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Le Guern AS, Savin C, Chereau F, Tessier S, Guglielmini J, Brémont S, Pizarro-Cerdá J. A novel cgMLST for genomic surveillance of Yersinia enterocolitica infections in France allowed the detection and investigation of outbreaks in 2017-2021. Microbiol Spectr 2024; 12:e0050424. [PMID: 38651883 PMCID: PMC11237650 DOI: 10.1128/spectrum.00504-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Enteric yersiniosis, the third most common food-borne zoonosis in Europe, is mainly caused by the pathogen Yersinia enterocolitica. In France, the yersiniosis microbiological surveillance is conducted at the Yersinia National Reference Laboratory (YNRL). Since 2017, isolates have been characterized by whole genome sequencing (WGS) followed by a 500-gene Yersinia-cgMLST. We report here the data of the WGS-based surveillance on Y. enterocolitica isolates for the 2017-2021 period. The YNRL characterized 7,642 Y. enterocolitica strains distributed in 2,497 non-pathogenic isolates from lineages 1Aa and 1Ab, and 5,145 specimens belonging to 8 pathogenic lineages. Among pathogenic isolates, lineage 4 was the most common (87.2%) followed by lineages 2/3-9b (10.6%), 2/3-5a (1.2%), 2/3-9a (0.6%), 3-3b, 3-3c, 1B, and 3-3d (0.1% per each). Importantly, we developed a routine surveillance system based on a new typing method consisting of a 1,727-genes core genome Multilocus Sequence Typing (cgMLST) specific to the species Y. enterocolitica followed by isolate clustering. Thresholds of allelic distances (AD) were determined and fixed for the clustering of isolates: AD ≤ 5 for lineages 4, 2/3-5a, and 2/3-9a, and AD ≤ 3 for lineage 2/3-9b. Clustering programs were implemented in 2019 in routine surveillance to detect genomic clusters of pathogenic isolates. In total, 419 clusters with at least 2 isolates were identified, representing 2,504 of the 3,503 isolates characterized between 2019 and 2021. Most clusters (n = 325) comprised 2 to 5 isolates. The new typing method proved to be useful for the molecular investigation of unusual grouping of cases as well as for the detection of genomic clusters in routine surveillance. IMPORTANCE We describe here the new typing method used for molecular surveillance of Yersinia enterocolitica infections in France based on a novel core genome Multilocus Sequence Typing (cgMLST) specific to Y. enterocolitica species. This method can reliably identify the pathogenic Y. enterocolitica subspecies and compare the isolates with a high discriminatory power. Between 2017 and 2021, 5,145 pathogenic isolates belonging to 8 lineages were characterized and lineage 4 was by far the most common followed by lineage 2/3-9b. A clustering program was implemented, and detection thresholds were cross-validated by the molecular and epidemiological investigation of three unusual groups of Y. enterocolitica infections. The routine molecular surveillance system has been able to detect genomic clusters, leading to epidemiological investigations.
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Affiliation(s)
- Anne-Sophie Le Guern
- Institut Pasteur, Université de Paris Cité, Yersinia Research Unit, Yersinia National Reference Laboratory, WHO Collaborating Centre for Plague Fra-140, Paris, France
| | - Cyril Savin
- Institut Pasteur, Université de Paris Cité, Yersinia Research Unit, Yersinia National Reference Laboratory, WHO Collaborating Centre for Plague Fra-140, Paris, France
| | - Fanny Chereau
- Santé publique France, Infectious Diseases Division, Saint-Maurice, France
| | - Sabrina Tessier
- Santé publique France, Regions Division, Bourgogne-Franche-Comté Office, Dijon, France
| | - Julien Guglielmini
- Institut Pasteur, Université de Paris Cité, Bioinformatics and Biostatistic Hub, Paris, France
| | - Sylvie Brémont
- Institut Pasteur, Université de Paris Cité, Yersinia Research Unit, Yersinia National Reference Laboratory, WHO Collaborating Centre for Plague Fra-140, Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université de Paris Cité, Yersinia Research Unit, Yersinia National Reference Laboratory, WHO Collaborating Centre for Plague Fra-140, Paris, France
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Prevalence, virulence determinants, and genetic diversity in Yersinia enterocolitica isolated from slaughtered pigs and pig carcasses. Int J Food Microbiol 2022; 376:109756. [DOI: 10.1016/j.ijfoodmicro.2022.109756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022]
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Savin C, Criscuolo A, Guglielmini J, Le Guern AS, Carniel E, Pizarro-Cerdá J, Brisse S. Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization. Microb Genom 2019; 5:e000301. [PMID: 31580794 PMCID: PMC6861861 DOI: 10.1099/mgen.0.000301] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/16/2019] [Indexed: 11/18/2022] Open
Abstract
The genus Yersinia comprises species that differ widely in their pathogenic potential and public-health significance. Yersinia pestis is responsible for plague, while Yersinia enterocolitica is a prominent enteropathogen. Strains within some species, including Y. enterocolitica, also vary in their pathogenic properties. Phenotypic identification of Yersinia species is time-consuming, labour-intensive and may lead to incorrect identifications. Here, we developed a method to automatically identify and subtype all Yersinia isolates from their genomic sequence. A phylogenetic analysis of Yersinia isolates based on a core subset of 500 shared genes clearly demarcated all existing Yersinia species and uncovered novel, yet undefined Yersinia taxa. An automated taxonomic assignment procedure was developed using species-specific thresholds based on core-genome multilocus sequence typing (cgMLST). The performance of this method was assessed on 1843 isolates prospectively collected by the French National Surveillance System and analysed in parallel using phenotypic reference methods, leading to nearly complete (1814; 98.4 %) agreement at species and infra-specific (biotype and serotype) levels. For 29 isolates, incorrect phenotypic assignments resulted from atypical biochemical characteristics or lack of phenotypic resolution. To provide an identification tool, a database of cgMLST profiles and reference taxonomic information has been made publicly accessible (https://bigsdb.pasteur.fr/yersinia). Genomic sequencing-based identification and subtyping of any Yersinia is a powerful and reliable novel approach to define the pathogenic potential of isolates of this medically important genus.
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Affiliation(s)
- Cyril Savin
- Yersinia Research Unit, Institut Pasteur, Paris, France
- National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France
| | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique – Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Julien Guglielmini
- Hub de Bioinformatique et Biostatistique – Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Anne-Sophie Le Guern
- Yersinia Research Unit, Institut Pasteur, Paris, France
- National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France
| | - Elisabeth Carniel
- Yersinia Research Unit, Institut Pasteur, Paris, France
- National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France
| | - Javier Pizarro-Cerdá
- Yersinia Research Unit, Institut Pasteur, Paris, France
- National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
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Raymond P, Houard E, Denis M, Esnault E. Diversity of Yersinia enterocolitica isolated from pigs in a French slaughterhouse over 2 years. Microbiologyopen 2019; 8:e00751. [PMID: 30350482 PMCID: PMC6562139 DOI: 10.1002/mbo3.751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 11/25/2022] Open
Abstract
The pig is one of the main reservoirs of Yersinia enterocolitica strains pathogenic to humans. A description of the Y. enterocolitica population in this reservoir, and accurate discriminatory techniques for typing isolates are needed for prevention, outbreak investigation, and surveillance. This study investigates the genetic diversity of pathogenic Y. enterocolitica isolates obtained from pig tonsils in a French pig slaughterhouse in 2009 (S1) and 2010 (S2). The use of Pulsed-Field Gel Electrophoresis (PFGE) and MLVA as typing techniques was also compared and evaluated. First, a total of 167 isolates (12 of biotype 3 recovered during S1, and 155 of biotype 4 recovered during S1 and S2) were typed by PFGE using the XbaI enzyme. MLVA was then tested on all the biotype 3 isolates in addition to 70 selected biotype 4 isolates recovered over the 2 years. PFGE generated two specific XbaI-PFGE profiles for biotype 3 isolates. Nine XbaI profiles were obtained for biotype 4, with a higher diversity (ID = 0.599) than biotype 3 (ID = 0.167). Two out of the nine XbaI profiles were reported during both surveys and at different months. MLVA improved the differentiation between isolates; the index of diversity reached 0.621 and 0.958, respectively, for biotype 3 (three MLVA types) and biotype 4 (32 MLVA types). The MLVA types for biotype 4 differed over the two surveys, but some isolates with different MLVA types were genetically closely related. This study provides an initial evaluation of the genetic diversity of Y. enterocolitica strains isolated from pigs in France. We show that some PFGE profiles are maintained in the pig production sector, and, through MLVA, that part of the Y. enterocolitica population remained genetically close over the two years. MLVA proved its effectiveness as a tool for investigating pathogenic Y. enterocolitica strains isolated from pigs.
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Affiliation(s)
- Pierre Raymond
- Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan/Plouzané LaboratoryANSES, University of Bretagne‐LoirePloufraganFrance
| | - Emmanuelle Houard
- Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan/Plouzané LaboratoryANSES, University of Bretagne‐LoirePloufraganFrance
| | - Martine Denis
- Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan/Plouzané LaboratoryANSES, University of Bretagne‐LoirePloufraganFrance
| | - Emilie Esnault
- Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan/Plouzané LaboratoryANSES, University of Bretagne‐LoirePloufraganFrance
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Identification of Yersinia at the Species and Subspecies Levels Is Challenging. CURRENT CLINICAL MICROBIOLOGY REPORTS 2018. [DOI: 10.1007/s40588-018-0088-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Saraka D, Savin C, Kouassi S, Cissé B, Koffi E, Cabanel N, Brémont S, Faye-Kette H, Dosso M, Carniel E. Yersinia enterocolitica, a Neglected Cause of Human Enteric Infections in Côte d'Ivoire. PLoS Negl Trop Dis 2017; 11:e0005216. [PMID: 28081123 PMCID: PMC5230755 DOI: 10.1371/journal.pntd.0005216] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/30/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Enteropathogenic Yersinia circulate in the pig reservoir and are the third bacterial cause of human gastrointestinal infections in Europe. In West Africa, reports of human yersiniosis are rare. This study was conducted to determine whether pathogenic Yersinia are circulating in pig farms and are responsible for human infections in the Abidjan District. METHODOLOGY/PRINCIPAL FINDINGS From June 2012 to December 2013, pig feces were collected monthly in 41 swine farms of the Abidjan district. Of the 781 samples collected, 19 Yersinia strains were isolated in 3 farms: 7 non-pathogenic Yersinia intermedia and 12 pathogenic Yersinia enterocolitica bioserotype 4/O:3. Farm animals other than pigs and wild animals were not found infected. Furthermore, 2 Y. enterocolitica 4/O:3 strains were isolated from 426 fecal samples of patients with digestive disorders. All 14 Y. enterocolitica strains shared the same PFGE and MLVA profile, indicating their close genetic relationship. However, while 6 of them displayed the usual phage type VIII, the other 8 had the highly infrequent phage type XI. Whole genome sequencing and SNP analysis of individual colonies revealed that phage type XI strains had unusually high rates of mutations. These strains displayed a hypermutator phenotype that was attributable to a large deletion in the mutS gene involved in DNA mismatch repair. CONCLUSIONS/SIGNIFICANCE This study demonstrates that pathogenic Y. enterocolitica circulate in the pig reservoir in Côte d'Ivoire and cause human infections with a prevalence comparable to that of many developed countries. The paucity of reports of yersiniosis in West Africa is most likely attributable to a lack of active detection rather than to an absence of the microorganism. The identification of hypermutator strains in pigs and humans is of concern as these strains can rapidly acquire selective advantages that may increase their fitness, pathogenicity or resistance to commonly used treatments.
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Affiliation(s)
- Daniel Saraka
- Environnement and Health department, Institut Pasteur, Abidjan, Côte d'Ivoire
- * E-mail: ,
| | - Cyril Savin
- Yersinia Research Unit and National Reference Laboratory, Institut Pasteur, Paris, France
| | - Stephane Kouassi
- Environnement and Health department, Institut Pasteur, Abidjan, Côte d'Ivoire
| | - Bakary Cissé
- Environnement and Health department, Institut Pasteur, Abidjan, Côte d'Ivoire
| | - Eugène Koffi
- Environnement and Health department, Institut Pasteur, Abidjan, Côte d'Ivoire
| | - Nicolas Cabanel
- Yersinia Research Unit and National Reference Laboratory, Institut Pasteur, Paris, France
| | - Sylvie Brémont
- Yersinia Research Unit and National Reference Laboratory, Institut Pasteur, Paris, France
| | - Hortense Faye-Kette
- Bacteriology and Virology department, Institut Pasteur, Abidjan, Côte d'Ivoire
| | - Mireille Dosso
- Bacteriology and Virology department, Institut Pasteur, Abidjan, Côte d'Ivoire
| | - Elisabeth Carniel
- Yersinia Research Unit and National Reference Laboratory, Institut Pasteur, Paris, France
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Petsios S, Fredriksson-Ahomaa M, Sakkas H, Papadopoulou C. Conventional and molecular methods used in the detection and subtyping of Yersinia enterocolitica in food. Int J Food Microbiol 2016; 237:55-72. [DOI: 10.1016/j.ijfoodmicro.2016.08.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 07/28/2016] [Accepted: 08/11/2016] [Indexed: 01/08/2023]
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