii) SEQ ID NO:21 and SEQ ID NO:47; (iii) SEQ ID NO:38 and SEQ ID NO:36; (iv) SEQ ID NO:35 and SEQ ID NO:40; (v) SEQ ID NO:12 and SEQ ID NO:28; (vi) SEQ ID NO:42 and SEQ ID NO:31; or (vii) SEQ ID NO:41 and SEQ ID NO:27; (b)(i) a C. jejuni-specific amplification oligomer set comprising first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:11 and SEQ ID NO:19, respectively; (c)(i) a C. coli specific amplification oligomer set comprising first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:8 and SEQ ID NO:10, respectively; (d) a Shigella-specific amplification oligomer set comprising first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:15 and SEQ ID NO:17, (ii) SEQ ID NO:34 and SEQ ID NO:22, or (iii) SEQ ID NO:32 and SEQ ID NO:33, respectively; and (e) a set of oligonucleotides, the set including at least one of a Shigatoxigenic E. coli (STEC)-specific amplification oligomer set, the set including first and second oligomers each comprising a target hybridization sequence substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:20 and SEQ ID NO:3, (ii) SEQ ID NO:49 and SEQ ID NO:3, or (iii) SEQ ID NO:4 and SEQ ID NO:7, respectively.

[0042] Embodiment 2 is the set of oligonucleotides of embodiment 1, comprising a Salmonella-specific amplification oligomer set.

[0043] Embodiment 3 is the set of oligonucleotides of embodiment 2, wherein the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:21 and SEQ ID NO:47, respectively.

[0044] Embodiment 4 is the set of oligonucleotides of embodiment 2, wherein the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:38 and SEQ ID NO:36, respectively.

[0045] Embodiment 5 is the set of oligonucleotides of embodiment 2, wherein the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:35 and SEQ ID NO:40, respectively.

[0046] Embodiment 6 is the set of oligonucleotides of embodiment 2, wherein the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:28, respectively.

[0047] Embodiment 7 is the set of oligonucleotides of embodiment 2, wherein the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:42 and SEQ ID NO:31, respectively.

[0048] Embodiment 8 is the set of oligonucleotides of embodiment 2, wherein the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:41 and SEQ ID NO:27, respectively.

[0049] Embodiment 9 is the set of oligonucleotides of any one of the preceding embodiments, comprising a C. jejuni-specific amplification oligomer set.

[0050] Embodiment 10 is the set of oligonucleotides of any one of the preceding embodiments, comprising a C. coli specific amplification oligomer set.

[0051] Embodiment 11 is the set of oligonucleotides of any one of the preceding embodiments, comprising a Shigella-specific amplification oligomer set.

[0052] Embodiment 12 is the set of oligonucleotides of embodiment 11, wherein the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:15 and SEQ ID NO:17, respectively.

[0053] Embodiment 13 is the set of oligonucleotides of embodiment 11, wherein the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:34 and SEQ ID NO:22, respectively.

[0054] Embodiment 14 is the set of oligonucleotides of embodiment 11, wherein the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:32 and SEQ ID NO:33, respectively.

[0055] Embodiment 15 is the set of oligonucleotides of any one of the preceding embodiments, comprising a STEC-specific amplification oligomer set.

[0056] Embodiment 16 is the set of oligonucleotides of any one of the preceding embodiments, comprising at least two of a Salmonella-specific amplification oligomer set, a C. jejuni-specific amplification oligomer set, a C. coli-specific amplification oligomer set, a Shigella-specific amplification oligomer set, and a STEC-specific amplification oligomer set.

[0057] Embodiment 17 is the set of oligonucleotides of any one of the preceding embodiments, comprising at least three of a Salmonella-specific amplification oligomer set, a C. jejuni-specific amplification oligomer set, a C. coli-specific amplification oligomer set, a Shigella-specific amplification oligomer set, and a STEC-specific amplification oligomer set.

[0058] Embodiment 18 is the set of oligonucleotides of any one of the preceding embodiments, comprising at least four of a Salmonella-specific amplification oligomer set, a C. jejuni-specific amplification oligomer set, a C. coli-specific amplification oligomer set, a Shigella-specific amplification oligomer set, and a STEC-specific amplification oligomer set.

[0059] Embodiment 19 is the set of oligonucleotides of any one of the preceding embodiments, comprising a Salmonella-specific amplification oligomer set, a C. jejuni-specific amplification oligomer set, a C. coli-specific amplification oligomer set, a Shigella-specific amplification oligomer set, and a STEC-specific amplification oligomer set.

[0060] Embodiment 20 is the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:14, respectively; the C. jejuni-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:11 and SEQ ID NO:19, respectively; the C. coli specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:8 and SEQ ID NO:10, respectively; the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:15 and SEQ ID NO:17, respectively; The set of oligonucleotides of the immediately preceding embodiment, wherein the STEC-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:20 and SEQ ID NO:3, and (ii) SEQ ID NO:4 and SEQ ID NO:7, respectively.

[0061] Embodiment 21 is When a Salmonella-specific amplification oligomer set includes first and second oligomers that contain target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:14, respectively, SEQ ID NO:13 When a Salmonella-specific amplification oligomer set includes first and second oligomers that contain target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:28, respectively, SEQ ID NO:13 When the Salmonella-specific amplification oligomer set includes first and second oligomers that contain target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:21 and SEQ ID NO:47, respectively, the set of SEQ ID NO:45 When the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:38 and SEQ ID NO:36, respectively, the set of oligomers may further comprise any of SEQ ID NO:44, SEQ ID NO:26, or SEQ ID NO:25, Where the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:35 and SEQ ID NO:40, respectively, SEQ ID NO:30, SEQ ID NO:23, or when the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:42 and SEQ ID NO:31, respectively. The set of oligonucleotides of any one of embodiments 2 to 20, further comprising a Salmonella detection probe comprising a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:43, when the Salmonella-specific amplification oligomer set comprises a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequence of SEQ ID NO:41 and SEQ ID NO:27, respectively.

[0062] Embodiment 22 is the set of oligonucleotides of embodiment 21, wherein one or more, or each, of nucleotides 2, 5, 7, and 14 in SEQ ID NO:23 comprises a 5-methylcytosine.

[0063] Embodiment 23 is the set of oligonucleotides of embodiment 21, wherein one or more, or each, of nucleotides 7, 9, 13, and 15 in SEQ ID NO:25 comprises a 5-methylcytosine.

[0064] Embodiment 24 is the set of oligonucleotides of embodiment 21, wherein one or more, or each, of nucleotides 9, 18, and 23 in SEQ ID NO:26 comprises a 5-methylcytosine.

[0065] Embodiment 25 is the set of oligonucleotides of embodiment 21, wherein one or more, or each, of nucleotides 6, 10, and 18 in SEQ ID NO:27 comprises a 5-methylcytosine.

[0066] Embodiment 26 is the set of oligonucleotides of embodiment 21, wherein one or more, or each, of nucleotides 2, 4, 18, 19, and 20 in SEQ ID NO:30 comprises a 5-methylcytosine.

[0067] Embodiment 27 is the set of oligonucleotides of embodiment 21, wherein one or more, or each, of nucleotides 2, 9, 12, 16, 17, 22, 23, and 26 in SEQ ID NO:43 comprises a 5-methylcytosine.

[0068] Embodiment 28 is the set of oligonucleotides of embodiment 21, wherein one or more, or each, of nucleotides 7, 9, 13, and 15 in SEQ ID NO:44 comprises a 5-methylcytosine.

[0069] Embodiment 29 is the set of oligonucleotides of embodiment 21, wherein one or more, or each, of nucleotides 3, 6, 8, and 17 in SEQ ID NO:45 comprises a 5-methylcytosine.

[0070] Embodiment 30 is the set of oligonucleotides of any one of embodiments 9 to 27, further comprising a C. jejuni detection probe, wherein the C. jejuni detection probe comprises a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:18.

[0071] Embodiment 31 is the set of oligonucleotides of embodiment 29, wherein in SEQ ID NO: 18, one or more of nucleotides 7, 12, and 25, or each of nucleotides 7 and 12, or each of nucleotides 7, 12, and 25, comprises 5-methylcytosine.

[0072] Embodiment 32 is a set of oligonucleotides of any one of embodiments 10 to 30, further comprising a C. coli detection probe, wherein the C. coli detection probe comprises a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:9, SEQ ID NO:37, or SEQ ID NO:39.

[0073] Embodiment 33 is the set of oligonucleotides of embodiment 31, wherein one or more, or each, of nucleotides 2, 6, 13, 16, 23, 26, 28, and 29 in SEQ ID NO: 9 contains a 5-methylcytosine.

[0074] Embodiment 34 is the set of oligonucleotides of embodiment 31, wherein one or more, or each, of nucleotides 17, 22, 23, and 27 in SEQ ID NO:37 comprises a 5-methylcytosine.

[0075] Embodiment 35 is the set of oligonucleotides of embodiment 31, wherein one or more, or each, of nucleotides 2, 9, 12, 19, 22, 24, and 25 in SEQ ID NO:39 comprises a 5-methylcytosine.

[0076] Embodiment 36 is The Shigella detection probe further comprises: When a Shigella-specific amplification oligomer set includes first and second oligomers that contain target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:15 and SEQ ID NO:17, respectively, SEQ ID NO:16, SEQ ID NO:46 or SEQ ID NO:29, when the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:34 and SEQ ID NO:22, respectively; The set of oligonucleotides of any one of embodiments 11 to 35, wherein the Shigella-specific amplification oligomer set comprises a first and a second oligomer comprising a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:32 and SEQ ID NO:33, respectively, and a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:24.

[0077] Embodiment 37 is the set of oligonucleotides of embodiment 36, wherein in SEQ ID NO:46, nucleotides 5, 11, and 12 each contain a 5-methylcytosine.

[0078] Embodiment 38 is The method further comprises the steps of: Where the STEC-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:20 and SEQ ID NO:3, respectively, SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:48, SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:48, where the STEC-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:49 and SEQ ID NO:3, respectively. When the STEC-specific amplification oligomer set comprises a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:4 and SEQ ID NO:7, respectively, the set of oligonucleotides of any one of embodiments 15 to 37 comprises a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:5 or SEQ ID NO:6.

[0079] Embodiment 39 is the set of oligonucleotides of embodiment 38, wherein one or more, or each, of nucleotides 6, 7, 9, 14, 17, and 24 in SEQ ID NO:1 comprises a 5-methylcytosine.

[0080] Embodiment 40 is the set of oligonucleotides of embodiment 38, wherein one or more, or each, of nucleotides 5, 8, 11, 13, 18, and 21 in SEQ ID NO:2 comprises a 5-methylcytosine.

[0081] Embodiment 41 is the set of oligonucleotides of embodiment 38, wherein one or more, or each, of nucleotides 3, 7, 8, 15, 20, 24, and 27 in SEQ ID NO:6 comprises a 5-methylcytosine.

[0082] Embodiment 42 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more of nucleotides 7 and 15, or each, in SEQ ID NO: 15 comprises a 5-methylcytosine.

[0083] Embodiment 43 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 1, 2, 7, 14, 15, 19, and 20 in SEQ ID NO: 19 comprises a 5-methylcytosine.

[0084] Embodiment 44 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 13, 17, and 24 in SEQ ID NO:21 comprises a 5-methylcytosine.

[0085] Embodiment 45 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 2, 4, 12, 14, 15, and 17 in SEQ ID NO:28 comprises a 5-methylcytosine.

[0086] Embodiment 46 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 6, 7, 8, 13, 23, 24, and 26 in SEQ ID NO:31 comprises a 5-methylcytosine.

[0087] Embodiment 47 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 5, 11, 12, and 15 in SEQ ID NO: 32 comprises a 5-methylcytosine.

[0088] Embodiment 48 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 2, 3, 4, 16, 18, 19, and 22 in SEQ ID NO: 36 comprises a 5-methylcytosine.

[0089] Embodiment 49 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 4, 6, 7, and 8 in SEQ ID NO: 38 comprises a 5-methylcytosine.

[0090] Embodiment 50 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 4, 13, 18, and 22 in SEQ ID NO:40 comprises a 5-methylcytosine.

[0091] Embodiment 51 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 11, 16, and 17 in SEQ ID NO:47 comprises a 5-methylcytosine.

[0092] Embodiment 52 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 3, 4, 18, and 19 in SEQ ID NO: 7 comprises a 5-methylcytosine.

[0093] Embodiment 53 is the set of oligonucleotides of any one of the preceding embodiments, wherein one or more, or each, of nucleotides 4, 11, 12, and 16 in SEQ ID NO: 12 comprises a 5-methylcytosine.

[0094] Embodiment 54 is the set of oligonucleotides of any one of the preceding embodiments, wherein, in SEQ ID NO:22, nucleotides 5 and 16 each comprise a 5-methylcytosine.

[0095] Embodiment 55 is the set of oligonucleotides of any one of embodiments 21 to 54, wherein one or more of the detection probes, or each, comprises a fluorescent dye compound.

[0096] Embodiment 56 is the set of oligonucleotides of the immediately preceding embodiment, wherein each of the detection probes further comprises a non-fluorescent quenching dye compound.

[0097] Embodiment 57 is an oligonucleotide for determining the presence or absence of at least one enteric pathogen, the oligonucleotide comprising: SEQ ID NO:15 (nucleotides 7 and 15 each contain a 5-methylcytosine); SEQ ID NO:16, SEQ ID NO:19 (nucleotides 1, 2, 7, 14, 15, 19, and 20 each contain a 5-methylcytosine); SEQ ID NO:21 (nucleotides 13, 17, and 24 each contain a 5-methylcytosine); SEQ ID NO:23 (nucleotides 2, 5, 7, and 14 each contain a 5-methylcytosine); SEQ ID NO:25 (nucleotides 7, 9, 13, and 15 each contain a 5-methylcytosine); SEQ ID NO:26 (nucleotides 9, 18, and 23 each contain a 5-methylcytosine); SEQ ID NO:27 (nucleotides 6, 10, and 18 each contain a 5-methylcytosine); SEQ ID NO:28 (nucleotides 2, 4, 12, 14, 15, and 17 each contain a 5-methylcytosine); SEQ ID NO:30 (nucleotides 2, 4, 18, 19, and 20 each contain a 5-methylcytosine); SEQ ID NO:31 (nucleotides 6, 7, 8, 13, 23, 24, and 26 each contain a 5-methylcytosine); SEQ ID NO:32 (nucleotides 5, 11, 12, and 15 each contain a 5-methylcytosine); SEQ ID NO:36 (nucleotides 2, 3, 4, 16, 18, 19, and 22 each contain a 5-methylcytosine); SEQ ID NO:38 (nucleotides 4, 6, 7, and 8 each contain a 5-methylcytosine); SEQ ID NO:39 (nucleotides 2, 9, 12, 19, 22, 24, and 25 each contain a 5-methylcytosine); SEQ ID NO:40 (nucleotides 4, 13, 18, and 22 each contain a 5-methylcytosine); SEQ ID NO:42, SEQ ID NO:43 (nucleotides 2, 9, 12, 16, 17, 22, 23, and 26 each contain a 5-methylcytosine); SEQ ID NO:44 (nucleotides 7, 9, 13, and 15 each contain a 5-methylcytosine); SEQ ID NO:45 (nucleotides 3, 6, 8, and 17 each contain a 5-methylcytosine); SEQ ID NO:47 (nucleotides 11, 16, and 17 each contain a 5-methylcytosine); SEQ ID NO:1 (nucleotides 6, 7, 9, 14, 17, and 24 each contain a 5-methylcytosine); SEQ ID NO:2 (nucleotides 5, 8, 11, 13, 18, and 21 each contain a 5-methylcytosine); SEQ ID NO:6 (nucleotides 3, 7, 8, 15, 20, 24, and 27 each contain a 5-methylcytosine); SEQ ID NO:7 (nucleotides 3, 4, 18, and 19 each contain a 5-methylcytosine); SEQ ID NO:9 (nucleotides 2, 6, 13, 16, 23, 26, 28, and 29 each contain a 5-methylcytosine); SEQ ID NO:12 (nucleotides 4, 11, 12, and 16 each contain a 5-methylcytosine); SEQ ID NO:18 (wherein each of nucleotides 7 and 12 or each of nucleotides 7, 12, and 25 contains a 5-methylcytosine); SEQ ID NO:22 (nucleotides 5 and 16 each contain a 5-methylcytosine); SEQ ID NO:37 (nucleotides 17, 22, 23, and 27 each contain a 5-methylcytosine), and It is an oligonucleotide comprising any one of the sequences of SEQ ID NO: 46 (each of nucleotides 5, 11, and 12 contains 5-methylcytosine).

[0098] Embodiment 58 is a method for producing an oligonucleotide comprising the steps of: SEQ ID NO:15 (nucleotides 7 and 15 each contain a 5-methylcytosine); SEQ ID NO:16, SEQ ID NO:19 (nucleotides 1, 2, 7, 14, 15, 19, and 20 each contain a 5-methylcytosine); SEQ ID NO:21 (nucleotides 13, 17, and 24 each contain a 5-methylcytosine); SEQ ID NO:23 (nucleotides 2, 5, 7, and 14 each contain a 5-methylcytosine); SEQ ID NO:25 (nucleotides 7, 9, 13, and 15 each contain a 5-methylcytosine); SEQ ID NO:26 (nucleotides 9, 18, and 23 each contain a 5-methylcytosine); SEQ ID NO:27 (nucleotides 6, 10, and 18 each contain a 5-methylcytosine); SEQ ID NO:28 (nucleotides 2, 4, 12, 14, 15, and 17 each contain a 5-methylcytosine); SEQ ID NO:30 (nucleotides 2, 4, 18, 19, and 20 each contain a 5-methylcytosine); SEQ ID NO:31 (nucleotides 6, 7, 8, 13, 23, 24, and 26 each contain a 5-methylcytosine); SEQ ID NO:32 (nucleotides 5, 11, 12, and 15 each contain a 5-methylcytosine); SEQ ID NO:36 (nucleotides 2, 3, 4, 16, 18, 19, and 22 each contain a 5-methylcytosine); SEQ ID NO:38 (nucleotides 4, 6, 7, and 8 each contain a 5-methylcytosine); SEQ ID NO:39 (nucleotides 2, 9, 12, 19, 22, 24, and 25 each contain a 5-methylcytosine); SEQ ID NO:40 (nucleotides 4, 13, 18, and 22 each contain a 5-methylcytosine); SEQ ID NO:42, SEQ ID NO:43 (nucleotides 2, 9, 12, 16, 17, 22, 23, and 26 each contain a 5-methylcytosine); SEQ ID NO:44 (nucleotides 7, 9, 13, and 15 each contain a 5-methylcytosine); SEQ ID NO:45 (nucleotides 3, 6, 8, and 17 each contain a 5-methylcytosine), and The oligonucleotide of the immediately preceding embodiment, comprising the sequence of any one of SEQ ID NO:47 (wherein nucleotides 11, 16, and 17 each comprise a 5-methylcytosine).

[0099] Embodiment 59 is a kit comprising the set of oligonucleotides according to any one of embodiments 1 to 56 or the oligonucleotides according to embodiment 57 or 58.

[0100] Embodiment 60 is a reaction mixture comprising the set of oligonucleotides of any one of embodiments 1 to 55 or the oligonucleotides of embodiment 57 or 58.

[0101] Embodiment 61 is the reaction mixture of the immediately preceding embodiment, further comprising α-cyclodextrin or polysorbate 20.

[0102] Embodiment 62 is the reaction mixture of embodiment 60 or 61, further comprising α-cyclodextrin and polysorbate 20.

[0103] Embodiment 63 is the reaction mixture of embodiment 61 or 62, wherein the concentration of α-cyclodextrin in the reaction mixture is from about 10 mg / mL to about 40 mg / mL.

[0104] Embodiment 64 is the reaction mixture of any one of embodiments 61 to 63, wherein the concentration of α-cyclodextrin in the reaction mixture is from about 16 mg / mL to about 30 mg / mL, from about 15 mg / mL to about 20 mg / mL, or from about 10 mg / mL to about 15 mg / mL.

[0105] Embodiment 65 is the reaction mixture of any one of embodiments 61-64, wherein the concentration of α-cyclodextrin in the reaction mixture is about 20 mg / mL, about 17.5 mg / mL, or about 12.5 mg / mL.

[0106] Embodiment 66 is the reaction mixture of any one of embodiments 61-65, wherein the concentration of polysorbate 20 in the reaction mixture is from about 0.002% to about 0.05% (v / v).

[0107] Embodiment 67 is the reaction mixture of any one of embodiments 61-66, wherein the concentration of polysorbate 20 in the reaction mixture is from about 0.003% to about 0.03% (v / v).

[0108] Embodiment 68 is the reaction mixture of any one of embodiments 61 to 67, wherein the concentration of polysorbate 20 in the reaction mixture is about 0.0042% (v / v), about 0.0035% (v / v), about 0.0026% (v / v), or about 0.02% (v / v).

[0109] Embodiment 69 is the reaction mixture of any one of embodiments 61 to 68, further comprising a detergent.

[0110] Embodiment 70 is the reaction mixture of the immediately preceding embodiment, wherein the detergent comprises sodium dodecyl sulfate.

[0111] Embodiment 71 is the reaction mixture of embodiment 69 or 70, wherein the concentration of detergent in the reaction mixture is from about 3 mg / mL to 300 mg / mL.

[0112] Embodiment 72 is the reaction mixture of any one of embodiments 69 to 71, wherein the concentration of the detergent in the reaction mixture is from about 10 mg / mL to 100 mg / mL.

[0113] Embodiment 73 is the reaction mixture of any one of embodiments 69 to 72, wherein the concentration of detergent in the reaction mixture is about 33.3 mg / mL.

[0114]

[0046] Embodiment 74 is a multiplexing method, comprising: (1) contacting a sample suspected of containing at least one enteric pathogen with a set of oligonucleotides according to any one of embodiments 1 to 56; (2) performing an in vitro nucleic acid amplification reaction in which any Salmonella, C. jejuni, C. coli, Shigella, and STEC target nucleic acids, if present in the sample, are used as templates to generate one or more amplification products corresponding to Salmonella, C. jejuni, C. coli, Shigella, and STEC target regions; (3) detecting the presence or absence of one or more amplification products; thereby determining the presence or absence of at least one of Salmonella, C. jejuni, C. coli, Shigella, and STEC in the sample.

[0115] Embodiment 74.1 is the multiplexing method of the immediately preceding embodiment, wherein the in vitro nucleic acid amplification reaction occurs in the reaction mixture of any one of embodiments 60-73.

[0116] Embodiment 75 is the multiplexing method of embodiment 74, wherein (3) is: contacting the sample with at least one of a Salmonella detection probe, a C. jejuni detection probe, a C. coli detection probe, a Shigella detection probe, and a STEC detection probe; performing electrophoresis on the sample; or determining the sequence, if any, of one or more of the amplification products.

[0117] Embodiment 75.1 is the multiplexing method of the immediately preceding embodiment, wherein the in vitro nucleic acid amplification reaction occurs in the reaction mixture of any one of embodiments 60-73.

[0118] Embodiment 76 is a method for synthesizing an oligonucleotide, comprising the steps of: (a) obtaining a solid support comprising at least one nucleobase residue, wherein the at least one nucleobase residue is covalently attached to the solid support at a 3′ position; (b) linking the 5'-position of the nucleobase residue furthest from the solid support to the 3'-position of another nucleobase residue; (c) repeating step (b) at least 13 additional times, thereby generating at least 15 consecutive nucleobase residues bound to the solid support; (d) cleaving at least 15 consecutive nucleobase residues produced in step (c), thereby obtaining an oligonucleotide; The oligonucleotide is SEQ ID NO:15 (nucleotides 7 and 15 each contain a 5-methylcytosine); SEQ ID NO:16, SEQ ID NO:19 (nucleotides 1, 2, 7, 14, 15, 19, and 20 each contain a 5-methylcytosine); SEQ ID NO:21 (nucleotides 13, 17, and 24 each contain a 5-methylcytosine); SEQ ID NO:23 (nucleotides 2, 5, 7, and 14 each contain a 5-methylcytosine); SEQ ID NO:25 (nucleotides 7, 9, 13, and 15 each contain a 5-methylcytosine); SEQ ID NO:26 (nucleotides 9, 18, and 23 each contain a 5-methylcytosine); SEQ ID NO:27 (nucleotides 6, 10, and 18 each contain a 5-methylcytosine); SEQ ID NO:28 (nucleotides 2, 4, 12, 14, 15, and 17 each contain a 5-methylcytosine); SEQ ID NO:30 (nucleotides 2, 4, 18, 19, and 20 each contain a 5-methylcytosine); SEQ ID NO:31 (nucleotides 6, 7, 8, 13, 23, 24, and 26 each contain a 5-methylcytosine); SEQ ID NO:32 (nucleotides 5, 11, 12, and 15 each contain a 5-methylcytosine); SEQ ID NO:36 (nucleotides 2, 3, 4, 16, 18, 19, and 22 each contain a 5-methylcytosine); SEQ ID NO:38 (nucleotides 4, 6, 7, and 8 each contain a 5-methylcytosine); SEQ ID NO:39 (nucleotides 2, 9, 12, 19, 22, 24, and 25 each contain a 5-methylcytosine); SEQ ID NO:40 (nucleotides 4, 13, 18, and 22 each contain a 5-methylcytosine); SEQ ID NO:42, SEQ ID NO:43 (nucleotides 2, 9, 12, 16, 17, 22, 23, and 26 each contain a 5-methylcytosine); SEQ ID NO:44 (nucleotides 7, 9, 13, and 15 each contain a 5-methylcytosine); SEQ ID NO:45 (nucleotides 3, 6, 8, and 17 each contain a 5-methylcytosine); SEQ ID NO:47 (nucleotides 11, 16, and 17 each contain a 5-methylcytosine); SEQ ID NO:1 (nucleotides 6, 7, 9, 14, 17, and 24 each contain a 5-methylcytosine); SEQ ID NO:2 (nucleotides 5, 8, 11, 13, 18, and 21 each contain a 5-methylcytosine); SEQ ID NO:6 (nucleotides 3, 7, 8, 15, 20, 24, and 27 each contain a 5-methylcytosine); SEQ ID NO:7 (nucleotides 3, 4, 18, and 19 each contain a 5-methylcytosine); SEQ ID NO:9 (nucleotides 2, 6, 13, 16, 23, 26, 28, and 29 each contain a 5-methylcytosine); SEQ ID NO:12 (nucleotides 4, 11, 12, and 16 each contain a 5-methylcytosine); SEQ ID NO:18 (wherein each of nucleotides 7 and 12 or each of nucleotides 7, 12, and 25 contains a 5-methylcytosine); SEQ ID NO:22 (nucleotides 5 and 16 each contain a 5-methylcytosine); SEQ ID NO:37 (nucleotides 17, 22, 23, and 27 each contain a 5-methylcytosine), and The method includes any one of the sequences of SEQ ID NO: 46 (wherein each of nucleotides 5, 11, and 12 contains a 5-methylcytosine).

[0119] Embodiment 77 is the method of embodiment 76, wherein the oligonucleotide has a length of 18 to 32 contiguous nucleobase residues, or 20 to 30 contiguous nucleobase residues.

[0120] Embodiment 78 is a method for synthesizing a pair of oligonucleotides, comprising synthesizing a first oligonucleotide and synthesizing a second oligonucleotide, Each of synthesizing a first oligonucleotide and synthesizing a second oligonucleotide comprises: (a) obtaining a solid support comprising at least one nucleobase residue, wherein the at least one nucleobase residue is covalently attached to the solid support at a 3′ position; (b) linking the 5'-position of the nucleobase residue furthest from the solid support to the 3'-position of another nucleobase residue; (c) repeating step (b) at least 13 additional times, thereby generating at least 15 consecutive nucleobase residues bound to the solid support; (d) cleaving at least 15 consecutive nucleobase residues produced in step (c), thereby obtaining an oligonucleotide; The first oligonucleotide and the second oligonucleotide each comprise: SEQ ID NO:12 and SEQ ID NO:14, SEQ ID NO: 21 and SEQ ID NO: 47, SEQ ID NO:38 and SEQ ID NO:36, SEQ ID NO: 35 and SEQ ID NO: 40, SEQ ID NO: 12 and SEQ ID NO: 28, SEQ ID NO: 42 and SEQ ID NO: 31, SEQ ID NO: 41 and SEQ ID NO: 27, SEQ ID NO:11 and SEQ ID NO:19, SEQ ID NO: 8 and SEQ ID NO: 10, SEQ ID NO: 15 and SEQ ID NO: 17, SEQ ID NO: 34 and SEQ ID NO: 22, SEQ ID NO: 32 and SEQ ID NO: 33, SEQ ID NO: 49 and SEQ ID NO: 3, SEQ ID NO: 20 and SEQ ID NO: 3, and The method includes any one of the sequences of SEQ ID NO: 4 and SEQ ID NO: 7.

[0121] Embodiment 79 is the method of embodiment 78, wherein each of the first oligonucleotide and the second oligonucleotide has a length of 18 to 32 contiguous nucleobase residues, or 20 to 30 contiguous nucleobase residues. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0122] definition Before describing the present teachings in detail, it should be understood that the present disclosure is not limited to specific compositions or process steps, as such may vary. As used herein and in the appended claims, it should be noted that the singular forms "a," "an," and "the" include plural references unless the context clearly dictates otherwise. Thus, for example, a reference to "an oligomer" includes a plurality of oligomers, etc. The conjunction "or" should be interpreted in an inclusive sense, i.e., equivalent to "and / or," unless an inclusive sense is unreasonable in the context.

[0123] It will be understood that there is an implicit "about" before temperatures, concentrations, times, etc. discussed in this disclosure, so that slight and negligible deviations are within the scope of the teachings herein. In general, the term "about" refers to negligible variations in the amounts of components of a composition that do not have any significant effect on the activity or stability of the composition. All ranges should be interpreted as including the endpoint in the absence of an explicit exclusion, such as "not including the endpoint," so that, for example, "within 10 to 15" includes the values ​​10 and 15. Also, the use of "comprise," "comprises," "comprising," "contain," "contains," "containing," "include," "includes," and "including" is not intended to be limiting. It should be understood that both the general description and the detailed description above are exemplary and are for illustrative purposes only and are not intended to limit the teachings. To the extent that any material incorporated by reference contradicts the explicit content of this disclosure, the explicit content controls.

[0124] Unless otherwise stated, embodiments herein that recite various components as "comprising" are also assumed to "consist" or "consist essentially of" the recited components. Embodiments herein that recite various components as "consisting of" are also assumed to "comprising" or "consist essentially of" the recited components. Embodiments herein that recite various components as "consisting essentially of" are also assumed to "consist" or "comprising" the recited components (this interchangeability does not apply to the use of these terms in the claims). "Consisting essentially of" means that additional component(s), composition(s), or method step(s) that do not substantially change the basic and novel characteristics of the compositions and methods described herein may be included in those compositions or methods. Such characteristics include the ability to detect the nucleic acid sequence of an enteric pathogen present in a sample with specificity that distinguishes the nucleic acid from other known pathogens, optionally with a sensitivity capable of detecting 75 to 150 CFU / mL of an enteric pathogen, and optionally within about 90 to about 180 minutes or about 120 to about 150 minutes, and / or about 30 cycles to about 60 cycles, about 40 cycles to about 50 cycles, or about 45 cycles from the start of the amplification reaction when a cyclic amplification reaction is used.

[0125] A "sample" or "specimen," including a "biological" or "clinical" sample, refers to any material that may contain or is suspected of containing one or more of Salmonella, Shigella, Campylobacter jejuni, Campylobacter coli, and STEC, or components thereof, such as nucleic acid or fragments of nucleic acid. A sample may be a complex mixture of components. Samples include "biological samples" including any tissue or material derived from a living or dead mammal or organism, including, for example, stool, blood, plasma, serum, blood cells, saliva, mucosa, and cerebrospinal fluid. A sample may include stool from an organism experiencing one or more symptoms of infection with one or more of Salmonella, Shigella, Campylobacter jejuni, Campylobacter coli, and STEC. The sample may also be a "spiked" sample, such as stool from an organism that has not experienced any symptoms of infection, but to which one or more of Salmonella, Shigella, Campylobacter jejuni, Campylobacter coli, and STEC are artificially added. The sample may also include a sample of in vitro cell culture components, including, for example, conditioned medium resulting from the growth of cells and tissues in culture medium. To prepare the sample for analysis, the sample may be chemically, physically, or mechanically treated to disrupt tissue or cell structures and release intracellular nucleic acids into a solution that may contain enzymes, buffers, salts, detergents, and the like. In one step of the method described herein, a sample is provided that is suspected of containing target nucleic acids of at least one enteric pathogen, such as Salmonella, Shigella, C. jejuni, C. coli, and STEC. This step therefore excludes the physical step of obtaining the sample from the subject.

[0126] "Nucleic acid" and "polynucleotide" refer to polymeric compounds that contain nucleosides or nucleoside analogs with nitrogenous heterocyclic bases or base analogs linked together to form polynucleotides, including polymers that are conventional RNA, DNA, mixed RNA-DNA, and analogs thereof. The nucleic acid "backbone" can be composed of a variety of linkages, including one or more of sugar phosphodiester linkages, peptide-nucleic acid linkages ("peptide nucleic acid" or PNA, PCT No. 95 / 32305), phosphorothioate linkages, methylphosphonate linkages, or combinations thereof. The sugar portion of the nucleic acid can be ribose, deoxyribose, or similar compounds with substitutions, such as 2' methoxy or 2' halide substitutions. The nitrogenous bases can be the conventional bases (A, G, C, T, U), their analogs (e.g., inosine or other, The Biochemistry of the Nucleic Acids 5-36, Adams et al., ed., 11 th ed., 1992), purine or pyrimidine derivatives (e.g., N 4 -methyldeoxyguanosine, deaza- or aza-purines, deaza- or aza-pyrimidines, pyrimidine bases having a substituent at the 5- or 6-position, purine bases having a substituent at the 2-, 6-, or 8-position, 2-amino-6-methylaminopurine, O 6 -methylguanine, 4-thio-pyrimidine, 4-amino-pyrimidine, 4-dimethylhydrazine-pyrimidine, and O 4-alkyl-pyrimidines, U.S. Pat. No. 5,378,825 and PCT No. 93 / 13121). Nucleic acids may contain one or more "abasic" residues where the backbone does not contain a nitrogenous base at the position(s) of the polymer (U.S. Pat. No. 5,585,481). Nucleic acids may contain only conventional RNA or DNA sugars, bases and linkages, or may contain both conventional moieties and substitutions (e.g., conventional bases with 2' methoxy linkages, or polymers containing both conventional bases and one or more base analogs). Nucleic acids include "locked nucleic acids" (LNAs), which are analogs that contain one or more LNA nucleotide monomers with bicyclic furanose units locked to an RNA-mimetic sugar structure, enhancing hybridization affinity to complementary RNA and DNA sequences (Vester and Wengel, 2004, Biochemistry 43(42):13233-41). Embodiments of oligomers that may affect the stability of a hybridization complex include PNA oligomers, oligomers containing 2'-methoxy or 2'-fluoro substituted RNA, or oligomers that affect the overall charge, charge density, or steric association of the hybridization complex, including oligomers containing charged linkages (e.g., phosphorothioates) or neutral groups (e.g., methylphosphonates). Unless otherwise indicated, 5-methylcytosine may be used with any of the above backbones / sugars / linkages, including RNA or DNA backbones (or mixtures thereof). When referring to a range for the length of an oligonucleotide, amplicon, or other nucleic acid, it is understood that the range includes all integers (e.g., a length of 19 to 25 contiguous nucleotides includes 19, 20, 21, 22, 23, 24, and 25).

[0127] A "C" or "cytosine" residue includes methylated and unmethylated cytosine, unless the context indicates otherwise.

[0128] "Oligonucleotide" or "oligomer" generally refers to a nucleic acid less than 1,000 nucleotides (nt), including those in a size range having a lower limit of about 2-5 nt and an upper limit of about 500-900 nt. Some particular embodiments are oligonucleotides in a size range having a lower limit of about 5-15, 16, 17, 18, 19, or 20 nt and an upper limit of about 50-600 nt, and other particular embodiments are in a size range having a lower limit of about 10-20 nt and an upper limit of about 22-100 nt. Oligonucleotides may be purified from naturally occurring sources, but may be synthesized by using any well-known enzymatic or chemical method. Oligonucleotides may be referred to by their functional name (e.g., capture probe, primer, or promoter primer), but one of skill in the art will understand that such terms refer to oligomers.

[0129] "Amplicon" or "amplification product" refers to a nucleic acid molecule produced in a nucleic acid amplification reaction and derived from a target nucleic acid. The amplicon or amplification product contains a target nucleic acid sequence that may be of the same or opposite orientation as the target nucleic acid.

[0130] "Amplification oligonucleotide" or "amplification oligomer" refers to an oligonucleotide, or its complement, that hybridizes to a target nucleic acid and participates in a nucleic acid amplification reaction, functioning, for example, as a primer or and promoter-primer. Certain amplification oligonucleotides contain at least about 10 contiguous bases, optionally at least 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 contiguous bases that are complementary to a region of the target nucleic acid sequence or its complementary strand. The contiguous bases may be at least about 80%, at least about 90%, or fully complementary to the target sequence to which the amplification oligomer binds. One of skill in the art will appreciate that the recited ranges include all integers and rational numbers within the range (e.g., 92% or 98.377%). Certain amplification oligonucleotides are about 10 to about 60 bases in length and may optionally contain modified nucleotides.

[0131] "Primer" refers to an oligonucleotide having a 3' end that hybridizes with a template nucleic acid and is extended by polymerization. A primer can be optionally modified, for example, by including a 5' region that is non-complementary to the target sequence. Such modifications can include functional additions, such as tags, promoters, or other sequences that are used or useful for manipulating or amplifying the primer or target oligonucleotide.

[0132] Within the context of transcription-mediated amplification, a primer modified with a 5' promoter sequence may be referred to as a "promoter-primer." Those skilled in the art of molecular biology or biochemistry will understand that an oligonucleotide capable of functioning as a primer can be modified to include a 5' promoter sequence and function as a promoter-primer, and similarly, any promoter-primer can function as a primer with or without its 5' promoter sequence.

[0133] "Nucleic acid amplification" refers to any in vitro procedure that produces multiple copies of a target nucleic acid sequence, or its complementary sequence, or fragments thereof (i.e., amplified sequences that contain less than the entire target nucleic acid). Examples of nucleic acid amplification procedures include transcription-related methods, such as transcription-mediated amplification (TMA), nucleic acid sequence-based amplification (NASBA), and others (e.g., U.S. Pat. Nos. 5,399,491, 5,554,516, 5,437,990, 5,130,238, 4,868,105, and 5,124,246), replicase-mediated amplification (e.g., U.S. Pat. Nos. 4,786,613, 4,786,616, 4,786,616, and 4,786,616). 00), polymerase chain reaction (PCR) (e.g., U.S. Pat. Nos. 4,683,195, 4,683,202, and 4,800,159), ligase chain reaction (LCR) (e.g., European Patent Application No. 0320308), helicase-dependent amplification (e.g., U.S. Pat. No. 7,282,328), and strand displacement amplification (SDA) (e.g., U.S. Pat. No. 5,422,252). Amplification can be linear or exponential. Replicase-mediated amplification uses self-replicating RNA molecules and a replicase such as QB-replicase. PCR amplification uses DNA polymerase, primers, and thermal cycling steps to synthesize multiple copies of two complementary strands of DNA or cDNA. LCR amplification uses at least four separate oligonucleotides to amplify a target and its complementary strand by using multiple cycles of hybridization, ligation, and denaturation. Helicase-dependent amplification uses a helicase to separate the two strands of a DNA duplex to generate a single-stranded template, followed by hybridization of a sequence-specific primer that hybridizes to the template and extension by a DNA polymerase that amplifies the target sequence. SDA uses a primer that contains a recognition site for a restriction endonuclease that will nick one strand of a hemi-modified DNA duplex containing the target sequence, followed by amplification in a series of primer extension and strand displacement steps. Certain embodiments use PCR or TMA, although it will be apparent to one of skill in the art that the oligonucleotides disclosed herein can be readily used as primers in other amplification methods.

[0134] Transcription-associated amplification uses DNA polymerase, RNA polymerase, deoxyribonucleoside triphosphates, ribonucleoside triphosphates, promoter-containing oligonucleotides, and optionally other oligonucleotides, to ultimately produce multiple RNA transcripts from a nucleic acid template (described in detail in U.S. Pat. Nos. 5,399,491 and 5,554,516, Kacian et al., U.S. Pat. No. 5,437,990, Burg et al., PCT Nos. 88 / 01302 and 88 / 10315, Gingeras et al., U.S. Pat. No. 5,130,238, Malek et al., U.S. Pat. Nos. 4,868,105 and 5,124,246, Urdea et al., PCT No. 94 / 03472, McDonough et al., PCT No. 95 / 03430, and Ryder et al.). Methods for using TMA have been described in detail previously (US Pat. Nos. 5,399,491 and 5,554,516).

[0135] In cyclic amplification methods that detect amplicons in real time, the term "threshold cycle" (Ct) is a measure of the time of appearance of a signal associated with the amplification of a target, and is generally 10 times the standard deviation of the normalized reporter signal. When the amplification reaches the "threshold cycle", it is generally considered that there is a positive amplification product of the sequence to which the probe binds. The identity of the amplification product can then be determined by methods known to those skilled in the art, such as gel electrophoresis, nucleic acid sequencing, and other such analytical procedures.

[0136] As used herein, the term "relative fluorescence unit" ("RFU") is a unit of measurement of fluorescence intensity. RFUs vary with the characteristics of the detection means used in the measurement and can be used as a measurement to compare relative intensities between samples and controls.

[0137] "Detection probe" or "probe" refers to an oligonucleotide that specifically hybridizes to a target sequence, including an amplified sequence, under conditions that promote nucleic acid hybridization for detection of a target nucleic acid. Detection can be either direct (i.e., a probe that hybridizes directly to a target) or indirect (i.e., a probe that hybridizes to an intermediate structure that binds the probe to a target). The target sequence of a probe generally refers to the specific sequence within a larger sequence to which the probe specifically hybridizes. Detection probes can include target-specific sequences and non-target-complementary sequences. Such non-target-complementary sequences can include sequences that will impart desired secondary or tertiary structures, such as hairpin structures, that can be used to promote detection and / or amplification (e.g., U.S. Pat. Nos. 5,118,801, 5,312,728, 6,835,542, and 6,849,412). Probes of defined sequences can be produced by techniques known to those of skill in the art, for example, by chemical synthesis and by in vitro or in vivo expression from recombinant nucleic acid molecules.

[0138] As used herein, a nucleic acid that is "substantially corresponding" to a specified nucleic acid sequence, or its complement, means that the oligonucleotide is sufficiently similar to the reference nucleic acid sequence to have similar hybridization properties to the reference nucleic acid sequence, in that the oligonucleotide will hybridize to the same target nucleic acid sequence under stringent hybridization conditions. A substantially corresponding nucleic acid differs from the particular nucleic acid by at least one nucleotide. This variation can be described in terms of the percentage of sequence identity or complementarity between the nucleic acid and the particular nucleic acid (e.g., less than 100% to about 80%). One of skill in the art will understand that the recited ranges include all integers and rational numbers in the range (e.g., 92%, 92.377%, etc.).

[0139] "Hybridization" or "hybridize" refers to the ability of two fully or partially complementary nucleic acid strands to come together under certain hybridization assay conditions, in parallel or antiparallel orientation, to form a stable structure having a double-stranded region. The two constituent strands of this double-stranded structure, sometimes called a hybrid, are held together by hydrogen bonds. These hydrogen bonds are most commonly formed between nucleotides containing the bases adenine and thymine or uracil (A and T or U) or cytosine and guanine (C and G) on a single nucleic acid strand, although base pairing can also be formed between bases that are not members of these "canonical" pairs. Non-canonical base pairing is well known in the art. (See, e.g., Adams et al., The Biochemistry of the Nucleic Acids (11th ed. 1992).)

[0140] "Preferentially hybridize" means that under stringent hybridization conditions, an amplification or detection probe oligonucleotide can hybridize to its target nucleic acid to form a stable oligonucleotide:target hybrid, but does not form a sufficient number of stable oligonucleotide:non-target hybrids. Amplification and detection oligonucleotides that hybridize preferentially to a target nucleic acid are useful for amplifying and detecting the target nucleic acid, but not to non-target organisms, especially organisms closely related phylogenetically. Thus, the oligonucleotide hybridizes to the target nucleic acid to a sufficiently greater extent than the non-target nucleic acid to allow the skilled artisan to accurately amplify and / or detect the presence (or absence) of nucleic acid from a specified enteric pathogen, as required. In general, reducing the degree of complementarity between an oligonucleotide sequence and its target sequence will reduce the degree or rate of hybridization of the oligonucleotide to its target region. However, the inclusion of one or more non-complementary nucleosides or nucleic acid bases may enhance the ability of the oligonucleotide to discriminate against non-target organisms.

[0141] Preferential hybridization can be measured using techniques known in the art and described herein, for example, in the examples provided below. In some embodiments, there is at least a 10-fold difference, at least a 100-fold difference, or at least a 1,000-fold difference between the target and non-target hybridization signals in the test sample. In some embodiments, the non-target hybridization signals in the test sample are at or below background signal levels.

[0142] "Stringent hybridization conditions" or "stringent conditions" refer to conditions that allow an oligomer to hybridize preferentially to a target nucleic acid (such as an enteric pathogen nucleic acid) but not to nucleic acids derived from closely related non-target nucleic acids. While the definition of stringent hybridization conditions is not variable, the actual reaction environment that can be used for stringent hybridization can vary depending on factors including the GC content and length of the oligonucleotide, the degree of similarity between the oligonucleotide sequence and the sequence of non-target nucleic acid that may be present in the test sample, and the target sequence. Hybridization conditions include the temperature and composition of the hybridization reagent or solution. Exemplary hybridization assay conditions for amplifying and / or detecting target nucleic acids derived from one or more target enteric pathogens with oligonucleotides of the present disclosure correspond to a temperature of about 60° C. when the salt concentration of a monovalent salt, such as KCl, is in the range of about 0.06-0.09 M. Specific hybridization assay conditions are described in the Examples section below. Other acceptable stringent hybridization conditions can be readily ascertained by one of ordinary skill in the art.

[0143] "Assay conditions" refers to conditions that allow for stable hybridization of an oligonucleotide to a target nucleic acid. Assay conditions do not require preferential hybridization of an oligonucleotide to a target nucleic acid.

[0144] "Label" or "detectable label" refers to a moiety or compound attached directly or indirectly to a probe that is detected or that results in a detectable signal. Direct attachment can use covalent or non-covalent interactions (e.g., hydrogen bonds, hydrophobic or ionic interactions, and chelate or coordinate complex formation), while indirect attachment can use a bridging moiety or linker (e.g., via an antibody or additional oligonucleotide(s)) that amplifies the detectable signal. Any detectable moiety can be used, such as radionuclides, ligands such as biotin or avidin, enzymes, enzyme substrates, reactive groups, chromophores such as dyes or particles (e.g., latex or metal beads) that impart a detectable color, luminescent compounds (e.g., bioluminescent, phosphorescent, or chemiluminescent compounds), and fluorescent compounds (i.e., fluorophores). Embodiments of fluorophores include those that absorb light in the range of about 495-690 nm and emit light in the range of about 520-705 nm, including those known as FAM™, TET™, CAL FLUOR™ (Orange or Red), and QUASAR™ compounds. Fluorophores may be used in combination with a quencher molecule that absorbs light when in close proximity to the fluorophore, thereby reducing background fluorescence. Such quenchers are well known in the art and include, for example, BLACK HOLE QUENCHER™ (or BHQ™) or TAMRA™ compounds. Certain embodiments include "homogeneous detectable labels" that are detectable in homogeneous systems in which bound labeled probes in a mixture exhibit a detectable change compared to unbound labeled probes, allowing the labels to be detected without physically removing hybridized labeled probes from unhybridized labeled probes (e.g., U.S. Pat. Nos. 5,283,174, 5,656,207, and 5,658,737). Certain homogeneous detectable labels include acridinium ester ("AE") compounds, such as chemiluminescent compounds including standard AE or AE derivatives, which are well known (U.S. Pat. Nos. 5,656,207, 5,658,737, and 5,639,604).Methods for synthesizing labels, binding labels to nucleic acids, and detecting signals from labels are well known (e.g., Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989), Chapter 10, and U.S. Patent Nos. 5,658,737, 5,656,207, 5,547,842, 5,283,174, and 4,581,333, and European Patent Application No. 0747706). Certain methods for binding AE compounds to nucleic acids are known (e.g., see U.S. Patent Nos. 5,585,481 and 5,639,604, column 10, row 6 to column 11, row 3, and Example 8). Specific AE labeling locations are the central region of the probe and near the region of A / T base pairs, the 3' or 5' end of the probe, or at or near the mismatch site with a known sequence where the probe should not be detected compared to the desired target sequence. Other detectably labeled probes include TaqMan™ probes, molecular torches, and molecular beacons. TaqMan™ probes contain donor and acceptor labels, and fluorescence is detected when the probe is enzymatically degraded during amplification to release the fluorophore from the presence of the quencher. Molecular torches and beacons exist in open and closed configurations, with the closed configuration quenching the fluorophore and the open position separating the fluorophore from the quencher to allow fluorescence. Hybridization to the target opens the otherwise closed probe.

[0145] A "non-extendable" oligonucleotide contains a blocking moiety at or near its 3' end to prevent extension. The blocking group near the 3' end is, in some embodiments, within 5 residues of the 3' end and large enough to limit the binding of a polymerase to the oligomer, while other embodiments contain a blocking group covalently attached to the 3' end. Many different chemical groups can be used to block the 3' end, such as alkyl groups, non-nucleotidic linkers, alkane-diol dideoxynucleotide residues, and cordycepin. Further examples of blocking moieties include 3'-deoxynucleotides (e.g., 2',3'-dideoxynucleotides); 3'-phosphorylated nucleotides; fluorophores, quenchers, or other labels that interfere with extension; inverted nucleotides (e.g., attached to the preceding nucleotide through a 3'- to -3' phosphodiester, optionally with an exposed 5'-OH or phosphate); or proteins or peptides attached to the oligonucleotide to prevent further extension of the nascent nucleic acid chain by a polymerase. Non-extendable oligonucleotides of the present disclosure can be at least 10 bases in length and can be up to 15, 20, 25, 30, 35, 40, 50, or more nucleotides in length. Non-extendable oligonucleotides that include a detectable label can be used as probes.

[0146] In particular, in the claims, references to "the sequence of SEQ ID NO:X" refer to the base sequence of the corresponding sequence listing entry, unless specifically indicated otherwise, and do not require identity of the backbone (e.g., RNA, 2'-O-Me RNA, or DNA) or base modifications (e.g., methylation of cytosine residues).

[0147] A "non-Watson-Crick" (NWC) position in an oligonucleotide refers to a position where the oligonucleotide is configured to hybridize to at least one target sequence with a non-Watson-Crick pairing, including through the use of inosine (e.g., via hypoxanthine (I) of inosine). Such NWC pairings include, for example, IA, IT, IC, IG, IU, GU, GT, and GA (any of I / A / T / C / G / U can be a base in the oligonucleotide). In some embodiments, the NWC position is configured to hybridize via an IA pair. In some embodiments, the NWC position is configured to hybridize via an IT pair. In some embodiments, the NWC position is configured to hybridize via an IC pair. In some embodiments, the NWC position is configured to hybridize via an IG pair. In some embodiments, the NWC position is configured to hybridize via an IU pair. In some embodiments, the NWC position is configured to hybridize via a wobble (GU) or purine-purine (GA) pair. In some embodiments, the NWC positions are configured to hybridize via a GT pair. In some embodiments, the NWC positions are configured to hybridize via a GU pair. In some embodiments, the NWC positions are configured to hybridize via a GA pair.

[0148] Unless otherwise defined, all scientific and technical terms used herein have the same meaning as commonly understood by those skilled in the relevant art. Common definitions can be found in technical books related to the field of molecular biology, such as DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY, 2nd ed. (Singleton et al., 1994, John Wiley&Sons, New York, NY) or THE HARPER COLLINS DICTIONARY OF BIOLOGY (Hale&Marham, 1991, Harper Perennial, New York, NY).

[0149] Exemplary Compositions, Kits, Methods, and Uses The present disclosure provides oligomers, compositions, and kits useful for determining the presence or absence of at least one enteric pathogen, such as Salmonella, C. jejuni, C. coli, Shigella, and STEC, in a sample.

[0150] In some embodiments, the oligonucleotides are provided, for example, in a kit or composition. The oligonucleotides generally include a target hybridization region configured to specifically hybridize to a target nucleic acid, for example, of an enteric pathogen. Although oligonucleotides of different lengths and base compositions can be used to amplify a target nucleic acid, in some embodiments, the oligonucleotides of the present disclosure have a target hybridization region of about 10-60 bases, about 14-50 bases, about 14-40 bases, about 14-35 bases, or about 15-30 bases. In some embodiments, the oligonucleotides include a region of a second sequence in addition to the target hybridization region, such as a promoter, which may be located 5' of the target hybridization region. In some embodiments, the oligonucleotides do not include a region of a second sequence.

[0151] In some embodiments, a set of oligonucleotides is provided, where one oligonucleotide is configured to hybridize to the sense strand of a target nucleic acid and the other oligonucleotide is configured to hybridize to the antisense strand of the target nucleic acid. Such oligonucleotides include amplification oligomer sets (e.g., primer pairs) for PCR or other forms of amplification.

[0152] In some embodiments, one or more oligonucleotides, such as a primer pair or a primer pair and a third oligonucleotide that is optionally labeled (e.g., for use as a probe), are configured to hybridize to a target nucleic acid of one or more enteric pathogens, including Salmonella, C. jejuni, C. coli, Shigella, and STEC. In some embodiments, a plurality of oligonucleotides, such as a plurality of primer pairs or a plurality of primer pairs and a third oligonucleotide that is optionally labeled (e.g., for use as a probe), are configured to collectively hybridize to one or more target nucleic acids of one or more enteric pathogens, including Salmonella, C. jejuni, C. coli, Shigella, or STEC.

[0153] In some embodiments, one or more oligonucleotides comprise a non-Watson-Crick (NWC) position. In some embodiments, the Salmonella primers, Salmonella primer pairs, and / or Salmonella probes comprise an NWC position, such as a position that includes an inosine. In some embodiments, the C. jejuni primers, C. jejuni primer pairs, and / or C. jejuni probes comprise an NWC position, such as a position that includes an inosine. In some embodiments, the C. coli primers, C. coli primer pairs, and / or C. coli probes comprise an NWC position, such as a position that includes an inosine. In some embodiments, the Shigella primers, Shigella primer pairs, and / or Shigella probes comprise an NWC position, such as a position that includes an inosine. In some embodiments, the STEC primers, STEC primer pairs, and / or STEC probes comprise an NWC position, such as a position that includes an inosine.

[0154] In some embodiments, one or more oligonucleotides comprise a position that includes a 5-methylcytosine. In some embodiments, the Salmonella primer, Salmonella primer pair, and / or Salmonella probe comprise a position that includes a 5-methylcytosine. In some embodiments, the C. jejuni primer, C. jejuni primer pair, and / or C. jejuni probe comprise a position that includes a 5-methylcytosine. In some embodiments, the C. coli primer, C. coli primer pair, and / or C. coli probe comprise a position that includes a 5-methylcytosine. In some embodiments, the Shigella primer, Shigella primer pair, and / or Shigella probe comprise a position that includes a 5-methylcytosine. In some embodiments, the STEC primer, STEC primer pair, and / or STEC probe comprise a position that includes a 5-methylcytosine.

[0155] In some embodiments, the first and second oligomers of the Salmonella-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO:12 and SEQ ID NO:14, respectively. In some embodiments, the first and second oligomers of the Salmonella-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO:21 and SEQ ID NO:47, respectively. In some embodiments, the first and second oligomers of the Salmonella-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO:38 and SEQ ID NO:36, respectively. In some embodiments, the first and second oligomers of the Salmonella-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO:35 and SEQ ID NO:40, respectively. In some embodiments, the first and second oligomers of the Salmonella-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO:12 and SEQ ID NO:28, respectively. In some embodiments, the first and second oligomers of the Salmonella-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO:42 and SEQ ID NO:31, respectively. In some embodiments, the first and second oligomers of the Salmonella-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO:41 and SEQ ID NO:27, respectively.

[0156] In some embodiments, the first and second oligomers of the C. jejuni-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO:11 and SEQ ID NO:19, respectively.

[0157] In some embodiments, the first and second oligomers of the C. jejuni-specific amplification oligomer set consist of target hybridization sequences comprising SEQ ID NO:11 and SEQ ID NO:19, respectively.

[0158] In some embodiments, the first and second oligomers of the C. coli specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO:8 and SEQ ID NO:10, respectively.

[0159] In some embodiments, the first and second oligomers of the C. coli specific amplification oligomer set consist of target hybridization sequences comprising SEQ ID NO:8 and SEQ ID NO:10, respectively.

[0160] In some embodiments, the first and second oligomers of the Shigella-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO: 15 and SEQ ID NO: 17, respectively. In some embodiments, the first and second oligomers of the Shigella-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO: 34 and SEQ ID NO: 22, respectively. In some embodiments, the first and second oligomers of the Shigella-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO: 32 and SEQ ID NO: 33, respectively.

[0161] In some embodiments, the first and second oligomers of the Shigella-specific amplification oligomer set consist of target hybridization sequences comprising SEQ ID NO: 15 and SEQ ID NO: 17, respectively. In some embodiments, the first and second oligomers of the Shigella-specific amplification oligomer set consist of target hybridization sequences comprising SEQ ID NO: 34 and SEQ ID NO: 22, respectively. In some embodiments, the first and second oligomers of the Shigella-specific amplification oligomer set consist of target hybridization sequences comprising SEQ ID NO: 32 and SEQ ID NO: 33, respectively.

[0162] In some embodiments, the first and second oligomers of a STEC-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO: 20 and SEQ ID NO: 3, respectively. In some embodiments, the first and second oligomers of a STEC-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO: 49 and SEQ ID NO: 3, respectively. In some embodiments, the first and second oligomers of a STEC-specific amplification oligomer set comprise target hybridization sequences comprising SEQ ID NO: 4 and SEQ ID NO: 7, respectively.

[0163] In some embodiments, the first and second oligomers of a STEC-specific amplification oligomer set consist of target hybridization sequences comprising SEQ ID NO: 20 and SEQ ID NO: 3, respectively. In some embodiments, the first and second oligomers of a STEC-specific amplification oligomer set consist of target hybridization sequences comprising SEQ ID NO: 49 and SEQ ID NO: 3, respectively. In some embodiments, the first and second oligomers of a STEC-specific amplification oligomer set consist of target hybridization sequences comprising SEQ ID NO: 4 and SEQ ID NO: 7, respectively.

[0164] Exemplary primer pairs and optional third oligomers (eg, probes) are set forth in Table A below.

[0165] [Table A]

[0166] In some embodiments, oligonucleotides are provided that include a label. Such oligonucleotides can be used as probes. In some embodiments, the labeled oligonucleotides have sequences that correspond to the SEQ ID NOs listed in the Oligomer 3 column of Table A. In some embodiments, the label is a non-nucleotide label. Suitable labels include compounds that emit detectable light signals, such as fluorophores or luminescent (e.g., chemiluminescent) compounds that can be detected in homogenous mixtures. More than one label, and more than one type of label, can be present on a particular probe, or detection can rely on using a mixture of probes, each of which is labeled with a compound that produces a detectable signal (see, for example, U.S. Patent Nos. 6,180,340 and 6,350,579, each of which is incorporated herein by reference). Labels can be attached to probes by a variety of means, including covalent binding, chelation, and ionic interactions, although in some embodiments, the labels are covalently attached. For example, in some embodiments, the detection probe has an attached chemiluminescent label, such as, for example, an acridinium ester (AE) compound (see, for example, U.S. Patent Nos. 5,185,439, 5,639,604, 5,585,481, and 5,656,744). Labels, such as fluorescent or chemiluminescent labels, can be attached to the probe by non-nucleotidic linkers (C Patent Nos. 5,585,481, 5,656,744, and 5,639,604). In some embodiments, the label can include one or more of Quasar 670, CalRed 610, CalOrange 560, fluorescein, ROX, FAM, and HEX.

[0167] In some embodiments, the probe (e.g., comprising a fluorescent label) further comprises a second label that interacts with the first label. For example, the second label can be a quencher. In some embodiments, the second label can comprise one or both of BHQ-1 and BHQ-2. Such probes can be used, for example, in TaqMan™ assays, where hybridization of the probe to a target or amplicon, followed by nucleolysis by a polymerase that comprises a 5'-3' exonuclease activity, results in release of the fluorescent label and thereby increased fluorescence, or fluorescence independent of interaction with the second label.

[0168] In some applications, one or more probes that exhibit at least some degree of self-complementarity are used to facilitate detection of probe:target duplexes in a test sample without first requiring removal of unhybridized probes prior to detection. Specific embodiments of such detection probes include probes that form conformations that are held together by intramolecular hybridization, such as conformations commonly referred to as hairpins. Suitable hairpin probes include "molecular torches" (see, e.g., U.S. Pat. Nos. 6,849,412, 6,835,542, 6,534,274, and 6,361,945) and "molecular beacons" (see, e.g., U.S. Pat. Nos. 5,118,801 and 5,312,728). Molecular torches contain separate regions of self-complementarity (coined "target binding domain" and "target closing domain") that are connected by a linking region (e.g., -(CH2CHO)3- linker) and hybridize to each other under predetermined hybridization assay conditions. When exposed to the appropriate target or denaturing conditions, the two complementary regions of the molecular torch (which may be fully or partially complementary) melt, making the target binding domain available for hybridization to the target sequence when the predetermined hybridization assay conditions are restored. Molecular torches are designed such that the target binding domain has a preference for hybridization to the target sequence relative to the target closing domain. The target binding domain and target closing domain of the molecular torch contain interactive labels (e.g., fluorescent / quencher) positioned such that a different signal is produced when the molecular torch is self-hybridized as opposed to when the molecular torch is hybridized to the target nucleic acid, thereby allowing detection of the probe:target duplex in a test sample in the presence of an unhybridized probe having a viable label associated therewith.

[0169] Examples of interacting donor / acceptor label pairs that may be used in connection with the present disclosure, without attempting to distinguish FRET from non-FRET pairs, include fluorescein / tetramethylrhodamine, IAEDANS / fluorescein, EDANS / DABCYL, coumarin / DABCYL, fluorescein / fluorescein, BODIPY FL / BODIPY FL, fluorescein / DABCYL, Lucifer Yellow / DABCYL, BODIPY / DABCYL, eosin / DABCYL, erythrosine / DABCYL, tetramethylrhodamine / DABCYL, Texas Red / DABCYL, CY5 / BHQ-1, CY5 / BHQ-2, CY3 / BHQ-1, CY3 / BHQ-2, and fluorescein / QSY7 dyes. Those skilled in the art will understand that when the donor and acceptor dyes are different, energy transfer can be detected by the appearance of sensitized fluorescence of the acceptor or by quenching of donor fluorescence. Non-fluorescent acceptors such as DABCYL and QSY7 dyes advantageously eliminate the potential problem of background fluorescence resulting from direct (i.e., non-sensitized) acceptor excitation. Exemplary fluorophore moieties that can be used as one member of a donor-acceptor pair include fluorescein, ROX, and CY dyes (such as CY5). Exemplary quencher moieties that can be used as another member of a donor-acceptor pair include DABCYL and Black Hole Quencher moieties available from Biosearch Technologies, Inc. (Novato, Calif.).

[0170] In some embodiments, the labeled oligonucleotide (e.g., probe) is non-extendable. For example, the labeled oligomer can be made non-extendable by 3'-phosphorylation, having a 3'-terminal 3'-deoxynucleotide (e.g., a terminal 2',3'-dideoxynucleotide), having a 3'-terminal inverted nucleotide (e.g., inverted so that the last nucleotide is attached to the penultimate nucleotide by a 3' to 3' phosphodiester bond or analog thereof, e.g., phosphorothioate), or having an attached fluorophore, quencher, or other label that interferes with extension (possibly, but not necessarily, attached through the 3' position of the terminal nucleotide). In some embodiments, the 3'-terminal nucleotide is unmethylated.

[0171] The present disclosure also provides a reaction mixture for determining the presence or absence of, or quantifying the amount of, a target nucleic acid of at least one enteric pathogen, such as Salmonella, C. jejuni, C. coli, Shigella, and STEC, in a sample. The reaction mixture according to the present disclosure comprises at least one or more of the following: an oligonucleotide described herein for amplifying a target nucleic acid, and an oligonucleotide (e.g., a probe) described herein for determining the presence or absence of an amplification product of the target nucleic acid. For a reaction mixture that includes a detection probe together with an amplification oligonucleotide combination, the amplification oligonucleotide and the detection probe oligonucleotide for the reaction mixture are bound by a common target region (i.e., the reaction mixture will include a probe that binds to a sequence that can be amplified by the amplification oligonucleotide combination of the reaction mixture).

[0172] The reaction mixture may further include a number of optional components, such as, for example, a capture probe, e.g., a poly-(k) capture probe as described in US2013 / 0209992, which is incorporated herein by reference, and / or a poly-(R) capture probe as described in US2020 / 0165599, which is incorporated herein by reference. For amplification reaction mixtures, the reaction mixture will typically include other reagents suitable for performing in vitro amplification, such as, for example, a buffer, a salt solution, appropriate nucleotide triphosphates (e.g., dATP, dCTP, dGTP, and dTTP, and / or ATP, CTP, GTP, and UTP), and / or enzymes (e.g., a thermostable DNA polymerase, or a reverse transcriptase and / or an RNA polymerase), and will typically include test sample components, which may or may not include a target nucleic acid. Suitable reagents include, for example, formulations containing lithium lauryl sulfate (LLS), sodium lauryl sulfate (SLS), NaH2PO4, Na2HPO4, EDTA, EGTA, LiOH, NaCl, KCl, MgCl2, NaOH, ethanol, methylparaben, propylparaben, trehalose, Tris Buffer, Triton® X-100, paramagnetic particles, target capture oligonucleotides, HEPES, succinic acid, polymerase (e.g., DNA polymerase, reverse transcriptase), and / or RNasin.

[0173] In some embodiments, the reaction mixture comprises KCl. In some embodiments, the KCl concentration is about 50 mM. In some embodiments, the KCl concentration is greater than about 50 mM, e.g., about 60-150 mM, about 75-125 mM, about 80-120 mM, about 85-115 mM, or about 90-110 mM. In some embodiments, the KCl concentration is 55-65, 65-75, 75-85, 85-95, 95-105, 105-115, 115-125, 125-135, or 135-145, each of the foregoing being in mM and optionally modified by "about." In some embodiments, a composition according to the present disclosure comprises KCl, e.g., at any of the foregoing concentrations. In some embodiments, a method according to the present disclosure comprises performing an amplification reaction in the presence of KCl, e.g., at any of the foregoing concentrations.

[0174] In some embodiments, the reaction mixture includes α-cyclodextrin and / or polysorbate 20. In some embodiments, the concentration of α-cyclodextrin in the reaction mixture is about 10 mg / mL to about 40 mg / mL. In some embodiments, the concentration of α-cyclodextrin in the reaction mixture is about 16 mg / mL to about 30 mg / mL, about 15 mg / mL to about 20 mg / mL, or about 10 mg / mL to about 15 mg / mL. In some embodiments, the concentration of α-cyclodextrin in the reaction mixture is about 20 mg / mL, about 17.5 mg / mL, or about 12.5 mg / mL. In some embodiments, the concentration of polysorbate 20 in the reaction mixture is about 0.002% to about 0.05% (v / v). In some embodiments, the concentration of polysorbate 20 in the reaction mixture is about 0.003% to about 0.03% (v / v). In some embodiments, the concentration of polysorbate 20 in the reaction mixture is about 0.0042% (v / v), about 0.0035% (v / v), about 0.0026% (v / v), or about 0.02% (v / v). In some embodiments, the reaction mixture includes a detergent. In some embodiments, the detergent includes sodium dodecyl sulfate. In some embodiments, the concentration of the detergent in the reaction mixture is about 3 mg / mL to 300 mg / mL. In some embodiments, the concentration of the detergent in the reaction mixture is about 10 mg / mL to 100 mg / mL. In some embodiments, the concentration of the detergent in the reaction mixture is about 33.3 mg / mL.

[0175] The present disclosure also provides a kit for carrying out the methods described herein. A kit according to the present disclosure includes at least one or more of the following: an oligonucleotide described herein for amplifying a target nucleic acid, and an oligonucleotide (e.g., a probe) described herein for determining the presence or absence of an amplification product of the target nucleic acid. In some embodiments, any of the oligonucleotide combinations described herein are present in the kit. The kit may further include a number of optional components, such as, for example, a capture probe, such as a poly-(k) capture probe as described in US2013 / 0209992, and / or a poly-(R) capture probe as described in US2020 / 0165599. Other reagents that may be present in the kit include reagents suitable for carrying out in vitro amplification, such as, for example, a buffer, a salt solution, appropriate nucleotide triphosphates (e.g., dATP, dCTP, dGTP, and dTTP, and / or ATP, CTP, GTP, and UTP), and / or enzymes (e.g., a thermostable DNA polymerase, or a reverse transcriptase and / or an RNA polymerase). The oligonucleotides described herein can be packaged in a variety of different embodiments, and those skilled in the art will understand that the present disclosure encompasses many different kit configurations. For example, the kit can include amplification oligonucleotides for only one, two, three, four, or all of Salmonella, C.jejuni, C.coli, Shigella, and STEC. In addition, for kits that include detection probes together with amplification oligomer combinations, the amplification oligonucleotides and detection probe oligonucleotides for the reaction mixture are bound by a common target region (i.e., the reaction mixture will include a probe that binds to a sequence that can be amplified by the amplification oligonucleotide combination of the reaction mixture). In certain embodiments, the kit further includes a set of instructions for carrying out the method according to the present disclosure, and the instructions can be associated with a package insert and / or packaging of the kit or its components.

[0176] The present disclosure also provides a method (e.g., a multiplex method) for determining the presence or absence of at least one enteric pathogen, including Salmonella, C.jejuni, C.coli, Shigella, and STEC, in a sample, for example, by using one or more of the oligonucleotides disclosed herein. Any method disclosed herein should also be understood as a disclosure of the corresponding use of the materials involved in the method directed to the object of the method. Any of the oligonucleotides, and any combinations (e.g., kits and compositions) comprising such oligonucleotides, should also be understood as being disclosed for use in detecting or quantifying at least one enteric pathogen, and for use in preparing compositions for detecting or quantifying at least one enteric pathogen.

[0177] Broadly speaking, the method may include one or more of the following components: target capture, where target nucleic acid (e.g., from a sample, such as a clinical sample) is annealed to a capture oligonucleotide; isolation, e.g., washing, to remove material not associated with the capture oligonucleotide; amplification; and amplicon detection, e.g., amplicon quantification, which may be performed in real time with amplification. Certain embodiments involve each of the aforementioned steps. Certain embodiments involve exponential amplification, optionally with a preceding linear amplification step. Certain embodiments involve exponential amplification and amplicon detection. Certain embodiments involve any two of the components listed above. Certain embodiments involve any two components listed adjacently above, e.g., washing and amplification, or amplification and detection.

[0178] In some embodiments, the amplification comprises: (1) contacting the sample with at least two oligonucleotides to amplify a target nucleic acid target region corresponding to the target nucleic acid, where the oligonucleotides comprise at least two amplification oligonucleotides described above (e.g., one or more oriented in a sense direction for exponential amplification and one or more oriented in an antisense direction); (2) performing an in vitro nucleic acid amplification reaction in which any target nucleic acid present in the sample is used as a template to generate an amplification product; and (3) detecting the presence or absence of the amplification product, thereby determining the presence or absence of at least one enteric pathogen, including Salmonella, C. jejuni, C. coli, Shigella, and STEC, in the sample or quantifying the amount of the target nucleic acid in the sample.

[0179] Detection methods according to the present disclosure can further include obtaining a sample to be subjected to subsequent steps of the method. In certain embodiments, "obtaining" a sample to be used includes, for example, receiving a sample at a testing facility or other location where one or more steps of the method are performed, and / or retrieving a sample from a location within the facility where one or more steps of the method are performed (e.g., from a storage or other depository).

[0180] In certain embodiments, the method further comprises purifying the target nucleic acid from other components in the sample prior to amplification, e.g., prior to the capture step. Such purification may include methods to separate and / or concentrate organisms contained in the sample from other sample components, or to remove or degrade non-nucleic acid sample components, e.g., proteins, carbohydrates, salts, lipids, etc. In some embodiments, the nucleic acids in the sample are degraded, e.g., with DNase, optionally removing or inactivating the DNase or removing the degraded nucleic acids.

[0181] In certain embodiments, purifying the target nucleic acid comprises capturing the target nucleic acid and specifically or non-specifically separating the target nucleic acid from other sample components. Non-specific target capture methods may involve selective precipitation of the nucleic acid from a substantially aqueous mixture, attachment of the nucleic acid to a support that is washed to remove other sample components, or other means of physically separating the nucleic acid from a mixture containing the target nucleic acid and other sample components.

[0182] Target capture typically occurs in a solution-phase mixture containing one or more capture probe oligonucleotides that hybridize to target nucleic acid sequences under hybridization conditions. For embodiments that include a capture probe tail, the target:capture-probe complex is captured by adjusting the hybridization conditions so that the capture probe tail hybridizes to the immobilized probe. Certain embodiments use particulate solid supports, such as paramagnetic beads.

[0183] Isolation can follow capture, with the complex on the solid support being separated from other sample components. Isolation can be accomplished by any suitable technique, for example, by washing the support associated with the target-sequence one or more times (e.g., two or three times) to remove other sample components and / or unbound oligomers. In embodiments using particulate solid supports such as paramagnetic beads, the particles associated with the target can be suspended in a wash solution and, in some embodiments, retrieved from the wash solution by using magnetic attraction. To limit the number of handling steps, the target nucleic acid can be amplified by simply mixing the target sequence in the complex on the support with the amplification oligomers and proceeding with the amplification step.

[0184] Exponentially amplifying the target sequence utilizes an in vitro amplification reaction that uses at least two amplification oligonucleotides that flank the target region to be amplified. In some embodiments, at least one oligonucleotide is provided as described above. In some embodiments, a plurality of oligonucleotide pairs is provided, the plurality comprising oligonucleotide pairs configured to hybridize at least one, two, three, four, or all of the Salmonella, C. jejuni, C. coli, Shigella, and STEC target nucleic acids. The amplification reaction can be cyclic or isothermal. Suitable amplification methods include, for example, replicase-mediated amplification, polymerase chain reaction (PCR), ligase chain reaction (LCR), strand displacement amplification (SDA), and transcription-mediated or transcription-associated amplification (TMA).

[0185] The detection step can be performed using any of a variety of known techniques for detecting signals specifically associated with the amplified target sequence, such as, for example, by hybridizing the amplification product with a labeled detection probe and detecting a signal resulting from the labeled probe (including, in some embodiments, from a label released from the probe after hybridization), performing electrophoresis on the sample and / or the amplification product, determining the sequence of the amplification product. In some embodiments, the labeled probe includes a second moiety, such as a quencher or other moiety that interacts with the first label, as discussed above. The detection step can also provide additional information about the amplified sequence, such as, for example, all or a portion of its nucleobase sequence. Detection can be performed after the amplification reaction is completed, or can be performed simultaneously with amplifying the target region, for example, in real time. In one embodiment, the detection step allows for homogenous detection, e.g., detection of hybridized probes without removal of unhybridized probes from the mixture (see, for example, U.S. Pat. Nos. 5,639,604 and 5,283,174). In some embodiments, the nucleic acid is associated with a surface that produces a physical change, such as a detectable change in electrical potential. The amplified nucleic acids can be detected by concentrating them in or on a matrix and detecting the nucleic acid or a dye associated with them (e.g., an intercalating agent such as ethidium bromide or SYBR Green), or by detecting an increase in a dye associated with the nucleic acid in the solution phase. Other detection methods can be by using a nucleic acid detection probe that is configured to specifically hybridize to a sequence in the amplified product and detect the presence of a probe:product complex, or by using a complex of probes that can amplify a detectable signal associated with the amplified product (see, for example, U.S. Patent Nos. 5,424,413, 5,451,503, and 5,849,481, each of which is incorporated by reference herein). A directly or indirectly labeled probe that specifically associates with the amplified product provides a detectable signal that indicates the presence of the target nucleic acid in the sample.In particular, the amplified product will contain a target sequence in or complementary to a target core sequence of at least one enteric pathogen, and the probe will bind directly or indirectly to a sequence contained in the amplified product to indicate the presence or absence of the pathogen in the tested sample.

[0186] In embodiments that detect amplified products near or at the end of the amplification step, linear detection probes can be used to provide a signal indicative of hybridization of the probe to the amplified product. One example of such detection uses a luminescently labeled probe that hybridizes to the target nucleic acid. The luminescent label is then hydrolyzed from the unhybridized probe. Detection is performed by chemiluminescence using a luminometer (see, for example, PCT Patent Application Publication No. 89 / 002476). In other embodiments that use real-time detection, the detection probe can be a hairpin probe, such as, for example, a molecular beacon, a molecular torch, or a hybridization switch probe, that is labeled with a reporter moiety that is detected when the probe binds to the amplified product. Such a probe can include a target hybridization sequence and a non-target hybridization sequence. Various forms of such probes are described, for example, in U.S. Pat. Nos. 5,118,801, 5,312,728, 5,925,517, 6,150,097, 6,849,412, 6,835,542, 6,534,274, and 6,361,945, and in U.S. Patent Application Publication Nos. 2006 / 0068417A1 and 2006 / 0194240A1.

[0187] In some embodiments, in the amplification reaction, the amplification oligonucleotides may hybridize preferentially to the target nucleic acid, such as the target sequence of the pathogen. In some embodiments, in the detection step, the probes may hybridize preferentially to the target nucleic acid, such as the amplification products. For example, under stringent hybridization conditions, the amplification or detection probe oligonucleotides may hybridize to their target nucleic acid to form stable oligonucleotide:target hybrids, but not form a sufficient number of stable oligonucleotide:non-target hybrids. In some embodiments, there is at least a 5-fold difference, at least a 10-fold difference, at least a 20-fold difference, at least a 50-fold difference, at least a 75-fold difference, at least a 100-fold difference, at least a 200-fold difference, at least a 500-fold difference, at least a 1,000-fold difference, or at least a 2,000-fold difference between the target and non-target hybridization signals in the test sample (i.e., the ratio of the signal intensities of the oligonucleotide:target hybrid and the oligonucleotide:non-target hybrid). In some embodiments, the non-target hybridization signals in the test sample are below background signal levels.

[0188] In some embodiments, the amplification reaction and / or detection step may be performed under stringent hybridization conditions. In some embodiments, such stringent hybridization conditions allow oligonucleotides (e.g., amplification oligonucleotides or probes) to preferentially hybridize to target nucleic acids (such as pathogen target sequences or amplification products) rather than nucleic acids derived from closely related non-target nucleic acids. In different embodiments, the actual reaction environment that can be used for stringent hybridization may vary depending on factors including the GC content and length of the oligonucleotide, the degree of similarity between the oligonucleotide sequence and the sequence of non-target nucleic acids that may be present in the test sample, and the target sequence. In some embodiments, hybridization conditions for the amplification reaction and / or detection step correspond to a temperature of about 55° C., about 56° C., about 57° C., about 58° C., about 59° C., about 60° C., about 61° C., about 62° C., about 63° C., about 64° C., or about 65° C. when the salt concentration of a monovalent salt, such as KCl, is about 0.5 M, about 0.6 M, about 0.7 M, about 0.8 M, about 0.9 M, or about 1.0 M.

[0189] For example, methods (e.g., multiplex methods) for determining the presence or absence of at least one enteric pathogen, including Salmonella, C. jejuni, C. coli, Shigella, and STEC, in a sample by using one or more of the oligonucleotides disclosed herein can be used to determine the presence or absence of at least one enteric pathogen, including Salmonella, C. jejuni, C. coli, Shigella, and STEC, at concentrations of 25-500 CFU / mL, 50-500 CFU / mL, 75-500 CFU / mL, 100-500 CFU / mL, 200-500 CFU / mL, 300-350 CFU / mL, 400-400 CFU / mL, 500-500 CFU / mL, 600-650 CFU / mL, 700-700 CFU / mL, 800-800 CFU / mL, 900-900 CFU / mL, 1000-1000 CFU / mL, 1500-1000 CFU / mL, 2000-2500 CFU / mL, 3000-4000 CFU / mL, 4000-500 CFU / mL, 5000-500 CFU / mL, 6000-7000 CFU / mL, 7000-8000 CFU / mL, 8000-9000 CFU / mL, 9000-1000 CFU / mL, 1000-1000 CFU / mL, 1500-1000 CFU / mL, 1000-1000 CFU / mL, 1500-1000 CFU / mL, 2000-2500 CFU / mL, 2000-2500 CFU / mL, 3000-300 The detection sensitivity may be 5 to 300 CFU / mL, 50 to 300 CFU / mL, 75 to 300 CFU / mL, 100 to 300 CFU / mL, 25 to 150 CFU / mL, 50 to 150 CFU / mL, 75 to 150 CFU / mL, 100 to 150 CFU / mL, 25 to 100 CFU / mL, 50 to 100 CFU / mL, 75 to 100 CFU / mL, 25 to 75 CFU / mL, 50 to 75 CFU / mL, or 25 to 50 CFU / mL.

[0190] The present disclosure also provides methods for synthesizing one or more (e.g., one or more pairs) of the oligonucleotides disclosed herein, where the oligonucleotides are useful for determining the presence or absence of at least one enteric pathogen, including Salmonella, C. jejuni, C. coli, Shigella, and STEC. The method may, for example, include the steps of: (a) obtaining a solid support comprising at least one nucleobase residue, where at least one nucleobase residue is attached (e.g., covalently attached) to the solid support at a 3' position; (b) attaching the 5' position of the nucleobase residue furthest from the solid support to the 3' position of another nucleobase residue; and (c) repeating step (b) an additional at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or at least 28 times, thereby obtaining at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, or at least 28 times. The method may include generating at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 contiguous solid support-bound nucleobase residues, and (d) cleaving at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 contiguous nucleobase residues generated in step (c), thereby obtaining an oligonucleotide or a plurality of oligonucleotides. In some embodiments, the oligonucleotide has a length of 18-32 contiguous nucleobase residues. In some embodiments, the oligonucleotide has a length of 20-30 contiguous nucleobase residues.

[0191] The method for synthesizing one or more of the oligonucleotides disclosed herein can be a solid-phase method.For example, phosphoramidite solid-phase chemistry for linking nucleotides by phosphodiester bond is described in Caruthers et al., "Chemical Synthesis of Deoxynucleotides by the Phosphoramidite Method," Methods Enzymol. 154:287 (1987).As another example, automated solid-phase chemical synthesis using cyanoethyl phosphoramidite precursors is described in Barone et al., "In Situ Activation of bis-dialkylaminephosphines-a New Method for Synthesizing Deoxyoligonucleotides on Polymer Supports," Nucleic Acids Res. 12(10):4051 (1984).As another example, U.S. Patent No. 5,449,769, entitled "Method and Reagent for Sulfurization of Organophosphorous Compounds," discloses a procedure for synthesizing oligonucleotides containing phosphorothioate bond. In addition, U.S. Patent No. 5,811,538, entitled "Process for the Purification of Oligomers," discloses the synthesis of oligonucleotides having different linkages, including methylphosphonate linkages. Further, methods for the organic synthesis of oligonucleotides are described, for example, in Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989), Chapter 10.

[0192] After synthesis and purification of a particular oligonucleotide, several different procedures can be utilized to purify and control the quality of the oligonucleotide. Suitable procedures include electrophoresis (e.g., polyacrylamide gel electrophoresis) or chromatography (e.g., high pressure liquid chromatography). EXAMPLES

[0193] The following examples are provided to illustrate certain disclosed embodiments and should not be construed as limiting the scope of the disclosure in any way.

[0194] Example 1 - Real-time PCR amplification and detection of GI-bacteria panel targets using different combinations of primers and probes Several primer and probe combinations were tested for real-time PCR amplification and detection of Salmonella, Campylobacter, Shigella / Enteroinvasive E. coli (Shigella / EIEC), and Shigatoxigenic E. coli (STEC) targets.

[0195] Amplification and detection reactions were performed using a Panther Fusion instrument (Hologic, Inc. San Diego, CA). Typically, 20 μL of amplification reagent was combined in a reaction well of a multi-well plate with 5 μL of target nucleic acid. The multi-well plate was placed in the Panther Fusion instrument and subjected to thermal cycling. Real-time amplification and detection reactions were performed by thermal cycling, typically over 45 cycles (denaturation at 95° C. for 8 seconds and annealing and extension at 60° C. for 25 seconds), with fluorescence emission measurements taken every 30 seconds. Fluorescence curve profiles for target nucleic acid were evaluated for Ct and RFU signals.

[0196] Example 2 - Analytical Sensitivity - Bacterial Detection Limit Analytical sensitivity experiments were performed to determine the limit of detection (LoD) of target nucleic acids for six individual bacterial organisms using multiplexed primer-probe combinations. Primers and probes used in the experiment are listed in Table 1. Known stock concentrations of each organism (available from American Type Tissue Culture, Manassas, VA) were serially diluted in live stool matrix to provide a series of five dilution concentrations for each organism. Salmonella typhimurium, Campylobacter coli, Campylobacter jejuni, Shigella sonnei, Shiga Toxin-producing Escherichia coli O157:H7 (STEC stx1 and STEC stx2) were each serially diluted to provide the following concentrations: 1,000 CFU / mL, 500 CFU / mL, 300 CFU / mL, 150 CFU / mL, and 100 CFU / mL. Campylobacter jejuni was serially diluted to provide the following concentrations: 1,000 CFU / mL, 500 CFU / mL, 300 CFU / mL, 100 CFU / mL, and 75 CFU / mL. Each of the dilutions was tested in replicates of 5, and the Ct and RFU data are shown in Table 2. The lowest concentration that was 100% positive for each organism was then further tested in replicates of 20 (dilutions made in both raw and Cary-Blair stool matrices), and the Ct and RFU data are shown in Table 3. Sample processing, target capture, amplification, and detection reactions were generally performed as described herein. An internal control nucleic acid was present in each amplification reaction.

[0197] [Table 1]

[0198] [Table 2]

[0199] [Table 3]

[0200] Data from this experiment showed 100% positivity (5 / 5) for Salmonella typhimurium, Shigella sonnei, STEC stx1, and STEC stx2 at concentrations as low as 100 CFU / mL. Campylobacter coli was 100% positive at 300 CFU / mL, 80% positive (4 / 5) at 100 CFU / mL, and Campylobacter jejuni was 100% positive at 75 CFU / mL. Confirmatory testing showed 100% positivity (20 / 20) for each of Campylobacter coli, Campylobacter jejuni, Shigella sonnei, STEC stx1, and STEC stx2 in two different stool matrices. Salmonella typhimurium was 90% positive in the live stool matrix and 95% positive in the Cary-Blair stool matrix. These data indicate that the multiplex primer / probe combination has a sensitivity of 75-150 CFU / mL.

[0201] Example 3 - Primer-probe combinations for amplification and detection of Salmonella Several primer and probe combinations were prepared and tested for amplification and detection of Salmonella enterica. The combinations are listed in Table 4 below. These primer-probe combinations were tested against Salmonella enterica at three serially diluted stock concentrations. Dilutions were made into sample transport reagent and concentrations of 500 CFU / mL, 150 CFU / mL, and 50 CFU / mL were tested. Negative reaction wells were sample transport medium. Reaction conditions were set up in triplicate and real-time amplification and detection reactions were performed. RFU and Ct results are shown in Table 5.

[0202] [Table 4-1] [Table 4-2]

[0203] [Table 5]

[0204] Primer and probe combinations 1 and 2 showed only negative results in this experiment and therefore the results are not shown in Table 5. Combinations 3-7 each showed a robust RFU over background. Combinations 4 and 5 showed the most robust RFU and fastest Ct in this experiment.

[0205] Example 4 - Analytical specificity and interference Analytical specificity was tested for an exemplary multiplexed assay for detecting Salmonella, Shigella, Campylobacter (C. jejuni and C. coli, undifferentiated), and STEC (stx-1 and stx-2 undifferentiated). The assays were performed as real-time, multiplexed PCR reactions utilizing the primer and probe combinations and cycling parameters in Table 1.

[0206] The analytical specificity of the PCR assay was determined using a total of 81 organisms divided into 17 panels listed in Table 6 and Table 6.1. These 81 organisms are commonly found in stool samples (organisms available from American Type Tissue Culture, Manassas, VA). The 17 organism panel was spiked into a negative Cary-Blair stool matrix. The concentrations of organisms were 1E6 CFU / mL in each test, except for Bifidobacterium adolescentis, Egglerthella lenta, and Peptostreptococcus micros, which had concentrations of 1E6 rRNA copies / mL, and Entamoeba histolytica, which had concentrations of 1E4 cells / mL. Positive controls were Salmonella enterica (strain V1796), Campylobacter coli (strain RO 268), Shigella flexneri (strain 24570), and STEC (strain CDC 1999-3302) spiked into Cary-Blair stool matrix at 3x LoD. Negative controls were Cary-Blair stool matrix only. Reactions were performed in triplicate. Reactivity or positivity was defined as an amplification curve exceeding the Ct threshold for each channel. Any curve below this threshold was considered negative or non-reactive. Ct thresholds used were: FAM, 600; HEX, 1000; ROX, 500; Q670, 600; and Q705, 1000. Results are shown in Tables 7, 7.1, 8, and 8.1.

[0207] [Table 6-1] [Table 6-2]

[0208] [Table 6.1]

[0209] [Table 7]

[0210] [Table 7.1]

[0211] [Table 8]

[0212] [Table 8.1]

[0213] The primers and probes did not react with any of the challenge organisms listed in Table 6, as shown in Table 7. Also, as shown in Table 8, the primers and probes were 100% positive when the target bacteria were present in the reaction wells. Thus, these primers and probes do not demonstrate cross-reactivity with organisms commonly found in stool or that cause similar disease conditions as the target organisms. The primers and probes showed high specificity even in the presence of commonly found non-target organisms.

[0214] In addition, because Shigella and EIEC have virtually identical ipaH genes, the Shigella primers and probes reacted with the organisms in Table 6.1, as shown in Table 7.1. The primers and probes also gave 100% positivity when the target bacteria was present in the reaction wells, as shown in Table 8.1. As such, the Shigella primers and probes can be used to detect the presence of EIEC in a sample.

[0215] Example 5 - Shigella primer and probe screening Several primer and probe combinations were prepared and tested for amplification and detection of Shigella sonnei. The combinations are listed in Table 9 below. These primer-probe combinations were tested against Shigella sonnei at three serially diluted stock concentrations. Dilutions were in sample transport reagent and concentrations of 500 CFU / mL, 150 CFU / mL, and 50 CFU / mL were tested. Negative reaction wells were sample transport medium. Reaction conditions were set up in triplicate and real-time amplification and detection reactions were performed. RFU and Ct results were analyzed and are shown below.

[0216] [Table 9]

[0217] Results showed 100% positivity (Ct threshold set at 1,000 RFU) for each primer-probe combination. Primer-probe combination 2 showed the highest RFU (approximately 12,000 RFU at 500 cfu / mL), but at 50 cfu / mL, one of the replicates dropped to approximately 2,000 RFU, while the other two replicates were approximately 8,000 RFU. Primer-probe combination 1.2 showed good overall results with consistent RFU and Ct values ​​for the replicate conditions tested. RFU and Ct results are shown in Table 10.

[0218] [Table 10-1] [Table 10-2]

[0219] Example 6 - Co-infection / competitive interference The ability to detect two or more target organisms in a single sample in a multiplex PCR assay was measured using the primer-probe combinations shown in Table 1. To generate coinfected samples, negative Cary-Blair stool matrices were spiked with high (1E6 CFU / mL) and low (3xLoD) concentrations of target organisms in combination, as shown in Table 11. Primer-probe combinations were tested against low concentrations of target organisms in the absence of coinfecting agents and further tested with combinations of low and high concentrations of distinct target organisms (see Table 12).

[0220] [Table 11]

[0221] [Table 12]

[0222] Detection of both high and low concentrations of all target bacteria was 100%. There were no false positives and no competitive interference was observed. The data show that the primer-probe combinations are capable of accurately detecting multiple target bacteria present in a single sample using multiplex PCR.

[0223] Example 7 - Reduction of inhibition of amplification reactions with α-cyclodextrin and / or polysorbate 20 For example, detergents present in wash buffers are known to inhibit or reduce nucleic acid amplification reactions. To investigate the ability of α-cyclodextrin and polysorbate 20 to mitigate such negative / inhibitory effects, several PCR reaction mixtures were prepared for testing with samples containing detergent.

[0224] A master mix was prepared containing 0.46 U / μL DNA polymerase, 0.5 U / μL reverse transcriptase, 0.2 U / μL RNase inhibitor, 0.25 mM each dNTP, 0.05 mM dUTP, 81 and 5.1 mM inorganic salts including KCl and MgCl2, 0.1 mM EDTA, and primers and probes for amplification and detection of target nucleic acids. The master mix was separated into conditions (A) to (F), where conditions (B) and (D) further contained polysorbate 20 at 0.025% (v / v), conditions (B), (C), and (F) further contained 12.5 mg / mL α-cyclodextrin, condition (C) further contained polysorbate 20 at 0.13% (v / v), and condition (E) further contained 50 mg / mL α-cyclodextrin. Samples were prepared by spiking the target nucleic acid into a suitable medium and incubated in a buffer reagent containing poly-T coated magnetic microparticles and target capture oligomers to bind the target nucleic acid to the magnetic solid support. The magnetic microparticles and bound nucleic acid were separated, and after additional separation and washing, an eluate containing the nucleic acid was collected. The eluate was split into separate containers, and one of the eluate portions was further spiked with 30% (v / v) wash buffer to produce an eluate containing 100 mg / mL sodium dodecyl sulfate to simulate carryover of wash buffer from an upstream sample processing step. Each of the master mix conditions (A)-(F) above was combined with an aliquot of wash buffer spiked or non-spiked eluate (20 μL master mix, 10 μL eluate, 30 μL total reaction volume per replicate). Thus, the final concentration of polysorbate 20 and / or α-cyclodextrin in each reaction mixture was 2 / 3 of the concentrations listed above for the master mix. Real-time amplification and detection reactions were set up for replication and run using a thermal cycler (Panther Fusion Instrument, Hologic, Inc., San Diego, Calif.) The results are shown in Table 13 below.

[0225] [Table 13]

[0226] The addition of α-cyclodextrin and polysorbate 20 to the reaction mixture mitigated the negative / inhibitory effect of detergent on nucleic acid amplification reactions. The Ct and RFU values ​​further indicate that the combination of these two reagents had a synergistic mitigating effect on detergent-induced inhibition compared to the mitigating effect observed using either α-cyclodextrin or polysorbate 20 alone.

[0227] [Table 14-1] [Table 14-2] [Table 14-3] [Table 14-4]

Claims

1. 1. A set of oligonucleotides for determining the presence or absence of at least one enteric pathogen, comprising at least (a): (a) a Salmonella-specific amplification oligomer set comprising first and second oligomers, each comprising a target hybridization sequence substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:12 and SEQ ID NO:14, (ii) SEQ ID NO:21 and SEQ ID NO:47, (iii) SEQ ID NO:38 and SEQ ID NO:36, (iv) SEQ ID NO:35 and SEQ ID NO:40, (v) SEQ ID NO:12 and SEQ ID NO:28, (vi) SEQ ID NO:42 and SEQ ID NO:31, or (vii) SEQ ID NO:41 and SEQ ID NO:

27. A set of oligonucleotides comprising:

2. (b) to (e): (b)(i) a C. jejuni-specific amplification oligomer set comprising first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:11 and SEQ ID NO:19, respectively; (c)(i) a C. coli specific amplification oligomer set comprising first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:8 and SEQ ID NO:10, respectively; (d) a Shigella-specific amplification oligomer set comprising first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:15 and SEQ ID NO:17, (ii) SEQ ID NO:34 and SEQ ID NO:22, or (iii) SEQ ID NO:32 and SEQ ID NO:33, respectively; and (e) a Shigatoxigenic E. coli (STEC)-specific amplification oligomer set comprising first and second oligomers each comprising a target hybridization sequence substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:20 and SEQ ID NO:3, (ii) SEQ ID NO:49 and SEQ ID NO:3, or (iii) SEQ ID NO:4 and SEQ ID NO:7, respectively. The set of oligonucleotides according to claim 1, further comprising at least one of:

3. 3. The set of oligonucleotides of claim 2, comprising the C. jejuni-specific amplification oligomer set.

4. 3. The set of oligonucleotides of claim 2, comprising the C. coli specific amplification oligomer set.

5. The set of oligonucleotides of claim 2 comprising said Shigella-specific amplification oligomer set.

6. The set of oligonucleotides according to claim 2 , comprising said STEC-specific amplification oligomer set.

7. 3. The set of oligonucleotides of claim 2, comprising the Salmonella-specific amplification oligomer set and at least one of the C. jejuni-specific amplification oligomer set, the C. coli-specific amplification oligomer set, the Shigella-specific amplification oligomer set, and the STEC-specific amplification oligomer set.

8. 3. The set of oligonucleotides of claim 2, comprising the Salmonella-specific amplification oligomer set and at least two of the C. jejuni-specific amplification oligomer set, the C. coli-specific amplification oligomer set, the Shigella-specific amplification oligomer set, and the STEC-specific amplification oligomer set.

9. 3. The set of oligonucleotides of claim 2, comprising the Salmonella-specific amplification oligomer set and at least three of the C. jejuni-specific amplification oligomer set, the C. coli-specific amplification oligomer set, the Shigella-specific amplification oligomer set, and the STEC-specific amplification oligomer set.

10. 3. The set of oligonucleotides of claim 2, comprising the Salmonella-specific amplification oligomer set, the C. jejuni-specific amplification oligomer set, the C. coli-specific amplification oligomer set, the Shigella-specific amplification oligomer set, and the STEC-specific amplification oligomer set.

11. the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:14, respectively; the C. jejuni-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:11 and SEQ ID NO:19, respectively; the C. coli specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:8 and SEQ ID NO:10, respectively; the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:15 and SEQ ID NO:17, respectively; The set of oligonucleotides described in claim 10, wherein the STEC-specific amplification oligomer set comprises first and second oligomers each comprising target hybridization sequences substantially corresponding to the nucleotide sequences of (i) SEQ ID NO:20 and SEQ ID NO:3 or (ii) SEQ ID NO:4 and SEQ ID NO:7, respectively. (a) when the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:14 or the nucleotide sequences of SEQ ID NO:12 and SEQ ID NO:28, respectively, the set of oligomers comprising SEQ ID NO:13, When the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:21 and SEQ ID NO:47, respectively, SEQ ID NO:45, When the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:38 and SEQ ID NO:36, respectively, the set of oligomers may further comprise any of SEQ ID NO:44, SEQ ID NO:26, or SEQ ID NO:25, When the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:35 and SEQ ID NO:40, respectively, SEQ ID NO:30, SEQ ID NO:23, or when the Salmonella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:42 and SEQ ID NO:31, respectively. When the Salmonella-specific amplification oligomer set includes first and second oligomers that include target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:41 and SEQ ID NO:27, respectively, the set of oligomers having the sequence SEQ ID NO:43 is a Salmonella detection probe comprising a target hybridization sequence substantially corresponding to the nucleotide sequence of (b) a C. jejuni detection probe comprising a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:18; (c) a C. coli detection probe comprising a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:9, SEQ ID NO:37, or SEQ ID NO:39; (d) When the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:15 and SEQ ID NO:17, respectively, SEQ ID NO:16, when the Shigella-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:34 and SEQ ID NO:22, respectively, SEQ ID NO:46 or SEQ ID NO:29, or When the Shigella-specific amplification oligomer set includes a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:32 and SEQ ID NO:33, respectively, the Shigella-specific amplification oligomer set includes a first and a second oligomer comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:24 and / or (e) a Shigella detection probe comprising a target hybridization sequence substantially corresponding to a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:48, when the STEC-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:20 and SEQ ID NO:3, or the nucleotide sequences of SEQ ID NO:49 and SEQ ID NO:3, respectively. a STEC detection probe comprising a target hybridization sequence substantially corresponding to the nucleotide sequence of SEQ ID NO:5 or SEQ ID NO:6, when the STEC-specific amplification oligomer set comprises first and second oligomers comprising target hybridization sequences substantially corresponding to the nucleotide sequences of SEQ ID NO:4 and SEQ ID NO:7, respectively; The set of oligonucleotides according to claim 10, further comprising:

13. 13. The set of oligonucleotides of claim 12, wherein one or more, or each, of the detection probes comprises a fluorescent dye compound.

14. 14. The set of oligonucleotides of claim 13, wherein each of the detection probes further comprises a non-fluorescent quenching dye compound.

15. An oligonucleotide for determining the presence or absence of at least one enteric pathogen, said oligonucleotide comprising: SEQ ID NO:21 (nucleotides 13, 17, and 24 each contain a 5-methylcytosine); SEQ ID NO:23 (nucleotides 2, 5, 7, and 14 each contain a 5-methylcytosine); SEQ ID NO:25 (nucleotides 7, 9, 13, and 15 each contain a 5-methylcytosine); SEQ ID NO:26 (nucleotides 9, 18, and 23 each contain a 5-methylcytosine); SEQ ID NO:27 (nucleotides 6, 10, and 18 each contain a 5-methylcytosine); SEQ ID NO:28 (nucleotides 2, 4, 12, 14, 15, and 17 each contain a 5-methylcytosine); SEQ ID NO:30 (nucleotides 2, 4, 18, 19, and 20 each contain a 5-methylcytosine); SEQ ID NO:31 (nucleotides 6, 7, 8, 13, 23, 24, and 26 each contain a 5-methylcytosine); SEQ ID NO:36 (nucleotides 2, 3, 4, 16, 18, 19, and 22 each contain a 5-methylcytosine); SEQ ID NO:38 (nucleotides 4, 6, 7, and 8 each contain a 5-methylcytosine); SEQ ID NO:40 (nucleotides 4, 13, 18, and 22 each contain a 5-methylcytosine); SEQ ID NO:42, SEQ ID NO:43 (nucleotides 2, 9, 12, 16, 17, 22, 23, and 26 each contain a 5-methylcytosine); SEQ ID NO:44 (nucleotides 7, 9, 13, and 15 each contain a 5-methylcytosine); SEQ ID NO:45 (nucleotides 3, 6, 8, and 17 each contain a 5-methylcytosine); SEQ ID NO:47 (nucleotides 11, 16, and 17 each contain a 5-methylcytosine), and SEQ ID NO:12 (nucleotides 4, 11, 12, and 16 each contain a 5-methylcytosine) An oligonucleotide comprising any one of the sequences:

16. A kit comprising a set of oligonucleotides according to any one of claims 1 to 14 or an oligonucleotide according to claim 15.

17. A reaction mixture comprising a set of oligonucleotides according to any one of claims 1 to 14 or an oligonucleotide according to claim 15.

18. A method for determining the presence or absence of Salmonella in a sample, the method comprising: (1) contacting a sample suspected of containing Salmonella with a Salmonella-specific amplification oligomer set for amplifying a target region of a Salmonella target nucleic acid, the Salmonella-specific amplification oligomer set comprising first and second oligomers each comprising a target hybridization sequence substantially corresponding to the nucleotide sequences of: (i) SEQ ID NO:12 and SEQ ID NO:14; (ii) SEQ ID NO:21 and SEQ ID NO:47; (iii) SEQ ID NO:38 and SEQ ID NO:36; (iv) SEQ ID NO:35 and SEQ ID NO:40; (v) SEQ ID NO:12 and SEQ ID NO:28; (vi) SEQ ID NO:42 and SEQ ID NO:31; or (vii) SEQ ID NO:41 and SEQ ID NO:27; (2) performing an in vitro nucleic acid amplification reaction, in which any Salmonella target nucleic acid, if present in the sample, is used as a template to generate an amplification product corresponding to the Salmonella target region; (3) detecting the presence or absence of the amplification product; thereby determining the presence or absence of Salmonella in the sample.

19. A multiplexing method for determining the presence or absence of Salmonella and at least one of C. jejuni, C. coli, Shigella, and Shigatoxigenic E. coli (STEC) in a sample, the method comprising: (1) contacting a sample suspected of containing at least one of Salmonella and C. jejuni, C. coli, Shigella, and STEC with a set of oligonucleotides for amplifying a target region of a Salmonella target nucleic acid and at least one of a C. jejuni target nucleic acid, a C. coli target nucleic acid, a Shigella target nucleic acid, and a STEC target nucleic acid, wherein the set of oligonucleotides is the set of oligonucleotides of any one of claims 2 to 11; (2) performing an in vitro nucleic acid amplification reaction, in which any Salmonella, C. jejuni, C. coli, Shigella, and STEC target nucleic acids, if present in the sample, are used as templates to generate one or more amplification products corresponding to the Salmonella, C. jejuni, C. coli, Shigella, and STEC target regions; (3) detecting the presence or absence of the one or more amplification products; thereby determining the presence or absence of Salmonella and at least one of C. jejuni, C. coli, Shigella, and STEC in said sample.

20. (3) contacting the sample with at least one of a Salmonella detection probe, a C. jejuni detection probe, a C. coli detection probe, a Shigella detection probe, and a STEC detection probe, each of said detection probes being as defined in claim 12; performing electrophoresis on the sample; or 20. The multiplexing method of claim 19, comprising determining the sequence, if present, of the one or more amplification products.

21. 1. A method for synthesizing an oligonucleotide, comprising: (a) obtaining a solid support comprising at least one nucleobase residue, said at least one nucleobase residue being covalently attached to said solid support at a 3′ position; (b) linking the 5′-position of the nucleobase residue furthest from the solid support to the 3′-position of another nucleobase residue; (c) repeating step (b) at least 13 additional times, thereby generating at least 15 consecutive nucleobase residues bound to said solid support; (d) cleaving the at least 15 consecutive nucleobase residues produced in step (c), thereby obtaining the oligonucleotide; The oligonucleotide is SEQ ID NO:21 (nucleotides 13, 17, and 24 each contain a 5-methylcytosine); SEQ ID NO:23 (nucleotides 2, 5, 7, and 14 each contain a 5-methylcytosine); SEQ ID NO:25 (nucleotides 7, 9, 13, and 15 each contain a 5-methylcytosine); SEQ ID NO:26 (nucleotides 9, 18, and 23 each contain a 5-methylcytosine); SEQ ID NO:27 (nucleotides 6, 10, and 18 each contain a 5-methylcytosine); SEQ ID NO:28 (nucleotides 2, 4, 12, 14, 15, and 17 each contain a 5-methylcytosine); SEQ ID NO:30 (nucleotides 2, 4, 18, 19, and 20 each contain a 5-methylcytosine); SEQ ID NO:31 (nucleotides 6, 7, 8, 13, 23, 24, and 26 each contain a 5-methylcytosine); SEQ ID NO:36 (nucleotides 2, 3, 4, 16, 18, 19, and 22 each contain a 5-methylcytosine); SEQ ID NO:38 (nucleotides 4, 6, 7, and 8 each contain a 5-methylcytosine); SEQ ID NO:40 (nucleotides 4, 13, 18, and 22 each contain a 5-methylcytosine); SEQ ID NO:42, SEQ ID NO:43 (nucleotides 2, 9, 12, 16, 17, 22, 23, and 26 each contain a 5-methylcytosine); SEQ ID NO:44 (nucleotides 7, 9, 13, and 15 each contain a 5-methylcytosine); SEQ ID NO:45 (nucleotides 3, 6, 8, and 17 each contain a 5-methylcytosine); SEQ ID NO:47 (nucleotides 11, 16, and 17 each contain a 5-methylcytosine), and SEQ ID NO:12 (nucleotides 4, 11, 12, and 16 each contain a 5-methylcytosine) The method of claim 1, comprising any one of the sequences:

22. 1. A method for synthesizing a pair of oligonucleotides, comprising: synthesizing a first oligonucleotide; and synthesizing a second oligonucleotide, Each of synthesizing the first oligonucleotide and synthesizing the second oligonucleotide comprises: (a) obtaining a solid support comprising at least one nucleobase residue, said at least one nucleobase residue being covalently attached to said solid support at a 3′ position; (b) linking the 5′-position of the nucleobase residue furthest from the solid support to the 3′-position of another nucleobase residue; (c) repeating step (b) at least 13 additional times, thereby generating at least 15 consecutive nucleobase residues bound to said solid support; (d) cleaving the at least 15 consecutive nucleobase residues produced in step (c), thereby obtaining the oligonucleotide; The first oligonucleotide and the second oligonucleotide each have SEQ ID NO: 12 and SEQ ID NO: 14, SEQ ID NO: 21 and SEQ ID NO: 47, SEQ ID NO:38 and SEQ ID NO:36, SEQ ID NO: 35 and SEQ ID NO: 40, SEQ ID NO: 12 and SEQ ID NO: 28, SEQ ID NO: 42 and SEQ ID NO: 31, and SEQ ID NO:41 and SEQ ID NO:27 The method of claim 1, comprising any one of the sequences: