Marc J.A. Stevens , Roger Stephan , Jule Anna Horlbog , Nicole Cernela , Magdalena Nüesch-Inderbinen
{"title":"基于全基因组序列对一家大型家禽屠宰场三年来从肉鸡屠体中分离出的弯曲杆菌进行特征分析,发现空肠弯曲杆菌具有高度的遗传多样性和重复出现的基因组系。","authors":"Marc J.A. Stevens , Roger Stephan , Jule Anna Horlbog , Nicole Cernela , Magdalena Nüesch-Inderbinen","doi":"10.1016/j.meegid.2024.105578","DOIUrl":null,"url":null,"abstract":"<div><p><em>Campylobacter</em> is among the most frequent agents of bacterial gastroenteritis in Europe and is primarily linked to the consumption of contaminated food. The aim of this study was to assess genomic diversity and to identify antimicrobial resistance and virulence genes of 155 <em>Campylobacter</em> isolated from broiler carcasses (neck skin samples) in a large-scale Swiss poultry abattoir over a three-year period. Samples originated from broilers from three different types of farming systems (particularly animal-friendly stabling (PAFS), free-range farms, and organic farms).</p><p><em>Campylobacter jejuni</em> (<em>n</em> = 127) <em>and Campylobacter coli</em> (<em>n</em> = 28) were analysed using a whole genome sequencing (WGS) approach (MiniSeq; Illumina). Sequence types (STs) were determined in silico from the WGS data and isolates were assigned into complex types (CTs) using the cgMLST SeqSphere+ scheme. Antimicrobial resistance genes were identified using the Resistance Gene Identifier (RGI), and virulence genes were identified using the virulence factor database (VFDB).</p><p>A high degree of genetic diversity was observed. Many sequence types (<em>C. jejuni</em> ST19, ST21, ST48, ST50, ST122, ST262 and <em>C. coli</em> ST827) occurred more than once and were distributed throughout the study period, irrespective of the year of isolation and of the broiler farming type. Antimicrobial resistance determinants included <em>bla</em><sub>OXA</sub> and <em>tet</em>(O) genes, as well as the T86I substitution within GyrA. Virulence genes known to play a role in human <em>Campylobacter</em> infection were identified such as the <em>wlaN, cstIII</em>, <em>neuA1, neuB1,</em> and <em>neuC1.</em> Subtyping of the <em>Campylobacter</em> isolates identified the occurrence of a highly clonal population of <em>C. jejuni</em> ST21 that was isolated throughout the three-year study period from carcasses from farms with geographically different locations and different farming systems.</p><p>The high rate of genetic diversity observed among broiler carcass isolates is consistent with previous studies. The identification of a persisting highly clonal <em>C. jejuni</em> ST21 subtype suggests that the slaughterhouse may represent an environment in which <em>C. jejuni</em> ST21 may survive, however, the ecological reservoir potentially maintaining this clone remains unknown.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6000,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000297/pdfft?md5=91dd88264d533898db1327fffae5bee9&pid=1-s2.0-S1567134824000297-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Whole genome sequence-based characterization of Campylobacter isolated from broiler carcasses over a three-year period in a big poultry slaughterhouse reveals high genetic diversity and a recurring genomic lineage of Campylobacter jejuni\",\"authors\":\"Marc J.A. Stevens , Roger Stephan , Jule Anna Horlbog , Nicole Cernela , Magdalena Nüesch-Inderbinen\",\"doi\":\"10.1016/j.meegid.2024.105578\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p><em>Campylobacter</em> is among the most frequent agents of bacterial gastroenteritis in Europe and is primarily linked to the consumption of contaminated food. The aim of this study was to assess genomic diversity and to identify antimicrobial resistance and virulence genes of 155 <em>Campylobacter</em> isolated from broiler carcasses (neck skin samples) in a large-scale Swiss poultry abattoir over a three-year period. Samples originated from broilers from three different types of farming systems (particularly animal-friendly stabling (PAFS), free-range farms, and organic farms).</p><p><em>Campylobacter jejuni</em> (<em>n</em> = 127) <em>and Campylobacter coli</em> (<em>n</em> = 28) were analysed using a whole genome sequencing (WGS) approach (MiniSeq; Illumina). Sequence types (STs) were determined in silico from the WGS data and isolates were assigned into complex types (CTs) using the cgMLST SeqSphere+ scheme. Antimicrobial resistance genes were identified using the Resistance Gene Identifier (RGI), and virulence genes were identified using the virulence factor database (VFDB).</p><p>A high degree of genetic diversity was observed. Many sequence types (<em>C. jejuni</em> ST19, ST21, ST48, ST50, ST122, ST262 and <em>C. coli</em> ST827) occurred more than once and were distributed throughout the study period, irrespective of the year of isolation and of the broiler farming type. Antimicrobial resistance determinants included <em>bla</em><sub>OXA</sub> and <em>tet</em>(O) genes, as well as the T86I substitution within GyrA. Virulence genes known to play a role in human <em>Campylobacter</em> infection were identified such as the <em>wlaN, cstIII</em>, <em>neuA1, neuB1,</em> and <em>neuC1.</em> Subtyping of the <em>Campylobacter</em> isolates identified the occurrence of a highly clonal population of <em>C. jejuni</em> ST21 that was isolated throughout the three-year study period from carcasses from farms with geographically different locations and different farming systems.</p><p>The high rate of genetic diversity observed among broiler carcass isolates is consistent with previous studies. The identification of a persisting highly clonal <em>C. jejuni</em> ST21 subtype suggests that the slaughterhouse may represent an environment in which <em>C. jejuni</em> ST21 may survive, however, the ecological reservoir potentially maintaining this clone remains unknown.</p></div>\",\"PeriodicalId\":54986,\"journal\":{\"name\":\"Infection Genetics and Evolution\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2024-02-27\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S1567134824000297/pdfft?md5=91dd88264d533898db1327fffae5bee9&pid=1-s2.0-S1567134824000297-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Infection Genetics and Evolution\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1567134824000297\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"INFECTIOUS DISEASES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Infection Genetics and Evolution","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1567134824000297","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}
Whole genome sequence-based characterization of Campylobacter isolated from broiler carcasses over a three-year period in a big poultry slaughterhouse reveals high genetic diversity and a recurring genomic lineage of Campylobacter jejuni
Campylobacter is among the most frequent agents of bacterial gastroenteritis in Europe and is primarily linked to the consumption of contaminated food. The aim of this study was to assess genomic diversity and to identify antimicrobial resistance and virulence genes of 155 Campylobacter isolated from broiler carcasses (neck skin samples) in a large-scale Swiss poultry abattoir over a three-year period. Samples originated from broilers from three different types of farming systems (particularly animal-friendly stabling (PAFS), free-range farms, and organic farms).
Campylobacter jejuni (n = 127) and Campylobacter coli (n = 28) were analysed using a whole genome sequencing (WGS) approach (MiniSeq; Illumina). Sequence types (STs) were determined in silico from the WGS data and isolates were assigned into complex types (CTs) using the cgMLST SeqSphere+ scheme. Antimicrobial resistance genes were identified using the Resistance Gene Identifier (RGI), and virulence genes were identified using the virulence factor database (VFDB).
A high degree of genetic diversity was observed. Many sequence types (C. jejuni ST19, ST21, ST48, ST50, ST122, ST262 and C. coli ST827) occurred more than once and were distributed throughout the study period, irrespective of the year of isolation and of the broiler farming type. Antimicrobial resistance determinants included blaOXA and tet(O) genes, as well as the T86I substitution within GyrA. Virulence genes known to play a role in human Campylobacter infection were identified such as the wlaN, cstIII, neuA1, neuB1, and neuC1. Subtyping of the Campylobacter isolates identified the occurrence of a highly clonal population of C. jejuni ST21 that was isolated throughout the three-year study period from carcasses from farms with geographically different locations and different farming systems.
The high rate of genetic diversity observed among broiler carcass isolates is consistent with previous studies. The identification of a persisting highly clonal C. jejuni ST21 subtype suggests that the slaughterhouse may represent an environment in which C. jejuni ST21 may survive, however, the ecological reservoir potentially maintaining this clone remains unknown.
期刊介绍:
(aka Journal of Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases -- MEEGID)
Infectious diseases constitute one of the main challenges to medical science in the coming century. The impressive development of molecular megatechnologies and of bioinformatics have greatly increased our knowledge of the evolution, transmission and pathogenicity of infectious diseases. Research has shown that host susceptibility to many infectious diseases has a genetic basis. Furthermore, much is now known on the molecular epidemiology, evolution and virulence of pathogenic agents, as well as their resistance to drugs, vaccines, and antibiotics. Equally, research on the genetics of disease vectors has greatly improved our understanding of their systematics, has increased our capacity to identify target populations for control or intervention, and has provided detailed information on the mechanisms of insecticide resistance.
However, the genetics and evolutionary biology of hosts, pathogens and vectors have tended to develop as three separate fields of research. This artificial compartmentalisation is of concern due to our growing appreciation of the strong co-evolutionary interactions among hosts, pathogens and vectors.
Infection, Genetics and Evolution and its companion congress [MEEGID](http://www.meegidconference.com/) (for Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases) are the main forum acting for the cross-fertilization between evolutionary science and biomedical research on infectious diseases.
Infection, Genetics and Evolution is the only journal that welcomes articles dealing with the genetics and evolutionary biology of hosts, pathogens and vectors, and coevolution processes among them in relation to infection and disease manifestation. All infectious models enter the scope of the journal, including pathogens of humans, animals and plants, either parasites, fungi, bacteria, viruses or prions. The journal welcomes articles dealing with genetics, population genetics, genomics, postgenomics, gene expression, evolutionary biology, population dynamics, mathematical modeling and bioinformatics. We also provide many author benefits, such as free PDFs, a liberal copyright policy, special discounts on Elsevier publications and much more. Please click here for more information on our author services .