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Pires J, Brandal LT, Naseer U. Development and implementation of a core genome multilocus sequence typing scheme for Yersinia enterocolitica: a tool for surveillance and outbreak detection. J Clin Microbiol 2024:e0004024. [PMID: 38990041 DOI: 10.1128/jcm.00040-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/06/2024] [Indexed: 07/12/2024] Open
Abstract
Yersinia enterocolitica (Y. enterocolitica) is the most frequent etiological agent of yersiniosis and has been responsible for several national outbreaks in Norway and elsewhere. A standardized high-resolution method, such as core genome Multilocus Sequence Typing (cgMLST), is needed for pathogen traceability at the national and international levels. In this study, we developed and implemented a cgMLST scheme for Y. enterocolitica. We designed a cgMLST scheme in SeqSphere + using high-quality genomes from different Y. enterocolitica biotype sublineages. The scheme was validated if more than 95% of targets were found across all tested Y. enterocolitica: 563 Norwegian genomes collected between 2012 and 2022 and 327 genomes from public data sets. We applied the scheme to known outbreaks to establish a threshold for identifying major complex types (CTs) based on the number of allelic differences. The final cgMLST scheme included 2,582 genes with a median of 97.9% (interquartile range 97.6%-98.8%) targets found across all tested genomes. Analysis of outbreaks identified all outbreak strains using single linkage clustering at four allelic differences. This threshold identified 311 unique CTs in Norway, of which CT18, CT12, and CT5 were identified as the most frequently associated with outbreaks. The cgMLST scheme showed a very good performance in typing Y. enterocolitica using diverse data sources and was able to identify outbreak clusters. We recommend the implementation of this scheme nationally and internationally to facilitate Y. enterocolitica surveillance and improve outbreak response in national and cross-border outbreaks.
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Affiliation(s)
- Joao Pires
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
- ECDC Fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Lin T Brandal
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Umaer Naseer
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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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 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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Powell J, Daly M, O'Connell NH, Dunne CP. Seek and you shall find: Yersinia enterocolitica in Ireland's drinking water. Ir J Med Sci 2024:10.1007/s11845-024-03641-5. [PMID: 38381378 DOI: 10.1007/s11845-024-03641-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
INTRODUCTION Three Yersinia species were identified from samples of drinking water from diverse geographic regions of Ireland. Conventional commercial biochemical identification systems classified them as Yersinia enterocolitica. Since this organism is the most common cause of bacterial gastroenteritis in some countries, further investigation was warranted. The aim of the study was to provide a microbial characterisation of three Yersinia species, to determine their pathogenicity, and to review the incidence rate of Yersinia enterocolitica detection in our region. METHODS Organism identification was performed using conventional commercial diagnostic systems MALDI-TOF, API 20E, API 50CHE, TREK Sensititre GNID and Vitek 2 GN, and whole genome sequencing (WGS) was performed. Historical data for detections was extracted from the lab system for 2008 to 2023. RESULTS All three isolates gave "good" identifications of Yersinia enterocolitica on conventional systems. Further analysis by WGS matched two of the isolates with recently described Yersinia proxima, and the third was a member of the non-pathogenic Yersinia enterocolitica clade 1Aa. DISCUSSION Our analysis of these three isolates deemed them to be Yersinia species not known currently to be pathogenic, but determining this necessitated the use of next-generation sequencing and advanced bioinformatics. Our work highlights the importance of having this technology available to public laboratories, either locally or in a national reference laboratory. The introduction of molecular technologies for the detection of Yersinia species may increase the rate of detections. Accurate identification of significant pathogens in environmental, public health and clinical microbiology laboratories is critically important for the protection of society.
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Affiliation(s)
- James Powell
- Department of Microbiology, University Hospital Limerick, Limerick, Ireland
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4I), University of Limerick, Limerick, Ireland
| | - Maureen Daly
- Department of Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Nuala H O'Connell
- Department of Microbiology, University Hospital Limerick, Limerick, Ireland
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4I), University of Limerick, Limerick, Ireland
| | - Colum P Dunne
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity (4I), University of Limerick, Limerick, Ireland.
- School of Medicine, University of Limerick, Limerick, Ireland.
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Lemarignier M, Savin C, Lê-Bury P, Dussurget O, Pizarro-Cerdá J. Complete genome sequence of Yersinia pseudotuberculosis strain SP-1303 from lineage 8, associated with Far East scarlet-like fever. Microbiol Resour Announc 2023; 12:e0083823. [PMID: 37906029 PMCID: PMC10652917 DOI: 10.1128/mra.00838-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
We report the complete genome sequence of Yersinia pseudotuberculosis strain SP-1303, identified as part of lineage 8 and associated with Far East scarlet-like fever. The genome includes the chromosome, the Yersinia-virulence plasmid (pYV) encoding a type III secretion system essential for virulence, the pVM82 plasmid, and two cryptic plasmids.
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Affiliation(s)
- Marion Lemarignier
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, Ile de France, France
| | - Cyril Savin
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, Ile de France, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-140, Paris, Île-de-France, France
| | - Pierre Lê-Bury
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, Ile de France, France
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, Ile de France, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, Ile de France, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-140, Paris, Île-de-France, France
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Huang S, Li Y, Hong C, Jin Y, Li S, Xu X, Xia Y, Zhang L, Lou Y, Guan W. Whole-genome sequencing-based analysis of antimicrobial resistance, virulence factors, and genetic diversity in Yersinia isolated in Wenzhou, China 2020. Mol Phylogenet Evol 2023; 188:107903. [PMID: 37574177 DOI: 10.1016/j.ympev.2023.107903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/20/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Yersinia spp. vary significantly in their ability to cause diseases that threaten public health. Their pathogenicity is frequently associated with increasing antimicrobial resistance (AMR) and various virulence factors. The aim of the study was to investigate the AMR genes, virulence factors, and genetic diversity of Yersinia strains isolated from meats and fish in Wenzhou in 2020 by using whole-genome sequencing (WGS). A total of 50 isolates were collected. The phylogenetic relationships among the Yersinia species were also analyzed using multilocus sequence typing (MLST), core genome multi-locus sequence typing (cgMLST), and single nucleotide polymorphism (SNP) analysis. According to the results, all the strains could be classified into five species, with most isolated from beef, followed by poultry, pork, and fish. AMR genes were identified in 23 strains. And the qnrD1 genes were all located in the Col3M plasmid. Virulence genes, such as yaxA, ystB, pla, and yplA, were also found in the 15 Y. enterocolitica strains. And this study also found the presence of icm/dot type IVB-related genes in one Yersinia massiliensis isolate. MLST analysis identified 43 sequence types (STs), 19 of which were newly detected in Yersinia. Moreover, cgMLST analysis revealed that no dense genotype clusters were formed (cgMLST 5341, 5344, 5346-5350, 5353-5390). Instead, the strains appeared to be dispersed over large distances, except when multiple isolates shared the same ST. Isolates Y4 and Y26 were closely related to strains originating from South Korea and Denmark. This study showed considerable diversity in Yersinia spp. isolated from local areas (Wenzhou City). The data generated in our study may enrich the molecular traceability database of Yersinia and provide a basis for the development of more effective antipathogen control strategies.
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Affiliation(s)
- Shaojie Huang
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Yi Li
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China.
| | - Chengji Hong
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China.
| | - Yafang Jin
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Shengkai Li
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Xuelian Xu
- Yuhang Center for Disease Control and Prevention, Yuhang, China.
| | - Yanmei Xia
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Leyi Zhang
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China.
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Wanchun Guan
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
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Łada P, Kończyk-Kmiecik K, Bancerz-Kisiel A. Isolation, characterization and antimicrobial resistance of Yersinia enterocolitica from Polish cattle and their carcasses. BMC Vet Res 2023; 19:143. [PMID: 37670289 PMCID: PMC10478351 DOI: 10.1186/s12917-023-03700-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Yersinia enterocolitica is a heterogeneous bacterial species that has been divided into six biotypes and more than 70 serotypes. Each year, the European Food Safety Authority classifies yersiniosis caused by Y. enterocolitica as one of the most important zoonotic diseases. The prevalence of Y. enterocolitica in cattle has not been thoroughly analyzed in Poland, and beef and bovine carcasses contaminated with antimicrobial resistant Y. enterocolitica pose a health risk for both, farm workers and consumers. Therefore, the aim of this study was to evaluate the prevalence of Y. enterocolitica in cattle and to determine the antimicrobial susceptibility of the isolated strains. RESULTS A total of 1020 samples were analyzed, including 660 rectal swabs collected from live cattle and 360 swabs from cold-stored beef carcasses. The results of this study indicate that Y. enterocolitica was isolated from three of the 15 examined cattle herds and the prevalence within these herds ranged from 0% to nearly 32%. Y. enterocolitica was isolated from 14.7% of the examined heifers, 7.4% of calves and 5.5% of adult cows. More than 65% of the strains were isolated from cold enrichment. The strains isolated from live cattle tested positive for the ystB gene, while ail and ystA genes were not found. Most of the isolated strains belonged to bioserotype 1A/NT. The majority of the isolated strains were resistant to ampicillin, cefalexin and amoxicillin with clavulanic acid, however these are expected phenotypes for Y. enterocolitica. CONCLUSIONS The results of this study indicate that Y. enterocolitica is present in cattle herds in Poland. The strains isolated from live cattle were ystB-positive, most of them belonged to bioserotype 1A/NT. The prevalence of Y. enterocolitica strains was generally low in cold-stored beef carcasses.
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Affiliation(s)
- Piotr Łada
- Department of Epizootiology, Faculty of Veterinary Medicine, University of Warmia and Mazury, Oczapowskiego 2 St, 10-719 Olsztyn, Poland
| | - Klaudia Kończyk-Kmiecik
- Department of Epizootiology, Faculty of Veterinary Medicine, University of Warmia and Mazury, Oczapowskiego 2 St, 10-719 Olsztyn, Poland
| | - Agata Bancerz-Kisiel
- Department of Epizootiology, Faculty of Veterinary Medicine, University of Warmia and Mazury, Oczapowskiego 2 St, 10-719 Olsztyn, Poland
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Piras F, Siddi G, Le Guern AS, Brémont S, Fredriksson-Ahomaa M, Sanna R, Meloni MP, De Santis EPL, Scarano C. Traceability, virulence and antimicrobial resistance of Yersinia enterocolitica in two industrial cheese-making plants. Int J Food Microbiol 2023; 398:110225. [PMID: 37126899 DOI: 10.1016/j.ijfoodmicro.2023.110225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023]
Abstract
Between 2018 and 2019, 309 environmental and food samples were collected from two industrial cheese-making plants located in Sardinia, in order to investigate Y. enterocolitica presence and to characterize the isolates. Y. enterocolitica isolates were further compared with isolates detected during a previous investigation from sheep and goat raw milk samples. Y. enterocolitica was detected in 7.4 % of the samples and the prevalence was higher, even if not significantly (P > 0.05) higher in non-food contact surface samples (10.2 %) than in food contact surface samples (3.8 %). The highest prevalence was detected in floor samples (13.5 %), followed by drain samples (7.2 %), which might serve as main harborage sites for further contamination. Y. enterocolitica was also detected in food contact surfaces, namely shelves of the Ricotta cooling room and packaging room, one cheese cutting machine surface and one raw milk filter sample. The biotype 1A isolates identified in this study were classified into six different serotypes. Additionally, a bioserotype 2/O:5,27 isolate was identified in one goat milk sample. All 1A isolates possessed the virulence genes invA and ystB while the 2/O:5,27 isolate showed the presence of ail, ystA, invA and yadA genes, thus confirming a pathogenic potential. The isolates showed intrinsic resistance to amoxicillin-clavulanic acid, ticarcillin and cefoxitin due to the presence of the blaA gene. Whole genome sequencing allowed to identify seven different sequence types among the 1A isolates, thus showing a high genetic diversity. The same Y. enterocolitica sequence type (ST3) was detected from three different areas of the same cheese-making plant, indicating a possible transfer of the microorganism along the processing lines. Y. enterocolitica contamination in cheese-making plants can pose a risk to human health. Preventive measures include the hygienic design of the plant layout and equipment, in association with proper cleaning and disinfection programmes.
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Affiliation(s)
- Francesca Piras
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy.
| | - Giuliana Siddi
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Anne-Sophie Le Guern
- Yersinia Research Unit and National Reference Laboratory for Plague and other Yersiniosis, Institut Pasteur, 28 Rue du Docteur Roux, 75724 Paris, France
| | - Sylvie Brémont
- Yersinia Research Unit and National Reference Laboratory for Plague and other Yersiniosis, Institut Pasteur, 28 Rue du Docteur Roux, 75724 Paris, France
| | - Maria Fredriksson-Ahomaa
- Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, 00790 Helsinki, Finland
| | - Rita Sanna
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Maria Pina Meloni
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | | | - Christian Scarano
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
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Yue Y, Zheng J, Sheng M, Liu X, Hao Q, Zhang S, Xu S, Liu Z, Hou X, Jing H, Liu Y, Zhou X, Li Z. Public health implications of Yersinia enterocolitica investigation: an ecological modeling and molecular epidemiology study. Infect Dis Poverty 2023; 12:41. [PMID: 37085902 PMCID: PMC10120104 DOI: 10.1186/s40249-023-01063-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 02/05/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Yersinia enterocolitica has been sporadically recovered from animals, foods, and human clinical samples in various regions of Ningxia, China. However, the ecological and molecular characteristics of Y. enterocolitica, as well as public health concerns about infection in the Ningxia Hui Autonomous Region, remain unclear. This study aims to analyze the ecological and molecular epidemiological characteristics of Y. enterocolitis in order to inform the public health intervention strategies for the contains of related diseases. METHODS A total of 270 samples were collected for isolation [animals (n = 208), food (n = 49), and patients (n = 13)], then suspect colonies were isolated and identified by the API20E biochemical identification system, serological tests, biotyping tests, and 16S rRNA-PCR. Then, we used an ecological epidemiological approach combined with machine learning algorithms (general linear model, random forest model, and eXtreme Gradient Boosting) to explore the associations between ecological factors and the pathogenicity of Y. enterocolitis. Furthermore, average nucleotide identity (ANI) estimation, single nucleotide polymorphism (SNP), and core gene multilocus sequence typing (cgMLST) were applied to characterize the molecular profile of isolates based on whole genome sequencing. The statistical test used single-factor analysis, Chi-square tests, t-tests/ANOVA-tests, Wilcoxon rank-sum tests, and Kruskal-Wallis tests. RESULTS A total of 270 isolates of Yersinia were identified from poultry and livestock (n = 191), food (n = 49), diarrhoea patients (n = 13), rats (n = 15), and hamsters (n = 2). The detection rates of samples from different hosts were statistically different (χ2 = 22.636, P < 0.001). According to the relatedness clustering results, 270 isolates were divided into 12 species, and Y. enterocolitica (n = 187) is a predominated species. Pathogenic isolates made up 52.4% (98/187), while non-pathogenic isolates made up 47.6% (89/187). Temperature and precipitation were strongly associated with the pathogenicity of the isolates (P < 0.001). The random forest (RF) prediction model showed the best performance. The prediction result shows a high risk of pathogenicity Y. enterocolitica was located in the northern, northwestern, and southern of the Ningxia Hui Autonomous Region. The Y. enterocolitica isolates were classified into 54 sequence types (STs) and 125 cgMLST types (CTs), with 4/O:3 being the dominant bioserotype in Ningxia. The dominant STs and dominant CTs of pathogenic isolates in Ningxia were ST429 and HC100_2571, respectively. CONCLUSIONS The data indicated geographical variations in the distribution of STs and CTs of Y. enterocolitica isolates in Ningxia. Our work offered the first evidence that the pathogenicity of isolates was directly related to fluctuations in temperature and precipitation of the environment. CgMLST typing strategies showed that the isolates were transmitted to the population via pigs and food. Therefore, strengthening health surveillance on pig farms in high-risk areas and focusing on testing food of pig origin are optional strategies to prevent disease outbreaks.
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Affiliation(s)
- Yuan Yue
- Key Laboratory of the Ministry of Education for the Conservation and Utilization of Special Biological Resources of Western China, Ningxia University, Yinchuan, People's Republic of China
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
- Ningxia Hui Autonomous Region Food Testing and Research Institute, Yinchuan, People's Republic of China
| | - Jinxin Zheng
- Department of Nephrology, Ruijin Hospital, Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- School of Global Health, Chinese Center for Tropical Diseases Research-Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Mei Sheng
- Ningxia Hui Autonomous Region Centre for Disease Control and Prevention, Yinchuan, People's Republic of China
| | - Xiang Liu
- Ningxia Hui Autonomous Region Centre for Disease Control and Prevention, Yinchuan, People's Republic of China
| | - Qiong Hao
- Ningxia Hui Autonomous Region Centre for Disease Control and Prevention, Yinchuan, People's Republic of China
| | - Shunxian Zhang
- School of Global Health, Chinese Center for Tropical Diseases Research-Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Shuai Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zhiguo Liu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Xuexin Hou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Huaiqi Jing
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yang Liu
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, Special Administrative Region, People's Republic of China
| | - Xuezhang Zhou
- Key Laboratory of the Ministry of Education for the Conservation and Utilization of Special Biological Resources of Western China, Ningxia University, Yinchuan, People's Republic of China.
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
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Wang YY, Xie L, Zhang WZ, Du XL, Li WG, Bia LL, Cui ZG, Wu Y, Lu JX. Application of a core genome sequence typing (cgMLST) pipeline for surveillance of Clostridioides difficile in China. Front Cell Infect Microbiol 2023; 13:1109153. [PMID: 36992688 PMCID: PMC10040748 DOI: 10.3389/fcimb.2023.1109153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/28/2023] [Indexed: 03/14/2023] Open
Abstract
IntroductionClostridioides difficile (C. difficile) is a nosocomial bacterial pathogen that causes antibiotic-associated diarrhea mediated by cellular exotoxins secreted into the intestine during bacterial growth. Multilocus sequence typing (MLST) and PCR ribotyping are the main molecular typing for C. difficile. Whole genome sequencing (WGS) core genome multilocus sequence typing (cgMLST) was developed for genetic evolution and outbreak investigation of C. difficile with higher precision and accuracy.MethodsA total of 699 whole (complete and draft) genome sequences of distinct C. difficile strains were used in this study to identify core gene set (2469 core genes) and the cgMLST scheme for the phylogeny analysis of C. difficile. This cgMLST pipeline was then carried the Chinese Pathogen Identification Net (China PIN) for surveillance of C. difficile in China. Within the China PIN, 195 WGS of C. difficile and an outbreak of CDI with 12 WGS of C. difficile were used to evaluate the cgMLST pipeline.ResultsThe result displayed that mostly tested C. difficile isolates could be successfully divided into 5 classic clades and the outbreak event was also successfully identified.DiscussionThe results are meaningful and offer a practicable pipeline for a national-wide surveillance of C. difficile in China.
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Affiliation(s)
- Yuan Yuan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lu Xie
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - Wen Zhu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiao li Du
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wen Ge Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lu Lu Bia
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhi Gang Cui
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
- *Correspondence: Yuan Wu,
| | - Jin Xing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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10
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Lê-Bury P, Druart K, Savin C, Lechat P, Mas Fiol G, Matondo M, Bécavin C, Dussurget O, Pizarro-Cerdá J. Yersiniomics, a Multi-Omics Interactive Database for Yersinia Species. Microbiol Spectr 2023; 11:e0382622. [PMID: 36847572 PMCID: PMC10100798 DOI: 10.1128/spectrum.03826-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/26/2023] [Indexed: 03/01/2023] Open
Abstract
The genus Yersinia includes a large variety of nonpathogenic and life-threatening pathogenic bacteria, which cause a broad spectrum of diseases in humans and animals, such as plague, enteritis, Far East scarlet-like fever (FESLF), and enteric redmouth disease. Like most clinically relevant microorganisms, Yersinia spp. are currently subjected to intense multi-omics investigations whose numbers have increased extensively in recent years, generating massive amounts of data useful for diagnostic and therapeutic developments. The lack of a simple and centralized way to exploit these data led us to design Yersiniomics, a web-based platform allowing straightforward analysis of Yersinia omics data. Yersiniomics contains a curated multi-omics database at its core, gathering 200 genomic, 317 transcriptomic, and 62 proteomic data sets for Yersinia species. It integrates genomic, transcriptomic, and proteomic browsers, a genome viewer, and a heatmap viewer to navigate within genomes and experimental conditions. For streamlined access to structural and functional properties, it directly links each gene to GenBank, the Kyoto Encyclopedia of Genes and Genomes (KEGG), UniProt, InterPro, IntAct, and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and each experiment to Gene Expression Omnibus (GEO), the European Nucleotide Archive (ENA), or the Proteomics Identifications Database (PRIDE). Yersiniomics provides a powerful tool for microbiologists to assist with investigations ranging from specific gene studies to systems biology studies. IMPORTANCE The expanding genus Yersinia is composed of multiple nonpathogenic species and a few pathogenic species, including the deadly etiologic agent of plague, Yersinia pestis. In 2 decades, the number of genomic, transcriptomic, and proteomic studies on Yersinia grew massively, delivering a wealth of data. We developed Yersiniomics, an interactive web-based platform, to centralize and analyze omics data sets on Yersinia species. The platform allows user-friendly navigation between genomic data, expression data, and experimental conditions. Yersiniomics will be a valuable tool to microbiologists.
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Affiliation(s)
- Pierre Lê-Bury
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
| | - Karen Druart
- Institut Pasteur, Université Paris Cité, CNRS USR2000, Mass Spectrometry for Biology Unit, Proteomic Platform, Paris, France
| | - Cyril Savin
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-140, Paris, France
| | - Pierre Lechat
- Institut Pasteur, Université Paris Cité, ALPS, Bioinformatic Hub, Paris, France
| | - Guillem Mas Fiol
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS USR2000, Mass Spectrometry for Biology Unit, Proteomic Platform, Paris, France
| | | | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Paris, France
- Institut Pasteur, Université Paris Cité, Yersinia National Reference Laboratory, WHO Collaborating Research & Reference Centre for Plague FRA-140, Paris, France
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11
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Sim EM, Koh B, Ng J, Nguyen T, Wang Q, Ginn AN, Brown M, Pham D, Sintchenko V. Case report: a genomics-guided reclassification of a blood culture isolate misassigned by MALDI-TOF as Yersinia pestis. Access Microbiol 2022; 4:acmi000422. [PMID: 36415732 PMCID: PMC9675175 DOI: 10.1099/acmi.0.000422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 08/18/2022] [Indexed: 01/25/2023] Open
Abstract
In this report, we describe a case where Gram-negative rods were isolated from a blood culture which subsequently presented a discordant Yersinia species result by MALDI-TOF. Rapid sequencing provided high-resolution identification of the isolate as Yersinia pseudotuberculosis , which was subsequently confirmed by biochemical tests.
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Affiliation(s)
- Eby M. Sim
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia,*Correspondence: Eby M. Sim,
| | - Bryant Koh
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Jimmy Ng
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Trang Nguyen
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Andrew N. Ginn
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
| | - Mitchell Brown
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - David Pham
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia,Centre for Infectious Diseases and Microbiology- Public Health, Westmead Hospital, Sydney, New South Wales, Australia
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12
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Palma F, Mangone I, Janowicz A, Moura A, Chiaverini A, Torresi M, Garofolo G, Criscuolo A, Brisse S, Di Pasquale A, Cammà C, Radomski N. In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes. BMC Genomics 2022; 23:235. [PMID: 35346021 PMCID: PMC8961897 DOI: 10.1186/s12864-022-08437-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/28/2022] [Indexed: 02/02/2023] Open
Abstract
Background Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles. Methods We used three L. monocytogenes reference genomes from different phylogenetic lineages and assessed the impact of in vitro (i.e. tested genomes, successive platings, replicates of DNA extraction and sequencing) and in silico parameters (i.e. targeted depth of coverage, depth of coverage, breadth of coverage, assembly metrics, cgMLST workflows, cgMLST completeness) on cgMLST precision made of 1748 core loci. Six cgMLST workflows were tested, comprising assembly-based (BIGSdb, INNUENDO, GENPAT, SeqSphere and BioNumerics) and assembly-free (i.e. kmer-based MentaLiST) allele callers. Principal component analyses and generalized linear models were used to identify the most impactful parameters on cgMLST precision. Results The isolate’s genetic background, cgMLST workflows, cgMLST completeness, as well as depth and breadth of coverage were the parameters that impacted most on cgMLST precision (i.e. identical alleles against reference circular genomes). All workflows performed well at ≥40X of depth of coverage, with high loci detection (> 99.54% for all, except for BioNumerics with 97.78%) and showed consistent cluster definitions using the reference cut-off of ≤7 allele differences. Conclusions This highlights that bioinformatics workflows dedicated to cgMLST allele calling are largely robust when paired-end reads are of high quality and when the sequencing depth is ≥40X. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08437-4.
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13
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What do we know about osmoadaptation of Yersinia pestis? Arch Microbiol 2021; 204:11. [PMID: 34878588 DOI: 10.1007/s00203-021-02610-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 10/19/2022]
Abstract
The plague agent Yersinia pestis mainly spreads among mammalian hosts and their associated fleas. Production of a successful mammal-flea-mammal life cycle implies that Y. pestis senses and responds to distinct cues in both host and vector. Among these cues, osmolarity is a fundamental parameter. The plague bacillus lives in a tightly regulated environment in the mammalian host, while osmolarity fluctuates in the flea gut (300-550 mOsM). Here, we review the mechanisms that enable Y. pestis to perceive fluctuations in osmolarity, as well as genomic plasticity and physiological adaptation of the bacterium to this stress.
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14
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Abdel-Glil MY, Fischer U, Steinhagen D, McCarthy U, Neubauer H, Sprague LD. Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis. Front Microbiol 2021; 12:782415. [PMID: 34867924 PMCID: PMC8640586 DOI: 10.3389/fmicb.2021.782415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM), a serious infection that affects global aquaculture with high economic impact. The present study used whole genome sequences to perform a comparative analysis on 10 Y. ruckeri strains and to explore their genetic relatedness to other members of the genus. Y. ruckeri, Yersinia entomophaga, and Yersinia nurmii formed a species complex that constitutes the most basal lineage of the genus. The results showed that the taxonomy of Y. ruckeri strains is better defined by using a core genome alignment and phylogenetic analysis. The distribution of accessory genes in all Yersinia species revealed the presence of 303 distinctive genes in Y. ruckeri. Of these, 169 genes were distributed in 17 genomic islands potentially involved in the pathogenesis of ERM via (1) encoding virulence factors such as Afp18, Yrp1, phage proteins and (2) improving the metabolic capabilities by enhancing utilization and metabolism of iron, amino acids (specifically, arginine and histidine), and carbohydrates. The genome of Y. ruckeri is highly conserved regarding gene structure, gene layout and functional categorization of genes. It contains various components of mobile genetic elements but lacks the CRISPR-Cas system and possesses a stable set of virulence genes possibly playing a critical role in pathogenicity. Distinct virulence plasmids were exclusively restricted to a specific clonal group of Y. ruckeri (CG4), possibly indicating a selective advantage. Phylogenetic analysis of Y. ruckeri genomes revealed the co-presence of multiple genetically distant lineages of Y. ruckeri strains circulating in Germany. Our results also suggest a possible dissemination of a specific group of strains in the United States, Peru, Germany, and Denmark. In conclusion, this study provides new insights into the taxonomy and evolution of Y. ruckeri and contributes to a better understanding of the pathogenicity of ERM in aquaculture. The genomic analysis presented here offers a framework for the development of more efficient control strategies for this pathogen.
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Affiliation(s)
- Mostafa Y Abdel-Glil
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | - Uwe Fischer
- Friedrich-Loeffler-Institut, Institute of Infectiology, Greifswald-Insel Riems, Germany
| | - Dieter Steinhagen
- Fish Disease Research Unit, Institute for Parasitology, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Una McCarthy
- Marine Laboratory, Marine Scotland, Aberdeen, United Kingdom
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
| | - Lisa D Sprague
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Jena, Germany
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15
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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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A Whole-Genome-Based Gene-by-Gene Typing System for Standardized High-Resolution Strain Typing of Bacillus anthracis. J Clin Microbiol 2021; 59:e0288920. [PMID: 33827898 PMCID: PMC8218748 DOI: 10.1128/jcm.02889-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequencing (WGS) has been established for bacterial subtyping and is regularly used to study pathogen transmission, to investigate outbreaks, and to perform routine surveillance. Core-genome multilocus sequence typing (cgMLST) is a bacterial subtyping method that uses WGS data to provide a high-resolution strain characterization. This study aimed at developing a novel cgMLST scheme for Bacillus anthracis, a notorious pathogen that causes anthrax in livestock and humans worldwide. The scheme comprises 3,803 genes that were conserved in 57 B. anthracis genomes spanning the whole phylogeny. The scheme has been evaluated and applied to 584 genomes from 50 countries. On average, 99.5% of the cgMLST targets were detected. The cgMLST results confirmed the classical canonical single-nucleotide-polymorphism (SNP) grouping of B. anthracis into major clades and subclades. Genetic distances calculated based on cgMLST were comparable to distances from whole-genome-based SNP analysis with similar phylogenetic topology and comparable discriminatory power. Additionally, the application of the cgMLST scheme to anthrax outbreaks from Germany and Italy led to a definition of a cutoff threshold of five allele differences to trace epidemiologically linked strains for cluster typing and transmission analysis. Finally, the association of two clusters of B. anthracis with human cases of injectional anthrax in four European countries was confirmed using cgMLST. In summary, this study presents a novel cgMLST scheme that provides high-resolution strain genotyping for B. anthracis. This scheme can be used in parallel with SNP typing methods to facilitate rapid and harmonized interlaboratory comparisons, essential for global surveillance and outbreak analysis. The scheme is publicly available for application by users, including those with little bioinformatics knowledge.
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Shevtsov V, Kairzhanova A, Shevtsov A, Shustov A, Kalendar R, Abdrakhmanov S, Lukhnova L, Izbanova U, Ramankulov Y, Vergnaud G. Genetic diversity of Francisella tularensis subsp. holarctica in Kazakhstan. PLoS Negl Trop Dis 2021; 15:e0009419. [PMID: 33999916 PMCID: PMC8158875 DOI: 10.1371/journal.pntd.0009419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/27/2021] [Accepted: 04/29/2021] [Indexed: 11/29/2022] Open
Abstract
Tularemia is a highly dangerous zoonotic infection due to the bacteria Francisella tularensis. Low genetic diversity promoted the use of polymorphic tandem repeats (MLVA) as first-line assay for genetic description. Whole genome sequencing (WGS) is becoming increasingly accessible, opening the perspective of a time when WGS might become the universal genotyping assay. The main goal of this study was to describe F. tularensis strains circulating in Kazakhstan based on WGS data and develop a MLVA assay compatible with in vitro and in silico analysis. In vitro MLVA genotyping and WGS were performed for the vaccine strain and for 38 strains isolated in Kazakhstan from natural water bodies, ticks, rodents, carnivores, and from one migratory bird, an Isabellina wheatear captured in a rodent burrow. The two genotyping approaches were congruent and allowed to attribute all strains to two F. tularensis holarctica lineages, B.4 and B.12. The seven tandem repeats polymorphic in the investigated strain collection could be typed in a single multiplex PCR assay. Identical MLVA genotypes were produced by in vitro and in silico analysis, demonstrating full compatibility between the two approaches. The strains from Kazakhstan were compared to all publicly available WGS data of worldwide origin by whole genome SNP (wgSNP) analysis. Genotypes differing at a single SNP position were collected within a time interval of more than fifty years, from locations separated from each other by more than one thousand kilometers, supporting a role for migratory birds in the worldwide spread of the bacteria. Genotyping of Francisella tularensis has become a routine practice in epidemiology. Despite rapidly accumulating knowledge, the phylogeography of the pathogen is still poorly understood and discussions about geographic and temporal origins continue. One important reason is the poor characterization of the pathogen in many tularemia-endemic countries. This article describes the genetic diversity of Francisella tularensis subsp. holarctica in Kazakhstan using tandem repeat polymorphisms as well as whole genome sequencing. Thirty-nine strains were analyzed and two lineages were identified, namely B.4 and B.12. The study demonstrates a wider distribution of genotype B.4 in Asia, and identified a more basal branching point in this subclade. The obtained data support the Asian origin hypothesis for F. tularensis. The finding of identical genotypes in strains separated in time by decades and a thousand-kilometers geographic distance, confirms the ability of the bacteria for long-term preservation and fast long distances spread. The isolation of F. tularensis subsp. holarctica from the bird species Isabellina wheatear allows speculating about a major contribution of birds to the phylogeography of the pathogen. A genotyping protocol was developed utilizing seven polymorphic tandem repeats, two of which were identified within the framework of this work. The in vitro and in silico results are identical when using sequencing reads of 300 base-pairs or more.
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Affiliation(s)
| | - Alma Kairzhanova
- National Center for Biotechnology, Nur Sultan, Kazakhstan
- S. Seifullin Kazakh Agrotechnical University, Nur Sultan, Kazakhstan
| | - Alexandr Shevtsov
- National Center for Biotechnology, Nur Sultan, Kazakhstan
- * E-mail: (AS); (GV)
| | | | | | | | - Larissa Lukhnova
- National Scientific Center for Especially Dangerous Infections named by Masgut Aykimbayev, Almaty, Kazakhstan
| | - Uinkul Izbanova
- National Scientific Center for Especially Dangerous Infections named by Masgut Aykimbayev, Almaty, Kazakhstan
| | - Yerlan Ramankulov
- National Center for Biotechnology, Nur Sultan, Kazakhstan
- School of Science and Technology Nazarbayev University, Nur Sultan, Kazakhstan
| | - Gilles Vergnaud
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
- * E-mail: (AS); (GV)
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18
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Obtaining Specific Sequence Tags for Yersinia pestis and Visually Detecting Them Using the CRISPR-Cas12a System. Pathogens 2021; 10:pathogens10050562. [PMID: 34066578 PMCID: PMC8148545 DOI: 10.3390/pathogens10050562] [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: 03/24/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022] Open
Abstract
Three worldwide historical plague pandemics resulted in millions of deaths. Yersinia pestis, the etiologic agent of plague, is also a potential bioterrorist weapon. Simple, rapid, and specific detection of Y. pestis is important to prevent and control plague. However, the high similarity between Y. pestis and its sister species within the same genus makes detection work problematic. Here, the genome sequence from the Y. pestis CO92 strain was electronically separated into millions of fragments. These fragments were analyzed and compared with the genome sequences of 539 Y. pestis strains and 572 strains of 20 species within the Yersinia genus. Altogether, 97 Y. pestis-specific tags containing two or more single nucleotide polymorphism sites were screened out. These 97 tags efficiently distinguished Y. pestis from all other closely related species. We chose four of these tags to design a Cas12a-based detection system. PCR–fluorescence methodology was used to test the specificity of these tags, and the results showed that the fluorescence intensity produced by Y. pestis was significantly higher than that of non-Y. pestis (p < 0.0001). We then employed recombinase polymerase amplification and lateral flow dipsticks to visualize the results. Our newly developed plasmid-independent, species-specific library of tags completely and effectively screened chromosomal sequences. The detection limit of our four-tag Cas12a system reached picogram levels.
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19
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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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20
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Rivas L, Strydom H, Paine S, Wang J, Wright J. Yersiniosis in New Zealand. Pathogens 2021; 10:191. [PMID: 33578727 PMCID: PMC7916520 DOI: 10.3390/pathogens10020191] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 01/27/2021] [Indexed: 11/19/2022] Open
Abstract
The rate of yersiniosis in New Zealand (NZ) is high compared with other developed countries, and rates have been increasing over recent years. Typically, >99% of human cases in NZ are attributed to Yersinia enterocolitica (YE), although in 2014, a large outbreak of 220 cases was caused by Yersinia pseudotuberculosis. Up until 2012, the most common NZ strain was YE biotype 4. The emergent strain since this time is YE biotype 2/3 serotype O:9. The pathogenic potential of some YE biotypes remains unclear. Most human cases of yersiniosis are considered sporadic without an identifiable source. Key restrictions in previous investigations included insufficient sensitivity for the isolation of Yersinia spp. from foods, although foodborne transmission is the most likely route of infection. In NZ, YE has been isolated from a variety of sick and healthy domestic and farm animals but the pathways from zoonotic reservoir to human remain unproven. Whole-genome sequencing provides unprecedented discriminatory power for typing Yersinia and is now being applied to NZ epidemiological investigations. A "One-Health" approach is necessary to elucidate the routes of transmission of Yersinia and consequently inform targeted interventions for the prevention and management of yersiniosis in NZ.
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Affiliation(s)
- Lucia Rivas
- Christchurch Science Centre, Institute of Environmental Science and Research Limited, Ilam, Christchurch 8041, New Zealand;
| | - Hugo Strydom
- National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research Limited, Upper Hutt, Wellington 5018, New Zealand;
| | - Shevaun Paine
- Kenepuru Science Centre, Institute of Environmental Science and Research Limited, Porirua, Wellington 5022, New Zealand; (S.P.); (J.W.)
| | - Jing Wang
- Kenepuru Science Centre, Institute of Environmental Science and Research Limited, Porirua, Wellington 5022, New Zealand; (S.P.); (J.W.)
| | - Jackie Wright
- National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research Limited, Upper Hutt, Wellington 5018, New Zealand;
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21
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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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22
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Leseigneur C, Lê-Bury P, Pizarro-Cerdá J, Dussurget O. Emerging Evasion Mechanisms of Macrophage Defenses by Pathogenic Bacteria. Front Cell Infect Microbiol 2020; 10:577559. [PMID: 33102257 PMCID: PMC7545029 DOI: 10.3389/fcimb.2020.577559] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/26/2020] [Indexed: 12/22/2022] Open
Abstract
Macrophages participate to the first line of defense against infectious agents. Microbial pathogens evolved sophisticated mechanisms to escape macrophage killing. Here, we review recent discoveries and emerging concepts on bacterial molecular strategies to subvert macrophage immune responses. We focus on the expanding number of fascinating subversive tools developed by Listeria monocytogenes, Staphylococcus aureus, and pathogenic Yersinia spp., illustrating diversity and commonality in mechanisms used by microorganisms with different pathogenic lifestyles.
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Affiliation(s)
- Clarisse Leseigneur
- Unité de Recherche Yersinia, Institut Pasteur, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Pierre Lê-Bury
- Unité de Recherche Yersinia, Institut Pasteur, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Javier Pizarro-Cerdá
- Unité de Recherche Yersinia, Institut Pasteur, Paris, France.,National Reference Laboratory Plague & Other Yersiniosis, Institut Pasteur, Paris, France.,WHO Collaborative Research & Reference Centre for Yersinia, Institut Pasteur, Paris, France
| | - Olivier Dussurget
- Unité de Recherche Yersinia, Institut Pasteur, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
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23
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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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24
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Abstract
Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries. Recent whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) approaches have been employed in epidemiological studies of specific human pathogens. However, this approach has not been reported in studies of S. mutans Here, we therefore developed a cgMLST scheme for S. mutans We surveyed 199 available S. mutans genomes as a means of identifying cgMLST targets, developing a scheme that incorporated 594 targets from the S. mutans UA159 reference genome. Sixty-eight sequence types (STs) were identified in this cgMLST scheme (cgSTs) in 80 S. mutans isolates from 40 children that were sequenced in this study, compared to 35 STs identified by multilocus sequence typing (MLST). Fifty-six cgSTs (82.35%) were associated with a single isolate based on our cgMLST scheme, which is significantly higher than in the MLST scheme (11.43%). In addition, 58.06% of all MLST profiles with ≥2 isolates were further differentiated by our cgMLST scheme. Topological analyses of the maximum likelihood phylogenetic trees revealed that our cgMLST scheme was more reliable than the MLST scheme. A minimum spanning tree of 145 S. mutans isolates from 10 countries developed based upon the cgMLST scheme highlighted the diverse population structure of S. mutans This cgMLST scheme thus offers a new molecular typing method suitable for evaluating the epidemiological distribution of this pathogen and has the potential to serve as a benchmark for future global studies of the epidemiological nature of dental caries.IMPORTANCE Streptococcus mutans is regarded as a major pathogen responsible for the onset of dental caries. S. mutans can transmit among people, especially within families. In this study, we established a new epidemiological approach to S. mutans classification. This approach can effectively differentiate among closely related isolates and offers superior reliability relative to that of the traditional MLST molecular typing method. As such, it has the potential to better support effective public health strategies centered around this bacterium that are aimed at preventing and treating dental caries.
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25
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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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