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Burns L, Giannakopoulou N, Zhu L, Xu YZ, Khan RH, Bekal S, Schurr E, Schmeing TM, Gruenheid S. A229 THE BACTERIAL VIRULENCE FACTOR NLEA UNDERGOES HOST-MEDIATED O-LINKED GLYCOSYLATION. J Can Assoc Gastroenterol 2023. [PMCID: PMC9991285 DOI: 10.1093/jcag/gwac036.229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
NOT PUBLISHED AT AUTHOR’S REQUEST
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Affiliation(s)
| | | | - L Zhu
- Microbiology & Immunology
| | - Y Z Xu
- Medicine, McGill University, Montreal
| | - R H Khan
- Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue,Microbiologie, Infectologie et Immunologie, Universite de Montreal, Montreal
| | - S Bekal
- Microbiologie, Infectologie et Immunologie, Universite de Montreal, Montreal,Institut National de Sante Publique du Quebec, Sainte-Anne-de-Bellevue
| | - E Schurr
- Biochemistry, McGill University, Montreal, Canada
| | - T M Schmeing
- Biochemistry, McGill University, Montreal, Canada
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Burns L, Giannakopoulou N, Zhu L, Xu YZ, Khan RH, Bekal S, Schurr E, Schmeing TM, Gruenheid S. The bacterial virulence factor NleA undergoes host-mediated O-linked glycosylation. Mol Microbiol 2023; 119:161-173. [PMID: 36196760 DOI: 10.1111/mmi.14989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 09/01/2022] [Accepted: 09/29/2022] [Indexed: 11/28/2022]
Abstract
Enterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC) are gastrointestinal pathogens responsible for severe diarrheal illness. EHEC and EPEC form "attaching and effacing" lesions during colonization and, upon adherence, inject proteins directly into host intestinal cells via the type III secretion system (T3SS). Injected bacterial proteins have a variety of functions but generally alter host cell biology to favor survival and/or replication of the pathogen. Non-LEE-encoded effector A (NleA) is a T3SS-injected effector of EHEC, EPEC, and the related mouse pathogen Citrobacter rodentium. Studies in mouse models indicate that NleA has an important role in bacterial virulence. However, the mechanism by which NleA contributes to disease remains unknown. We have determined that the following translocation into host cells, a serine and threonine-rich region of NleA is modified by host-mediated mucin-type O-linked glycosylation. Surprisingly, this region was not present in several clinical EHEC isolates. When expressed in C. rodentium, a non-modifiable variant of NleA was indistinguishable from wildtype NleA in an acute mortality model but conferred a modest increase in persistence over the course of infection in mixed infections in C57BL/6J mice. This is the first known example of a bacterial effector being modified by host-mediated O-linked glycosylation. Our data also suggests that this modification may confer a selective disadvantage to the bacteria during in vivo infection.
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Affiliation(s)
- Lindsay Burns
- McGill Research Centre on Complex Traits and Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Natalia Giannakopoulou
- McGill Research Centre on Complex Traits and Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Lei Zhu
- McGill Research Centre on Complex Traits and Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Yong Zhong Xu
- Program in Infectious Diseases and Global Health, The Research Institute of the McGill University Health Centre and McGill International TB Centre, Department of Medicine, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Rufaida H Khan
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada.,Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
| | - Erwin Schurr
- Program in Infectious Diseases and Global Health, The Research Institute of the McGill University Health Centre and McGill International TB Centre, Department of Medicine, Faculty of Medicine, McGill University, Montréal, Québec, Canada.,Department of Biochemistry, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - T Martin Schmeing
- Department of Biochemistry, Faculty of Medicine, McGill University, Montréal, Québec, Canada.,Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec, Canada
| | - Samantha Gruenheid
- McGill Research Centre on Complex Traits and Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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3
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Dion R, Ayres Hutter J, Umutanguha A, Bekal S. 396 – Labovigilance des infections humaines à Salmonella au Québec, Canada, 2002 à 2016. Rev Epidemiol Sante Publique 2022. [DOI: 10.1016/j.respe.2022.06.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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Bharat A, Mataseje L, Parmley EJ, Avery BP, Cox G, Carson CA, Irwin RJ, Deckert AE, Daignault D, Alexander DC, Allen V, El Bailey S, Bekal S, German GJ, Haldane D, Hoang L, Chui L, Minion J, Zahariadis G, Reid-Smith RJ, Mulvey MR. One Health Genomic Analysis of Extended-Spectrum β-Lactamase‒Producing Salmonella enterica, Canada, 2012‒2016. Emerg Infect Dis 2022; 28:1410-1420. [PMID: 35731173 PMCID: PMC9239887 DOI: 10.3201/eid2807.211528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Extended-spectrum β-lactamases (ESBLs) confer resistance to extended-spectrum cephalosporins, a major class of clinical antimicrobial drugs. We used genomic analysis to investigate whether domestic food animals, retail meat, and pets were reservoirs of ESBL-producing Salmonella for human infection in Canada. Of 30,303 Salmonella isolates tested during 2012–2016, we detected 95 ESBL producers. ESBL serotypes and alleles were mostly different between humans (n = 54) and animals/meat (n = 41). Two exceptions were blaSHV-2 and blaCTX-M-1 IncI1 plasmids, which were found in both sources. A subclade of S. enterica serovar Heidelberg isolates carrying the same IncI1-blaSHV-2 plasmid differed by only 1–7 single nucleotide variants. The most common ESBL producer in humans was Salmonella Infantis carrying blaCTX-M-65, which has since emerged in poultry in other countries. There were few instances of similar isolates and plasmids, suggesting that domestic animals and retail meat might have been minor reservoirs of ESBL-producing Salmonella for human infection.
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Doualla-Bell F, Boyd DA, Savard P, Yousfi K, Bernaquez I, Wong S, Usongo V, Mataseje LF, Mulvey MR, Bekal S. Analysis of an IncR Plasmid Carrying blaNDM-1 Linked to an Azithromycin Resistance Region in Enterobacter hormaechei Involved in an Outbreak in Quebec. Microbiol Spectr 2021; 9:e0199821. [PMID: 34937191 PMCID: PMC8694144 DOI: 10.1128/spectrum.01998-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/24/2021] [Indexed: 11/20/2022] Open
Abstract
In the context of a recent rise in prevalence of NDM-encoding carbapenemase-producing Enterobacterales (CPE) in the province of QC, Canada, the genetic environment of blaNDM-1 was investigated. Three NDM-producing clinical isolates of Enterobacter hormaechei recovered from hospitalized patients involved in a putative outbreak were further characterized by whole-genome sequencing (WGS). Two isolates were confirmed by pulsed-field gel electrophoresis and WGS to be closely related. In addition to a ∼128 kb IncFII conjugative multidrug-resistance (MDR) plasmid, these isolates possessed a ∼45 kb mobilizable IncR MDR plasmid containing 2 MDR regions: a complex class 1 integron harboring blaNDM-1 and 7 other AMR genes, and the IS26-mph(A)-mrx-mphR(A)-IS6100 azithromycin resistance unit. The predicted antimicrobial resistance (AMR) genes correlated with the antimicrobial susceptibility testing results. The multidrug-resistant phenotype in addition to the presence of two important mobile genetic elements, suggest a potent role as a reservoir of antibiotic resistance for such a small IncR plasmid. IMPORTANCE Analyzing the genetic environment of clinically relevant MDR genes can provide information on the way in which such genes are maintained and disseminated. Understanding this phenomenon is of interest for clinicians as it can also provide insight on where these genes might have been sourced, possibly supporting outbreak investigations.
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Affiliation(s)
- Florence Doualla-Bell
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - David A. Boyd
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Patrice Savard
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
- Département clinique de médecine des laboratoires OPTILAB-CHUM and CRCHUM, Université de Montréal, Montréal, Quebec, Canada
| | - Khadidja Yousfi
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Isabelle Bernaquez
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Simon Wong
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Valentine Usongo
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Laura F. Mataseje
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
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Bernaquez I, Gaudreau C, Pilon PA, Bekal S. Evaluation of whole-genome sequencing-based subtyping methods for the surveillance of Shigella spp. and the confounding effect of mobile genetic elements in long-term outbreaks. Microb Genom 2021; 7. [PMID: 34730485 PMCID: PMC8743557 DOI: 10.1099/mgen.0.000672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Many public health laboratories across the world have implemented whole-genome sequencing (WGS) for the surveillance and outbreak detection of foodborne pathogens. PulseNet-affiliated laboratories have determined that most single-strain foodborne outbreaks are contained within 0–10 multi-locus sequence typing (MLST)-based allele differences and/or core genome single-nucleotide variants (SNVs). In addition to being a food- and travel-associated outbreak pathogen, most
Shigella
spp. cases occur through continuous person-to-person transmission, predominantly involving men who have sex with men (MSM), leading to long-term and recurrent outbreaks. Continuous transmission patterns coupled to genetic evolution under antibiotic treatment pressure require an assessment of existing WGS-based subtyping methods and interpretation criteria for cluster inclusion/exclusion. An evaluation of 4 WGS-based subtyping methods [SNVPhyl, coreMLST, core genome MLST (cgMLST) and whole-genome MLST (wgMLST)] was performed on 9 foodborne-, travel- and MSM-related retrospective outbreaks from a collection of 91
Shigella flexneri
and 232
Shigella sonnei
isolates to determine the methods’ epidemiological concordance, discriminatory power, robustness and ability to generate stable interpretation criteria. The discriminatory powers were ranked as follows: coreMLST<SNVPhyl<cgMLST<wgMLST (range: 0.970–1.000). The genetic differences observed for non-MSM-related
Shigella
spp. outbreaks respect the standard 0–10 allele/SNV guideline; however, mobile genetic element (MGE)-encoded loci caused inflated genetic variation and discrepant phylogenies for prolonged MSM-related
S. sonnei
outbreaks via wgMLST. The
S. sonnei
correlation coefficients of wgMLST were also the lowest at 0.680, 0.703 and 0.712 for SNVPhyl, coreMLST and cgMLST, respectively. Plasmid maintenance, mobilization and conjugation-associated genes were found to be the main source of genetic distance inflation in addition to prophage-related genes. Duplicated alleles arising from the repeated nature of IS elements were also responsible for many false cg/wgMLST differences. The coreMLST approach was shown to be the most robust, followed by SNVPhyl and wgMLST for inter-laboratory comparability. Our results highlight the need for validating species-specific subtyping methods based on microbial genome plasticity and outbreak dynamics in addition to the importance of filtering confounding MGEs for cluster detection.
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Affiliation(s)
- Isabelle Bernaquez
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, H9X 3R5, Canada
| | - Christiane Gaudreau
- Microbiologie médicale et infectiologie, Centre Hospitalier de l’Université de Montréal (CHUM), Montreal, QC, H2X 3E4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Pierre A. Pilon
- Direction régionale de santé publique, Centre intégré universitaire de santé et de services sociaux du Centre-Sud-de-l’île-de-Montréal, Montreal, QC, H2L 4M1, Canada
- Département de médecine sociale et préventive, Université de Montréal, Montreal, QC, H3N 1X9, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, H9X 3R5, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, QC, H3C 3J7, Canada
- *Correspondence: Sadjia Bekal,
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Cavestri C, Savard P, Fliss I, Emond-Rhéault JG, Hamel J, Kukavica-Ibrulj I, Boyle B, Daigle F, Malo D, Bekal S, Harris LJ, Levesque RC, Goodridge L, LaPointe G. Salmonella enterica subsp. enterica virulence potential can be linked to higher survival within a dynamic in vitro human gastrointestinal model. Food Microbiol 2021; 101:103877. [PMID: 34579845 DOI: 10.1016/j.fm.2021.103877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/04/2022]
Abstract
Salmonella enterica subsp. enterica is one of the leading causes of human foodborne infections and several outbreaks are now associated with the consumption of fresh fruit and vegetables. This study aims at evaluating whether Salmonella virulence can be linked to an enhanced ability to survive successive digestive environments. Thirteen S. enterica strains were selected according to high and low virulence phenotypes. Lettuce inoculated separately with each S. enterica strain was used as food matrix in the TNO gastrointestinal model (TIM-1) of the human upper gastrointestinal tract. During the passage in the stomach, counts determined using PMA-qPCR were 2-5 logs higher than the cultivable counts for all strains indicating the presence of viable but non-cultivable cells. Bacterial growth was observed in the duodenum compartment after 180 min for all but one strain and growth continued into the ileal compartment. After passage through the simulated gastrointestinal tract, both virulent and avirulent S. enterica strains survived but high virulence strains had a significantly (p = 0.004) better average survival rate (1003 %-3753 %) than low virulence strains (from 25 % to 3730%). The survival rates of S. enterica strains could be linked to the presence of genes associated with acid and bile resistance and their predicted products. The presence of single nucleotide polymorphisms may also impact the function of virulence associated genes and play a role in the resulting phenotype. These data provide an understanding of the relationship between measured virulence potential and survival of S. enterica during dynamic simulated gastrointestinal transit.
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Affiliation(s)
- Camille Cavestri
- Institute of Nutrition and Functional Foods, Université Laval, Québec, Canada
| | - Patricia Savard
- Institute of Nutrition and Functional Foods, Université Laval, Québec, Canada
| | - Ismail Fliss
- Institute of Nutrition and Functional Foods, Université Laval, Québec, Canada
| | | | - Jérémie Hamel
- Institute for Integrative and Systems Biology, Université Laval, Québec, Canada
| | | | - Brian Boyle
- Institute for Integrative and Systems Biology, Université Laval, Québec, Canada
| | - France Daigle
- Département de Microbiologie Infectiologie et Immunologie, Université de Montréal, Montréal, Canada
| | - Danielle Malo
- Department of Medicine, McGill University, Montreal, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique Du Québec, Ste-Anne de Bellevue, Canada
| | - Linda J Harris
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Roger C Levesque
- Institute for Integrative and Systems Biology, Université Laval, Québec, Canada
| | | | - Gisèle LaPointe
- Department of Food Science, University of Guelph, Guelph, Canada.
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Greninger AL, Addetia A, Starr K, Cybulski RJ, Stewart MK, Salipante SJ, Bryan AB, Cookson B, Gaudreau C, Bekal S, Fang FC. International Spread of Multidrug-Resistant Campylobacter coli in Men Who Have Sex With Men in Washington State and Québec, 2015-2018. Clin Infect Dis 2021; 71:1896-1904. [PMID: 31665255 PMCID: PMC7643735 DOI: 10.1093/cid/ciz1060] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Background Campylobacter species are among the most common causes of enteric bacterial infections worldwide. Men who have sex with men (MSM) are at increased risk for sexually transmitted enteric infections, including globally distributed strains of multidrug-resistant Shigella species. Methods This was a retrospective study of MSM-associated Campylobacter in Seattle, Washington and Montréal, Québec with phenotypic antimicrobial resistance profiles and whole genome sequencing (WGS). Results We report the isolation of 2 clonal lineages of multidrug-resistant Campylobacter coli from MSM in Seattle and Montréal. WGS revealed nearly identical strains obtained from the 2 regions over a 4-year period. Comparison with the National Center for Biotechnology Information’s Pathogen Detection database revealed extensive Campylobacter species clusters carrying multiple drug resistance genes that segregated with these isolates. Examination of the genetic basis of antimicrobial resistance revealed multiple macrolide resistance determinants including a novel ribosomal RNA methyltransferase situated in a CRISPR (clustered regularly interspaced short palindromic repeats) array locus in a C. coli isolate. Conclusions As previously reported for Shigella, specific multidrug-resistant strains of Campylobacter are circulating by sexual transmission in MSM populations across diverse geographic locations, suggesting a need to incorporate sexual behavior in the investigation of clusters of foodborne pathogens revealed by WGS data.
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Affiliation(s)
- Alexander L Greninger
- Departments of Laboratory Medicine and Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Correspondence: A. L. Greninger, University of Washington, 1616 Eastlake Ave E, Suite 320, Seattle, WA 98102 ()
| | - Amin Addetia
- Departments of Laboratory Medicine and Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kimberly Starr
- Departments of Laboratory Medicine and Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Robert J Cybulski
- Department of Pathology and Area Laboratory Services, Brooke Army Medical Center, San Antonio, Texas, USA
| | - Mary K Stewart
- Departments of Laboratory Medicine and Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J Salipante
- Departments of Laboratory Medicine and Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Andrew B Bryan
- Departments of Laboratory Medicine and Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Brad Cookson
- Departments of Laboratory Medicine and Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Christiane Gaudreau
- Microbiologie médicale et infectiologie, Centre hospitalier de l’Université de Montréal, Québec, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Québec, Canada
| | - Sadjia Bekal
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Québec, Canada
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Ferric C Fang
- Departments of Laboratory Medicine and Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
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Cherifi T, Arsenault J, Pagotto F, Quessy S, Côté JC, Neira K, Fournaise S, Bekal S, Fravalo P. Distribution, diversity and persistence of Listeria monocytogenes in swine slaughterhouses and their association with food and human listeriosis strains. PLoS One 2020; 15:e0236807. [PMID: 32760141 PMCID: PMC7410256 DOI: 10.1371/journal.pone.0236807] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/13/2020] [Indexed: 02/05/2023] Open
Abstract
Listeria monocytogenes is the etiological agent of listeriosis, a major foodborne disease and an important public health concern. Contamination of meat with L. monocytogenes occurs frequently at the slaughterhouse. Our aims were; 1) to investigate the distribution of L. monocytogenes in the processing areas of four swine slaughterhouses; 2) to describe the diversity of L. monocytogenes strains by pulsed-field gel electrophoresis; 3) to identify persistent L. monocytogenes strains and describe their distribution; 4) to investigate the associations between persistence of strains and their following characteristics: detection in food isolates, detection in human clinical isolates, and the presence of benzalkonium chloride (BAC) resistance genes. Various operation areas within the four swine slaughterhouses were sampled on four occasions. A total of 2496 samples were analyzed, and L. monocytogenes was successfully isolated from 243 samples. The proportion of positive samples ranged from 32 to 58% in each slaughterhouse and from 24 to 68% in each operation area. Fifty-eight different pulsotypes were identified and eight pulsotypes, present in samples collected during 4 visits, were considered persistent. The persistent pulsotypes were significantly more likely to be detected in food (P < 0.01, exact χ²) and human clinical cases (P < 0.01, exact χ²), respectively. Among pulsotypes harboring the BAC bcrABC resistance cassette or the emrE multidrug transporter gene, 42.8% were persistent compared to 4.5% for pulsotypes without these resistance genes (P < 0.01, exact χ²). Our study highlights the importance of persistent L. monocytogenes strains in the environmental contamination of slaughterhouses, which may lead to repeated contamination of meat products. It also shows that the presence of disinfectants resistance genes is an important contributing factor.
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Affiliation(s)
- Tamazight Cherifi
- Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Centre de recherche en infectiologie porcine et avicole (CRIPA-FQRNT), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Groupe de recherche et d’enseignement en salubrité des aliments (GRESA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- * E-mail: (TC); (PF)
| | - Julie Arsenault
- Centre de recherche en infectiologie porcine et avicole (CRIPA-FQRNT), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Epidemiology of Zoonoses and Public Health Research Unit (GREZOSP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Franco Pagotto
- Listeriosis Reference Service, Microbiology Research Division, Bureau of Microbial Hazards, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Sylvain Quessy
- Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Groupe de recherche et d’enseignement en salubrité des aliments (GRESA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Jean-Charles Côté
- Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Groupe de recherche et d’enseignement en salubrité des aliments (GRESA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Kersti Neira
- Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Centre de recherche en infectiologie porcine et avicole (CRIPA-FQRNT), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Groupe de recherche et d’enseignement en salubrité des aliments (GRESA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | | | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Philippe Fravalo
- Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Centre de recherche en infectiologie porcine et avicole (CRIPA-FQRNT), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- Epidemiology of Zoonoses and Public Health Research Unit (GREZOSP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
- * E-mail: (TC); (PF)
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10
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Yousfi K, Usongo V, Berry C, Khan RH, Tremblay DM, Moineau S, Mulvey MR, Doualla-Bell F, Fournier E, Nadon C, Goodridge L, Bekal S. Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012. Front Microbiol 2020; 11:1317. [PMID: 32625190 PMCID: PMC7311582 DOI: 10.3389/fmicb.2020.01317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
Whole-genome sequencing (WGS) is the method of choice for bacterial subtyping and it is rapidly replacing the more traditional methods such as pulsed-field gel electrophoresis (PFGE). Here we used the high-resolution core genome single nucleotide variant (cgSNV) typing method to characterize clinical and food from Salmonella enterica serovar Heidelberg isolates in the context of source attribution. Additionally, clustered regularly interspaced short palindromic repeats (CRISPR) analysis was included to further support this method. Our results revealed that cgSNV was highly discriminatory and separated the outbreak isolates into distinct clusters (0-4 SNVs). CRISPR analysis was also able to distinguish outbreak strains from epidemiologically unrelated isolates. Specifically, our data clearly demonstrated the strength of these two methods to determine the probable source(s) of a 2012 epidemiologically characterized outbreak of S. Heidelberg. Using molecular cut-off of 0-10 SNVs, the cgSNV analysis of 246 clinical and food isolates of S. Heidelberg collected in Québec, in the same year of the outbreak event, revealed that retail and abattoir chicken isolates likely represent an important source of human infection to S. Heidelberg. Interestingly, the isolates genetically related by cgSNV also harbored the same CRISPR as outbreak isolates and clusters. This indicates that CRISPR profiles can be useful as a complementary approach to determine source attribution in foodborne outbreaks. Use of the genomic analysis also allowed to identify a large number of cases that were missed by PFGE, indicating that most outbreaks are probably underestimated. Although epidemiological information must still support WGS-based results, cgSNV method is a highly discriminatory method for the resolution of outbreak events and the attribution of these events to their respective sources. CRISPR typing can serve as a complimentary tool to this analysis during source tracking.
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Affiliation(s)
- Khadidja Yousfi
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.,Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Valentine Usongo
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.,Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Rufaida H Khan
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.,Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Denise M Tremblay
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Florence Doualla-Bell
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Celine Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Lawrence Goodridge
- Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
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11
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Pilar AVC, Petronella N, Dussault FM, Verster AJ, Bekal S, Levesque RC, Goodridge L, Tamber S. Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries. BMC Genomics 2020; 21:377. [PMID: 32471418 PMCID: PMC7257147 DOI: 10.1186/s12864-020-06780-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/13/2020] [Indexed: 12/14/2022] Open
Abstract
Background Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presence of background microflora that may present as Salmonella (false positives). False positive isolates belonging to the genus Citrobacter can be difficult to distinguish from Salmonella due to similarities in their genetics, cell surface antigens, and other phenotypes. In order to understand the genetic basis of these similarities, a comparative genomic approach was used to define the pan-, core, accessory, and unique coding sequences of a representative population of Salmonella and Citrobacter strains. Results Analysis of the genomic content of 58 S. enterica strains and 37 Citrobacter strains revealed the presence of 31,130 and 1540 coding sequences within the pan- and core genome of this population. Amino acid sequences unique to either Salmonella (n = 1112) or Citrobacter (n = 195) were identified and revealed potential niche-specific adaptations. Phylogenetic network analysis of the protein families encoded by the pan-genome indicated that genetic exchange between Salmonella and Citrobacter may have led to the acquisition of similar traits and also diversification within the genera. Conclusions Core genome analysis suggests that the Salmonella enterica and Citrobacter populations investigated here share a common evolutionary history. Comparative analysis of the core and pan-genomes was able to define the genetic features that distinguish Salmonella from Citrobacter and highlight niche specific adaptations.
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Affiliation(s)
| | - Nicholas Petronella
- Bureau of Food Surveillance and Science Integration, Health Canada, Ottawa, Ontario, Canada
| | - Forest M Dussault
- Bureau of Food Surveillance and Science Integration, Health Canada, Ottawa, Ontario, Canada
| | - Adrian J Verster
- Bureau of Food Surveillance and Science Integration, Health Canada, Ottawa, Ontario, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Roger C Levesque
- Institute for Integrative and Systems Biology (IBIS), Université Laval, Quebec, Quebec, Canada
| | - Lawrence Goodridge
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada.,Food Science Department, University of Guelph, Guelph, Ontario, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, Ottawa, Ontario, Canada.
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12
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Currie A, Honish L, Cutler J, Locas A, Lavoie MC, Gaulin C, Galanis E, Tschetter L, Chui L, Taylor M, Jamieson F, Gilmour M, Ng C, Mutti S, Mah V, Hamel M, Martinez A, Buenaventura E, Hoang L, Pacagnella A, Ramsay D, Bekal S, Coetzee K, Berry C, Farber J, Team OBOTNI. Outbreak of Escherichia coli O157:H7 Infections Linked to Mechanically Tenderized Beef and the Largest Beef Recall in Canada, 2012. J Food Prot 2019; 82:1532-1538. [PMID: 31414901 DOI: 10.4315/0362-028x.jfp-19-005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Contaminated beef is a known vehicle of Escherichia coli O157:H7 infection, although more attention is given to the control of E. coli O157:H7 in ground, rather than whole-cut, beef products. In September 2012, an investigation was initiated at an Alberta, Canada, beef plant after the detection of E. coli O157:H7 in two samples of trim cut from beef originating from this plant. Later in September 2012, Alberta Health Services identified five laboratory-confirmed infections of E. coli O157:H7, and case patients reported eating needle-tenderized beef steaks purchased at a store in Edmonton, Alberta, produced with beef from the Alberta plant. In total, 18 laboratory-confirmed illnesses in Canada in September and October 2012 were linked to beef from the Alberta plant, including the five individuals who ate needle-tenderized steaks purchased at the Edmonton store. A unique strain of E. coli O157:H7, defined by molecular subtyping and whole genome sequencing, was detected in clinical isolates, four samples of leftover beef from case patient homes, and eight samples of Alberta plant beef tested by industry and food safety partners. Investigators identified several deficiencies in the control of E. coli O157:H7 at the plant; in particular, the evaluation of, and response to, the detection of E. coli O157 in beef samples during routine testing were inadequate. To control the outbreak, 4,000 tons of beef products were recalled, making it the largest beef recall in Canadian history. This outbreak, in combination with similar outbreaks in the United States and research demonstrating that mechanical tenderization can transfer foodborne pathogens present on the surface into the interior of beef cuts, prompted amendments to Canada's Food and Drug Regulations requiring mechanically tenderized beef to be labeled as such and to provide safe cooking instructions to consumers. A detailed review of this event also led to recommendations and action to improve the safety of Canada's beef supply.
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Affiliation(s)
- Andrea Currie
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada N1H 8J1
| | - Lance Honish
- Alberta Health Services, Edmonton, Alberta, Canada T5J 2Y2
| | - Jennifer Cutler
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada N1H 8J1
| | - Annie Locas
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0Y9
| | | | - Colette Gaulin
- Ministère de la Santé et des Services Sociaux du Québec, Québec, Québec, Canada G1S 2M1
| | - Eleni Galanis
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada V5Z 4R4
| | - Lorelee Tschetter
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada R3E 3R2
| | - Linda Chui
- Provincial Laboratory for Public Health: Alberta Public Laboratories, Alberta, Canada T6G 2J2
| | - Marsha Taylor
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada V5Z 4R4
| | - Fred Jamieson
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0Y9
| | - Matthew Gilmour
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada R3E 3R2
| | - Constance Ng
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0Y9
| | - Sarbjit Mutti
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0Y9
| | - Victor Mah
- Alberta Health, Edmonton, Alberta, Canada T5J 1S6
| | - Meghan Hamel
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada N1H 8J1
| | - Amalia Martinez
- Bureau of Microbial Hazards, Health Canada, Ottawa, Ontario, Canada K1A 0K9
| | | | - Linda Hoang
- British Columbia Public Health Microbiology and Reference Laboratory, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada V5Z 4R4
| | - Ana Pacagnella
- British Columbia Public Health Microbiology and Reference Laboratory, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada V5Z 4R4
| | - Danielle Ramsay
- Ministère de l'Agriculture, des Pêcheries et de l'Alimentation du Québec, 200 Chemin Ste-Foy, 11ème étage, Québec, Québec, Canada G1R 4X6
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne de Bellevue, Québec, Canada H9X 3Y3
| | - Kelly Coetzee
- Department of Health and Community Services, Government of Newfoundland and Labrador, St. John's, Newfoundland and Labrador, Canada A1B 4J6
| | - Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada R3E 3R2
| | - Jeff Farber
- University of Guelph, Guelph, Ontario, Canada N1G 2W1
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13
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Mangat CS, Bekal S, Avery BP, Côté G, Daignault D, Doualla-Bell F, Finley R, Lefebvre B, Bharat A, Parmley EJ, Reid-Smith RJ, Longtin J, Irwin RJ, Mulvey MR. Genomic Investigation of the Emergence of Invasive Multidrug-Resistant Salmonella enterica Serovar Dublin in Humans and Animals in Canada. Antimicrob Agents Chemother 2019; 63:e00108-19. [PMID: 31036694 PMCID: PMC6535508 DOI: 10.1128/aac.00108-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/07/2019] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Dublin is a zoonotic pathogen that often leads to invasive bloodstream infections in humans that are multidrug resistant. Described here are the results of Canadian national surveillance of S Dublin from 2003 to 2015 in humans and bovines, principally collected through the Canadian Integrated Program for Antibiotic Resistance Surveillance (CIPARS). An increase in human infections due to multidrug-resistant (MDR) S Dublin was observed in 2010, many of which were bloodstream infections. Phylogenomic analysis of human and bovine isolates revealed a closely related network that differed by only 0 to 17 single nucleotide variants (SNVs), suggesting some potential transmission between humans and bovines. Phylogenomic comparison of global publicly available sequences of S Dublin showed that Canadian isolates clustered closely with those from the United States. A high correlation between phenotypic and genotypic antimicrobial susceptibility was observed in Canadian isolates. IS26 replication was widespread among U.S. and Canadian isolates and caused the truncation and inactivation of the resistance genes strA and blaTEM-1B A hybrid virulence and MDR plasmid (pN13-01125) isolated from a Canadian S Dublin isolate was searched against NCBI SRA data of bacteria. The pN13-01125 coding sequences were found in 13 Salmonella serovars, but S Dublin appears to be a specific reservoir. In summary, we have observed the rise of invasive MDR S Dublin in humans in Canada and found that they are closely related to bovine isolates and to American isolates in their mobile and chromosomal contents.
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Affiliation(s)
- Chand S Mangat
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Brent P Avery
- Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Geneviève Côté
- Ministère de l'Agriculture, des Pêcheries et de l'Alimentation du Québec, Québec, Canada
| | | | | | - Rita Finley
- Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Brigitte Lefebvre
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Amrita Bharat
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | | | | | - Jean Longtin
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
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14
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Reimer A, Weedmark K, Petkau A, Peterson CL, Walker M, Knox N, Kent H, Mabon P, Berry C, Tyler S, Tschetter L, Jerome M, Allen V, Hoang L, Bekal S, Clark C, Nadon C, Van Domselaar G, Pagotto F, Graham M, Farber J, Gilmour M. Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria. Microb Genom 2019; 5. [PMID: 30648944 PMCID: PMC6412057 DOI: 10.1099/mgen.0.000237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The persuasiveness of genomic evidence has pressured scientific agencies to supplement or replace well-established methodologies to inform public health and food safety decision-making. This study of 52 epidemiologically defined Listeria monocytogenes isolates, collected between 1981 and 2011, including nine outbreaks, was undertaken (1) to characterize their phylogenetic relationship at finished genome-level resolution, (2) to elucidate the underlying genetic diversity within an endemic subtype, CC8, and (3) to re-evaluate the genetic relationship and epidemiology of a CC8-delimited outbreak in Canada in 2008. Genomes representing Canadian Listeria outbreaks between 1981 and 2010 were closed and manually annotated. Single nucleotide variants (SNVs) and horizontally acquired traits were used to generate phylogenomic models. Phylogenomic relationships were congruent with classical subtyping and epidemiology, except for CC8 outbreaks, wherein the distribution of SNV and prophages revealed multiple co-evolving lineages. Chronophyletic reconstruction of CC8 evolution indicates that prophage-related genetic changes among CC8 strains manifest as PFGE subtype reversions, obscuring the relationship between CC8 isolates, and complicating the public health interpretation of subtyping data, even at maximum genome resolution. The size of the shared genome interrogated did not change the genetic relationship measured between highly related isolates near the tips of the phylogenetic tree, illustrating the robustness of these approaches for routine public health applications where the focus is recent ancestry. The possibility exists for temporally and epidemiologically distinct events to appear related even at maximum genome resolution, highlighting the continued importance of epidemiological evidence.
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Affiliation(s)
- Aleisha Reimer
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Kelly Weedmark
- 2Health Canada, Bureau of Microbial Hazards, Ottawa, ON, K1A 0K9, Canada
| | - Aaron Petkau
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Matthew Walker
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Natalie Knox
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Heather Kent
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Philip Mabon
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Chrystal Berry
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Shaun Tyler
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Morganne Jerome
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Vanessa Allen
- 3Public Health Ontario, Toronto, ON, M5G 1M1, Canada
| | - Linda Hoang
- 4British Columbia Centre for Disease Control, Public Health Microbiology and Reference Laboratory, Vancouver, BC V5Z 4R4, Canada
| | - Sadjia Bekal
- 5Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, H9X 3R5, Canada
| | - Clifford Clark
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Celine Nadon
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | | | - Franco Pagotto
- 2Health Canada, Bureau of Microbial Hazards, Ottawa, ON, K1A 0K9, Canada
| | - Morag Graham
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
| | - Jeff Farber
- 6University of Guelph, Guelph, ON, N1G 2W, Canada
| | - Matthew Gilmour
- 1Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada
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15
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Labbé G, Rankin MA, Robertson J, Moffat J, Giang E, Lee LK, Ziebell K, MacKinnon J, Laing CR, Parmley EJ, Agunos A, Daignault D, Bekal S, Chui L, MacDonald KA, Hoang L, Slavic D, Ramsay D, Pollari F, Nash JHE, Johnson RP. Targeting discriminatory SNPs in Salmonella enterica serovar Heidelberg genomes using RNase H2-dependent PCR. J Microbiol Methods 2018; 157:81-87. [PMID: 30592979 DOI: 10.1016/j.mimet.2018.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 11/16/2022]
Abstract
We report a novel RNase H2-dependent PCR (rhPCR) genotyping assay for a small number of discriminatory single-nucleotide polymorphisms (SNPs) that identify lineages and sub-lineages of the highly clonal pathogen Salmonella Heidelberg (SH). Standard PCR primers targeting numerous SNP locations were initially designed in silico, modified to be RNase H2-compatible, and then optimized by laboratory testing. Optimization often required repeated cycling through variations in primer design, assay conditions, reagent concentrations and selection of alternative SNP targets. The final rhPCR assay uses 28 independent rhPCR reactions to target 14 DNA bases that can distinguish 15 possible lineages and sub-lineages of SH. On evaluation, the assay correctly identified the 12 lineages and sub-lineages represented in a panel of 75 diverse SH strains. Non-specific amplicons were observed in 160 (15.2%) of the 1050 reactions, but due to their low intensity did not compromise assay performance. Furthermore, in silico analysis of 500 closed genomes from 103 Salmonella serovars and laboratory rhPCR testing of five prevalent Salmonella serovars including SH indicated the assay can identify Salmonella isolates as SH, since only SH isolates generated amplicons from all 14 target SNPs. The genotyping results can be fully correlated with whole genome sequencing (WGS) data in silico. This fast and economical assay, which can identify SH isolates and classify them into related or unrelated lineages and sub-lineages, has potential applications in outbreak identification, source attribution and microbial source tracking.
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Affiliation(s)
- Geneviève Labbé
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Marisa A Rankin
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Jonathan Moffat
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Elissa Giang
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Lok Kan Lee
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Joanne MacKinnon
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Chad R Laing
- National Centres for Animal Disease Lethbridge Laboratory, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - E Jane Parmley
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Agnes Agunos
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Danielle Daignault
- National Microbiology Laboratory, Public Health Agency of Canada, St-Hyacinthe, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Linda Chui
- Provincial Laboratory for Public Health-Alberta Public Laboratories, Edmonton, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kimberley A MacDonald
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; British Columbia Centre for Disease Control, Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
| | - Linda Hoang
- British Columbia Centre for Disease Control, Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
| | - Durda Slavic
- Animal Health Laboratory, Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada
| | - Danielle Ramsay
- Ministère de l'Agriculture, des Pêcheries, et de l'Alimentation du Québec, Québec, Canada
| | - Frank Pollari
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - John H E Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Toronto, Ontario, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada.
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16
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Yousfi K, Touati A, Lefebvre B, Garneau P, Brahmi S, Gharout-Sait A, Harel J, Bekal S. Characterization of multidrug-resistant Gram-negative bacilli isolated from hospitals effluents: first report of a bla OXA-48-like in Klebsiella oxytoca, Algeria. Braz J Microbiol 2018; 50:175-183. [PMID: 30637660 DOI: 10.1007/s42770-018-0010-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/02/2018] [Indexed: 12/17/2022] Open
Abstract
The antibiotic susceptibility profile and antimicrobial resistance determinants were characterized on Gram-negative bacilli (GNB) isolated from Algerian hospital effluents. Among the 94 isolates, Enterobacteriaceae was the predominant family, with Escherichia coli and Klebsiella pneumoniae being the most isolated species. In non-Enterobacteriaceae, Acinetobacter and Aeromonas were the predominant species followed by Pseudomonas, Comamonas, Pasteurella, and Shewanella spp. The majority of the isolates were multidrug-resistant (MDR) and carried different antimicrobial resistance genes including blaCTX-M, blaTEM, blaSHV, blaOXA-48-like, blaOXA-23, blaOXA-51, qnrB, qnrS, tet(A), tet(B), tet(C), dfrA1, aac(3)-IIc (aacC2), aac(6')-1b, sul1, and sul2. The qacEΔ1-sul1 and intI2 signatures of class 1 and class 2 integrons, respectively, were also detected. Microarray hybridization on MDR E. coli revealed additional resistance genes (aadA1 and aph3strA, tet30, mphA, dfrA12, blacmy2, blaROB1, and cmlA1) and classified the tested strains as commensals, thus highlighting the potential role of humans in antibiotic resistance dissemination. This study is the first report of blaOXA-48-like in Klebsiella oxytoca in Algeria and blaOXA-23 in A. baumannii in Algerian hospital effluents. The presence of these bacteria and resistance genes in hospital effluents represents a serious public health concern since they can be disseminated in the environment and can colonize other hosts.
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Affiliation(s)
- Khadidja Yousfi
- Laboratoire d'Écologie Microbienne, FSNV, Université de Béjaia, 06000, Béjaia, Algeria.,Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, H9X 3R5, Canada
| | - Abdelaziz Touati
- Laboratoire d'Écologie Microbienne, FSNV, Université de Béjaia, 06000, Béjaia, Algeria
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, H9X 3R5, Canada
| | - Philippe Garneau
- Faculté de Médecine Vétérinaire, Centre de Recherche en Infectiologie Porcine, Université de Montréal, St-Hyacinthe, QC, Canada
| | - Soumia Brahmi
- Laboratoire d'Écologie Microbienne, FSNV, Université de Béjaia, 06000, Béjaia, Algeria
| | - Alima Gharout-Sait
- Laboratoire d'Écologie Microbienne, FSNV, Université de Béjaia, 06000, Béjaia, Algeria
| | - Josée Harel
- Faculté de Médecine Vétérinaire, Centre de Recherche en Infectiologie Porcine, Université de Montréal, St-Hyacinthe, QC, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, H9X 3R5, Canada. .,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada.
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17
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Cadieux B, Colavecchio A, Jeukens J, Freschi L, Emond-Rheault JG, Kukavica-Ibrulj I, Levesque RC, Bekal S, Chandler JC, Coleman SM, Bisha B, Goodridge LD. Prophage induction reduces Shiga toxin producing Escherichia coli (STEC) and Salmonella enterica on tomatoes and spinach: A model study. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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18
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Marchand-Senécal X, Bekal S, Pilon PA, Sylvestre JL, Gaudreau C. Campylobacter fetus Cluster Among Men Who Have Sex With Men, Montreal, Quebec, Canada, 2014-2016. Clin Infect Dis 2018; 65:1751-1753. [PMID: 29020280 DOI: 10.1093/cid/cix610] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/07/2017] [Indexed: 11/13/2022] Open
Abstract
From March 2014 to December 2016, a cluster of 13 cases of Campylobacter fetus intestinal and extraintestinal infections, including 2 patients with an aortic mycotic aneurysm, caused significant morbidity. The cluster likely resulted from sexual transmission between men having sex with men living in the greater Montreal area, Quebec, Canada.
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Affiliation(s)
- Xavier Marchand-Senécal
- Département de microbiologie médicale et infectiologie, Centre Hospitalier de l'Université de Montréal-Hôpital Saint-Luc.,Département de microbiologie, immunologie et infectiologie, Université de Montréal
| | - Sadjia Bekal
- Département de microbiologie, immunologie et infectiologie, Université de Montréal.,Laboratoire de Santé Publique du Québec/Institut National de Santé publique du Québec
| | - Pierre A Pilon
- Direction de santé publique, Centre intégré universitaire de santé et de services sociaux du Centre-Sud-de-l'île-de-Montréal.,Département de médecine sociale et préventive, Université de Montréal, Québec, Canada
| | - Jean-Loup Sylvestre
- Direction de santé publique, Centre intégré universitaire de santé et de services sociaux du Centre-Sud-de-l'île-de-Montréal
| | - Christiane Gaudreau
- Département de microbiologie médicale et infectiologie, Centre Hospitalier de l'Université de Montréal-Hôpital Saint-Luc.,Département de microbiologie, immunologie et infectiologie, Université de Montréal
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19
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Mottawea W, Duceppe MO, Dupras AA, Usongo V, Jeukens J, Freschi L, Emond-Rheault JG, Hamel J, Kukavica-Ibrulj I, Boyle B, Gill A, Burnett E, Franz E, Arya G, Weadge JT, Gruenheid S, Wiedmann M, Huang H, Daigle F, Moineau S, Bekal S, Levesque RC, Goodridge LD, Ogunremi D. Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping. Front Microbiol 2018; 9:836. [PMID: 29780368 PMCID: PMC5945981 DOI: 10.3389/fmicb.2018.00836] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/12/2018] [Indexed: 12/30/2022] Open
Abstract
Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR) of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.
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Affiliation(s)
- Walid Mottawea
- Department of Food Science and Agricultural Chemistry, McGill University, Ste Anne de Bellevue, QC, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.,Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Marc-Olivier Duceppe
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Andrée A Dupras
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Valentine Usongo
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique due Québec, Ste Anne de Bellevue, QC, Canada
| | - Julie Jeukens
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Luca Freschi
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | | | - Jeremie Hamel
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Irena Kukavica-Ibrulj
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Alexander Gill
- Health Canada, Bureau of Microbial Hazards, Ottawa, ON, Canada
| | - Elton Burnett
- Institute of Parasitology, McGill University, Montreal, QC, Canada
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Gitanjali Arya
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Joel T Weadge
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Samantha Gruenheid
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Hongsheng Huang
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - France Daigle
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bioinformatique, Université Laval, Québec City, QC, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique due Québec, Ste Anne de Bellevue, QC, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Lawrence D Goodridge
- Department of Food Science and Agricultural Chemistry, McGill University, Ste Anne de Bellevue, QC, Canada
| | - Dele Ogunremi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
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20
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Usongo V, Berry C, Yousfi K, Doualla-Bell F, Labbé G, Johnson R, Fournier E, Nadon C, Goodridge L, Bekal S. Impact of the choice of reference genome on the ability of the core genome SNV methodology to distinguish strains of Salmonella enterica serovar Heidelberg. PLoS One 2018; 13:e0192233. [PMID: 29401524 PMCID: PMC5798827 DOI: 10.1371/journal.pone.0192233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/18/2018] [Indexed: 12/15/2022] Open
Abstract
Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. The core genome single nucleotide variant pipeline (cgSNV) is one of several whole genome based sequence typing methods used for the laboratory investigation of foodborne pathogens. SNV detection using this method requires a reference genome. The purpose of this study was to investigate the impact of the choice of the reference genome on the cgSNV-informed phylogenetic clustering and inferred isolate relationships. We found that using a draft or closed genome of S. Heidelberg as reference did not impact the ability of the cgSNV methodology to differentiate among 145 S. Heidelberg isolates involved in foodborne outbreaks. We also found that using a distantly related genome such as S. Dublin as choice of reference led to a loss in resolution since some sporadic isolates were found to cluster together with outbreak isolates. In addition, the genetic distances between outbreak isolates as well as between outbreak and sporadic isolates were overall reduced when S. Dublin was used as the reference genome as opposed to S. Heidelberg.
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Affiliation(s)
- Valentine Usongo
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Department of Food Science and Agricultural Chemistry, Food Safety and Quality Program, McGill University, Ste Anne de Bellevue, Québec, Canada
| | - Chrystal Berry
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Khadidja Yousfi
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | | | - Genevieve Labbé
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Roger Johnson
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Celine Nadon
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lawrence Goodridge
- Department of Food Science and Agricultural Chemistry, Food Safety and Quality Program, McGill University, Ste Anne de Bellevue, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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21
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Gaudreau C, Pilon PA, Sylvestre JL, Boucher F, Bekal S. Multidrug-Resistant Campylobacter coli in Men Who Have Sex with Men, Quebec, Canada, 2015. Emerg Infect Dis 2018; 22:1661-3. [PMID: 27533504 PMCID: PMC4994334 DOI: 10.3201/eid2209.151695] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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22
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Gaudreau C, Pilon PA, Cornut G, Marchand-Senecal X, Bekal S. Shigella flexneri with Ciprofloxacin Resistance and Reduced Azithromycin Susceptibility, Canada, 2015. Emerg Infect Dis 2018; 22:2016-2018. [PMID: 27767915 PMCID: PMC5088001 DOI: 10.3201/eid2211.160883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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23
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Mauffrey F, Fournier É, Demczuk W, Martin I, Mulvey M, Martineau C, Lévesque S, Bekal S, Domingo MC, Doualla-Bell F, Longtin J, Lefebvre B. Comparison of sequential multiplex PCR, sequetyping and whole genome sequencing for serotyping of Streptococcus pneumoniae. PLoS One 2017; 12:e0189163. [PMID: 29236737 PMCID: PMC5728576 DOI: 10.1371/journal.pone.0189163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/20/2017] [Indexed: 01/22/2023] Open
Abstract
Streptococcus pneumoniae is one of the major causes of pneumonia, meningitis and other pneumococcal infections in young children and elders. Determination of circulating S. pneumoniae serotypes is an essential service by public health laboratories for the monitoring of putative serotype replacement following the introduction of pneumococcal conjugate vaccines (PCVs) and of the efficacy of the immunization program. The Quellung method remains the gold standard for typing S. pneumoniae. Although this method is very effective, it is also costly, time consuming and not totally reliable due to its subjective nature. The objectives of this study were to test and evaluate the efficiency of 3 different molecular methods compared to the Quellung method. Sequential multiplex PCR, sequetyping and whole genome sequencing (WGS) were chosen and tested using a set of diverse S. pneumoniae. One-hundred and eighteen isolates covering 83 serotypes were subjected to multiplex PCR and sequetyping while 88 isolates covering 53 serotypes were subjected to WGS. Sequential multiplex PCR allowed the identification of a significant proportion (49%) of serotypes at the serogroup or subset level but only 27% were identified at the serotype level. Using WGS, 55% to 60% of isolates were identified at the serotype level depending on the analysis strategy used. Finally, sequetyping demonstrated the lowest performance, with 17% of misidentified serotypes. The use of Jin cpsB database instead of the GenBank database slightly improved results but did not significantly impact the efficiency of sequetyping. Although none of these molecular methods may currently replace the Quellung method, WGS remains the most promising molecular pneumococcal serotyping method.
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Affiliation(s)
- Florian Mauffrey
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Éric Fournier
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Christine Martineau
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Simon Lévesque
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Marc-Christian Domingo
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Florence Doualla-Bell
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Jean Longtin
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
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24
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Iraola G, Forster SC, Kumar N, Lehours P, Bekal S, García-Peña FJ, Paolicchi F, Morsella C, Hotzel H, Hsueh PR, Vidal A, Lévesque S, Yamazaki W, Balzan C, Vargas A, Piccirillo A, Chaban B, Hill JE, Betancor L, Collado L, Truyers I, Midwinter AC, Dagi HT, Mégraud F, Calleros L, Pérez R, Naya H, Lawley TD. Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota. Nat Commun 2017; 8:1367. [PMID: 29118316 PMCID: PMC5678084 DOI: 10.1038/s41467-017-01449-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/15/2017] [Indexed: 12/31/2022] Open
Abstract
Campylobacter fetus is a venereal pathogen of cattle and sheep, and an opportunistic human pathogen. It is often assumed that C. fetus infection occurs in humans as a zoonosis through food chain transmission. Here we show that mammalian C. fetus consists of distinct evolutionary lineages, primarily associated with either human or bovine hosts. We use whole-genome phylogenetics on 182 strains from 17 countries to provide evidence that C. fetus may have originated in humans around 10,500 years ago and may have "jumped" into cattle during the livestock domestication period. We detect C. fetus genomes in 8% of healthy human fecal metagenomes, where the human-associated lineages are the dominant type (78%). Thus, our work suggests that C. fetus is an unappreciated human intestinal pathobiont likely spread by human to human transmission. This genome-based evolutionary framework will facilitate C. fetus epidemiology research and the development of improved molecular diagnostics and prevention schemes for this neglected pathogen.
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Affiliation(s)
- Gregorio Iraola
- Unidad de Bioinformática, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay. .,Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay. .,Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK
| | - Philippe Lehours
- Bordeaux Research in Translational Oncology, INSERM UMR1053, University of Bordeaux, 33076, Bordeaux, France.,French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, 33076, Bordeaux, France
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada, H9X 3Y3.,Départment de Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, QC, Canada, H3T 1J4
| | - Francisco J García-Peña
- Departamento de Bacteriología, Laboratorio Central de Veterinaria de Algete (MAGRAMA), 28110, Algete, Spain
| | - Fernando Paolicchi
- Laboratorio de Bacteriología, EEA-INTA Balcarce, Balcarce, 7620, Argentina
| | - Claudia Morsella
- Laboratorio de Bacteriología, EEA-INTA Balcarce, Balcarce, 7620, Argentina
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, 07743, Jena, Germany
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, Taipei, 10617, Taiwan
| | - Ana Vidal
- Animal and Plant Health Association (APHA), Addlestone, KT15 3NB, UK
| | - Simon Lévesque
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada, H9X 3Y3
| | - Wataru Yamazaki
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Claudia Balzan
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Agueda Vargas
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Alessandra Piccirillo
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, 35122, Italy
| | - Bonnie Chaban
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatchewan, SK, Canada, S7N 5A2
| | - Laura Betancor
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, 11600, Uruguay
| | - Luis Collado
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, 5090000, Valdivia, Chile
| | - Isabelle Truyers
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Anne C Midwinter
- EpiLab, Infectious Disease Research Centre, Massey University, Palmerston North, 4442, New Zealand
| | - Hatice T Dagi
- Department of Microbiology, Faculty of Medicine, Selçuk University, Selçuklu, 42250, Turkey
| | - Francis Mégraud
- Bordeaux Research in Translational Oncology, INSERM UMR1053, University of Bordeaux, 33076, Bordeaux, France.,French National Reference Center for Campylobacters and Helicobacters, University of Bordeaux, 33076, Bordeaux, France
| | - Lucía Calleros
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, 11400, Montevideo, Uruguay
| | - Hugo Naya
- Unidad de Bioinformática, Institut Pasteur Montevideo, 11400, Montevideo, Uruguay.,Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, 12900, Montevideo, Uruguay
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, UK.
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25
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Marinier E, Zaheer R, Berry C, Weedmark KA, Domaratzki M, Mabon P, Knox NC, Reimer AR, Graham MR, Chui L, Patterson-Fortin L, Zhang J, Pagotto F, Farber J, Mahony J, Seyer K, Bekal S, Tremblay C, Isaac-Renton J, Prystajecky N, Chen J, Slade P, Van Domselaar G. Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations. Nucleic Acids Res 2017; 45:e159. [PMID: 29048594 PMCID: PMC5737611 DOI: 10.1093/nar/gkx702] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 08/01/2017] [Indexed: 11/13/2022] Open
Abstract
The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using 'big data' approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune's loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-targets using probabilistic models. Neptune uses parallel computing to efficiently identify and extract these loci from draft genome assemblies without requiring multiple sequence alignments or other computationally expensive comparative sequence analyses. Tests on simulated and real datasets showed that Neptune rapidly identifies regions that are both sensitive and specific. We demonstrate that this system can identify trait-specific loci from different bacterial lineages. Neptune is broadly applicable for comparative bacterial analyses, yet will particularly benefit pathogenomic applications, owing to efficient and sensitive discovery of differentially abundant genomic loci. The software is available for download at: http://github.com/phac-nml/neptune.
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Affiliation(s)
- Eric Marinier
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Rahat Zaheer
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Kelly A Weedmark
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Michael Domaratzki
- Department of Computer Science, University of Manitoba, 66 Chancellors Circle, Winnipeg, MB R3T 2N2, Canada
| | - Philip Mabon
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Natalie C Knox
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Aleisha R Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada
| | - Morag R Graham
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada
| | - Linda Chui
- Provincial Laboratory for Public Health, 8440 112 St NW, Edmonton, AB T6G 2P4, Canada.,Department of Laboratory Medicine and Pathology, University of Alberta, 116 St. and 85 Ave., Edmonton, AB T6G 2R3, Canada
| | - Laura Patterson-Fortin
- Department of Laboratory Medicine and Pathology, University of Alberta, 116 St. and 85 Ave., Edmonton, AB T6G 2R3, Canada
| | - Jian Zhang
- Alberta Innovates-Technology Futures, 250 Karl Clark Road, Edmonton, AB T6N 1E4, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Health Canada, 251 Sir Frederick Banting Driveway, Tunney's Pasture, Ottawa, ON K1A 0K9, Canada
| | - Jeff Farber
- Bureau of Microbial Hazards, Health Canada, 251 Sir Frederick Banting Driveway, Tunney's Pasture, Ottawa, ON K1A 0K9, Canada
| | - Jim Mahony
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Karine Seyer
- Canadian Food Inspection Agency, St. Hyacinthe Laboratory, 3400 Boulevard Casavant O, Saint-Hyacinthe, QC J2S 8E3, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, 20045 Ch Ste-Marie, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada.,Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Pavillon Roger-Gaudry, Université de Montréal, C.P. 6128, Succ. Centre-ville Montréal, QC H3C 3J7, Canada
| | - Cécile Tremblay
- Laboratoire de santé publique du Québec, 20045 Ch Ste-Marie, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada.,Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Pavillon Roger-Gaudry, Université de Montréal, C.P. 6128, Succ. Centre-ville Montréal, QC H3C 3J7, Canada
| | - Judy Isaac-Renton
- BC Public Health and Microbiology Reference Laboratory, 655 W. 12th Avenue, Vancouver, BC V5Z 4R4, Canada
| | - Natalie Prystajecky
- BC Public Health and Microbiology Reference Laboratory, 655 W. 12th Avenue, Vancouver, BC V5Z 4R4, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Rm. G227 - 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Jessica Chen
- Department of Food Science, Food, Nutrition and Health, University of British Columbia, 2329 West Mall, Vancouver, BC V6T 1Z4, Canada
| | - Peter Slade
- Maple Leaf Foods, 6897 Financial Drive, Mississauga, ON L5N 0A8, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, MB R3E 3R2, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada
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26
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Colavecchio A, D'Souza Y, Tompkins E, Jeukens J, Freschi L, Emond-Rheault JG, Kukavica-Ibrulj I, Boyle B, Bekal S, Tamber S, Levesque RC, Goodridge LD. Prophage Integrase Typing Is a Useful Indicator of Genomic Diversity in Salmonella enterica. Front Microbiol 2017; 8:1283. [PMID: 28740489 PMCID: PMC5502288 DOI: 10.3389/fmicb.2017.01283] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 06/26/2017] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica is a bacterial species that is a major cause of illness in humans and food-producing animals. S. enterica exhibits considerable inter-serovar diversity, as evidenced by the large number of host adapted serovars that have been identified. The development of methods to assess genome diversity in S. enterica will help to further define the limits of diversity in this foodborne pathogen. Thus, we evaluated a PCR assay, which targets prophage integrase genes, as a rapid method to investigate S. enterica genome diversity. To evaluate the PCR prophage integrase assay, 49 isolates of S. enterica were selected, including 19 clinical isolates from clonal serovars (Enteritidis and Heidelberg) that commonly cause human illness, and 30 isolates from food-associated Salmonella serovars that rarely cause human illness. The number of integrase genes identified by the PCR assay was compared to the number of integrase genes within intact prophages identified by whole genome sequencing and phage finding program PHASTER. The PCR assay identified a total of 147 prophage integrase genes within the 49 S. enterica genomes (79 integrase genes in the food-associated Salmonella isolates, 50 integrase genes in S. Enteritidis, and 18 integrase genes in S. Heidelberg). In comparison, whole genome sequencing and PHASTER identified a total of 75 prophage integrase genes within 102 intact prophages in the 49 S. enterica genomes (44 integrase genes in the food-associated Salmonella isolates, 21 integrase genes in S. Enteritidis, and 9 integrase genes in S. Heidelberg). Collectively, both the PCR assay and PHASTER identified the presence of a large diversity of prophage integrase genes in the food-associated isolates compared to the clinical isolates, thus indicating a high degree of diversity in the food-associated isolates, and confirming the clonal nature of S. Enteritidis and S. Heidelberg. Moreover, PHASTER revealed a diversity of 29 different types of prophages and 23 different integrase genes within the food-associated isolates, but only identified four different phages and integrase genes within clonal isolates of S. Enteritidis and S. Heidelberg. These results demonstrate the potential usefulness of PCR based detection of prophage integrase genes as a rapid indicator of genome diversity in S. enterica.
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Affiliation(s)
- Anna Colavecchio
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-BellevueQC, Canada
| | - Yasmin D'Souza
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-BellevueQC, Canada
| | - Elizabeth Tompkins
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-BellevueQC, Canada
| | - Julie Jeukens
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec CityQC, Canada
| | - Luca Freschi
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec CityQC, Canada
| | | | - Irena Kukavica-Ibrulj
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec CityQC, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec CityQC, Canada
| | - Sadjia Bekal
- Pathogènes entériques et Bioterrorisme, Laboratoire de santé publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Sandeep Tamber
- Salmonella Research Laboratory, Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec CityQC, Canada
| | - Lawrence D Goodridge
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-BellevueQC, Canada
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27
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Emond-Rheault JG, Jeukens J, Freschi L, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Colavecchio A, Barrere V, Cadieux B, Arya G, Bekal S, Berry C, Burnett E, Cavestri C, Chapin TK, Crouse A, Daigle F, Danyluk MD, Delaquis P, Dewar K, Doualla-Bell F, Fliss I, Fong K, Fournier E, Franz E, Garduno R, Gill A, Gruenheid S, Harris L, Huang CB, Huang H, Johnson R, Joly Y, Kerhoas M, Kong N, Lapointe G, Larivière L, Loignon S, Malo D, Moineau S, Mottawea W, Mukhopadhyay K, Nadon C, Nash J, Ngueng Feze I, Ogunremi D, Perets A, Pilar AV, Reimer AR, Robertson J, Rohde J, Sanderson KE, Song L, Stephan R, Tamber S, Thomassin P, Tremblay D, Usongo V, Vincent C, Wang S, Weadge JT, Wiedmann M, Wijnands L, Wilson ED, Wittum T, Yoshida C, Youfsi K, Zhu L, Weimer BC, Goodridge L, Levesque RC. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis. Front Microbiol 2017. [PMID: 28626454 PMCID: PMC5454079 DOI: 10.3389/fmicb.2017.00996] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.
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Affiliation(s)
| | - Julie Jeukens
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Luca Freschi
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Irena Kukavica-Ibrulj
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Brian Boyle
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Marie-Josée Dupont
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | | | | | | | - Gitanjali Arya
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | | | - Travis K Chapin
- Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
| | | | - France Daigle
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| | - Michelle D Danyluk
- Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
| | | | - Ken Dewar
- McGill University, MontréalQC, Canada.,Génome Québec Innovation Center, MontréalQC, Canada
| | | | | | - Karen Fong
- Food Safety Engineering, Faculty of Land and Food Systems, University of British Columbia, VancouverBC, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Eelco Franz
- National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | | | - Alexander Gill
- Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
| | | | - Linda Harris
- UC Davis Food Science and Technology, DavisCA, United States
| | - Carol B Huang
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | - Roger Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Yann Joly
- McGill University, MontréalQC, Canada
| | - Maud Kerhoas
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| | - Nguyet Kong
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | | | | | | | | | - Walid Mottawea
- McGill University, MontréalQC, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura UniversityMansoura, Egypt
| | | | - Céline Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - John Nash
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | | | - Ann Perets
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | - Aleisha R Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - John Rohde
- Department of Microbiology and Immunology, Dalhousie University, HalifaxNS, Canada
| | | | | | - Roger Stephan
- Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
| | | | | | - Valentine Usongo
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Caroline Vincent
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Siyun Wang
- Food Safety Engineering, Faculty of Land and Food Systems, University of British Columbia, VancouverBC, Canada
| | - Joel T Weadge
- Biological and Chemical Sciences, Wilfrid Laurier University, WaterlooON, Canada
| | - Martin Wiedmann
- Department of Food Science, Cornell University, IthacaNY, United States
| | - Lucas Wijnands
- National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | - Emily D Wilson
- Biological and Chemical Sciences, Wilfrid Laurier University, WaterlooON, Canada
| | - Thomas Wittum
- College of Veterinary Medicine, The Ohio State University, ColumbusOH, United States
| | - Catherine Yoshida
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Khadija Youfsi
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Lei Zhu
- McGill University, MontréalQC, Canada
| | - Bart C Weimer
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | - Roger C Levesque
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
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28
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Yousfi K, Touati A, Lefebvre B, Fournier É, Côté JC, Soualhine H, Walker M, Bougdour D, Tremblay C, Bekal S. A Novel Plasmid, pSx1, Harboring a New Tn1696 Derivative from Extensively Drug-Resistant Shewanella xiamenensis Encoding OXA-416. Microb Drug Resist 2017; 23:429-436. [DOI: 10.1089/mdr.2016.0025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Khadidja Yousfi
- Laboratoire d'Écologie Microbienne, FSNV, Université A/MIRA de Bejaia, Bejaia, Algérie
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Abdelaziz Touati
- Laboratoire d'Écologie Microbienne, FSNV, Université A/MIRA de Bejaia, Bejaia, Algérie
| | - Brigitte Lefebvre
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Éric Fournier
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Jean-Charles Côté
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Hafid Soualhine
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Matthew Walker
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Djamila Bougdour
- Laboratoire d'Écologie Microbienne, FSNV, Université A/MIRA de Bejaia, Bejaia, Algérie
| | - Cécile Tremblay
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Canada
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29
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Fravalo P, Cherifi T, Neira Feliciano KD, Letellier A, Fairbrother JH, Bekal S. Characterisation of InlA truncation in Listeria monocytogenes isolates from farm animals and human cases in the province of Quebec. Vet Rec Open 2017; 4:e000199. [PMID: 28761668 PMCID: PMC5520022 DOI: 10.1136/vetreco-2016-000199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/21/2016] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
The introduction of Listeria monocytogenes into the food production chain is a concern, with numerous grouped cases of listeriosis associated with milk-derived or pork-derived products have been documented. Management of this zoonotic pathogen considers all strains as an equal risk. Recently, a new perspective for characterisation of strain virulence was introduced with the discovery of the unaltered sequence of InlA as a determinant of strain virulence; this has also been reported as an infrequent finding among so-called environmental strains, that is, strains isolated from food or from surfaces in food industries. The aim of this study was to differentiate L monocytogenes strains isolated from animal cases versus those from human cases and to differentiate clinical strains from environmental ones using a Caenorhabditis elegans virulence testing model. In Quebec in 2013/2014, the surveillance of L monocytogenes clinical isolates registered a total of 20 strains of animal origin and 16 pulsed-field gel electrophoresis types isolated from human cases. The mixed PCR multiplex agglutination protocol used for geno-serotyping clearly discriminated genogroup IVB strains from bovine and human origins. The presence of a premature stop codon single nucleotide polymorphism in the inlA gene sequence in clinical strains and the identical behaviour of particular strains in the C elegans model are discussed in this paper from the perspective of industrial management of L monocytogenes risk.
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Affiliation(s)
- Philippe Fravalo
- University of Montreal, Faculty veterinary medicine, Dpt Pathology Microbiology 3190 Sicotte J2S2M2, Saint Hyacinthe, QC, Canada
| | - Tamazight Cherifi
- University of Montreal, Faculty veterinary medicine, Dpt Pathology Microbiology 3190 Sicotte J2S2M2, Saint Hyacinthe, QC, Canada
| | - Kersti Dina Neira Feliciano
- University of Montreal, Faculty veterinary medicine, Dpt Pathology Microbiology 3190 Sicotte J2S2M2, Saint Hyacinthe, QC, Canada
| | - Ann Letellier
- University of Montreal, Faculty veterinary medicine, Dpt Pathology Microbiology 3190 Sicotte J2S2M2, Saint Hyacinthe, QC, Canada
| | - Julie-Hélène Fairbrother
- Laboratoire d'épidémiosurveillance animale du Québec Ministry of Agriculture, Fisheries and Food, Saint Hyacinthe, QC, Canada
| | - Sadjia Bekal
- Provincial Public Health Laboratory (LSPQ), QC, Canada
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30
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Yousfi K, Bekal S, Usongo V, Touati A. Current trends of human infections and antibiotic resistance of the genus Shewanella. Eur J Clin Microbiol Infect Dis 2017; 36:1353-1362. [PMID: 28299457 DOI: 10.1007/s10096-017-2962-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/05/2017] [Indexed: 10/20/2022]
Abstract
Shewanella spp. are commonly known as environmental bacteria and are most frequently isolated from aquatic areas. Currently, diseases syndromes and multidrug resistance have increasingly been reported in the genus Shewanella. Some species are associated with various infections, such as skin and soft tissue infections, as well as bacteremia. Generally, these bacteria are opportunistic and mostly affect people with an impaired immune system. This genus is also a probable vehicle and progenitor of antibiotic resistance genes. In fact, several resistance genes and mobile genetic elements have been identified in some resistant species isolated from environmental or clinical settings. These genes confer resistance to different antibiotic classes, including those used in therapies such as β-lactams and quinolones, and are generally located on the chromosome. Recently, a multidrug-resistant (MDR) plasmid harboring several drug resistance genes associated with transposons and integrons has been identified in Shewanella xiamenensis. These antibiotic resistance genes can circulate in the environment and contribute to the emergence of antibiotic resistance. This review describes different aspects of Shewanella, focusing on the infections caused by this genus, as well as their role in the propagation of antibiotic resistance via mobile genetic elements.
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Affiliation(s)
- K Yousfi
- Laboratoire d'Écologie Microbienne, FSNV, Université de Bejaia, Bejaia, 06000, Algeria.,Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - S Bekal
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - V Usongo
- Laboratoire d'Écologie Microbienne, FSNV, Université de Bejaia, Bejaia, 06000, Algeria.,Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC, Canada
| | - A Touati
- Laboratoire d'Écologie Microbienne, FSNV, Université de Bejaia, Bejaia, 06000, Algeria.
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31
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Marchand-Senécal X, Bekal S, Pilon PA, Sylvestre JL, Gaudreau C. Campylobacter fetus Outbreak in Montreal, Quebec, Canada: A Retrospective Analysis. Open Forum Infect Dis 2016. [DOI: 10.1093/ofid/ofw172.901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Xavier Marchand-Senécal
- Département De Microbiologie Médicale Et Infectiologie, CHUM-Hôpital Saint-Luc, Montreal, Quebec, Canada
- Département De Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Quebec, Canada
| | - Sadjia Bekal
- Département De Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Quebec, Canada
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Pierre A. Pilon
- Direction de Santé Publique, Centre Intégré Universitaire de Santé et de Services Sociaux du Centre-Sud-de-l'île-de-Montréal, Montreal, Quebec, Canada
- Département De Médecine Sociale et Préventive, Université de Montréal, Montreal, Quebec, Canada
| | - Jean-Loup Sylvestre
- Direction de Santé Publique, Centre Intégré Universitaire de Santé et de Services Sociaux du Centre-Sud-de-l'île-de-Montréal, Montreal, Quebec, Canada
| | - Christiane Gaudreau
- Département De Microbiologie Médicale Et Infectiologie, CHUM-Hôpital Saint-Luc, Montreal, Quebec, Canada
- Département De Microbiologie, Immunologie et Infectiologie, Université de Montréal, Montreal, Quebec, Canada
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32
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Lévesque S, Lemay F, Bekal S, Frost EH, Michaud S. First reported case of Campylobacter lanienae enteritis in a human. JMM Case Rep 2016; 3:e005045. [PMID: 28348764 PMCID: PMC5330232 DOI: 10.1099/jmmcr.0.005045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/05/2016] [Accepted: 04/29/2016] [Indexed: 01/05/2023] Open
Abstract
Introduction: Campylobacters are the most frequently identified bacteria causing diarrhoea in humans worldwide. Campylobacter lanienae was isolated for the first time in 2000 from faecal samples of two asymptomatic abattoir workers in Switzerland during a routine hygiene screen, but has never been associated with human disease. Case presentation: At hospital admission, the patient reported diarrhoea, lower abdominal cramps, nausea, one episode of bilious vomiting and low-grade fever of 38 °C. The patient was having 10 or more diarrheic stools per day as well as during the night, and had noticed blood mixed with the stools on several occasions. Stool cultures were negative for species of Salmonella and Shigella, Escherichia coli O157:H7 and Yersinia enterocolitica, but were positive for C. lanienae. Identification was made by classical biochemical testing, as well as 16S rRNA gene and cpn60 sequencing. The patient slowly improved without antibiotic treatment and was discharged nine days after admission with complete resolution of symptoms. Conclusion: On the whole it seems very likely that C. lanienae was the causative agent. Clinical microbiologists should be aware of this micro-organism which can be identified by phenotypic and molecular methods. The real burden of C. lanienae infection in humans might be underestimated and should be further investigated as a potential cause of human diarrhoea disease.
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Affiliation(s)
- Simon Lévesque
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec , Canada
| | - Frédéric Lemay
- Faculté de Médecine et des sciences de la santé de l'Université de Sherbrooke, Sherbrooke, Québec, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke(CHUS), Sherbrooke, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec/Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec , Canada
| | - Eric H Frost
- Faculté de Médecine et des sciences de la santé de l'Université de Sherbrooke, Sherbrooke, Québec, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke(CHUS), Sherbrooke, Québec, Canada
| | - Sophie Michaud
- Faculté de Médecine et des sciences de la santé de l'Université de Sherbrooke, Sherbrooke, Québec , Canada
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33
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Bekal S, Vincent A, Lin A, Harel J, Côté JC, Tremblay C. A Fatal Case of Necrotizing Fasciitis Caused by a Highly Virulent Escherichia coli Strain. Can J Infect Dis Med Microbiol 2016; 2016:2796412. [PMID: 27366162 PMCID: PMC4906195 DOI: 10.1155/2016/2796412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/12/2016] [Indexed: 12/17/2022]
Abstract
Necrotizing fasciitis is a serious disease characterized by the necrosis of the subcutaneous tissues and fascia. E. coli as the etiologic agent of necrotizing fasciitis is a rare occurrence. A 66-year-old woman underwent total abdominal hysterectomy with bilateral salpingo-oophorectomy. She rapidly developed necrotizing fasciitis which led to her death 68 hours following surgery. An E. coli strain was isolated from blood and fascia cultures. DNA microarray revealed the presence of 20 virulence genes.
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Affiliation(s)
- Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada H9X 3R5
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada H3T 1J4
| | - André Vincent
- Centre Hospitalier Affilié Universitaire, Hôtel-Dieu de Lévis, Lévis, QC, Canada G6V 3Z1
| | - Alex Lin
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada H9X 3R5
| | - Josée Harel
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada J2S 2M2
| | - Jean-Charles Côté
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada H9X 3R5
| | - Cécile Tremblay
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada H9X 3R5
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada H3T 1J4
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Abstract
An outbreak of Shigella sonnei that occurred in the ultra-Orthodox Jewish community (UOJC) was the subject of an investigation and response by the Montréal Regional Public Health Department (DRSP), who collaborated with several health and community partners. A total of 27 confirmed cases were reported in this outbreak, which lasted from February to June 2015. The epidemic curve was compatible with a point source with secondary person-to-person transmission. In 11 of the 27 cases, pulsed-field gel electrophoresis (PFGE) analysis of strains found a single PFGE pattern newly identified in Quebec. Almost all strains tested showed resistance to ampicillin and trimethoprim-sulfamethoxazole (TMP/SMX). All the cases resided in Montréal Centre-West. Most of the cases were under 5 years old and attended a daycare centre, an environment recognized to be conducive to the transmission of enteric diseases. DRSP sent timely information to families, daycare and school stakeholders, community partners and synagogues in the UOJC, which helped reduce the transmission of shigellosis in the community.
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Affiliation(s)
- PA Pilon
- Infectious Disease and Prevention Control, Montréal Regional Public Health Department, Montréal, QC
- School of Public Health, Université de Montréal, Montréal, QC
| | - B Camara
- Infectious Disease and Prevention Control, Montréal Regional Public Health Department, Montréal, QC
| | - S Bekal
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC
- Department of Microbiology and Immunology, Université de Montréal, Montréal, QC
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Labbé G, Edirmanasinghe R, Ziebell K, Nash JHE, Bekal S, Parmley EJ, Mulvey MR, Johnson RP. Complete Genome and Plasmid Sequences of Three Canadian Isolates of Salmonella enterica subsp. enterica Serovar Heidelberg from Human and Food Sources. Genome Announc 2016; 4:e01526-15. [PMID: 26769926 PMCID: PMC4714108 DOI: 10.1128/genomea.01526-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/18/2015] [Indexed: 11/20/2022]
Abstract
Isolates of Salmonella enterica subsp. enterica serovar Heidelberg are often associated with poultry products and may cause severe human illness. Here, we report the fully assembled genome and plasmid sequences of three S. Heidelberg strains with phage types 9, 29, and 41.
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Affiliation(s)
- Geneviève Labbé
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Romaine Edirmanasinghe
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada National Microbiology Laboratory at the Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kim Ziebell
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - John H E Nash
- National Microbiology Laboratory at Toronto, Public Health Agency of Canada, Toronto, Ontario, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - E Jane Parmley
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada National Microbiology Laboratory at the Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Roger P Johnson
- National Microbiology Laboratory at Guelph, Public Health Agency of Canada, Guelph, Ontario, Canada
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Bekal S, Pilon PA, Cloutier N, Doualla-Bell F, Longtin J. Identification of Shigella flexneri isolates carrying the Shiga toxin 1-producing gene in Quebec, Canada, linked to travel to Haiti. Can J Microbiol 2015; 61:995-6. [PMID: 26401981 DOI: 10.1139/cjm-2015-0538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Sadjia Bekal
- a Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada.,b Département de Microbiologie, Infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Pierre A Pilon
- c Direction régionale de santé publique de Montréal, Quebec, Canada
| | - Nancy Cloutier
- a Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Florence Doualla-Bell
- a Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada.,d Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Quebec, Canada
| | - Jean Longtin
- a Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada.,e Centre de recherche en infectiologie de l'Université Laval, Quebec, Canada
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Gaudreau C, Rodrigues-Coutlée S, Pilon PA, Coutlée F, Bekal S. Long-Lasting Outbreak of Erythromycin- and Ciprofloxacin-Resistant Campylobacter jejuni Subspecies jejuni From 2003 to 2013 in Men Who Have Sex With Men, Quebec, Canada. Clin Infect Dis 2015; 61:1549-52. [PMID: 26187024 DOI: 10.1093/cid/civ570] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 07/08/2015] [Indexed: 11/13/2022] Open
Abstract
From January 2003 to December 2013, sexual transmission of 2 clades of Campylobacter jejuni subspecies jejuni isolates resulted in a prolonged outbreak among men who have sex with men living in Quebec, Canada. The outbreak isolates were acquired locally and were resistant to erythromycin and ciprofloxacin.
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Affiliation(s)
- Christiane Gaudreau
- Département de microbiologie médicale et infectiologie, Centre hospitalier de l'Université de Montréal Département de microbiologie, infectiologie et immunologie, Université de Montréal Laboratoire de Santé Publique du Québec/Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue
| | - Sophie Rodrigues-Coutlée
- Département de microbiologie médicale et infectiologie, Centre hospitalier de l'Université de Montréal
| | - Pierre A Pilon
- Direction de santé publique, Agence de la santé et des services sociaux de Montréal Département de médecine sociale et préventive, Université de Montréal, Québec, Canada
| | - François Coutlée
- Département de microbiologie médicale et infectiologie, Centre hospitalier de l'Université de Montréal Département de microbiologie, infectiologie et immunologie, Université de Montréal
| | - Sadjia Bekal
- Département de microbiologie, infectiologie et immunologie, Université de Montréal Laboratoire de Santé Publique du Québec/Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue
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Gaulin C, Ramsay D, Catford A, Bekal S. Escherichia coliO157:H7 Outbreak Associated with the Consumption of Beef and Veal Tartares in the Province of Quebec, Canada, in 2013. Foodborne Pathog Dis 2015; 12:612-8. [DOI: 10.1089/fpd.2014.1919] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Colette Gaulin
- Ministère de la Santé et des Services Sociaux, Québec, Canada
| | - Danielle Ramsay
- Ministère de l'Agriculture, des Pêcheries, et de l'Alimentation du Québec, Québec, Canada
| | - Angela Catford
- Health Canada, Health Products and Food Branch, Ottawa, Ontario, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec (INSPQ), Sainte-Anne de Bellevue, Province de Québec, Canada
- Département de Microbiologie, Infectiologie, et Immunologie, Université de Montréal, Montréal, Québec, Canada
- Institut National de Santé Publique du Québec, Montréal, Québec, Canada
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Currie A, Farber JM, Nadon C, Sharma D, Whitfield Y, Gaulin C, Galanis E, Bekal S, Flint J, Tschetter L, Pagotto F, Lee B, Jamieson F, Badiani T, MacDonald D, Ellis A, May-Hadford J, McCormick R, Savelli C, Middleton D, Allen V, Tremblay FW, MacDougall L, Hoang L, Shyng S, Everett D, Chui L, Louie M, Bangura H, Levett PN, Wilkinson K, Wylie J, Reid J, Major B, Engel D, Douey D, Huszczynski G, Di Lecci J, Strazds J, Rousseau J, Ma K, Isaac L, Sierpinska U. Multi-Province Listeriosis Outbreak Linked to Contaminated Deli Meat Consumed Primarily in Institutional Settings, Canada, 2008. Foodborne Pathog Dis 2015; 12:645-52. [PMID: 26258258 DOI: 10.1089/fpd.2015.1939] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A multi-province outbreak of listeriosis occurred in Canada from June to November 2008. Fifty-seven persons were infected with 1 of 3 similar outbreak strains defined by pulsed-field gel electrophoresis, and 24 (42%) individuals died. Forty-one (72%) of 57 individuals were residents of long-term care facilities or hospital inpatients during their exposure period. Descriptive epidemiology, product traceback, and detection of the outbreak strains of Listeria monocytogenes in food samples and the plant environment confirmed delicatessen meat manufactured by one establishment and purchased primarily by institutions was the source of the outbreak. The food safety investigation identified a plant environment conducive to the introduction and proliferation of L. monocytogenes and persistently contaminated with Listeria spp. This outbreak demonstrated the need for improved listeriosis surveillance, strict control of L. monocytogenes in establishments producing ready-to-eat foods, and advice to vulnerable populations and institutions serving these populations regarding which high-risk foods to avoid.
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Affiliation(s)
- Andrea Currie
- 1 Centre for Foodborne, Environmental, and Zoonotic Infectious Diseases , Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Jeffrey M Farber
- 2 Bureau of Microbial Hazards , Health Canada, Ottawa, Ontario, Canada
| | - Céline Nadon
- 3 National Microbiology Laboratory , Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | | | - Yvonne Whitfield
- 5 Public Health Division, Ontario Ministry of Health and Long-Term Care , Toronto, Ontario, Canada
| | - Colette Gaulin
- 6 Ministère de la santé et des services sociaux du Québec , Québec, Province de Québec, Canada
| | - Eleni Galanis
- 7 Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control , Vancouver, British Columbia, Canada
| | - Sadjia Bekal
- 8 Laboratoire de santé publique du Québec , Sainte-Anne de Bellevue, Province de Québec, Canada
| | - James Flint
- 1 Centre for Foodborne, Environmental, and Zoonotic Infectious Diseases , Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Lorelee Tschetter
- 3 National Microbiology Laboratory , Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Franco Pagotto
- 2 Bureau of Microbial Hazards , Health Canada, Ottawa, Ontario, Canada
| | - Brenda Lee
- 5 Public Health Division, Ontario Ministry of Health and Long-Term Care , Toronto, Ontario, Canada
| | - Fred Jamieson
- 4 Canadian Food Inspection Agency , Ottawa, Ontario, Canada
| | - Tina Badiani
- 5 Public Health Division, Ontario Ministry of Health and Long-Term Care , Toronto, Ontario, Canada
| | - Diane MacDonald
- 1 Centre for Foodborne, Environmental, and Zoonotic Infectious Diseases , Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Andrea Ellis
- 1 Centre for Foodborne, Environmental, and Zoonotic Infectious Diseases , Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Jennifer May-Hadford
- 9 Canadian Field Epidemiology Program, Public Health Agency of Canada , Ottawa, Ontario, Canada
| | - Rachel McCormick
- 9 Canadian Field Epidemiology Program, Public Health Agency of Canada , Ottawa, Ontario, Canada
| | - Carmen Savelli
- 1 Centre for Foodborne, Environmental, and Zoonotic Infectious Diseases , Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Dean Middleton
- 5 Public Health Division, Ontario Ministry of Health and Long-Term Care , Toronto, Ontario, Canada
| | - Vanessa Allen
- 10 Provincial Public Health Laboratory, Ontario Ministry of Health and Long-Term Care , Toronto, Ontario, Canada
| | | | - Laura MacDougall
- 7 Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control , Vancouver, British Columbia, Canada
| | - Linda Hoang
- 11 British Columbia Public Health Microbiology and Reference Laboratory, British Columbia Centre for Disease Control , Vancouver, British Columbia, Canada
| | - Sion Shyng
- 12 Environmental Health Services, British Columbia Centre for Disease Control , Vancouver, British Columbia, Canada
| | | | - Linda Chui
- 14 Provincial Laboratory for Public Health , Edmonton, Alberta, Canada
| | - Marie Louie
- 14 Provincial Laboratory for Public Health , Edmonton, Alberta, Canada
| | - Helen Bangura
- 15 Saskatchewan Ministry of Health , Regina, Saskatchewan, Canada
| | - Paul N Levett
- 16 Saskatchewan Disease Control Laboratory , Regina, Saskatchewan, Canada
| | - Krista Wilkinson
- 17 Manitoba Health , Healthy Living and Seniors, Winnipeg, Manitoba, Canada
| | - John Wylie
- 18 Cadham Provincial Laboratory , Manitoba Health, Winnipeg, Manitoba, Canada
| | - Janet Reid
- 19 New Brunswick Enteric Reference Laboratory , Saint John, New Brunswick, Canada
| | - Brian Major
- 4 Canadian Food Inspection Agency , Ottawa, Ontario, Canada
| | - Dave Engel
- 4 Canadian Food Inspection Agency , Ottawa, Ontario, Canada
| | - Donna Douey
- 4 Canadian Food Inspection Agency , Ottawa, Ontario, Canada
| | | | - Joe Di Lecci
- 4 Canadian Food Inspection Agency , Ottawa, Ontario, Canada
| | - Judy Strazds
- 4 Canadian Food Inspection Agency , Ottawa, Ontario, Canada
| | - Josée Rousseau
- 4 Canadian Food Inspection Agency , Ottawa, Ontario, Canada
| | - Kenneth Ma
- 4 Canadian Food Inspection Agency , Ottawa, Ontario, Canada
| | - Leah Isaac
- 4 Canadian Food Inspection Agency , Ottawa, Ontario, Canada
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Antonation KS, Bekal S, Côté G, Dallaire A, Corbett CR. Multiple-locus variable-number tandem-repeat analysis of Francisella tularensis from Quebec, Canada. Lett Appl Microbiol 2015; 60:328-33. [PMID: 25442329 DOI: 10.1111/lam.12371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 12/01/2022]
Abstract
UNLABELLED Francisella tularensis is ubiquitous in the Northern Hemisphere. Yet, little is known about the disease and its ecology within Canada as few serological studies have shown exposure to the disease and fewer case studies have been reported. This report is the first to describe the molecular subtyping of F. tularensis isolates within eastern Canada using multiple-locus variable-number tandem-repeat analysis. From 1998 to 2011, a total of 73 specimens were isolated from unique human and animal sources. As expected, F. tularensis subsp. tularensis AI and F. tularensis subsp. holarctica subtypes were observed, corresponding to the known geographical division within this species. The majority of human isolates (78%) and all animal (hare) isolates were of the more virulent, AI type. Half of the B isolates were isolated from patients living in a region of Quebec where muskrat densities are known to be high. A relatively high level of marker diversity was found, suggestive of multiple introductions of the organism to the region, or more likely ongoing endemicity. There was no evidence of ongoing outbreaks or transmission, and the bulk of cases were likely due to interaction between human activity and the environment (e.g. hunting/trapping activities). SIGNIFICANCE AND IMPACT OF THE STUDY This study reveals the diversity of Francisella tularensis in eastern Canada using multiple-locus variable-number tandem-repeat analysis. It was initiated to further the understanding of the species within North America as previous studies elucidating the diversity and phylogeography of the species have consisted mostly of specimens from the United States. Type A tularaemia, the most life-threatening subtype of the species and a Category A biothreat agent, is restricted to North America, and this study serves to broaden the knowledge of the epidemiology and diversity of the organism.
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Affiliation(s)
- K S Antonation
- Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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41
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Abstract
During 2012-2013 in Montreal, Canada, 4 locally acquired Shigella spp. pulse types with the mph(A) gene and reduced susceptibility to azithromycin were identified from 9 men who have sex with men, 7 of whom were HIV infected. Counseling about prevention of enteric sexually transmitted infections might help slow transmission of these organisms.
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Larivière-Gauthier G, Letellier A, Kérouanton A, Bekal S, Quessy S, Fournaise S, Fravalo P. Analysis of Listeria monocytogenes strain distribution in a pork slaughter and cutting plant in the province of Quebec. J Food Prot 2014; 77:2121-8. [PMID: 25474060 DOI: 10.4315/0362-028x.jfp-14-192] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Following the 2008 Canadian listeriosis outbreak associated with ready-to-eat (RTE) meat products, regulations on the presence of Listeria monocytogenes in RTE food production facilities were modified by Health Canada, confirming the need to control this pathogen, not only in the final product but also in the plant environment. Information on the occurrence of this microorganism during the early steps of production, such as the slaughtering process and in the cutting area, is scarce in Canada. In this study, we sampled different production steps in a slaughtering and cutting plant in the province of Quebec over a 2-year period. The lairage pens, representative areas of the slaughter line, and cutting zones were targeted after their respective cleaning procedures. A total of 874 samples were analyzed for the presence of L. monocytogenes. Characterization was done by first genoserogrouping the isolates using multiplex PCR and then using a pulsed-field gel electrophoresis approach. L. monocytogenes was detected throughout all production stages. The 108 positive samples found were analyzed further, and we established that there were 4 different serogroups, with serogroup IIb being the most prevalent. The results of pulsed-field gel electrophoresis analysis showed a significant decrease in the diversity of strains from the first areas of the plant to the cutting room (10 pulsotypes in 13 positive samples in lairage and 9 in 86 positive samples in cutting) and also showed the overrepresentation of a single predominant strain in the cutting room environment (type 1, representing 96.1% of the isolates). Biofilm formation analysis of the strains cannot exclusively explain the transitions we observed. A strong genotypic similarity between strains isolated in the early production areas and some strains in the cutting room was shown. These results support the need for better surveillance of L. monocytogenes prior to RTE food production in order to design control strategies that are better adapted from a public health perspective.
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Affiliation(s)
- Guillaume Larivière-Gauthier
- Chaire de Recherche en Salubrité des Viandes (CRSV), Groupe de Recherche et d'Enseignement en Salubrité Alimentaire (GRESA), Groupe de Recherche sur les Maladies Infectieuses du Porc (GREMIP), and Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA), Department of Pathology and Microbiology, University of Montreal, Faculty of Veterinary Medicine, 3200 Sicotte Street, Saint-Hyacinthe, Quebec, Canada J2S 7C6
| | - Ann Letellier
- Chaire de Recherche en Salubrité des Viandes (CRSV), Groupe de Recherche et d'Enseignement en Salubrité Alimentaire (GRESA), Groupe de Recherche sur les Maladies Infectieuses du Porc (GREMIP), and Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA), Department of Pathology and Microbiology, University of Montreal, Faculty of Veterinary Medicine, 3200 Sicotte Street, Saint-Hyacinthe, Quebec, Canada J2S 7C6
| | - Annaëlle Kérouanton
- Anses, Laboratoire de Ploufragan-Plouzané, Unité Hygiène et Qualité des Produits Avicoles et Porcines (HQPAP), BP 53, Ploufragan, 22440, France
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, 20045 Sainte-Marie Ch, Sainte-Anne-de-Bellevue, Québec, Canada H9X 3R5
| | - Sylvain Quessy
- Chaire de Recherche en Salubrité des Viandes (CRSV), Groupe de Recherche et d'Enseignement en Salubrité Alimentaire (GRESA), Groupe de Recherche sur les Maladies Infectieuses du Porc (GREMIP), and Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA), Department of Pathology and Microbiology, University of Montreal, Faculty of Veterinary Medicine, 3200 Sicotte Street, Saint-Hyacinthe, Quebec, Canada J2S 7C6
| | - Sylvain Fournaise
- Olymel S.E.C./L.P., 1580 Eiffel Street, Boucherville, Québec, Canada J4B 5Y1
| | - Philippe Fravalo
- Chaire de Recherche en Salubrité des Viandes (CRSV), Groupe de Recherche et d'Enseignement en Salubrité Alimentaire (GRESA), Groupe de Recherche sur les Maladies Infectieuses du Porc (GREMIP), and Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA), Department of Pathology and Microbiology, University of Montreal, Faculty of Veterinary Medicine, 3200 Sicotte Street, Saint-Hyacinthe, Quebec, Canada J2S 7C6.
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Gaulin C, Currie A, Gravel G, Hamel M, Leblanc MA, Ramsay D, Bekal S. Summary of 11 years of enteric outbreak investigations and criteria to initiate an investigation, Province of Quebec, 2002 through 2012. J Food Prot 2014; 77:1563-70. [PMID: 25198848 DOI: 10.4315/0362-028x.jfp-13-530] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This article presents a retrospective analysis of enteric disease outbreak investigations led by or conducted in collaboration with provincial health authorities in the Province of Quebec from 2002 through 2012. Objectives were to characterize enteric disease outbreaks, quantify and describe those for which a source was identified (including the control measures implemented), identify factors that contributed to or impeded identification of the source, and recommend areas for improvement in outbreak investigations (including establishment of criteria to initiate investigations). A descriptive analysis of enteric disease outbreak summaries recorded in a provincial database since 2002 was conducted, and corresponding outbreak reports were reviewed. Among 61 enteric disease outbreaks investigated, primary pathogens involved were Salmonella (46%), Escherichia coli O157:H7 (25%), and Listeria monocytogenes (13%). Sources were identified for 37 (61%) of 61 of the outbreaks, and descriptive studies were sufficient to identify the source for 26 (70%) of these. During the descriptive phase of the investigation, the causes of 21 (81%) of 26 outbreaks were identified by promptly collecting samples of suspected foods based on case interviews. Causes of outbreaks were more likely to be detected by weekly surveillance or alert systems (odds ratio = 6.0, P = 0.04) than by serotyping or molecular typing surveillance and were more likely to be associated with a common event or location (odds ratio = 11.0, P = 0.023). Among the 37 outbreaks for which causes were identified, 24 (65%) were associated with contaminated food, and recalls were the primary control measure implemented (54%). Review of enteric outbreaks investigated at the provincial level in Québec has increased the province's ability to quantify success and identify factors that can promote success. Multiple criteria should be taken into account to identify case clusters that are more likely to be resolved.
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Affiliation(s)
- Colette Gaulin
- Ministère de la Santé et des Services sociaux du Québec, 1075 chemin Ste-Foy, Québec, Province de Québec, Canada G1S 2M1.
| | - Andrea Currie
- Outbreak Management Division, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Unit 120, 255 Woodlawn Road West, Guelph, Ontario, Canada N1H 8J1
| | - Geneviève Gravel
- Ministère de la Santé et des Services sociaux, 201 rue Crémazie Est, Montréal, Province de Québec, Canada H2M 1L2
| | - Meghan Hamel
- Outbreak Management Division, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, 2932 Baseline Road, Tower A, Room 327B, AL 3303B, Ottawa, Ontario, Canada K1A 0K9
| | - Marie-Andree Leblanc
- Ministère de la Santé et des Services sociaux du Québec, 1075 chemin Ste-Foy, Québec, Province de Québec, Canada G1S 2M1
| | - Danielle Ramsay
- Ministère de l'Agriculture, des Pêcheries et de l'Alimentation du Québec, 200 chemin Ste-Foy, 11ème étage, Québec, Province de Québec, Canada G1R 4X6
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, 20045 chemin Ste-Marie, Sainte-Anne de Bellevue, Québec, Province de Québec, Canada H9X 3R5
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Bekal S, Ramsay D, Rallu F, Pilon P, Gilmour M, Johnson R, Tremblay C. First documented case of human infection with ovine Shiga-toxin-producingEscherichia coliserotype O52:H45. Can J Microbiol 2014; 60:417-8. [DOI: 10.1139/cjm-2014-0159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report a concurrent case of infection with non-O157 Shiga-toxin-producing Escherichia coli (STEC) strain in an 8-month-old child. Laboratory and epidemiological investigations indicated child exposure to contaminated sheep meat following the Muslim feast of sacrifice (Eid al-Adha). Microbiological and molecular typing confirmed that the ovine strain O52:H45 (stx1+, eae–, hlyA–) was the causal agent. This is the first documented case of human infection to this STEC serotype.
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Affiliation(s)
- Sadjia Bekal
- Laboratoire de santé publique du Québec, 20045 chemin Ste-Marie, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada
- Université de Montréal, Montréal, Que., Canada
| | - Danielle Ramsay
- Ministère de l’Agriculture, des Pêcheries et de l’Alimentation du Québec, 200 chemin Ste-Foy, Québec, QC G1R 4X6, Canada
| | | | - Pierre Pilon
- Agence de la santé et des services sociaux de Montréal, Université de Montréal, 3725, rue Saint Denis, Montréal, QC H2X 3L9, Canada
| | - Matthew Gilmour
- National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada
| | - Roger Johnson
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON N1G 3W4, Canada
| | - Cécile Tremblay
- Laboratoire de santé publique du Québec, 20045 chemin Ste-Marie, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada
- Université de Montréal, Montréal, Que., Canada
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Gaulin C, Gravel G, Bekal S, Currie A, Ramsay D, Roy S. Challenges in Listeriosis Cluster and Outbreak Investigations, Province of Quebec, 1997–2011. Foodborne Pathog Dis 2014; 11:1-7. [DOI: 10.1089/fpd.2013.1574] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Colette Gaulin
- Ministère de la Santé et des Services Sociaux, Québec, Québec, Canada
| | - Geneviève Gravel
- Ministère de la Santé et des Services Sociaux, Montréal, Québec, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Québec, Canada
| | - Andrea Currie
- Public Health Agency of Canada, Outbreak Management Division, Centre for Food-borne, Environmental, and Zoonotic Infectious Diseases, Infectious Disease and Emergency Preparedness Branch, Guelph, Ontario, Canada
| | - Danielle Ramsay
- Ministère de l'Agriculture, des Pêcheries, et de l'Alimentation du Québec, Québec, Canada
| | - Sophie Roy
- Ministère de l'Agriculture, des Pêcheries, et de l'Alimentation du Québec, Direction des Laboratoires d'Expertises, Québec, Canada
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Gaudreau C, Helferty M, Sylvestre JL, Allard R, Pilon PA, Poisson M, Bekal S. Campylobacter coli outbreak in men who have sex with men, Quebec, Canada, 2010-2011. Emerg Infect Dis 2013; 19:764-7. [PMID: 23647786 PMCID: PMC3647503 DOI: 10.3201/eid1905.121344] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
During September 2010–November 2011, a cluster of erythromycin-susceptible, tetracycline- and ciprofloxacin-resistant Campylobacter coli pulsovar 1 infections was documented, involving 10 case-patients, in Montreal, Quebec, Canada. The findings suggested sexual transmission of an enteric infection among men who have sex with men.
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Affiliation(s)
- Christiane Gaudreau
- Centre Hospitalier de l'Université de Montréal–Hôpital Saint-Luc, Montreal, Quebec, Canada.
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Mulvey MR, Boyd DA, Finley R, Fakharuddin K, Langner S, Allen V, Ang L, Bekal S, El Bailey S, Haldane D, Hoang L, Horsman G, Louis M, Robberts L, Wylie J. Ciprofloxacin-resistant Salmonella enterica serovar Kentucky in Canada. Emerg Infect Dis 2013; 19:999-1001. [PMID: 23735312 PMCID: PMC3713822 DOI: 10.3201/eid1906.121351] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report emergence of ciprofloxacin-resistant Salmonella enterica serovar Kentucky in Canada during 2003-2009. All isolates had similar macrorestriction patterns and were multilocus sequence type ST198, which has been observed in Europe and Africa. Ciprofloxacin-resistant S. enterica serovar Kentucky represents 66% of all ciprofloxacin-resistant nontyphoidal Salmonella sp. isolates observed in Canada since 2003.
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Affiliation(s)
- Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
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Leclair D, Fung J, Isaac-Renton JL, Proulx JF, May-Hadford J, Ellis A, Ashton E, Bekal S, Farber JM, Blanchfield B, Austin JW. Foodborne botulism in Canada, 1985-2005. Emerg Infect Dis 2013; 19:961-8. [PMID: 23735780 PMCID: PMC3713816 DOI: 10.3201/eid1906.120873] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During 1985-2005, a total of 91 laboratory-confirmed outbreaks of foodborne botulism occurred in Canada; these outbreaks involved 205 cases and 11 deaths. Of the outbreaks, 75 (86.2%) were caused by Clostridium botulinum type E, followed by types A (7, 8.1%) and B (5, 5.7%). Approximately 85% of the outbreaks occurred in Alaska Native communities, particularly the Inuit of Nunavik in northern Quebec and the First Nations population of the Pacific coast of British Columbia. These populations were predominantly exposed to type E botulinum toxin through the consumption of traditionally prepared marine mammal and fish products. Two botulism outbreaks were attributed to commercial ready-to-eat meat products and 3 to foods served in restaurants; several cases were attributed to non-Native home-prepared foods. Three affected pregnant women delivered healthy infants. Improvements in botulism case identification and early treatment have resulted in a reduction in the case-fatality rate in Canada.
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Mulvey MR, Finley R, Allen V, Ang L, Bekal S, El Bailey S, Haldane D, Hoang L, Horsman G, Louie M, Robberts L, Wylie J, McCracken M, Langner S, Ahmed R, Tabor H, Gilmour M. Emergence of multidrug-resistant Salmonella enterica serotype 4,[5],12:i:- involving human cases in Canada: results from the Canadian Integrated Program on Antimicrobial Resistance Surveillance (CIPARS), 2003-10. J Antimicrob Chemother 2013; 68:1982-6. [PMID: 23710071 DOI: 10.1093/jac/dkt149] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Over the last decade, a marked increase in Salmonella enterica serotype 4,[5],12:i:- with a core resistance to ampicillin, streptomycin, sulphonamides and tetracycline (ASSuT) has been observed in Europe. This study describes the emergence and characterization of isolates of multidrug-resistant Salmonella 4,[5],12:i:- in Canada. METHODS Human clinical isolates of Salmonella 4,[5],12:i:- were identified by provincial laboratories from 2003 to 2010. Serotyping and phage typing were performed by standardized methodologies. MIC values were determined using broth microdilution. PCR was used to determine the presence of resistance genes. Multilocus sequence typing was performed on a selected number of isolates. RESULTS A total of 26 251 Salmonella were submitted as part of the Canadian Integrated Program on Antibiotic Resistance Surveillance (CIPARS). Of these, Salmonella 4,[5],12:i:- accounted for a total of 766 isolates (2.9%), and the number increased significantly from 42 (1.4%) in 2003 to 164 (4.8%) in 2010. The ASSuT+ phenotype was observed in 11.9% (n = 91) of Salmonella 4,[5],12:i:- isolates and increased from two isolates in 2003 to 35 isolates in 2010. Two sequence types (STs) were observed. ST34 was mainly associated with the ASSuT isolates (n = 24; 38%), which contained blaTEM, strA-strB, tet(B) and sul2. ST19 was more likely to be associated with the ACSSuT phenotype and contained blaTEM, floR, strA-strB, sul2 and tet(A) or blaPSE-1, floR, aadA2, sul1 and tet(G). CONCLUSIONS The prevalence of Salmonella 4,[5],12:i:- has significantly increased from 2003 to 2010 and it is now the fifth most common serotype reported in Canada causing human disease. Similar antimicrobial resistance patterns, phage types and STs have been observed in Europe.
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Bekal S, Lefebvre B, Bergevin M, Tremblay C. CTX-M-15 type ESBL-producing Salmonella Havana associated with international adoption in Canada. Can J Microbiol 2012; 59:57. [PMID: 23391231 DOI: 10.1139/cjm-2012-0667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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