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Prevalence, bio-serotype, antibiotic susceptibility and genotype of Yersinia enterocolitica and other Yersinia species isolated from retail and processed meats in Shaanxi Province, China. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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2
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Platt-Samoraj A, Kończyk-Kmiecik K, Bakuła T. Occurrence and Genetic Correlations of Yersinia spp. Isolated from Commensal Rodents in Northeastern Poland. Pathogens 2021; 10:pathogens10101247. [PMID: 34684196 PMCID: PMC8537150 DOI: 10.3390/pathogens10101247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/08/2023] Open
Abstract
Rodents can be a potential Yersinia spp. vector responsible for farm facilities contamination. The aim of the study was to determine the prevalence of Yersinia spp. in commensal rodents found in the farms and fodder factory areas to characterize the obtained isolates and epidemiological risk. Intestinal samples were subjected to bacteriological, bioserotype, and PCR examination for virulence markers ail, ystA, ystB, and inv presence. Yersinia spp. was isolated from 43 out of 244 (17.6%) rodents (Apodemus agrarius n = 132, Mus musculus n = 102, Apodemus sylvaticus n = 8, Rattus norvegicus n = 2). Y. enterocolitica was isolated from 41 rodents (16.8%), and from one Y. pseudotuberculosis and one Y. kristensenii. In three cases, two Y. enterocolitica isolates were obtained from one rodent. All Y. enetrocolitica contained ystB and belonged to biotype 1A, considered as potentially pathogenic. One isolate additionally had the ail gene typical for pathogenic strains. The sequence analysis of the ystB, ail, and inv fragments showed a high similarity to those from clinical cases. The current study revealed a high prevalence of Y. enetrocolitica among commensal rodents, but the classification of all of Y. enterocolitica isolates into biotype 1A and the sporadic isolation of Y. pseudotuberculosis do not indicate a high epidemiological risk.
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Affiliation(s)
- Aleksandra Platt-Samoraj
- Department of Epizootiology, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13 Str., 10-718 Olsztyn, Poland;
- Correspondence:
| | - Klaudia Kończyk-Kmiecik
- Department of Epizootiology, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13 Str., 10-718 Olsztyn, Poland;
| | - Tadeusz Bakuła
- Department of Veterinary Prevention and Feed Hygiene, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego 13 Str., 10-718 Olsztyn, Poland;
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Analysis of Yersinia pseudotuberculosis Isolates Recovered from Deceased Mammals of a German Zoo Animal Collection. J Clin Microbiol 2021; 59:JCM.03125-20. [PMID: 33789956 PMCID: PMC8315957 DOI: 10.1128/jcm.03125-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/19/2021] [Indexed: 11/20/2022] Open
Abstract
Yersinia pseudotuberculosis is an important pathogen for both humans and animals. It can infect livestock, as well as pets and wild animals. During recent years, a number of reports have described the isolation of Y. pseudotuberculosis from zoo animals, mainly birds and mammals, for which the infection was mostly lethal. Between 2005 and 2019, there were at least 17 cases of deceased mammals, belonging to five different species, which suffered from a Y. pseudotuberculosis infection at the Zoo Wuppertal, Germany. Since only scarce information exists on the properties of Y. pseudotuberculosis from zoo animals, we characterized eight isolates, covering all infected species, in detail. All isolates were members of biotype 1, but belonged to five serotypes, five sequence types (STs), and seven core-genome multilocus sequence types (cgMLSTs). Using pulsed-field gel electrophoresis (PFGE) analysis and whole-genome sequencing (WGS), the seven isolates could be discriminated from each other. They differed significantly regarding their virulence genes and mobile genetic elements. While the virulence plasmid pYV existed in all serotypes (five isolates), a complete high-pathogenicity island (HPI) was detected only in the serotypes O:1a, O:1b, and O:13 (four isolates), but not in O:2a and O:2b. Similarly, the content of other plasmids and prophages varied greatly between the isolates. The data demonstrate that the deceased mammals were infected by seven individual isolates and not by a single type predominating in the zoo animals.
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Nguyen SV, Cunningham SA, Jeraldo P, Tran A, Patel R. Yersinia occitanica is a later heterotypic synonym of Yersinia kristensenii subsp. rochesterensis and elevation of Yersinia kristensenii subsp. rochesterensis to species status. Int J Syst Evol Microbiol 2021; 71. [PMID: 33406034 DOI: 10.1099/ijsem.0.004626] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of Yersinia kristensenii subsp. rochesterensis and Yersinia occitanica was re-evaluated by genomic analysis. Average nucleotide identity (ANI), digital DNA-DNA hybridization values, and phylogenetic analyses of the type strains indicate that Y. kristensenii subsp. rochesterensis and Y. occitanica are the same genospecies. Additionally, the overall genomic relatedness index (OGRI) values reveal that Y. kristensenii subsp. rochesterensis should be elevated to species status as Yersinia rochesterensis sp. nov.
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Affiliation(s)
- Scott Van Nguyen
- District of Columbia Department of Forensic Sciences, Public Health Laboratory Division, Washington, District of Columbia, USA
| | - Scott A Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Rochester, Minnesota, USA
| | - Patricio Jeraldo
- Microbiome Program, Center for Individualized Medicine, Rochester, Minnesota, USA.,Department of Surgery, Rochester, Minnesota, USA
| | - Anthony Tran
- District of Columbia Department of Forensic Sciences, Public Health Laboratory Division, Washington, District of Columbia, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Rochester, Minnesota, USA.,Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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5
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Le Guern AS, Savin C, Angermeier H, Brémont S, Clermont D, Mühle E, Orozova P, Najdenski H, Pizarro-Cerdá J. Yersinia artesiana sp. nov., Yersinia proxima sp. nov., Yersinia alsatica sp. nov., Yersina vastinensis sp. nov., Yersinia thracica sp. nov. and Yersinia occitanica sp. nov., isolated from humans and animals. Int J Syst Evol Microbiol 2020; 70:5363-5372. [PMID: 32853134 PMCID: PMC7660898 DOI: 10.1099/ijsem.0.004417] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/06/2020] [Indexed: 12/30/2022] Open
Abstract
Thirty-three Yersinia strains previously characterized by the French Yersinia National Reference Laboratory (YNRL) and isolated from humans and animals were suspected to belong to six novel species by a recently described core genome multilocus sequence typing scheme. These strains and five additional strains from the YNRL were characterized using a polyphasic taxonomic approach including a phylogenetic analysis based on 500 core genes, determination of average nucleotide identity (ANI), determination of DNA G+C content and identification of phenotypic features. Phylogenetic analysis confirmed that the 38 studied strains formed six well-demarcated clades. ANI values between these clades and their closest relatives were <94.7 % and ANI values within each putative novel species were >97.5 %. Distinctive biochemical characteristics were identified in five out of the six novel species. All of these data demonstrated that the 38 strains belong to six novel species of the genus Yersinia: Yersinia artesiana sp. nov., type strain IP42281T (=CIP 111845T=DSM 110725T); Yersinia proxima sp. nov., type strain IP37424T (=CIP 111847T=DSM 110727T); Yersinia alsatica sp. nov., type strain IP38850T (=CIP 111848T=DSM 110726T); Yersinia vastinensis sp. nov., type strain IP38594T (=CIP 111844T=DSM 110738T); Yersinia thracica sp. nov., type strain IP34646T (=CIP 111842T=DSM 110736T); and Yersinia occitanica sp. nov., type strain IP35638T (=CIP 111843T=DSM 110739T).
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Affiliation(s)
- Anne-Sophie Le Guern
- Yersinia National Reference Laboratory, Institut Pasteur, F-75724 Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, F-75724 Paris, France
- Yersinia Research Unit, Institut Pasteur, F-75724 Paris, France
| | - Cyril Savin
- Yersinia National Reference Laboratory, Institut Pasteur, F-75724 Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, F-75724 Paris, France
- Yersinia Research Unit, Institut Pasteur, F-75724 Paris, France
- Université de Paris, F-75013, Paris, France
| | - Hilde Angermeier
- Yersinia National Reference Laboratory, Institut Pasteur, F-75724 Paris, France
- European Programme for Public Health Microbiology (EUPHEM), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Sylvie Brémont
- Yersinia National Reference Laboratory, Institut Pasteur, F-75724 Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, F-75724 Paris, France
- Yersinia Research Unit, Institut Pasteur, F-75724 Paris, France
| | | | - Estelle Mühle
- Collection of Institut Pasteur, Institut Pasteur, F-75724 Paris, France
| | - Petya Orozova
- National Reference Laboratory for Fish, Mollusc and Crustacean Diseases, National Diagnostics and Research Veterinary Medical Institute, Sofia, Bulgaria
| | | | - Javier Pizarro-Cerdá
- Yersinia National Reference Laboratory, Institut Pasteur, F-75724 Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, F-75724 Paris, France
- Yersinia Research Unit, Institut Pasteur, F-75724 Paris, France
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Nguyen SV, Muthappa DM, Eshwar AK, Buckley JF, Murphy BP, Stephan R, Lehner A, Fanning S. Comparative genomic insights into Yersinia hibernica - a commonly misidentified Yersinia enterocolitica-like organism. Microb Genom 2020; 6:mgen000411. [PMID: 32701425 PMCID: PMC7643974 DOI: 10.1099/mgen.0.000411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/07/2020] [Indexed: 11/18/2022] Open
Abstract
Food-associated outbreaks linked to enteropathogenic Yersinia enterocolitica are of concern to public health. Pigs and their meat are recognized risk factors for transmission of Y. enterocolitica. This study aimed to describe the comparative genomics of Y. enterocolitica along with a number of misclassified Yersinia isolates, now constituting the recently described Yersinia hibernica. The latter was originally cultured from an environmental sample taken at a pig slaughterhouse. Unique features were identified in the genome of Y. hibernica, including a novel integrative conjugative element (ICE), denoted as ICEYh-1 contained within a 255 kbp region of plasticity. In addition, a zebrafish embryo infection model was adapted and applied to assess the virulence potential among Yersinia isolates including Y. hibernica.
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Affiliation(s)
- Scott Van Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Dechamma Mundanda Muthappa
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Athmanya K. Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - James F. Buckley
- Veterinary Food Safety Laboratory, Cork County Council, Inniscarra, Co. Cork and Department of Microbiology, National University of Ireland, Cork, College Road, Cork, Ireland
| | - Brenda P. Murphy
- Veterinary Food Safety Laboratory, Cork County Council, Inniscarra, Co. Cork and Department of Microbiology, National University of Ireland, Cork, College Road, Cork, Ireland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
- Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5AG, UK
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7
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Two copies of the ail gene found in Yersinia enterocolitica and Yersinia kristensenii. Vet Microbiol 2020; 247:108798. [PMID: 32768239 DOI: 10.1016/j.vetmic.2020.108798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/07/2020] [Accepted: 07/11/2020] [Indexed: 12/20/2022]
Abstract
Yersinia enterocolitica is the most common Yersinia species causing foodborne infections in humans. Pathogenic strains carry the chromosomal ail gene, which is essential for bacterial attachment to and invasion into host cells and for serum resistance. This gene is commonly amplified in several PCR assays detecting pathogenic Y. enterocolitica in food samples and discriminating pathogenic isolates from non-pathogenic ones. We have isolated several non-pathogenic ail-positive Yersinia strains from various sources in Finland. For this study, we selected 16 ail-positive Yersinia strains, which were phenotypically and genotypically characterised. Eleven strains were confirmed to belong to Y. enterocolitica and five strains to Yersinia kristensenii using whole-genome alignment, Parsnp and the SNP phylogenetic tree. All Y. enterocolitica strains belonged to non-pathogenic biotype 1A. We found two copies of the ail gene (ail1 and ail2) in all five Y. kristensenii strains and in one Y. enterocolitica biotype 1A strain. All 16 Yersinia strains carried the ail1 gene consisting of three different sequence patterns (A6-A8), which were highly similar with the ail gene found in high-pathogenic Y. enterocolitica biotype 1B strains (A2). The Ail protein encoded by the ail1 gene was highly conserved compared to the Ail protein encoded by the ail2 gene. Multiple sequence alignment of the ail gene and Ail protein were conducted with MAFF. In total, 10 ail sequence variations have been identified, of which 8 conserved ones belonged to the ail1 gene. According to our results, the detection of ail alone is not sufficient to predict the pathogenicity of Yersinia isolates.
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Nguyen SV, Greig DR, Hurley D, Donoghue O, Cao Y, McCabe E, Mitchell M, Schaffer K, Jenkins C, Fanning S. Yersinia canariae sp. nov., isolated from a human yersiniosis case. Int J Syst Evol Microbiol 2020; 70:2382-2387. [DOI: 10.1099/ijsem.0.004047] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A Gram-negative rod from the
Yersinia
genus was isolated from a clinical case of yersiniosis in the United Kingdom. Long read sequencing data from an Oxford Nanopore Technologies (ONT) MinION in conjunction with Illumina HiSeq reads were used to generate a finished quality genome of this strain. Overall Genome Related Index (OGRI) of the strain was used to determine that it was a novel species within
Yersinia
, despite biochemical similarities to
Yersinia enterocolitica
. The 16S ribosomal RNA gene accessions are MN434982-MN434987 and the accession number for the complete and closed chromosome is CP043727. The type strain is SRR7544370T (=NCTC 14382T/=LMG 31573T).
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Affiliation(s)
- Scott V. Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - David R. Greig
- National Infection Services, Public Health England, 61 Colindale Avenue, London NW9 5HT, UK
| | - Daniel Hurley
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Orla Donoghue
- Department of Microbiology, St Vincent's University Hospital, 196 Merrion Road, Elm Park, Dublin D04 T6F4, Ireland
| | - Yu Cao
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Evonne McCabe
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Molly Mitchell
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Kirsten Schaffer
- Department of Microbiology, St Vincent's University Hospital, 196 Merrion Road, Elm Park, Dublin D04 T6F4, Ireland
| | - Claire Jenkins
- National Infection Services, Public Health England, 61 Colindale Avenue, London NW9 5HT, UK
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
- Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
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Type III Secretion Effectors with Arginine N-Glycosyltransferase Activity. Microorganisms 2020; 8:microorganisms8030357. [PMID: 32131463 PMCID: PMC7142665 DOI: 10.3390/microorganisms8030357] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 01/31/2023] Open
Abstract
Type III secretion systems are used by many Gram-negative bacterial pathogens to inject proteins, known as effectors, into the cytosol of host cells. These virulence factors interfere with a diverse array of host signal transduction pathways and cellular processes. Many effectors have catalytic activities to promote post-translational modifications of host proteins. This review focuses on a family of effectors with glycosyltransferase activity that catalyze addition of N-acetyl-d-glucosamine to specific arginine residues in target proteins, leading to reduced NF-κB pathway activation and impaired host cell death. This family includes NleB from Citrobacter rodentium, NleB1 and NleB2 from enteropathogenic and enterohemorrhagic Escherichia coli, and SseK1, SseK2, and SseK3 from Salmonella enterica. First, we place these effectors in the general framework of the glycosyltransferase superfamily and in the particular context of the role of glycosylation in bacterial pathogenesis. Then, we provide detailed information about currently known members of this family, their role in virulence, and their targets.
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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: 18] [Impact Index Per Article: 3.6] [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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