Chlamydia psittaci cgMLST molecular typing method

Abstract

The invention discloses a chlamydia psittaci cgMLST molecular typing method, and belongs to the field of microbial molecular typing and tracing. According to the invention, an operation technology for carrying out molecular typing on chlamydia psittaci by using a core genome multi-site sequence typing system (cgMLST) is established for the first time. The chlamydia psittaci cgMLST system is established through the processes of collecting chlamydia psittaci genomes in a disclosed genome database, obtaining core genomes through quality control screening and generic genome analysis, screening core genes suitable for typing under multiple screening conditions and the like. And comparing with a phylogenetic analysis result based on core genome SNP difference to confirm the resolution and reliability of the typing system. According to the typing technology, the core genome of the chlamydia psittaci is determined for the first time, and the typing technology can be used for molecular typing and epidemiological monitoring of the chlamydia psittaci.

Description

Technical Field

[0001] This invention belongs to the field of microbial molecular typing and tracing, and particularly relates to a method for typing Chlamydia psittaci using the Core Genome Multilocus Sequence Typing System (cgMLST). Background Technology

[0002] Chlamydia psittaci is a Gram-negative bacterium that primarily infects birds, especially parrots, but cattle, horses, and cats can also carry it. Healthy individuals can become infected by inhaling dried feces or respiratory secretions from infected animals, or through direct contact. Patients infected with Chlamydia psittaci often experience symptoms such as high fever, cough, and shortness of breath. Severe cases can lead to acute respiratory distress syndrome, severe pneumonia, shock, and have a poor prognosis, threatening life.

[0003] Globally, cases of Chlamydia psittaci infection are gradually increasing, particularly in specific environments or among specific populations. This bacterium not only affects susceptible groups such as pet owners and bird lovers, but can also cause localized outbreaks in places with high animal interaction (such as bird markets and farms). Moreover, human-to-human transmission has occurred in rare cases. Therefore, early and accurate monitoring and identification of Chlamydia psittaci is of great importance to public health.

[0004] Although the pathogenic mechanism of *Chlamydia psittaci* is relatively well understood, current molecular typing systems for this pathogen remain insufficient. Existing typing techniques largely rely on PCR amplification of specific target gene sequences followed by sequence analysis. These methods have limitations in terms of accuracy, sensitivity, and versatility. For example, while traditional multi-site sequence typing (MLST) can type strains, it has a limited number of target genes included, relatively low resolution, and is complex and time-consuming, making it difficult to meet the needs of rapid monitoring and large-scale epidemiological surveys. As a zoonotic transmissible pathogen, *Chlamydia psittaci* urgently requires effective and reliable molecular typing methods to monitor its prevalence and outbreaks.

[0005] Core genome multilocus sequence typing (cgMLST) is an emerging molecular typing technique that has achieved significant results in the epidemiological studies of various pathogens, such as Staphylococcus aureus, Staphylococcus capitulata, Brucella, and Klebsiella pneumoniae. This system provides extremely high resolution and stability by identifying stable core genome sequences within the species, making it suitable for highly diverse microbial communities. However, a cgMLST system for Chlamydia psittaci has not yet been constructed. Therefore, we collected Chlamydia psittaci genomes from public genome databases and constructed a cgMLST system suitable for Chlamydia psittaci using a series of methods. We then compared the resolution with that based on phylogenetic analysis of core genome SNP differences, demonstrating that our cgMLST system can provide sufficient resolution for the epidemiological study of Chlamydia psittaci. Summary of the Invention

[0006] The purpose of this invention is to address the deficiencies in existing technologies by providing a cgMLST molecular typing method for Chlamydia psittaci.

[0007] The objective of this invention is achieved through the following technical solution:

[0008] 1. Collect, quality control, and screen Chlamydia psittaci genomes.

[0009] All assembled genomes of *Chlamydia psittaci* strains and raw sequences from next-generation whole-genome sequencing were downloaded from the NCBI public genome database. After assembly and annotation, the number of contigs and genes in each genome were counted, and genomes with obvious contamination or fewer than 900 genes were removed. ANI analysis was then performed using the complete genome of *Chlamydia psittaci* 6BC (accession number: NC_017287.1) as the alignment standard, and genomes with an ANI value below 0.95 were removed. Finally, BUSCO analysis was performed to assess genome integrity, and genomes with integrity below 95% were removed. A total of 88 assembled genomes and 44 raw genomes were included.

[0010] 2. Pan-genome analysis to obtain the initial core genome

[0011] For the 88 assembled genomes included in the study, pan-genome analysis was performed using Panaroo software after genome annotation. A 95% carrier rate was used as the standard for screening, resulting in 949 initial core genomes.

[0012] 3. Screening the initial core genome to obtain the cgMLST system

[0013] Genes in the initial core genome were removed if they met any of the following criteria: 1. No initial codon; 2. No or multiple stop codons; 3. Length less than 50 bp; 4. Repetitive genes with similar sequences; 5. Carried on plasmids; 6. Similar to mobile genes. Additionally, if two genes overlapped, only the longer gene was retained. A total of 870 core genes were ultimately included as the initial cgMLST system.

[0014] Subsequently, the chewBBACA software was used to analyze all assembled and original genomes included in the studies using the initial cgMLST system. The carrier rate of each gene was calculated, and genes with a carrier rate below 95% were removed. A final cgMLST system of 846 genes was obtained. The core genes in the final cgMLST system were mapped onto standard genome chromosomes, such as... Figure 1 As shown.

[0015] 4. Evaluate the resolution of the cgMLST system

[0016] Subsequently, a phylogenetic analysis based on core genomic SNP differences was performed on all included genomes, and the results were visualized and compared with the cgMLST analysis results to clarify the genotyping accuracy and high resolution of the cgMLST system constructed in this invention. Specific results are as follows: Figure 2 As shown.

[0017] Compared with existing technologies and products, the present invention has the following technical effects:

[0018] The molecular typing method for *Chlamydia psittaci* described in this invention demonstrates excellent typing and clustering effects on high-quality collected genomic data. The results show good consistency with clones identified through phylogenetic analysis. Using the cgMLST system, the clonal affiliation of *Chlamydia psittaci* can be accurately determined. This invention has identified the core genome of *Chlamydia psittaci* through rigorous screening. Molecular typing of currently known high-quality *Chlamydia psittaci* genomes clarifies the system's ability to identify different clones, and the identified core genome is publicly disclosed. The aim is to address the increased medical burden caused by the spread of this pathogen, providing a reliable molecular typing tool for controlling the spread of *Chlamydia psittaci*, and providing a foundational tool for further research on the transmission and drug resistance mechanisms of this bacterium. Attached Figure Description

[0019] Figure 1 This is a diagram showing the distribution of each gene on the chromosome in the cgMLST system of this invention;

[0020] Figure 2 This is a comparison plot of cgMLST analysis and SNP-based phylogenetic analysis clustering. Detailed Implementation

[0021] To facilitate understanding and implementation of the present invention by those skilled in the art, the present invention will be further described in detail below with reference to the accompanying drawings and specific embodiments.

[0022] Example 1: Construction of the cgMLST system for Chlamydia psittaci.

[0023] 1. Collect, quality control, and screen Chlamydia psittaci genomes.

[0024] All assembled genomes of *Chlamydia psittaci* strains and raw sequences from next-generation whole-genome sequencing were downloaded from the NCBI public genome database. After assembly and annotation, the number of contigs and genes in each genome were counted, and genomes with obvious contamination or fewer than 900 genes were removed. ANI analysis was then performed using the complete genome of *Chlamydia psittaci* 6BC (accession number: NC_017287.1) as the alignment standard, and genomes with an ANI value below 0.95 were removed. Finally, BUSCO analysis was performed to assess genome integrity, and genomes with integrity below 95% were removed. A total of 88 assembled genomes and 44 raw genomes were included.

[0025] 2. Pan-genome analysis to obtain the initial core genome

[0026] For the 88 assembled genomes included in the study, pan-genome analysis was performed using Panaroo software after genome annotation. A 95% carrier rate was used as the standard for screening, resulting in 949 initial core genomes.

[0027] 3. Screening the initial core genome to obtain the cgMLST system

[0028] Genes in the initial core genome were removed if they met any of the following criteria: 1. No initial codon; 2. No or multiple stop codons; 3. Length less than 50 bp; 4. Sequence-similar repetitive genes (identity > 0.9 and coverage > 0.9); 5. Carried on plasmids; 6. Similar to mobile genes (identity > 0.9 and coverage > 0.9). Additionally, if two genes overlapped, only the longer gene was retained. A total of 870 core genes were ultimately included as the initial cgMLST system.

[0029] Subsequently, the chewBBACA software was used to analyze all assembled and original genomes included in the studies using the initial cgMLST system. The carrier rate of each gene was calculated, and genes with a carrier rate below 95% were removed. A final cgMLST system of 846 genes was obtained. The core genes in the final cgMLST system were mapped onto standard genome chromosomes, such as... Figure 1 As shown.

[0030] 4. Evaluate the resolution of the cgMLST system

[0031] Subsequently, a phylogenetic analysis based on core genomic SNP differences was performed on all included genomes, and the results were visualized and compared with the cgMLST analysis results to clarify the genotyping accuracy and high resolution of the cgMLST system constructed in this invention. Specific results are as follows: Figure 2 As shown, the left side presents the cgMLST analysis results, and the right side presents the phylogenetic analysis results based on differences in core genome SNPs. The two methods are consistent in their clustering results.

[0032] Example 2: cgMLST molecular typing based on the core genome of Chlamydia psittaci.

[0033] Based on Example 1, the core genome of Chlamydia psittaci was constructed, containing the following genes:

[0034] G5O_RS07550,G5O_RS07400,G5O_RS06475,G5O_RS08070,G5O_RS06320,G5O_RS10155,G5O_RS10015,G5O_RS08245,G5O_RS08905,G5O_RS07190,G5O_RS08885,G5O_RS05230,G5O_RS06820,G5O_RS07730,G5O_RS07270,G5O_RS07335,G5O_RS07095,G5O_RS05935,G5O_RS06085,G5O_RS10455,G5O_RS07165,G5O_RS06480,G5O_RS09865,G5O_RS06455,G5O_RS10185,G5O_RS10530,G5O_RS08495,G5O_RS10045,G5O_RS09870,G5O_RS06350,G5O_RS06785,G5O_RS05760,G5O_RS10165,G5O_RS08205,G5O_RS05350,G5O_RS09880,G5O_RS07305,G5O_RS08220,G5O_RS05185,G5O_RS07640,G5O_RS09440,G5O_RS09795,G5O_RS09250,G5O_RS06575,G5O_RS05970,G5O_RS05630,G5O_RS05495,G5O_RS08940,G5O_RS10035,G5O_RS09295,G5O_RS06760,G5O_RS07870,G5O_RS09355,G5O_RS08780,G5O_RS08785,G5O_RS08790,G5O_RS07935,G5O_RS07940,G5O_RS06890,G5O_RS07595,G5O_RS07505,G5O_RS07845,G5O_RS10365,G5O_RS10055,G5O_RS09600,G5O_RS06235,G5O_RS07040,G5O_RS09495,G5O_RS08480,G5O_RS07885,G5O_RS06045,G5O_RS08770,G5O_RS06485,G5O_RS07665,G5O_RS07895,G5O_RS08695,G5O_RS05555,G5O_RS05960,G5O_RS08555,G5O_RS08545,G5O_RS08565,G5O_RS06265,G5O_RS07570,G5O_RS08065,G5O_RS07545,G5O_RS06800,G5O_RS08735,G5O_RS09350,G5O_RS08660,G5O_RS09650,G5O_RS09800,G5O_RS09415,G5O_RS09640,G5O_RS05990,G5O_RS09760,G5O_RS06060,G5O_RS06935,G5O_RS09750,G5O_RS09755,G5O_RS06055,G5O_RS07740,G5O_RS07915,G5O_RS09480,G5O_RS05525,G5O_RS07600,G5O_RS09425,G5O_RS08285,G5O_RS06155,G5O_RS09365,G5O_RS09325,G5O_RS05505,G5O_RS08685,G5O_RS08700,G5O_RS09050,G5O_RS06425,G5O_RS08875,G5O_RS07180,G5O_RS07625,G5O_RS06275,G5O_RS06740,G5O_RS09765,G5O_RS07080,G5O_RS05590,G5O_RS07525,G5O_RS07000,G5O_RS05790,G5O_RS05535,G5O_RS09285,G5O_RS06795,G5O_RS06385,G5O_RS07390,G5O_RS08140,G5O_RS05895,G5O_RS09335,G5O_RS10010,G5O_RS10110,G5O_RS06895,G5O_RS07370,G5O_RS06710,G5O_RS07745,G5O_RS07930,G5O_RS09490,G5O_RS09970,G5O_RS09885,G5O_RS07585,G5O_RS09385,G5O_RS07590,G5O_RS07580,G5O_RS07100,G5O_RS05610,G5O_RS07655,G5O_RS10150,G5O_RS08085,G5O_RS08420,G5O_RS09840,G5O_RS05620,G5O_RS07405,G5O_RS10160,G5O_RS10000,G5O_RS09995,G5O_RS05380,G5O_RS08955,G5O_RS07025,G5O_RS09580,G5O_RS09070,G5O_RS08880,G5O_RS07650,G5O_RS05745,G5O_RS06625,G5O_RS06620,G5O_RS06955,G5O_RS06145,G5O_RS09245,G5O_RS06515,G5O_RS07195,G5O_RS09090,G5O_RS09085,G5O_RS10205,G5O_RS06095,G5O_RS06310,G5O_RS09260,G5O_RS08395,G5O_RS07325,G5O_RS09705,G5O_RS08350,G5O_RS10065,G5O_RS09475,G5O_RS08345,G5O_RS10025,G5O_RS05260,G5O_RS09280,G5O_RS10145,G5O_RS05625,G5O_RS05810,G5O_RS08460,G5O_RS08455,G5O_RS07105,G5O_RS08445,G5O_RS08440,G5O_RS05545,G5O_RS09920,G5O_RS06775,G5O_RS10490,G5O_RS08720,G5O_RS09430,G5O_RS06465,G5O_RS06305,G5O_RS08320,G5O_RS08370,G5O_RS08575,G5O_RS10395,G5O_RS06375,G5O_RS08890,G5O_RS07200,G5O_RS05910,G5O_RS06125,G5O_RS06840,G5O_RS06715,G5O_RS09275,G5O_RS07825,G5O_RS05210,G5O_RS07380,G5O_RS06660,G5O_RS07860,G5O_RS05300,G5O_RS06360,G5O_RS08540,G5O_RS10075,G5O_RS08645,G5O_RS08560,G5O_RS09180,G5O_RS06910,G5O_RS05530,G5O_RS08530,G5O_RS05310,G5O_RS06130,G5O_RS06120,G5O_RS05215,G5O_RS06835,G5O_RS10195,G5O_RS08835,G5O_RS08845,G5O_RS05480,G5O_RS06855,G5O_RS05305,G5O_RS09780,G5O_RS10100,G5O_RS10405,G5O_RS05340,G5O_RS07540,G5O_RS07555,G5O_RS09320,G5O_RS05985,G5O_RS07005,G5O_RS07210,G5O_RS09055,G5O_RS07660,G5O_RS05750,G5O_RS09635,G5O_RS05465,G5O_RS05365,G5O_RS06905,G5O_RS05830,G5O_RS08920,G5O_RS05295,G5O_RS07365,G5O_RS06020,G5O_RS06030,G5O_RS07345,G5O_RS05490,G5O_RS06965,G5O_RS09605,G5O_RS06345,G5O_RS09770,G5O_RS06615,G5O_RS09875,G5O_RS09045,G5O_RS07610,G5O_RS05320,G5O_RS09530,G5O_RS07375,G5O_RS08570,G5O_RS06370,G5O_RS07415,G5O_RS08775,G5O_RS08415,G5O_RS05870,G5O_RS07135,G5O_RS06295,G5O_RS10080,G5O_RS09695,G5O_RS05270,G5O_RS08240,G5O_RS05510,G5O_RS09720,G5O_RS08465,G5O_RS10340,G5O_RS08825,G5O_RS06635,G5O_RS09450,G5O_RS09380,G5O_RS10115,G5O_RS08620,G5O_RS07710,G5O_RS07630,G5O_RS08250,G5O_RS09205,G5O_RS08865,G5O_RS06460,G5O_RS05335,G5O_RS08325,G5O_RS06655,G5O_RS06440,G5O_RS06450,G5O_RS08935,G5O_RS08650,G5O_RS09165,G5O_RS07800,G5O_RS07565,G5O_RS06115,G5O_RS08970,G5O_RS06035,G5O_RS07170,G5O_RS05485,G5O_RS08840,G5O_RS06850,G5O_RS07145,G5O_RS07110,G5O_RS05975,G5O_RS09710,G5O_RS10425,G5O_RS10515,G5O_RS05920,G5O_RS10180,G5O_RS06640,G5O_RS07245,G5O_RS06090,G5O_RS08710,G5O_RS10005,G5O_RS06010,G5O_RS06230,G5O_RS06435,G5O_RS08930,G5O_RS07090,G5O_RS05520,G5O_RS07795,G5O_RS06915,G5O_RS07280,G5O_RS08855,G5O_RS07140,G5O_RS05965,G5O_RS08680,G5O_RS05880,G5O_RS07775,G5O_RS08895,G5O_RS07070,G5O_RS06645,G5O_RS07010,G5O_RS05445,G5O_RS09015,G5O_RS06225,G5O_RS06430,G5O_RS06195,G5O_RS05500,G5O_RS08665,G5O_RS07790,G5O_RS08675,G5O_RS10430,G5O_RS06490,G5O_RS10520,G5O_RS06405,G5O_RS06220,G5O_RS09545,G5O_RS06410,G5O_RS06420,G5O_RS06995,G5O_RS08105,G5O_RS06415,G5O_RS06510,G5O_RS06520,G5O_RS06945,G5O_RS06525,G5O_RS08080,G5O_RS08075,G5O_RS08280,G5O_RS08355,G5O_RS08850,G5O_RS09110,G5O_RS06355,G5O_RS09955,G5O_RS08910,G5O_RS10050,G5O_RS06790,G5O_RS09610,G5O_RS10070,G5O_RS08390,G5O_RS10435,G5O_RS06990,G5O_RS09485,G5O_RS08305,G5O_RS08915,G5O_RS07285,G5O_RS05245,G5O_RS10310,G5O_RS09805,G5O_RS09590,G5O_RS10415,G5O_RS10420,G5O_RS07450,G5O_RS06920,G5O_RS07510,G5O_RS09310,G5O_RS09655,G5O_RS05315,G5O_RS09040,G5O_RS09270,G5O_RS06745,G5O_RS09990,G5O_RS07605,G5O_RS07615,G5O_RS06925,G5O_RS05170,G5O_RS09935,G5O_RS09950,G5O_RS09675,G5O_RS07420,G5O_RS05595,G5O_RS09360,G5O_RS09810,G5O_RS06875,G5O_RS05470,G5O_RS07815,G5O_RS10135,G5O_RS07705,G5O_RS09595,G5O_RS09825,G5O_RS08470,G5O_RS07055,G5O_RS09855,G5O_RS07445,G5O_RS05190,G5O_RS07175,G5O_RS09680,G5O_RS09830,G5O_RS05865,G5O_RS09860,G5O_RS07085,G5O_RS09895,G5O_RS08435,G5O_RS07960,G5O_RS07750,G5O_RS10210,G5O_RS07850,G5O_RS07685,G5O_RS07130,G5O_RS06290,G5O_RS05855,G5O_RS06695,G5O_RS05925,G5O_RS09155,G5O_RS07855,G5O_RS06810,G5O_RS06750,G5O_RS08300,G5O_RS07720,G5O_RS09925,G5O_RS06735,G5O_RS08975,G5O_RS08800,G5O_RS08175,G5O_RS06470,G5O_RS10380,G5O_RS09300,G5O_RS07680,G5O_RS05275,G5O_RS09985,G5O_RS08235,G5O_RS09190,G5O_RS08505,G5O_RS06070,G5O_RS09715,G5O_RS10220,G5O_RS07645,G5O_RS09915,G5O_RS07295,G5O_RS07410,G5O_RS05150,G5O_RS10175,G5O_RS08475,G5O_RS06165,G5O_RS07255,G5O_RS08215,G5O_RS07315,G5O_RS07620,G5O_RS08745,G5O_RS07900,G5O_RS08230,G5O_RS09845,G5O_RS09265,G5O_RS08965,G5O_RS06325,G5O_RS06700,G5O_RS06390,G5O_RS07695,G5O_RS05280,G5O_RS05285,G5O_RS07690,G5O_RS05290,G5O_RS05140,G5O_RS06860,G5O_RS05860,G5O_RS08295,G5O_RS07250,G5O_RS09525,G5O_RS06500,G5O_RS05950,G5O_RS06395,G5O_RS07050,G5O_RS08450,G5O_RS07920,G5O_RS08640,G5O_RS07485,G5O_RS09000,G5O_RS07160,G5O_RS06000,G5O_RS09210,G5O_RS06160,G5O_RS07275,G5O_RS08860,G5O_RS05250,G5O_RS06285,G5O_RS09370,G5O_RS07330,G5O_RS08200,G5O_RS07515,G5O_RS09820,G5O_RS05600,G5O_RS07820,G5O_RS06780,G5O_RS05780,G5O_RS05240,G5O_RS09100,G5O_RS05605,G5O_RS07560,G5O_RS06005,G5O_RS06270,G5O_RS08500,G5O_RS06240,G5O_RS08690,G5O_RS09330,G5O_RS06755,G5O_RS07535,G5O_RS07440,G5O_RS06900,G5O_RS08900,G5O_RS07125,G5O_RS05360,G5O_RS08805,G5O_RS06330,G5O_RS07675,G5O_RS08210,G5O_RS09410,G5O_RS08290,G5O_RS06930,G5O_RS08795,G5O_RS05785,G5O_RS10305,G5O_RS06335,G5O_RS09405,G5O_RS07075,G5O_RS06340,G5O_RS09460,G5O_RS05415,G5O_RS05410,G5O_RS09645,G5O_RS09730,G5O_RS07065,G5O_RS06040,G5O_RS09010,G5O_RS09435,G5O_RS09455,G5O_RS09465,G5O_RS05205,G5O_RS09910,G5O_RS09290,G5O_RS07120,G5O_RS07455,G5O_RS05775,G5O_RS05200,G5O_RS08155,G5O_RS05145,G5O_RS06985,G5O_RS06980,G5O_RS06975,G5O_RS06970,G5O_RS09550,G5O_RS09025,G5O_RS06250,G5O_RS09030,G5O_RS08550,G5O_RS08535,G5O_RS07490,G5O_RS09005,G5O_RS08615,G5O_RS05905,G5O_RS06105,G5O_RS06110,G5O_RS07875,G5O_RS08125,G5O_RS08135,G5O_RS05900,G5O_RS05460,G5O_RS05455,G5O_RS09725,G5O_RS09095,G5O_RS06280,G5O_RS07215,G5O_RS08340,G5O_RS08170,G5O_RS08180,G5O_RS06880,G5O_RS08815,G5O_RS05475,G5O_RS07865,G5O_RS05800,G5O_RS08985,G5O_RS05915,G5O_RS08225,G5O_RS06050,G5O_RS09170,G5O_RS06605,G5O_RS06215,G5O_RS06540,G5O_RS06550,G5O_RS06545,G5O_RS07495,G5O_RS08950,G5O_RS09375,G5O_RS08430,G5O_RS08425,G5O_RS06400,G5O_RS09785,G5O_RS09230,G5O_RS09195,G5O_RS06825,G5O_RS08510,G5O_RS05835,G5O_RS05385,G5O_RS06865,G5O_RS09735,G5O_RS07480,G5O_RS06495,G5O_RS06770,G5O_RS10140,G5O_RS05175,G5O_RS05180,G5O_RS07385,G5O_RS06080,G5O_RS05940,G5O_RS07575,G5O_RS10090,G5O_RS05825,G5O_RS09620,G5O_RS06255,G5O_RS09625,G5O_RS07470,G5O_RS09615,G5O_RS09660,G5O_RS07115,G5O_RS05265,G5O_RS06870,G5O_RS09185,G5O_RS08400,G5O_RS06650,G5O_RS09315,G5O_RS06380,G5O_RS08310,G5O_RS08605,G5O_RS05645,G5O_RS05635,G5O_RS05690,G5O_RS05700,G5O_RS09215,G5O_RS08600,G5O_RS08610,G5O_RS08595,G5O_RS07830,G5O_RS05680,G5O_RS05715,G5O_RS05665,G5O_RS05740,G5O_RS05705,G5O_RS08405,G5O_RS08990,G5O_RS06175,G5O_RS05655,G5O_RS05640,G5O_RS05685,G5O_RS09235,G5O_RS06180,G5O_RS07435,G5O_RS09175,G5O_RS07810,G5O_RS08995,G5O_RS05735,G5O_RS10095,G5O_RS05395,G5O_RS05660,G5O_RS05195,G5O_RS09225,G5O_RS06140,G5O_RS05695,G5O_RS07835,G5O_RS05730,G5O_RS06135,G5O_RS05725,G5O_RS09305,G5O_RS08945,G5O_RS05675,G5O_RS09220,G5O_RS05650,G5O_RS05515,G5O_RS09390,G5O_RS06705,G5O_RS05850,G5O_RS07230,G5O_RS05770,G5O_RS07185,G5O_RS05765,G5O_RS09775,G5O_RS06075,G5O_RS05720,G5O_RS09630,G5O_RS07310,G5O_RS07725,G5O_RS07395,G5O_RS06885,G5O_RS09945,G5O_RS09850,G5O_RS05450,G5O_RS07265,G5O_RS09065,G5O_RS09060,G5O_RS05425,G5O_RS07765,G5O_RS08580,G5O_RS09940,G5O_RS10225,G5O_RS09745,G5O_RS08960,G5O_RS09500,G5O_RS05805,G5O_RS10105,G5O_RS06730,G5O_RS08410,G5O_RS05565,G5O_RS09960,G5O_RS05995,G5O_RS07475,G5O_RS05570,G5O_RS07715,G5O_RS07880,G5O_RS05585,G5O_RS05390,G5O_RS07770,G5O_RS08630,G5O_RS05165,G5O_RS09080,G5O_RS07320,G5O_RS07430,G5O_RS05540,G5O_RS10085,G5O_RS06065,G5O_RS09965,G5O_RS08525,G5O_RS08195,G5O_RS06765,G5O_RS06725,G5O_RS06720,G5O_RS06830,G5O_RS06365,G5O_RS08335,G5O_RS09075,G5O_RS07465,G5O_RS08165,G5O_RS07520,G5O_RS10290,G5O_RS07840,G5O_RS06245,G5O_RS09905,G5O_RS08120,G5O_RS09835,G5O_RS05325,G5O_RS07460,G5O_RS08375,G5O_RS08485,G5O_RS06190,G5O_RS08585,G5O_RS08590,G5O_RS07905,G5O_RS06535,G5O_RS08520,G5O_RS08275,G5O_RS09890,G5O_RS05155,G5O_RS09980,G5O_RS08385,G5O_RS08130,G5O_RS07340,G5O_RS08365,G5O_RS05345,G5O_RS09200,G5O_RS05840,G5O_RS09930,G5O_RS09160,G5O_RS08870,G5O_RS09540,G5O_RS09445,G5O_RS07425,G5O_RS06185,G5O_RS07500,G5O_RS08820,G5O_RS05440,G5O_RS06210,G5O_RS07355,G5O_RS07155,G5O_RS06630,G5O_RS10200,G5O_RS05405,G5O_RS08515,G5O_RS09510, G5O_RS08925, G5O_RS05435, G5O_RS06950, G5O_RS06150, G5O_RS10170, G5O_RS10130, G5O_RS08160, G5O_RS06675, G5O_RS06845, G5O_RS05945, G5O_RS08670; gene numbers are derived from the complete genome accession number of Chlamydia psittaci 6BC: NC_017287.1.

[0035] Based on the core genome, cgMLST molecular typing can be performed: the core genome of a group of isolated bacteria with unknown phylogenetic relationships is typed to obtain a core genome typing result matrix; based on the core genome analysis result matrix, cluster analysis is performed on the strains included in the analysis, and the strains with smaller differences are more closely related.

[0036] It should be noted that the above description is merely a preferred embodiment of the present invention and is not intended to limit the present invention. For those skilled in the art, the present invention can have various modifications and variations. Any modifications, equivalent substitutions, improvements, etc., made without creative effort should be included within the protection scope of the present invention.

Claims

1. A method for constructing a cgMLST system for Chlamydia psittaci, characterized in that, Includes the following steps: (1) Download the assembled genomes of all Chlamydia psittaci from the NCBI public genome database and the original sequences of second-generation whole genome sequencing, and perform quality control and screening. Those that meet the requirements are included in the study, including assembled genomes and original genomes. (2) After genome annotation, the assembled genomes included in the study were subjected to pan-genome analysis, and the initial core genomes were obtained by screening based on the carrier rate. (3) Remove genes from the initial core genome that have any of the following characteristics: no initial codon, no or multiple stop codons, length less than 50 bp, repetitive genes with similar sequences, carried on plasmids, or similar to mobile genes. If there is overlap between two genes, only the one with the longer gene length is retained; those that meet the requirements are included in the initial cgMLST system; the initial cgMLST system is used to analyze all the assembled genomes and original genomes included in the study, and the carrier rate of each gene is calculated. If the carrier rate is lower than the threshold, the gene is removed, and the rest are used as the final cgMLST system for Chlamydia psittaci. The core genes in the final cgMLST system are mapped onto the standard genome chromosome.

2. The method for constructing the *Chlamydia psittaci* cgMLST system according to claim 1, characterized in that, In step (1), the quality control and screening are specifically as follows: after splicing and annotation, the number of contigs and genes of each genome are counted, and genomes with obvious contamination and fewer than 900 genes are removed; then, ANI analysis is performed using the complete genome of Chlamydia psittaci 6BC as the alignment standard sequence, and genomes with an ANI value below 0.95 are removed; then, BUSCO analysis is performed to assess genome integrity, and genomes with integrity below 95% are removed.

3. The method for constructing the *Chlamydia psittaci* cgMLST system according to claim 1, characterized in that, In step (2), the pan-genome analysis is performed using Panaroo software; in step (3), the analysis of all assembled genomes and original genomes included in the study and the statistical analysis of the carrier rate of each gene are performed using ChewBBACA software.

4. The method for constructing the *Chlamydia psittaci* cgMLST system according to claim 1, characterized in that, In steps (2) and (3), the carrying rate threshold is set to 95%.

5. The method for constructing the *Chlamydia psittaci* cgMLST system according to claim 1, characterized in that, In step (3), the similarity judgment criteria are: sequence consistency greater than 0.9 and coverage greater than 0.

9.

6. The method for constructing the *Chlamydia psittaci* cgMLST system according to claim 1, characterized in that, It also includes evaluating the resolution of the cgMLST system after obtaining the final Chlamydia psittaci cgMLST system. Specifically, this involves performing a phylogenetic analysis based on core genome SNP differences on all included genomes, visualizing the results, comparing them with the cgMLST analysis results, and evaluating the genotyping accuracy and resolution of the cgMLST system.

7. A Chlamydia psittaci core genome for cgMLST molecular typing, characterized in that, Includes the following genes: G5O_RS07550,G5O_RS07400,G5O_RS06475,G5O_RS08070,G5O_RS06320,G5O_RS10155,G5O_RS10015,G5O_RS08245,G5O_RS08905,G5O_RS07190,G5O_RS08885,G5O_RS 05230,G5O_RS06820,G5O_RS07730,G5O_RS07270,G5O_RS07335,G5O_RS07095,G5O_RS05935,G5O_RS06085,G5O_RS10455,G5O_RS07165,G5O_RS06480,G5O_RS09865,G5O_RS06455,G5O_RS10185,G5O_RS10530,G5O_RS08495,G5O_RS10045,G5O_RS09870,G5O_RS06350,G5O_RS06785,G5O_RS05760,G5O_RS10165,G5O_RS08205,G5O_RS 05350,G5O_RS09880,G5O_RS07305,G5O_RS08220,G5O_RS05185,G5O_RS07640,G5O_RS09440,G5O_RS09795,G5O_RS09250,G5O_RS06575,G5O_RS05970,G5O_RS05630,G5O_RS05495,G5O_RS08940,G5O_RS10035,G5O_RS09295,G5O_RS06760,G5O_RS07870,G5O_RS09355,G5O_RS08780,G5O_RS08785,G5O_RS08790,G5O_RS07935,G5O_RS 07940,G5O_RS06890,G5O_RS07595,G5O_RS07505,G5O_RS07845,G5O_RS10365,G5O_RS10055,G5O_RS09600,G5O_RS06235,G5O_RS07040,G5O_RS09495,G5O_RS08480,G5O_RS07885,G5O_RS06045,G5O_RS08770,G5O_RS06485,G5O_RS07665,G5O_RS07895,G5O_RS08695,G5O_RS05555,G5O_RS05960,G5O_RS08555,G5O_RS08545,G5O_RS 08565,G5O_RS06265,G5O_RS07570,G5O_RS08065,G5O_RS07545,G5O_RS06800,G5O_RS08735,G5O_RS09350,G5O_RS08660,G5O_RS09650,G5O_RS09800,G5O_RS09415,G5O_RS09640,G5O_RS05990,G5O_RS09760,G5O_RS06060,G5O_RS06935,G5O_RS09750,G5O_RS09755,G5O_RS06055,G5O_RS07740,G5O_RS07915,G5O_RS09480,G5O_RS 05525,G5O_RS07600,G5O_RS09425,G5O_RS08285,G5O_RS06155,G5O_RS09365,G5O_RS09325,G5O_RS05505,G5O_RS08685,G5O_RS08700,G5O_RS09050,G5O_RS06425,G5O_RS08875,G5O_RS07180,G5O_RS07625,G5O_RS06275,G5O_RS06740,G5O_RS09765,G5O_RS07080,G5O_RS05590,G5O_RS07525,G5O_RS07000,G5O_RS05790,G5O_RS05535,G5O_RS09285,G5O_RS06795,G5O_RS06385,G5O_RS07390,G5O_RS08140,G5O_RS05895,G5O_RS09335,G5O_RS10010,G5O_RS10110,G5O_RS06895,G5O_RS07370,G5O_RS06710,G5O_RS07745,G5O_RS07930,G5O_RS09490,G5O_RS09970,G5O_RS09885,G5O_RS07585,G5O_RS09385,G5O_RS07590,G5O_RS07580,G5O_RS07100,G5O_RS 05610,G5O_RS07655,G5O_RS10150,G5O_RS08085,G5O_RS08420,G5O_RS09840,G5O_RS05620,G5O_RS07405,G5O_RS10160,G5O_RS10000,G5O_RS09995,G5O_RS05380,G5O_RS08955,G5O_RS07025,G5O_RS09580,G5O_RS09070,G5O_RS08880,G5O_RS07650,G5O_RS05745,G5O_RS06625,G5O_RS06620,G5O_RS06955,G5O_RS06145,G5O_RS 09245,G5O_RS06515,G5O_RS07195,G5O_RS09090,G5O_RS09085,G5O_RS10205,G5O_RS06095,G5O_RS06310,G5O_RS09260,G5O_RS08395,G5O_RS07325,G5O_RS09705,G5O_RS08350,G5O_RS10065,G5O_RS09475,G5O_RS08345,G5O_RS10025,G5O_RS05260,G5O_RS09280,G5O_RS10145,G5O_RS05625,G5O_RS05810,G5O_RS08460,G5O_RS 08455,G5O_RS07105,G5O_RS08445,G5O_RS08440,G5O_RS05545,G5O_RS09920,G5O_RS06775,G5O_RS10490,G5O_RS08720,G5O_RS09430,G5O_RS06465,G5O_RS06305,G5O_RS08320,G5O_RS08370,G5O_RS08575,G5O_RS10395,G5O_RS06375,G5O_RS08890,G5O_RS07200,G5O_RS05910,G5O_RS06125,G5O_RS06840,G5O_RS06715,G5O_RS 09275,G5O_RS07825,G5O_RS05210,G5O_RS07380,G5O_RS06660,G5O_RS07860,G5O_RS05300,G5O_RS06360,G5O_RS08540,G5O_RS10075,G5O_RS08645,G5O_RS08560,G5O_RS09180,G5O_RS06910,G5O_RS05530,G5O_RS08530,G5O_RS05310,G5O_RS06130,G5O_RS06120,G5O_RS05215,G5O_RS06835,G5O_RS10195,G5O_RS08835,G5O_RS 08845,G5O_RS05480,G5O_RS06855,G5O_RS05305,G5O_RS09780,G5O_RS10100,G5O_RS10405,G5O_RS05340,G5O_RS07540,G5O_RS07555,G5O_RS09320,G5O_RS05985,G5O_RS07005,G5O_RS07210,G5O_RS09055,G5O_RS07660,G5O_RS05750,G5O_RS09635,G5O_RS05465,G5O_RS05365,G5O_RS06905,G5O_RS05830,G5O_RS08920,G5O_RS05295,G5O_RS07365,G5O_RS06020,G5O_RS06030,G5O_RS07345,G5O_RS05490,G5O_RS06965,G5O_RS09605,G5O_RS06345,G5O_RS09770,G5O_RS06615,G5O_RS09875,G5O_RS09045,G5O_RS07610,G5O_RS05320,G5O_RS09530,G5O_RS07375,G5O_RS08570,G5O_RS06370,G5O_RS07415,G5O_RS08775,G5O_RS08415,G5O_RS05870,G5O_RS 07135,G5O_RS06295,G5O_RS10080,G5O_RS09695,G5O_RS05270,G5O_RS08240,G5O_RS05510,G5O_RS09720,G5O_RS08465,G5O_RS10340,G5O_RS08825,G5O_RS06635,G5O_RS09450,G5O_RS09380,G5O_RS10115,G5O_RS08620,G5O_RS07710,G5O_RS07630,G5O_RS08250,G5O_RS09205,G5O_RS08865,G5O_RS06460,G5O_RS05335,G5O_RS 08325,G5O_RS06655,G5O_RS06440,G5O_RS06450,G5O_RS08935,G5O_RS08650,G5O_RS09165,G5O_RS07800,G5O_RS07565,G5O_RS06115,G5O_RS08970,G5O_RS06035,G5O_RS07170,G5O_RS05485,G5O_RS08840,G5O_RS06850,G5O_RS07145,G5O_RS07110,G5O_RS05975,G5O_RS09710,G5O_RS10425,G5O_RS10515,G5O_RS05920,G5O_RS 10180,G5O_RS06640,G5O_RS07245,G5O_RS06090,G5O_RS08710,G5O_RS10005,G5O_RS06010,G5O_RS06230,G5O_RS06435,G5O_RS08930,G5O_RS07090,G5O_RS05520,G5O_RS07795,G5O_RS06915,G5O_RS07280,G5O_RS08855,G5O_RS07140,G5O_RS05965,G5O_RS08680,G5O_RS05880,G5O_RS07775,G5O_RS08895,G5O_RS07070,G5O_RS 06645,G5O_RS07010,G5O_RS05445,G5O_RS09015,G5O_RS06225,G5O_RS06430,G5O_RS06195,G5O_RS05500,G5O_RS08665,G5O_RS07790,G5O_RS08675,G5O_RS10430,G5O_RS06490,G5O_RS10520,G5O_RS06405,G5O_RS06220,G5O_RS09545,G5O_RS06410,G5O_RS06420,G5O_RS06995,G5O_RS08105,G5O_RS06415,G5O_RS06510,G5O_RS 06520,G5O_RS06945,G5O_RS06525,G5O_RS08080,G5O_RS08075,G5O_RS08280,G5O_RS08355,G5O_RS08850,G5O_RS09110,G5O_RS06355,G5O_RS09955,G5O_RS08910,G5O_RS10050,G5O_RS06790,G5O_RS09610,G5O_RS10070,G5O_RS08390,G5O_RS10435,G5O_RS06990,G5O_RS09485,G5O_RS08305,G5O_RS08915,G5O_RS07285,G5O_RS05245,G5O_RS10310,G5O_RS09805,G5O_RS09590,G5O_RS10415,G5O_RS10420,G5O_RS07450,G5O_RS06920,G5O_RS07510,G5O_RS09310,G5O_RS09655,G5O_RS05315,G5O_RS09040,G5O_RS09270,G5O_RS06745,G5O_RS09990,G5O_RS07605,G5O_RS07615,G5O_RS06925,G5O_RS05170,G5O_RS09935,G5O_RS09950,G5O_RS09675,G5O_RS 07420,G5O_RS05595,G5O_RS09360,G5O_RS09810,G5O_RS06875,G5O_RS05470,G5O_RS07815,G5O_RS10135,G5O_RS07705,G5O_RS09595,G5O_RS09825,G5O_RS08470,G5O_RS07055,G5O_RS09855,G5O_RS07445,G5O_RS05190,G5O_RS07175,G5O_RS09680,G5O_RS09830,G5O_RS05865,G5O_RS09860,G5O_RS07085,G5O_RS09895,G5O_RS 08435,G5O_RS07960,G5O_RS07750,G5O_RS10210,G5O_RS07850,G5O_RS07685,G5O_RS07130,G5O_RS06290,G5O_RS05855,G5O_RS06695,G5O_RS05925,G5O_RS09155,G5O_RS07855,G5O_RS06810,G5O_RS06750,G5O_RS08300,G5O_RS07720,G5O_RS09925,G5O_RS06735,G5O_RS08975,G5O_RS08800,G5O_RS08175,G5O_RS06470,G5O_RS 10380,G5O_RS09300,G5O_RS07680,G5O_RS05275,G5O_RS09985,G5O_RS08235,G5O_RS09190,G5O_RS08505,G5O_RS06070,G5O_RS09715,G5O_RS10220,G5O_RS07645,G5O_RS09915,G5O_RS07295,G5O_RS07410,G5O_RS05150,G5O_RS10175,G5O_RS08475,G5O_RS06165,G5O_RS07255,G5O_RS08215,G5O_RS07315,G5O_RS07620,G5O_RS 08745,G5O_RS07900,G5O_RS08230,G5O_RS09845,G5O_RS09265,G5O_RS08965,G5O_RS06325,G5O_RS06700,G5O_RS06390,G5O_RS07695,G5O_RS05280,G5O_RS05285,G5O_RS07690,G5O_RS05290,G5O_RS05140,G5O_RS06860,G5O_RS05860,G5O_RS08295,G5O_RS07250,G5O_RS09525,G5O_RS06500,G5O_RS05950,G5O_RS06395,G5O_RS 07050,G5O_RS08450,G5O_RS07920,G5O_RS08640,G5O_RS07485,G5O_RS09000,G5O_RS07160,G5O_RS06000,G5O_RS09210,G5O_RS06160,G5O_RS07275,G5O_RS08860,G5O_RS05250,G5O_RS06285,G5O_RS09370,G5O_RS07330,G5O_RS08200,G5O_RS07515,G5O_RS09820,G5O_RS05600,G5O_RS07820,G5O_RS06780,G5O_RS05780,G5O_RS05240,G5O_RS09100,G5O_RS05605,G5O_RS07560,G5O_RS06005,G5O_RS06270,G5O_RS08500,G5O_RS06240,G5O_RS08690,G5O_RS09330,G5O_RS06755,G5O_RS07535,G5O_RS07440,G5O_RS06900,G5O_RS08900,G5O_RS07125,G5O_RS05360,G5O_RS08805,G5O_RS06330,G5O_RS07675,G5O_RS08210,G5O_RS09410,G5O_RS08290,G5O_RS 06930,G5O_RS08795,G5O_RS05785,G5O_RS10305,G5O_RS06335,G5O_RS09405,G5O_RS07075,G5O_RS06340,G5O_RS09460,G5O_RS05415,G5O_RS05410,G5O_RS09645,G5O_RS09730,G5O_RS07065,G5O_RS06040,G5O_RS09010,G5O_RS09435,G5O_RS09455,G5O_RS09465,G5O_RS05205,G5O_RS09910,G5O_RS09290,G5O_RS07120,G5O_RS 07455,G5O_RS05775,G5O_RS05200,G5O_RS08155,G5O_RS05145,G5O_RS06985,G5O_RS06980,G5O_RS06975,G5O_RS06970,G5O_RS09550,G5O_RS09025,G5O_RS06250,G5O_RS09030,G5O_RS08550,G5O_RS08535,G5O_RS07490,G5O_RS09005,G5O_RS08615,G5O_RS05905,G5O_RS06105,G5O_RS06110,G5O_RS07875,G5O_RS08125,G5O_RS 08135,G5O_RS05900,G5O_RS05460,G5O_RS05455,G5O_RS09725,G5O_RS09095,G5O_RS06280,G5O_RS07215,G5O_RS08340,G5O_RS08170,G5O_RS08180,G5O_RS06880,G5O_RS08815,G5O_RS05475,G5O_RS07865,G5O_RS05800,G5O_RS08985,G5O_RS05915,G5O_RS08225,G5O_RS06050,G5O_RS09170,G5O_RS06605,G5O_RS06215,G5O_RS06540,G5O_RS06550,G5O_RS06545,G5O_RS07495,G5O_RS08950,G5O_RS09375,G5O_RS08430,G5O_RS08425,G5O_RS06400,G5O_RS09785,G5O_RS09230,G5O_RS09195,G5O_RS06825,G5O_RS08510,G5O_RS05835,G5O_RS05385,G5O_RS06865,G5O_RS09735,G5O_RS07480,G5O_RS06495,G5O_RS06770,G5O_RS10140,G5O_RS05175,G5O_RS 05180,G5O_RS07385,G5O_RS06080,G5O_RS05940,G5O_RS07575,G5O_RS10090,G5O_RS05825,G5O_RS09620,G5O_RS06255,G5O_RS09625,G5O_RS07470,G5O_RS09615,G5O_RS09660,G5O_RS07115,G5O_RS05265,G5O_RS06870,G5O_RS09185,G5O_RS08400,G5O_RS06650,G5O_RS09315,G5O_RS06380,G5O_RS08310,G5O_RS08605,G5O_RS05645,G5O_RS05635,G5O_RS05690,G5O_RS05700,G5O_RS09215,G5O_RS08600,G5O_RS08610,G5O_RS08595,G5O_RS07830,G5O_RS05680,G5O_RS05715,G5O_RS05665,G5O_RS05740,G5O_RS05705,G5O_RS08405,G5O_RS08990,G5O_RS06175,G5O_RS05655,G5O_RS05640,G5O_RS05685,G5O_RS09235,G5O_RS06180,G5O_RS07435,G5O_RS 09175,G5O_RS07810,G5O_RS08995,G5O_RS05735,G5O_RS10095,G5O_RS05395,G5O_RS05660,G5O_RS05195,G5O_RS09225,G5O_RS06140,G5O_RS05695,G5O_RS07835,G5O_RS05730,G5O_RS06135,G5O_RS05725,G5O_RS09305,G5O_RS08945,G5O_RS05675,G5O_RS09220,G5O_RS05650,G5O_RS05515,G5O_RS09390,G5O_RS06705,G5O_RS 05850,G5O_RS07230,G5O_RS05770,G5O_RS07185,G5O_RS05765,G5O_RS09775,G5O_RS06075,G5O_RS05720,G5O_RS09630,G5O_RS07310,G5O_RS07725,G5O_RS07395,G5O_RS06885,G5O_RS09945,G5O_RS09850,G5O_RS05450,G5O_RS07265,G5O_RS09065,G5O_RS09060,G5O_RS05425,G5O_RS07765,G5O_RS08580,G5O_RS09940,G5O_RS 10225,G5O_RS09745,G5O_RS08960,G5O_RS09500,G5O_RS05805,G5O_RS10105,G5O_RS06730,G5O_RS08410,G5O_RS05565,G5O_RS09960,G5O_RS05995,G5O_RS07475,G5O_RS05570,G5O_RS07715,G5O_RS07880,G5O_RS05585,G5O_RS05390,G5O_RS07770,G5O_RS08630,G5O_RS05165,G5O_RS09080,G5O_RS07320,G5O_RS07430,G5O_RS 05540,G5O_RS10085,G5O_RS06065,G5O_RS09965,G5O_RS08525,G5O_RS08195,G5O_RS06765,G5O_RS06725,G5O_RS06720,G5O_RS06830,G5O_RS06365,G5O_RS08335,G5O_RS09075,G5O_RS07465,G5O_RS08165,G5O_RS07520,G5O_RS10290,G5O_RS07840,G5O_RS06245,G5O_RS09905,G5O_RS08120,G5O_RS09835,G5O_RS05325,G5O_RS 07460,G5O_RS08375,G5O_RS08485,G5O_RS06190,G5O_RS08585,G5O_RS08590,G5O_RS07905,G5O_RS06535,G5O_RS08520,G5O_RS08275,G5O_RS09890,G5O_RS05155,G5O_RS09980,G5O_RS08385,G5O_RS08130,G5O_RS07340,G5O_RS08365,G5O_RS05345,G5O_RS09200,G5O_RS05840,G5O_RS09930,G5O_RS09160,G5O_RS08870,G5O_RS09540,G5O_RS09445,G5O_RS07425,G5O_RS06185,G5O_RS07500,G5O_RS08820,G5O_RS05440,G5O_RS06210,G5O_RS07355,G5O_RS07155,G5O_RS06630,G5O_RS10200,G5O_RS05405,G5O_RS08515,G5O_RS09510, G5O_RS08925, G5O_RS05435, G5O_RS06950, G5O_RS06150, G5O_RS10170, G5O_RS10130, G5O_RS08160, G5O_RS06675, G5O_RS06845, G5O_RS05945, G5O_RS08670; gene numbers are derived from the complete genome of Chlamydia psittaci 6BC, accession number: NC_017287.

1.

8. A method for molecular typing of Chlamydia psittaci cgMLST based on the core genome of claim 7, characterized in that, The method is as follows: based on the core genome, a group of isolated bacteria with unknown phylogenetic relationships are genotyped to obtain a core genome genotyping result matrix; Cluster analysis was performed on the included strains based on the matrix of core genome analysis results, and the strains with smaller differences were more closely related.

9. The method according to claim 8, characterized in that, The cluster analysis was performed using either ChewBBACA or Ridom software.

Images