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Babin A, Schurr F, Delannoy S, Fach P, Huyen Ton Nu Nguyet M, Bougeard S, de Miranda JR, Rundlöf M, Wintermantel D, Albrecht M, Attridge E, Bottero I, Cini E, Costa C, De la Rúa P, Di Prisco G, Dominik C, Dzul D, Hodge S, Klein AM, Knapp J, Knauer AC, Mänd M, Martínez-López V, Medrzycki P, Pereira-Peixoto MH, Potts SG, Raimets R, Schweiger O, Senapathi D, Serrano J, Stout JC, Tamburini G, Brown MJF, Laurent M, Rivière MP, Chauzat MP, Dubois E. Distribution of infectious and parasitic agents among three sentinel bee species across European agricultural landscapes. Sci Rep 2024; 14:3524. [PMID: 38347035 PMCID: PMC10861508 DOI: 10.1038/s41598-024-53357-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/31/2024] [Indexed: 02/15/2024] Open
Abstract
Infectious and parasitic agents (IPAs) and their associated diseases are major environmental stressors that jeopardize bee health, both alone and in interaction with other stressors. Their impact on pollinator communities can be assessed by studying multiple sentinel bee species. Here, we analysed the field exposure of three sentinel managed bee species (Apis mellifera, Bombus terrestris and Osmia bicornis) to 11 IPAs (six RNA viruses, two bacteria, three microsporidia). The sentinel bees were deployed at 128 sites in eight European countries adjacent to either oilseed rape fields or apple orchards during crop bloom. Adult bees of each species were sampled before their placement and after crop bloom. The IPAs were detected and quantified using a harmonised, high-throughput and semi-automatized qPCR workflow. We describe differences among bee species in IPA profiles (richness, diversity, detection frequencies, loads and their change upon field exposure, and exposure risk), with no clear patterns related to the country or focal crop. Our results suggest that the most frequent IPAs in adult bees are more appropriate for assessing the bees' IPA exposure risk. We also report positive correlations of IPA loads supporting the potential IPA transmission among sentinels, suggesting careful consideration should be taken when introducing managed pollinators in ecologically sensitive environments.
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Affiliation(s)
- Aurélie Babin
- ANSES, Sophia Antipolis Laboratory, Unit of Honey bee Pathology, 06902, Sophia Antipolis, France.
| | - Frank Schurr
- ANSES, Sophia Antipolis Laboratory, Unit of Honey bee Pathology, 06902, Sophia Antipolis, France
| | - Sabine Delannoy
- IdentyPath Genomics Platform, Food Safety Laboratory, ANSES, 94701, Maisons-Alfort, France
| | - Patrick Fach
- IdentyPath Genomics Platform, Food Safety Laboratory, ANSES, 94701, Maisons-Alfort, France
| | | | - Stéphanie Bougeard
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Epidemiology and Welfare, France
| | - Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Maj Rundlöf
- Department of Biology, Lund University, Lund, Sweden
| | - Dimitry Wintermantel
- Chair of Nature Conservation and Landscape Ecology, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
| | - Matthias Albrecht
- Agroecology and Environment, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Eleanor Attridge
- Federation of Irish Beekeepers' Associations, Tullamore, Ireland
| | - Irene Bottero
- Botany, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Elena Cini
- Centre for Agri-Environmental Research, School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Cecilia Costa
- CREA Research Centre for Agriculture and Environment, Via di Corticella 133, 40128, Bologna, Italy
| | - Pilar De la Rúa
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, 30100, Murcia, Spain
| | - Gennaro Di Prisco
- CREA Research Centre for Agriculture and Environment, Via di Corticella 133, 40128, Bologna, Italy
- Institute for Sustainable Plant Protection, The Italian National Research Council, Piazzale E. Ferni 1, 80055, Portici, Napoli, Italy
| | - Christophe Dominik
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, 06120, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
| | - Daniel Dzul
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, 30100, Murcia, Spain
| | - Simon Hodge
- Botany, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Alexandra-Maria Klein
- Chair of Nature Conservation and Landscape Ecology, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
| | - Jessica Knapp
- Department of Biology, Lund University, Lund, Sweden
- Botany, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Anina C Knauer
- Agroecology and Environment, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Marika Mänd
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Vicente Martínez-López
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, 30100, Murcia, Spain
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Bioscience Building, L69 7ZB, Liverpool, UK
| | - Piotr Medrzycki
- CREA Research Centre for Agriculture and Environment, Via di Corticella 133, 40128, Bologna, Italy
| | - Maria Helena Pereira-Peixoto
- Chair of Nature Conservation and Landscape Ecology, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
| | - Simon G Potts
- Centre for Agri-Environmental Research, School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Risto Raimets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Oliver Schweiger
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, 06120, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
| | - Deepa Senapathi
- Centre for Agri-Environmental Research, School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - José Serrano
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, 30100, Murcia, Spain
| | - Jane C Stout
- Botany, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Giovanni Tamburini
- Chair of Nature Conservation and Landscape Ecology, University of Freiburg, Tennenbacher Straße 4, 79106, Freiburg, Germany
- University of Bari, Department of Soil, Plant and Food Sciences (DiSSPA-Entomology and Zoology), Bari, Italy
| | - Mark J F Brown
- Centre for Ecology, Evolution & Behaviour, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, UK
| | - Marion Laurent
- ANSES, Sophia Antipolis Laboratory, Unit of Honey bee Pathology, 06902, Sophia Antipolis, France
| | - Marie-Pierre Rivière
- ANSES, Sophia Antipolis Laboratory, Unit of Honey bee Pathology, 06902, Sophia Antipolis, France
| | - Marie-Pierre Chauzat
- ANSES, Sophia Antipolis Laboratory, Unit of Honey bee Pathology, 06902, Sophia Antipolis, France
- Paris-Est University, ANSES, Laboratory for Animal Health, 94701, Maisons-Alfort, France
| | - Eric Dubois
- ANSES, Sophia Antipolis Laboratory, Unit of Honey bee Pathology, 06902, Sophia Antipolis, France.
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Hoyle DV, Wee BA, Macleod K, Chase-Topping ME, Bease AG, Tongue SC, Gally DL, Delannoy S, Fach P, Pearce MC, Gunn GJ, Holmes A, Allison L. Phylogenetic relationship and virulence composition of Escherichia coli O26:H11 cattle and human strain collections in Scotland; 2002-2020. Front Microbiol 2023; 14:1260422. [PMID: 38029122 PMCID: PMC10657854 DOI: 10.3389/fmicb.2023.1260422] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
O26 is the commonest non-O157 Shiga toxin (stx)-producing Escherichia coli serogroup reported in human infections worldwide. Ruminants, particularly cattle, are the primary reservoir source for human infection. In this study, we compared the whole genomes and virulence profiles of O26:H11 strains (n = 99) isolated from Scottish cattle with strains from human infections (n = 96) held by the Scottish Escherichia coli O157/STEC Reference Laboratory, isolated between 2002 and 2020. Bovine strains were from two national cross-sectional cattle surveys conducted between 2002-2004 and 2014-2015. A maximum likelihood phylogeny was constructed from a core-genome alignment with the O26:H11 strain 11368 reference genome. Genomes were screened against a panel of 2,710 virulence genes using the Virulence Finder Database. All stx-positive bovine O26:H11 strains belonged to the ST21 lineage and were grouped into three main clades. Bovine and human source strains were interspersed, and the stx subtype was relatively clade-specific. Highly pathogenic stx2a-only ST21 strains were identified in two herds sampled in the second cattle survey and in human clinical infections from 2010 onwards. The closest pairwise distance was 9 single-nucleotide polymorphisms (SNPs) between Scottish bovine and human strains and 69 SNPs between the two cattle surveys. Bovine O26:H11 was compared to public EnteroBase ST29 complex genomes and found to have the greatest commonality with O26:H11 strains from the rest of the UK, followed by France, Italy, and Belgium. Virulence profiles of stx-positive bovine and human strains were similar but more conserved for the stx2a subtype. O26:H11 stx-negative ST29 (n = 17) and ST396 strains (n = 5) were isolated from 19 cattle herds; all were eae-positive, and 10 of these herds yielded strains positive for ehxA, espK, and Z2098, gene markers suggestive of enterohaemorrhagic potential. There was a significant association (p < 0.001) between nucleotide sequence percent identity and stx status for the bacteriophage insertion site genes yecE for stx2 and yehV for stx1. Acquired antimicrobial resistance genes were identified in silico in 12.1% of bovine and 17.7% of human O26:H11 strains, with sul2, tet, aph(3″), and aph(6″) being most common. This study describes the diversity among Scottish bovine O26:H11 strains and investigates their relationship to human STEC infections.
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Affiliation(s)
- Deborah V. Hoyle
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Bryan A. Wee
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Kareen Macleod
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Margo E. Chase-Topping
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Andrew G. Bease
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Sue C. Tongue
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, North Faculty, Scotland’s Rural College (SRUC), Inverness, United Kingdom
| | - David L. Gally
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Sabine Delannoy
- Unité ColiPath – Plateforme IdentyPath, Laboratoire de Sécurité des Aliments, Agence Nationale De Sécurité Sanitaire de l’alimentation, de l’environnement et du travail (ANSES), Maisons-Alfort, France
| | - Patrick Fach
- Unité ColiPath – Plateforme IdentyPath, Laboratoire de Sécurité des Aliments, Agence Nationale De Sécurité Sanitaire de l’alimentation, de l’environnement et du travail (ANSES), Maisons-Alfort, France
| | - Michael C. Pearce
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, North Faculty, Scotland’s Rural College (SRUC), Inverness, United Kingdom
| | - George J. Gunn
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, North Faculty, Scotland’s Rural College (SRUC), Inverness, United Kingdom
| | - Anne Holmes
- Scottish E. coli O157/STEC Reference Laboratory (SERL), Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Lesley Allison
- Scottish E. coli O157/STEC Reference Laboratory (SERL), Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
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Delannoy S, Hoffer C, Tran ML, Madec JY, Brisabois A, Fach P, Haenni M. High throughput qPCR analyses suggest that Enterobacterales of French sheep and cow cheese rarely carry genes conferring resistances to critically important antibiotics for human medicine. Int J Food Microbiol 2023; 403:110303. [PMID: 37384974 DOI: 10.1016/j.ijfoodmicro.2023.110303] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023]
Abstract
Bacteria present in raw milk can carry acquired or intrinsic antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, only a few studies have evaluated raw milk cheese as a potential reservoir of ARGs. This study thus aimed at providing new data regarding resistance markers present in raw milk cheese. Sheep (n = 360) and cow (n = 360) cheese samples produced in France were incubated in buffered peptone water supplemented with acriflavin or novobiocin; as corroborated by 16S metabarcoding, samples were enriched in Gram-negative bacteria since Escherichia coli and Hafnia alvei respectively accounted for 40 % and 20 % of the samples' microbiota. Screening of the samples for the presence of 30 ARGs and 16 MGEs by high throughput qPCR array showed that nine ARGs conferring resistances to 1st-generation beta-lactams, aminoglycosides, trimethoprim/sulfonamides and tetracyclines occurred in >75 % of both sheep and cow samples. This is neither surprising nor alarming since these resistance genes are widely spread across the One Health human, animal and environmental sectors. Conversely, genes conferring resistances to last-generations cephalosporins were rarely identified, while those conferring resistances to carbapenems or amikacin, which are restricted to human use, were never detected. Multiple MGEs were detected, the most frequent ones being IncF plasmids, confirming the potential transmission of ARGs. Our results are in line with the few studies of the resistome of milk or milk cheese showing that genes conferring resistances to 1st-generation beta-lactams, aminoglycosides and tetracyclines families are widespread, while those conferring resistances to critically important antibiotics are rare or absent.
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Affiliation(s)
- Sabine Delannoy
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France.
| | - Corine Hoffer
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Maï-Lan Tran
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, 69007 Lyon, France
| | - Anne Brisabois
- Strategy and Programs Department, ANSES, 94700 Maisons-Alfort, France
| | - Patrick Fach
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, 69007 Lyon, France
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Michelet L, Tambosco J, Biet F, Fach P, Delannoy S, Boschiroli ML. Deciphering the evolution of the temporal and geographic distribution of French Mycobacterium bovis genotypes using a high throughput SNP-targeted amplicon sequencing method. Infect Genet Evol 2023; 114:105497. [PMID: 37657678 DOI: 10.1016/j.meegid.2023.105497] [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] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Mycobacterium bovis, which belongs to the Mycobacterium tuberculosis complex, is a highly clonal pathogen. However, several lineages of M. bovis have been described worldwide and nine different clusters were identified in France. Targeted amplicon sequencing using next-generation sequencing technology of eighty-eight phylogenetically informative single nucleotide polymorphisms (SNPs) were used to infer the phylogenetic relationship of 630 strains of the National Reference Laboratory isolated between 1979 and 2018 from various animal species. This study allowed classifying 618 different genotypic profiles (combination of a spoligotype and 8 loci-MIRU-VNTR profiles) into the nine previously identified clusters. A global analysis of the entire collection of the National Reference Laboratory has made it possible to represent the evolution of clonal complexes and clusters in time and space for better assessing epidemiological changes of bovine tuberculosis in France.
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Affiliation(s)
- Lorraine Michelet
- Université Paris-Est, ANSES Animal Health Laboratory, National reference laboratory for Tuberculosis, 94706 Maisons-Alfort, France.
| | - Jennifer Tambosco
- Université Paris-Est, ANSES Animal Health Laboratory, National reference laboratory for Tuberculosis, 94706 Maisons-Alfort, France
| | | | - Patrick Fach
- IdentyPath Genomics Platform, Laboratory for Food Safety, Anses, 94706 Maisons-Alfort, France
| | - Sabine Delannoy
- IdentyPath Genomics Platform, Laboratory for Food Safety, Anses, 94706 Maisons-Alfort, France
| | - María Laura Boschiroli
- Université Paris-Est, ANSES Animal Health Laboratory, National reference laboratory for Tuberculosis, 94706 Maisons-Alfort, France
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Jaudou S, Deneke C, Tran ML, Salzinger C, Vorimore F, Goehler A, Schuh E, Malorny B, Fach P, Grützke J, Delannoy S. Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-Producing Escherichia coli in Presence of Commensal E. coli. Microorganisms 2023; 11:2043. [PMID: 37630603 PMCID: PMC10458860 DOI: 10.3390/microorganisms11082043] [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: 06/26/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The characterization of Shiga toxin-producing Escherichia coli (STEC) is necessary to assess their pathogenic potential, but isolation of the strain from complex matrices such as milk remains challenging. In previous work, we have shown the potential of long-read metagenomics to characterize eae-positive STEC from artificially contaminated raw milk without isolating the strain. The presence of multiple E. coli strains in the sample was shown to potentially hinder the correct characterization of the STEC strain. Here, we aimed at determining the STEC:commensal ratio that would prevent the characterization of the STEC. We artificially contaminated pasteurized milk with different ratios of an eae-positive STEC and a commensal E. coli and applied the method previously developed. Results showed that the STEC strain growth was better than the commensal E. coli after enrichment in acriflavine-supplemented BPW. The STEC was successfully characterized in all samples with at least 10 times more STEC post-enrichment compared to the commensal E. coli. However, the presence of equivalent proportions of STEC and commensal E. coli prevented the full characterization of the STEC strain. This study confirms the potential of long-read metagenomics for STEC characterization in an isolation-free manner while refining its limit regarding the presence of background E. coli strains.
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Affiliation(s)
- Sandra Jaudou
- COLiPATH Unit, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (S.J.)
- National Study Center for Sequencing in Risk Assessment, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Carlus Deneke
- National Study Center for Sequencing in Risk Assessment, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Mai-Lan Tran
- COLiPATH Unit, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (S.J.)
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Carina Salzinger
- National Reference Laboratory for Escherichia coli Including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Fabien Vorimore
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - André Goehler
- National Reference Laboratory for Escherichia coli Including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Elisabeth Schuh
- National Reference Laboratory for Escherichia coli Including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Burkhard Malorny
- National Study Center for Sequencing in Risk Assessment, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Patrick Fach
- COLiPATH Unit, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (S.J.)
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
| | - Josephine Grützke
- National Study Center for Sequencing in Risk Assessment, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Sabine Delannoy
- COLiPATH Unit, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (S.J.)
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France
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Félix B, Capitaine K, Te S, Felten A, Gillot G, Feurer C, van den Bosch T, Torresi M, Sréterné Lancz Z, Delannoy S, Brauge T, Midelet G, Leblanc JC, Roussel S. Identification by High-Throughput Real-Time PCR of 30 Major Circulating Listeria monocytogenes Clonal Complexes in Europe. Microbiol Spectr 2023; 11:e0395422. [PMID: 37158749 PMCID: PMC10269651 DOI: 10.1128/spectrum.03954-22] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Listeria monocytogenes is a ubiquitous bacterium that causes a foodborne illness, listeriosis. Most strains can be classified into major clonal complexes (CCs) that account for the majority of outbreaks and sporadic cases in Europe. In addition to the 20 CCs known to account for the majority of human and animal clinical cases, 10 CCs are frequently reported in food production, thereby posing a serious challenge for the agrifood industry. Therefore, there is a need for a rapid and reliable method to identify these 30 major CCs. The high-throughput real-time PCR assay presented here provides accurate identification of these 30 CCs and eight genetic subdivisions within four CCs, splitting each CC into two distinct subpopulations, along with the molecular serogroup of a strain. Based on the BioMark high-throughput real-time PCR system, our assay analyzes 46 strains against 40 real-time PCR arrays in a single experiment. This European study (i) designed the assay from a broad panel of 3,342 L. monocytogenes genomes, (ii) tested its sensitivity and specificity on 597 sequenced strains collected from 24 European countries, and (iii) evaluated its performance in the typing of 526 strains collected during surveillance activities. The assay was then optimized for conventional multiplex real-time PCR for easy implementation in food laboratories. It has already been used for outbreak investigations. It represents a key tool for assisting food laboratories to establish strain relatedness with human clinical strains during outbreak investigations and for helping food business operators by improving their microbiological management plans. IMPORTANCE Multilocus sequence typing (MLST) is the reference method for Listeria monocytogenes typing but is expensive and takes time to perform, from 3 to 5 days for laboratories that outsource sequencing. Thirty major MLST clonal complexes (CCs) are circulating in the food chain and are currently identifiable only by sequencing. Therefore, there is a need for a rapid and reliable method to identify these CCs. The method presented here enables the rapid identification, by real-time PCR, of 30 CCs and eight genetic subdivisions within four CCs, splitting each CC into two distinct subpopulations. The assay was then optimized on different conventional multiplex real-time PCR systems for easy implementation in food laboratories. The two assays will be used for frontline identification of L. monocytogenes isolates prior to whole-genome sequencing. Such assays are of great interest for all food industry stakeholders and public agencies for tracking L. monocytogenes food contamination.
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Affiliation(s)
- Benjamin Félix
- ANSES, European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, Maisons-Alfort, France
| | - Karine Capitaine
- ANSES, European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, Maisons-Alfort, France
| | - Sandrine Te
- ANSES, European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, Maisons-Alfort, France
| | - Arnaud Felten
- ANSES, Ploufragan/Plouzané/Niort Laboratory, Viral Genetics and Bio-Security Unit, Université Européenne de Bretagne, Ploufragan, France
| | | | - Carole Feurer
- IFIP–The French Pig and Pork Institute, Department of Fresh and Processed Meat, Le Rheu, France
| | - Tijs van den Bosch
- Wageningen Food Safety Research, Department of Bacteriology, Molecular Technology and Antimicrobial Resistance, Wageningen, The Netherlands
| | - Marina Torresi
- National Reference Laboratory for Listeria monocytogenes, Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise “G. Caporale” Via Campo Boario, Teramo, Italy
| | - Zsuzsanna Sréterné Lancz
- Microbiological National Reference Laboratory, National Food Chain Safety Office, Food Chain Safety Laboratory Directorate, Budapest, Hungary
| | - Sabine Delannoy
- ANSES, Laboratory for Food Safety, IdentyPath Platform, Maisons-Alfort, France
| | - Thomas Brauge
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne-sur-Mer, France
| | - Graziella Midelet
- ANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne-sur-Mer, France
| | - Jean-Charles Leblanc
- ANSES, European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, Maisons-Alfort, France
| | - Sophie Roussel
- ANSES, European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Salmonella and Listeria Unit, University of Paris-Est, Maisons-Alfort, France
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Vorimore F, Jaudou S, Tran ML, Richard H, Fach P, Delannoy S. Combination of whole genome sequencing and supervised machine learning provides unambiguous identification of eae-positive Shiga toxin-producing Escherichia coli. Front Microbiol 2023; 14:1118158. [PMID: 37250024 PMCID: PMC10213463 DOI: 10.3389/fmicb.2023.1118158] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/21/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction The objective of this study was to develop, using a genome wide machine learning approach, an unambiguous model to predict the presence of highly pathogenic STEC in E. coli reads assemblies derived from complex samples containing potentially multiple E. coli strains. Our approach has taken into account the high genomic plasticity of E. coli and utilized the stratification of STEC and E. coli pathogroups classification based on the serotype and virulence factors to identify specific combinations of biomarkers for improved characterization of eae-positive STEC (also named EHEC for enterohemorrhagic E.coli) which are associated with bloody diarrhea and hemolytic uremic syndrome (HUS) in human. Methods The Machine Learning (ML) approach was used in this study on a large curated dataset composed of 1,493 E. coli genome sequences and 1,178 Coding Sequences (CDS). Feature selection has been performed using eight classification algorithms, resulting in a reduction of the number of CDS to six. From this reduced dataset, the eight ML models were trained with hyper-parameter tuning and cross-validation steps. Results and discussion It is remarkable that only using these six genes, EHEC can be clearly identified from E. coli read assemblies obtained from in silico mixtures and complex samples such as milk metagenomes. These various combinations of discriminative biomarkers can be implemented as novel marker genes for the unambiguous EHEC characterization from different E. coli strains mixtures as well as from raw milk metagenomes.
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Affiliation(s)
- Fabien Vorimore
- ANSES, Laboratory for Food Safety, Genomics Platform IdentyPath, Maisons-Alfort, France
| | - Sandra Jaudou
- ANSES, Laboratory for Food Safety, Genomics Platform IdentyPath, Maisons-Alfort, France
- ANSES, Laboratory for Food Safety, COLiPATH Unit, Maisons-Alfort, France
| | - Mai-Lan Tran
- ANSES, Laboratory for Food Safety, Genomics Platform IdentyPath, Maisons-Alfort, France
- ANSES, Laboratory for Food Safety, COLiPATH Unit, Maisons-Alfort, France
| | - Hugues Richard
- Bioinformatics Unit, Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Patrick Fach
- ANSES, Laboratory for Food Safety, Genomics Platform IdentyPath, Maisons-Alfort, France
- ANSES, Laboratory for Food Safety, COLiPATH Unit, Maisons-Alfort, France
| | - Sabine Delannoy
- ANSES, Laboratory for Food Safety, Genomics Platform IdentyPath, Maisons-Alfort, France
- ANSES, Laboratory for Food Safety, COLiPATH Unit, Maisons-Alfort, France
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8
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Jaudou S, Deneke C, Tran ML, Schuh E, Goehler A, Vorimore F, Malorny B, Fach P, Grützke J, Delannoy S. A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics. Microb Genom 2022; 8:mgen000911. [PMID: 36748417 PMCID: PMC9836091 DOI: 10.1099/mgen.0.000911] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are a cause of severe human illness and are frequently associated with haemolytic uraemic syndrome (HUS) in children. It remains difficult to identify virulence factors for STEC that absolutely predict the potential to cause human disease. In addition to the Shiga-toxin (stx genes), many additional factors have been reported, such as intimin (eae gene), which is clearly an aggravating factor for developing HUS. Current STEC detection methods classically rely on real-time PCR (qPCR) to detect the presence of the key virulence markers (stx and eae). Although qPCR gives an insight into the presence of these virulence markers, it is not appropriate for confirming their presence in the same strain. Therefore, isolation steps are necessary to confirm STEC viability and characterize STEC genomes. While STEC isolation is laborious and time-consuming, metagenomics has the potential to accelerate the STEC characterization process in an isolation-free manner. Recently, short-read sequencing metagenomics have been applied for this purpose, but assembly quality and contiguity suffer from the high proportion of mobile genetic elements occurring in STEC strains. To circumvent this problem, we used long-read sequencing metagenomics for identifying eae-positive STEC strains using raw cow's milk as a causative matrix for STEC food-borne outbreaks. By comparing enrichment conditions, optimizing library preparation for MinION sequencing and generating an easy-to-use STEC characterization pipeline, the direct identification of an eae-positive STEC strain was successful after enrichment of artificially contaminated raw cow's milk samples at a contamination level as low as 5 c.f.u. ml-1. Our newly developed method combines optimized enrichment conditions of STEC in raw milk in combination with a complete STEC analysis pipeline from long-read sequencing metagenomics data. This study shows the potential of the innovative methodology for characterizing STEC strains from complex matrices. Further developments will nonetheless be necessary for this method to be applied in STEC surveillance.
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Affiliation(s)
- Sandra Jaudou
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany,*Correspondence: Sandra Jaudou,
| | - Carlus Deneke
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Mai-Lan Tran
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Elisabeth Schuh
- National Reference Laboratory for Escherichia coli including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - André Goehler
- National Reference Laboratory for Escherichia coli including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Fabien Vorimore
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Burkhard Malorny
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Patrick Fach
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Josephine Grützke
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Sabine Delannoy
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,*Correspondence: Sabine Delannoy,
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9
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Lucas C, Delannoy S, Schouler C, Souillard R, Le Devendec L, Lucas P, Keita A, Fach P, Puterflam J, Bougeard S, Kempf I. Description and validation of a new set of PCR markers predictive of avian pathogenic Escherichia coli virulence. Vet Microbiol 2022; 273:109530. [DOI: 10.1016/j.vetmic.2022.109530] [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] [Received: 03/28/2022] [Accepted: 08/02/2022] [Indexed: 10/16/2022]
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10
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Jaudou S, Tran ML, Vorimore F, Fach P, Delannoy S. Evaluation of high molecular weight DNA extraction methods for long-read sequencing of Shiga toxin-producing Escherichia coli. PLoS One 2022; 17:e0270751. [PMID: 35830426 PMCID: PMC9278759 DOI: 10.1371/journal.pone.0270751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/26/2021] [Accepted: 06/16/2022] [Indexed: 11/18/2022] Open
Abstract
Next generation sequencing has become essential for pathogen characterization and typing. The most popular second generation sequencing technique produces data of high quality with very low error rates and high depths. One major drawback of this technique is the short reads. Indeed, short-read sequencing data of Shiga toxin-producing Escherichia coli (STEC) are difficult to assemble because of the presence of numerous mobile genetic elements (MGEs), which contain repeated elements. The resulting draft assemblies are often highly fragmented, which results in a loss of information, especially concerning MGEs or large structural variations. The use of long-read sequencing can circumvent these problems and produce complete or nearly complete genomes. The ONT MinION, for its small size and minimal investment requirements, is particularly popular. The ultra-long reads generated with the MinION can easily span prophages and repeat regions. In order to take full advantage of this technology it requires High Molecular Weight (HMW) DNA of high quality in high quantity. In this study, we have tested three different extraction methods: bead-based, solid-phase and salting-out, and evaluated their impact on STEC DNA yield, quality and integrity as well as performance in MinION long-read sequencing. Both the bead-based and salting-out methods allowed the recovery of large quantities of HMW STEC DNA suitable for MinION library preparation. The DNA extracted using the salting-out method consistently produced longer reads in the subsequent MinION runs, compared with the bead-based methods. While both methods performed similarly in subsequent STEC genome assembly, DNA extraction based on salting-out appeared to be the overall best method to produce high quantity of pure HMW STEC DNA for MinION sequencing.
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Affiliation(s)
- Sandra Jaudou
- Pathogenic E. coli Unit, Laboratory for Food Safety, Anses, Maisons-Alfort, France
| | - Mai-Lan Tran
- Pathogenic E. coli Unit, Laboratory for Food Safety, Anses, Maisons-Alfort, France
- IdentyPath Platform, Laboratory for Food Safety, Anses, Maisons-Alfort, France
| | - Fabien Vorimore
- IdentyPath Platform, Laboratory for Food Safety, Anses, Maisons-Alfort, France
| | - Patrick Fach
- Pathogenic E. coli Unit, Laboratory for Food Safety, Anses, Maisons-Alfort, France
- IdentyPath Platform, Laboratory for Food Safety, Anses, Maisons-Alfort, France
| | - Sabine Delannoy
- Pathogenic E. coli Unit, Laboratory for Food Safety, Anses, Maisons-Alfort, France
- IdentyPath Platform, Laboratory for Food Safety, Anses, Maisons-Alfort, France
- * E-mail:
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11
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Delannoy S, Hoffer C, Youf R, Dauvergne E, Webb HE, Brauge T, Tran ML, Midelet G, Granier SA, Haenni M, Fach P, Brisabois A. High Throughput Screening of Antimicrobial Resistance Genes in Gram-Negative Seafood Bacteria. Microorganisms 2022; 10:microorganisms10061225. [PMID: 35744743 PMCID: PMC9230514 DOI: 10.3390/microorganisms10061225] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 03/28/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 01/24/2023] Open
Abstract
From a global view of antimicrobial resistance over different sectors, seafood and the marine environment are often considered as potential reservoirs of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs); however, there are few studies and sparse results on this sector. This study aims to provide new data and insights regarding the content of resistance markers in various seafood samples and sources, and therefore the potential exposure to humans in a global One Health approach. An innovative high throughput qPCR screening was developed and validated in order to simultaneously investigate the presence of 41 ARGs and 33 MGEs including plasmid replicons, integrons, and insertion sequences in Gram-negative bacteria. Analysis of 268 seafood isolates from the bacterial microflora of cod (n = 24), shellfish (n = 66), flat fishes (n = 53), shrimp (n = 10), and horse mackerel (n = 115) show the occurrence of sul-1, ant(3″)-Ia, aph(3')-Ia, strA, strB, dfrA1, qnrA, and blaCTX-M-9 genes in Pseudomonas spp., Providencia spp., Klebsiella spp., Proteus spp., and Shewanella spp. isolates and the presence of MGEs in all bacterial species investigated. We found that the occurrence of MGE may be associated with the seafood type and the environmental, farming, and harvest conditions. Moreover, even if MGE were detected in half of the seafood isolates investigated, association with ARG was only identified for twelve isolates. The results corroborate the hypothesis that the incidence of antimicrobial-resistant bacteria (ARB) and ARG decreases with increasing distance from potential sources of fecal contamination. This unique and original high throughput micro-array designed for the screening of ARG and MGE in Gram-negative bacteria could be easily implementable for monitoring antimicrobial resistance gene markers in diverse contexts.
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Affiliation(s)
- Sabine Delannoy
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
- Correspondence:
| | - Corine Hoffer
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Raphaëlle Youf
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Emilie Dauvergne
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Hattie E. Webb
- Department of Animal and Food Sciences, International Center for Food Safety Excellence, Texas Tech University, Lubbock, TX 79409, USA;
| | - Thomas Brauge
- Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Laboratory for Food Safety, ANSES, 62200 Boulogne-sur-Mer, France; (T.B.); (G.M.)
| | - Mai-Lan Tran
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Graziella Midelet
- Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Laboratory for Food Safety, ANSES, 62200 Boulogne-sur-Mer, France; (T.B.); (G.M.)
| | - Sophie A. Granier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, ANSES, 35306 Fougères, France;
| | - Marisa Haenni
- Antimicrobial Resistance and Bacterial Virulence Unit, Lyon Laboratory, Université de Lyon, ANSES, 69364 Lyon, France;
| | - Patrick Fach
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Anne Brisabois
- Strategy and Programs Department, ANSES, 94700 Maisons-Alfort, France;
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12
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Keita A, Le Devendec L, Amelot M, Puterflam J, Lucas C, Bougeard S, Delannoy S, Schouler C, Fach P, Lucas P, Souillard R, Kempf I. Efficacy of passive immunization in broiler chicks via an inactivated Escherichia coli autogenous vaccine administered to broiler breeder hens. Avian Pathol 2022; 51:445-456. [DOI: 10.1080/03079457.2022.2084362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Alassane Keita
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Laetitia Le Devendec
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Michel Amelot
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | | | - Camille Lucas
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Stéphanie Bougeard
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Sabine Delannoy
- ANSES – French Agency for Food, Environmental and Occupational Health and Safety Food Research Laboratory, Platform IdentyPath, 94700 Maisons-Alfort, France
| | | | - Patrick Fach
- ANSES – French Agency for Food, Environmental and Occupational Health and Safety Food Research Laboratory, Platform IdentyPath, 94700 Maisons-Alfort, France
| | - Pierrick Lucas
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Rozenn Souillard
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Isabelle Kempf
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
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13
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Valat C, Haenni M, Arnaout Y, Drapeau A, Hirchaud E, Touzain F, Boyer T, Delannoy S, Vorimore F, Fach P, Madec JY. F74 plasmids are major vectors of virulence genes in bovine NTEC2. Lett Appl Microbiol 2022; 75:355-362. [PMID: 35509148 DOI: 10.1111/lam.13733] [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: 03/03/2022] [Revised: 04/08/2022] [Accepted: 04/29/2022] [Indexed: 11/28/2022]
Abstract
Necrotoxigenic Escherichia coli 2 (NTEC2) are defined as E. coli producing the toxin known as cytotoxic necrotizing factor 2 (CNF2), a potent toxin primarily found in bovine but also in humans. NTEC2 are mostly associated with bovine, and cnf2 is known to be carried by pVir-like plasmids. In this study, we looked for NTEC2 in a collection of E. coli collected between 2011 and 2018 in French bovine. Thirty-two isolates, collected from both sick (n=19) and healthy (n=13) animals, were identified and characterized using whole-genome sequencing. One F74 plasmid of this bacterial collection was long-read sequenced: its size was 138 121 bp and it carried the cnf2, F17cA-eG, cdtB, iutA, iucC, and ompP virulence factors (VFs), but no resistance gene. A large variety of genetic backgrounds was observed, but all cnf2-carrying plasmids belonged to the IncF family, and most of them (78.1%) were of the F74 group. Similar F74 plasmids were also reported from bovine in the United Kingdom and USA, as identified in the publically available databases. Consequently, these F74 plasmids, which are widely disseminated among E. coli from cattle in the French territory, are vectors of virulence determinants that largely went unnoticed until now.
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Affiliation(s)
- Charlotte Valat
- Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire (ANSES) - Université de Lyon, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire (ANSES) - Université de Lyon, Lyon, France
| | - Youssef Arnaout
- Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire (ANSES) - Université de Lyon, Lyon, France
| | - Antoine Drapeau
- Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire (ANSES) - Université de Lyon, Lyon, France
| | - Edouard Hirchaud
- Unité Génétique Virale et Biosécurité, Agence Nationale de Sécurité Sanitaire (ANSES), Ploufragan, France
| | - Fabrice Touzain
- Unité Génétique Virale et Biosécurité, Agence Nationale de Sécurité Sanitaire (ANSES), Ploufragan, France
| | - Théophile Boyer
- Unité Epidémiologie et appui à la surveillance, Agence Nationale de Sécurité Sanitaire (ANSES) - Université de Lyon, Lyon, France
| | - Sabine Delannoy
- Unité COLiPATH / Plateforme d'identification et de typage des agents pathogènes (IdentyPath) du laboratoire de sécurité des aliments, Agence Nationale de Sécurité Sanitaire (ANSES), Maisons-Alfort, France
| | - Fabien Vorimore
- Unité COLiPATH / Plateforme d'identification et de typage des agents pathogènes (IdentyPath) du laboratoire de sécurité des aliments, Agence Nationale de Sécurité Sanitaire (ANSES), Maisons-Alfort, France
| | - Patrick Fach
- Unité COLiPATH / Plateforme d'identification et de typage des agents pathogènes (IdentyPath) du laboratoire de sécurité des aliments, Agence Nationale de Sécurité Sanitaire (ANSES), Maisons-Alfort, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire (ANSES) - Université de Lyon, Lyon, France
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Delannoy S, Tran ML, Fach P. Insights into the assessment of highly pathogenic Shiga toxin-producing Escherichia coli in raw milk and raw milk cheeses by High Throughput Real-time PCR. Int J Food Microbiol 2022; 366:109564. [DOI: 10.1016/j.ijfoodmicro.2022.109564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/27/2022]
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15
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Zhi S, Parsons BD, Szelewicki J, Yuen YTK, Fach P, Delannoy S, Li V, Ferrato C, Freedman SB, Lee BE, Pang XL, Chui L. Identification of Shiga-Toxin-Producing Shigella Infections in Travel and Non-Travel Related Cases in Alberta, Canada. Toxins (Basel) 2021; 13:toxins13110755. [PMID: 34822539 PMCID: PMC8618429 DOI: 10.3390/toxins13110755] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 01/21/2023] Open
Abstract
It has long been accepted that Shiga toxin (Stx) only exists in Shigella dysenteriae serotype 1. However, in recent decades, the presence of Shiga toxin genes (stx) in other Shigella spp. have been reported. We screened 366 Shigella flexneri strains from Alberta, Canada (2003 to 2016) for stx and 26 positive strains were identified. These isolates are highly related with the majority originating from the Dominican Republic and three isolates with Haiti origin. Both phylogenetic and spanning tree analysis of the 26 Alberta and 29 stx positive S. flexneri originating from the U.S., France, Canada (Quebec) and Haiti suggests that there are geographic specific distribution patterns (Haiti and Dominican Republic clades). This study provides the first comprehensive whole genome based phylogenetic analysis of stx positive S. flexneri strains as well as their global transmission, which signify the public health risks of global spreading of these strains.
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Affiliation(s)
- Shuai Zhi
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315000, China;
- School of Medicine, Ningbo University, Ningbo 315000, China
| | - Brendon D. Parsons
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
| | - Jonas Szelewicki
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
| | - Yue T. K. Yuen
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
| | - Patrick Fach
- Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, COLiPATH Research Unit & IDPA Genomics Platform, FR-94700 Maisons-Alfort, France; (P.F.); (S.D.)
| | - Sabine Delannoy
- Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, COLiPATH Research Unit & IDPA Genomics Platform, FR-94700 Maisons-Alfort, France; (P.F.); (S.D.)
| | - Vincent Li
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
| | - Christina Ferrato
- Alberta Precision Laboratories-ProvLab, Calgary, AB T2N 4W4, Canada;
| | - Stephen B. Freedman
- Alberta Children’s Hospital, Division of Pediatric Emergency Medicine and Gastroenterology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Alberta Children’s Hospital Research Institute, Department of Emergency Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine & Dentistry, Women and Children’s Health Research Institute, Stollery Children’s Hospital, University of Alberta, Edmonton, AB T6G 1C9, Canada;
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2B7, Canada; (B.D.P.); (J.S.); (Y.T.K.Y.); (X.-L.P.)
- Alberta Precision Laboratories-ProvLab, Edmonton, AB T6G 2J2, Canada;
- Correspondence:
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Cointe A, Bizot E, Delannoy S, Fach P, Bidet P, Birgy A, Weill FX, Lefèvre S, Mariani-Kurkdjian P, Bonacorsi S. Emergence of New ST301 Shiga Toxin-Producing Escherichia coli Clones Harboring Extra-Intestinal Virulence Traits in Europe. Toxins (Basel) 2021; 13:toxins13100686. [PMID: 34678979 PMCID: PMC8537712 DOI: 10.3390/toxins13100686] [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: 08/25/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
O80:H2 enterohemorrhagic Escherichia coli (EHEC) of sequence type ST301 is one of the main serotypes causing European hemolytic and uremic syndrome, but also invasive infections, due to extra-intestinal virulence factors (VFs). Here, we determined whether other such heteropathotypes exist among ST301. EnteroBase was screened for ST301 strains that were included in a general SNP-phylogeny. French strains belonging to a new heteropathotype clone were sequenced. ST, hierarchical clusters (HC), serotype, resistome, and virulome were determined using EnteroBase, the CGE website, and local BLAST. The ST301 general phylogeny shows two groups. Group A (n = 25) is mainly composed of enteropathogenic E. coli, whereas group B (n = 55) includes mostly EHEC. Three serotypes, O186:H2, O45:H2 and O55:H9, share the same virulome as one of the O80:H2 sub-clones from which they derive subsequent O-antigen switches. The O55:H9 clone, mainly present in France (n = 29), as well as in the UK (n = 5) and Germany (n = 1), has a low background of genetic diversity (four HC20), although it has three Stx subtypes, an H-antigen switch, and genes encoding the major extra-intestinal VF yersiniabactin, and extended-spectrum beta-lactamases. Diverse heteropathotype clones genetically close to the O80:H2 clone are present among the ST301, requiring close European monitoring, especially the virulent O55:H9 clone.
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Affiliation(s)
- Aurélie Cointe
- Service de Microbiologie, Centre National de Référence Escherichia coli, AP-HP, Hôpital Robert-Debré, Université de Paris, IAME, UMR 1137, INSERM, 75018 Paris, France; (E.B.); (P.B.); (A.B.); (P.M.-K.); (S.B.)
- Correspondence:
| | - Etienne Bizot
- Service de Microbiologie, Centre National de Référence Escherichia coli, AP-HP, Hôpital Robert-Debré, Université de Paris, IAME, UMR 1137, INSERM, 75018 Paris, France; (E.B.); (P.B.); (A.B.); (P.M.-K.); (S.B.)
| | - Sabine Delannoy
- Platform Identy Path, Food Safety Laboratory, ANSES, Université Paris-Est, 94701 Maisons-Alfort, France; (S.D.); (P.F.)
| | - Patrick Fach
- Platform Identy Path, Food Safety Laboratory, ANSES, Université Paris-Est, 94701 Maisons-Alfort, France; (S.D.); (P.F.)
| | - Philippe Bidet
- Service de Microbiologie, Centre National de Référence Escherichia coli, AP-HP, Hôpital Robert-Debré, Université de Paris, IAME, UMR 1137, INSERM, 75018 Paris, France; (E.B.); (P.B.); (A.B.); (P.M.-K.); (S.B.)
| | - André Birgy
- Service de Microbiologie, Centre National de Référence Escherichia coli, AP-HP, Hôpital Robert-Debré, Université de Paris, IAME, UMR 1137, INSERM, 75018 Paris, France; (E.B.); (P.B.); (A.B.); (P.M.-K.); (S.B.)
| | - François-Xavier Weill
- Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Unités des Bactéries Pathogènes Entériques, 75015 Paris, France; (F.-X.W.); (S.L.)
| | - Sophie Lefèvre
- Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Unités des Bactéries Pathogènes Entériques, 75015 Paris, France; (F.-X.W.); (S.L.)
| | - Patricia Mariani-Kurkdjian
- Service de Microbiologie, Centre National de Référence Escherichia coli, AP-HP, Hôpital Robert-Debré, Université de Paris, IAME, UMR 1137, INSERM, 75018 Paris, France; (E.B.); (P.B.); (A.B.); (P.M.-K.); (S.B.)
| | - Stéphane Bonacorsi
- Service de Microbiologie, Centre National de Référence Escherichia coli, AP-HP, Hôpital Robert-Debré, Université de Paris, IAME, UMR 1137, INSERM, 75018 Paris, France; (E.B.); (P.B.); (A.B.); (P.M.-K.); (S.B.)
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17
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Cointe A, Birgy A, Bridier-Nahmias A, Mariani-Kurkdjian P, Walewski V, Lévy C, Cohen R, Fach P, Delannoy S, Bidet P, Bonacorsi S. Escherichia coli O80 hybrid pathotype strains producing Shiga toxin and ESBL: molecular characterization and potential therapeutic options. J Antimicrob Chemother 2021; 75:537-542. [PMID: 31773130 DOI: 10.1093/jac/dkz484] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 10/03/2019] [Accepted: 10/22/2019] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Enterohaemorrhagic Escherichia coli (EHEC) infections may be complicated by haemolytic uraemic syndrome (HUS). The emerging worldwide EHEC serogroup O80 has acquired a mosaic plasmid combining extraintestinal virulence and antibiotic resistance. This hybrid pathotype is associated with invasive infections that require antibiotic therapy, classically not recommended in EHEC infections, increasing the risk of HUS. We characterized two ESBL-producing O80 EHEC strains, which is an unusual resistance mechanism among EHECs, and determined the safest therapy to be used for invasive infections. METHODS WGS of two strains isolated from the stools of an asymptomatic carrier and a patient with HUS was performed using Illumina and Nanopore technologies. Generated reads were combined to assemble genomes. We determined the safest therapy by comparing Shiga toxin (Stx) production by the two strains in the presence of several antibiotics. RESULTS The strains were genetically close to the O80 EHEC clone, belonging to ST301 and harbouring stx2d, eae-ξ, ehxA and genes characteristic of the extraintestinal virulence plasmid pS88. Long-read sequencing identified the acquisition of an additional plasmid harbouring CTX-M-type genes (blaCTX-M-14 and blaCTX-M-1). Azithromycin decreased Stx production at subinhibitory concentrations, ciprofloxacin increased it and imipenem had no major effect. The combination of azithromycin and imipenem overall reduced Stx production. CONCLUSIONS Acquisition of an additional plasmid harbouring ESBL genes is a step towards increasing the risk of O80 EHEC dissemination and represents a serious public health concern. The combination of azithromycin and imipenem reduced Stx production and suggests that this combination could be tested in clinical trials.
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Affiliation(s)
- Aurélie Cointe
- Université de Paris, IAME, INSERM, F-75018 Paris, France.,Service de Microbiologie, Centre National de Référence Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - André Birgy
- Université de Paris, IAME, INSERM, F-75018 Paris, France.,Service de Microbiologie, Centre National de Référence Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | | | - Patricia Mariani-Kurkdjian
- Université de Paris, IAME, INSERM, F-75018 Paris, France.,Service de Microbiologie, Centre National de Référence Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Violaine Walewski
- Université de Paris, IAME, INSERM, F-75018 Paris, France.,Service de Microbiologie, Hôpital Avicenne, AP-HP, Paris, France
| | - Corinne Lévy
- ACTIV, Association Clinique et Thérapeutique Infantile du Val-de-Marne, Saint Maur-des-Fossés, France.,Université Paris Est, IMRB-GRC GEMINI, Clinical Research Center (CRC), Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Robert Cohen
- ACTIV, Association Clinique et Thérapeutique Infantile du Val-de-Marne, Saint Maur-des-Fossés, France.,Université Paris Est, IMRB-GRC GEMINI, Clinical Research Center (CRC), Centre Hospitalier Intercommunal de Créteil, Créteil, France.,Unité Court Séjour, Petits Nourrissons, Service de Néonatalogie, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Patrick Fach
- ANSES, Plateforme IdentyPath, Maisons-Alfort, France
| | | | - Philippe Bidet
- Université de Paris, IAME, INSERM, F-75018 Paris, France.,Service de Microbiologie, Centre National de Référence Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Stéphane Bonacorsi
- Université de Paris, IAME, INSERM, F-75018 Paris, France.,Service de Microbiologie, Centre National de Référence Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
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18
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Vorimore F, Hölzer M, Liebler-Tenorio EM, Barf LM, Delannoy S, Vittecoq M, Wedlarski R, Lécu A, Scharf S, Blanchard Y, Fach P, Hsia RC, Bavoil PM, Rosselló-Móra R, Laroucau K, Sachse K. Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus): Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov. Syst Appl Microbiol 2021; 44:126200. [PMID: 34298369 DOI: 10.1016/j.syapm.2021.126200] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/01/2021] [Accepted: 03/18/2021] [Indexed: 11/17/2022]
Abstract
The family Chlamydiaceae currently comprises a single genus Chlamydia, with 11 validly published species and seven more taxa. It includes the human pathogens Chlamydia (C.) trachomatis, C. pneumoniae and C. psittaci, a zoonotic agent causing avian chlamydiosis and human psittacosis, as well as other proven or potential pathogens in ruminants, birds, snakes, reptiles and turtles. During routine testing of 15 apparently healthy captive flamingos in a zoo in 2011, an atypical strain of Chlamydiaceae was detected by real-time PCR of cloacal swab samples. Sequence analysis of the 16S rRNA gene revealed high similarity to the uncultured Chlamydiales bacterium clone 122, which previously had been found in gulls. As more samples were collected during annual campaigns of the flamingo ringing program in southern France from 2012 to 2015, Chlamydiaceae-specific DNA was detected by PCR in 30.9% of wild birds. From these samples, three strains were successfully grown in cell culture. Ultrastructural analysis, comparison of 16S and 23S rRNA gene sequences, whole-genome analysis based on de novo hybrid-assembled sequences of the new strains as well as subsequent calculation of taxonomic parameters revealed that the relatedness of the flamingo isolates to established members of the family Chlamydiaceae was sufficiently distant to indicate that the three strains belong to two distinct species within a new genus. Based on these data, we propose the introduction of Chlamydiifrater gen. nov., as a new genus, and Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov., as two new species of the genus.
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Affiliation(s)
- F Vorimore
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France.
| | - M Hölzer
- Robert Koch Institute, MF1 Bioinformatics, Berlin, Germany
| | - E M Liebler-Tenorio
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Germany
| | - L-M Barf
- Friedrich-Schiller-Universität Jena, RNA Bioinformatics and High-Throughput Analysis, Jena, Germany
| | - S Delannoy
- University Paris-Est, Anses, Food Research Laboratory, IdentyPath Platform, Maisons-Alfort, France
| | - M Vittecoq
- Tour du Valat, Centre de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles, France
| | - R Wedlarski
- Bioparc - Zoo de Doué la fontaine, 103 rue de Cholet, 49700 Doué la Fontaine, France
| | - A Lécu
- Parc Zoologique de Paris, avenue de Daumesnil, 75012 Paris, France
| | - S Scharf
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Germany
| | - Y Blanchard
- Unit of Viral Genetics and Biosafety, ANSES, Laboratory of Ploufragan, Ploufragan, France
| | - P Fach
- University Paris-Est, Anses, Food Research Laboratory, IdentyPath Platform, Maisons-Alfort, France
| | - R C Hsia
- University of Maryland, Electron Microscopy Core Imaging Facility, Baltimore, MD 21201, USA
| | - P M Bavoil
- University of Maryland, Department of Microbial Pathogenesis, Baltimore, MD 21201, USA
| | - R Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies, 07190 Esporles, Spain
| | - K Laroucau
- University Paris-Est, Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France
| | - K Sachse
- Friedrich-Schiller-Universität Jena, RNA Bioinformatics and High-Throughput Analysis, Jena, Germany
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19
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Delannoy S, Schouler C, Souillard R, Yousfi L, Le Devendec L, Lucas C, Bougeard S, Keita A, Fach P, Galliot P, Balaine L, Puterflam J, Kempf I. Diversity of Escherichia coli strains isolated from day-old broiler chicks, their environment and colibacillosis lesions in 80 flocks in France. Vet Microbiol 2020; 252:108923. [PMID: 33221068 DOI: 10.1016/j.vetmic.2020.108923] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 09/12/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
Avian colibacillosis is the most common bacterial disease affecting broilers. To better evaluate the diversity and the origin of the causative Escherichia coli strains infecting birds, we conducted a study on 80 broiler flocks. Just before the arrival of chicks on the farm, samples were collected in the farm environment (walls, feeders, air inlets, etc.) and, upon delivery, day-old chicks (DOCs) and the transport boxes were also sampled. Isolates were obtained from these samples, and from organs of chickens exhibiting typical colibacillosis symptoms. The isolates were characterized using high-throughput qPCR to detect a range of genetic markers (phylogroups, main serogroups virulence markers, etc.). A total of 967 isolates were studied, including 203 from 28 colibacillosis episodes, 484 from DOCs, 162 from transport boxes and 118 from the farm environment. These isolates yielded 416 different genetic profiles, of which 267 were detected in single isolates, and the others were observed in up to 44 isolates from nine farms. The distributions of isolates across phylogroups and the main serogroups varied with the origin of isolation. The isolates obtained from colibacillosis cases either shared a single genetic profile or were different. In a few cases, we observed the same profile for isolates obtained from DOCs and colibacillosis lesions in the same flock or different flocks. However, some flocks receiving DOCs contaminated with isolates bearing the genetic profile of colibacillosis cases identified in other flocks remained healthy. This study highlights the huge diversity among avian E. coli isolated from diseased and non diseased birds.
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Affiliation(s)
- Sabine Delannoy
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, 94701, Maisons-Alfort, France
| | | | | | - Léna Yousfi
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, 94701, Maisons-Alfort, France
| | | | | | | | | | - Patrick Fach
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, 94701, Maisons-Alfort, France
| | | | - Loïc Balaine
- ANSES, Ploufragan-Plouzané-Niort Laboratory, France
| | | | - Isabelle Kempf
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, 94701, Maisons-Alfort, France.
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20
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Merino VR, Nakano V, Delannoy S, Fach P, Alberca GGF, Farfan MJ, Piazza RMF, Avila-Campos MJ. Prevalence of Enteropathogens and Virulence Traits in Brazilian Children With and Without Diarrhea. Front Cell Infect Microbiol 2020; 10:549919. [PMID: 33102252 PMCID: PMC7545120 DOI: 10.3389/fcimb.2020.549919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/07/2020] [Accepted: 08/25/2020] [Indexed: 11/13/2022] Open
Abstract
The use of molecular diagnostics for pathogen detection in epidemiological studies have allowed us to get a wider view of the pathogens associated with diarrhea, but the presence of enteropathogens in asymptomatic individuals has raised several challenges in understanding the etiology of diarrhea, and the use of these platforms in clinical diagnosis as well. To characterize the presence of the most relevant bacterial enteropathogens in diarrheal episodes, we evaluated here the prevalence of diarrheagenic E. coli pathotypes, Salmonella spp., and Yersinia enterocolitica in stool samples of children with and without diarrhea using real-time quantitative PCR (qPCR). We found that the presence of genetic markers associated with bacterial pathogens was significantly higher in stool samples from the diarrhea group compared to the control (P < 0.001). Bacterial loads in samples positive for eae and aggR markers were also determined. Compared to samples from asymptomatic children, a significantly higher number of copies of the eae gene were found in diarrhea samples. Also, the presence of genetic markers associated with STEC strains with clinical significance was evaluated in eae-positive samples by high-throughput real-time PCR. The data presented herein demonstrated that asymptomatic children of an urban area in Brazil might be enteropathogen reservoirs, especially for STEC.
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Affiliation(s)
- Victor R Merino
- Laboratório de Anaeróbios, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade of São Paulo, São Paulo, Brazil
| | - Viviane Nakano
- Laboratório de Anaeróbios, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade of São Paulo, São Paulo, Brazil
| | - Sabine Delannoy
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Food Safety Laboratory, Université Paris-Est, Champs-sur-Marne, France
| | - Patrick Fach
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Food Safety Laboratory, Université Paris-Est, Champs-sur-Marne, France
| | - Gabriela G F Alberca
- Laboratório de Anaeróbios, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade of São Paulo, São Paulo, Brazil
| | - Mauricio J Farfan
- Departamento de Pediatría y Cirugía Infantil, Facultad de Medicina, Campus Oriente-Hospital Dr. Luis Calvo Mackenna, Universidad de Chile, Santiago, Chile
| | | | - Mario J Avila-Campos
- Laboratório de Anaeróbios, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade of São Paulo, São Paulo, Brazil
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21
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Mourand G, Le Devendec L, Delannoy S, Fach P, Keita A, Amelot M, Jaunet H, Dia MEH, Kempf I. Variations of the Escherichia coli population in the digestive tract of broilers. Avian Pathol 2020; 49:678-688. [PMID: 32835506 DOI: 10.1080/03079457.2020.1814201] [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] [Indexed: 10/23/2022]
Abstract
We explored the between-group and temporal variations in the intestinal Escherichia coli populations of broilers under experimental conditions, taking both antimicrobial resistance and virulence into consideration. Four replicates of 45 commercial chicks were reared in four animal facilities. On their first day of life (Day 0), they were orally inoculated with two extended-spectrum-cephalosporin-resistant (ESCR) E. coli (2.72 log10 CFU of a bla CMY-2- and 2.55 log10 CFU of a bla CTX-M-carrying E. coli). Faecal samples were then collected weekly and caecal samples were obtained from birds sacrificed on Days 21 or 42. The total, ESC-, ciprofloxacin- and gentamicin-resistant E. coli populations were enumerated on MacConkey (MC) and MC-supplemented media, and eight virulence-associated genes (VAGs) (iroN, iutA, iss, ompT, hlyF, vat, frzorf4 , and fyuA) were sought by PCR on isolates obtained on MC agar. The results showed significant between-group differences in the size of the resistant sub-populations and the presence of VAGs. Contrary to bla CTX-M-positive strains, bla CMY-positive strains persisted up to Day 42, but represented only a minor fraction of the total E. coli population. The ESC-, gentamicin- and ciprofloxacin-resistant populations decreased over time. Isolates obtained during the first week contained a mean of 5.1 VAGs. The percentages of some VAG profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. The fluctuations or differences between E. coli isolates according to group, age, and faecal or caecal origin need to be considered when designing experimental protocols and seeking to improve colibacillosis control. RESEARCH HIGHLIGHTS Temporal variations in the intestinal E. coli populations of broilers was studied. The antibiotic-resistant populations decreased over time. Virulence profiles differed between faecal isolates on Day 41 and caecal isolates on Day 42. Strains with the highest numbers of virulence genes were present during the first days.
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Affiliation(s)
- Gwenaëlle Mourand
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Zoopôle les croix, Ploufragan, France
| | - Laëtitia Le Devendec
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Zoopôle les croix, Ploufragan, France
| | - Sabine Delannoy
- ANSES - French Agency for Food, Environmental and Occupational Health & Safety Food Research Laboratory, Platform IdentyPath, Maisons-Alfort, France
| | - Patrick Fach
- ANSES - French Agency for Food, Environmental and Occupational Health & Safety Food Research Laboratory, Platform IdentyPath, Maisons-Alfort, France
| | - Alassane Keita
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Zoopôle les croix, Ploufragan, France
| | - Michel Amelot
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Zoopôle les croix, Ploufragan, France
| | | | | | - Isabelle Kempf
- ANSES Laboratoire de Ploufragan-Plouzané-Niort, Zoopôle les croix, Ploufragan, France
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Laroucau K, Aaziz R, Vorimore F, Varghese K, Deshayes T, Bertin C, Delannoy S, Sami AM, Al Batel M, El Shorbagy M, Almutawaa KAW, Alanezi SJ, Alazemi YSN, Guernier-Cambert V, Wernery U. A genetic variant of Burkholderia mallei detected in Kuwait: Consequences for the PCR diagnosis of glanders. Transbound Emerg Dis 2020; 68:960-963. [PMID: 33245616 DOI: 10.1111/tbed.13777] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 11/26/2022]
Abstract
Glanders is a contagious zoonotic disease caused by Burkholderia mallei. Following the detection of glanders positive horses using the OIE complement fixation test, the tissues of two horses were analysed by PCR. While PCR systems targeting the Burkholderia pseudomallei complex gave positive signals, the species-specific PCR systems targeting B. mallei (fliP-IS407A) and B. pseudomallei (orf11)-the OIE recommended targets-resulted in negative signals. However, the presence of B. mallei in these tissues was confirmed with a recently described B. mallei-specific real-time PCR system and genotyping with MLST- and SNP-based methods, performed on the most positive tissue, identified a genotype closely related to B. mallei strains recently isolated in the Middle East. This study leads to recommendations regarding the use of PCR systems for the molecular diagnosis of glanders, especially in regions where the circulating B. mallei strains have not yet been fully genetically characterized.
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Affiliation(s)
- Karine Laroucau
- Laboratory for Animal Health, Bacterial Zoonosis Unit, European and OIE Reference Laboratory for Glanders, Paris-Est University, ANSES, Maisons-Alfort, France
| | - Rachid Aaziz
- Laboratory for Animal Health, Bacterial Zoonosis Unit, European and OIE Reference Laboratory for Glanders, Paris-Est University, ANSES, Maisons-Alfort, France
| | - Fabien Vorimore
- Laboratory for Animal Health, Bacterial Zoonosis Unit, European and OIE Reference Laboratory for Glanders, Paris-Est University, ANSES, Maisons-Alfort, France
| | - Koshy Varghese
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Thomas Deshayes
- Laboratory for Animal Health, Bacterial Zoonosis Unit, European and OIE Reference Laboratory for Glanders, Paris-Est University, ANSES, Maisons-Alfort, France
| | - Claire Bertin
- Laboratory for Animal Health, Bacterial Zoonosis Unit, European and OIE Reference Laboratory for Glanders, Paris-Est University, ANSES, Maisons-Alfort, France
| | - Sabine Delannoy
- Food Research Laboratory, IdentyPath Platform, University Paris-Est, ANSES, Maisons-Alfort, France
| | - Attia M Sami
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Maha Al Batel
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Mamdouh El Shorbagy
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Khaled A W Almutawaa
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Saad J Alanezi
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Yousef S N Alazemi
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Vanina Guernier-Cambert
- Agricultural Research Service, National Animal Disease Center, United States Department of Agriculture, Ames, IA, USA
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, OIE Reference Laboratory for Glanders, Dubai, United Arab Emirates
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Gondard M, Delannoy S, Pinarello V, Aprelon R, Devillers E, Galon C, Pradel J, Vayssier-Taussat M, Albina E, Moutailler S. Upscaling the Surveillance of Tick-borne Pathogens in the French Caribbean Islands. Pathogens 2020; 9:pathogens9030176. [PMID: 32121571 PMCID: PMC7157729 DOI: 10.3390/pathogens9030176] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/24/2020] [Accepted: 02/28/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the high burden of vector-borne disease in (sub)tropical areas, few information are available regarding the diversity of tick and tick-borne pathogens circulating in the Caribbean. Management and control of vector-borne disease require actual epidemiological data to better assess and anticipate the risk of (re)emergence of tick-borne diseases in the region. To simplify and reduce the costs of such large-scale surveys, we implemented a high-throughput microfluidic real-time PCR system suitable for the screening of the main bacterial and parasitic genera involved in tick-borne disease and potentially circulating in the area. We used the new screening tool to perform an exploratory epidemiological study on 132 adult specimens of Amblyomma variegatum and 446 of Rhipicephalus microplus collected in Guadeloupe and Martinique. Not only the system was able to detect the main pathogens of the area-Ehrlichia ruminantium, Rickettsia africae, Anaplasma marginale, Babesia bigemina and Babesia bovis-but the system also provided evidence of unsuspected microorganisms in Caribbean ticks, belonging to the Anaplasma, Ehrlichia, Borrelia and Leishmania genera. Our study demonstrated how high-throughput microfluidic real-time PCR technology can assist large-scale epidemiological studies, providing a rapid overview of tick-borne pathogen and microorganism diversity, and opening up new research perspectives for the epidemiology of tick-borne pathogens.
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Affiliation(s)
- Mathilde Gondard
- UMR BIPAR, Animal Health Laboratory, ANSES, INRAE, National Veterinary School of Alfort, Paris-Est University, Maisons-Alfort, 94700 Paris, France; (M.G.); (E.D.); (C.G.); (M.V.-T.)
- CIRAD, UMR ASTRE, F-97170 Petit-Bourg, 97170 Guadeloupe, France; (V.P.); (R.A.); (J.P.); (E.A.)
| | - Sabine Delannoy
- IdentyPath Platform, Laboratory for Food Safety, ANSES, Maisons-Alfort, 94700 Paris, France;
| | - Valérie Pinarello
- CIRAD, UMR ASTRE, F-97170 Petit-Bourg, 97170 Guadeloupe, France; (V.P.); (R.A.); (J.P.); (E.A.)
- ASTRE, Univ Montpellier, CIRAD, INRAE, 34000 Montpellier, France
| | - Rosalie Aprelon
- CIRAD, UMR ASTRE, F-97170 Petit-Bourg, 97170 Guadeloupe, France; (V.P.); (R.A.); (J.P.); (E.A.)
- ASTRE, Univ Montpellier, CIRAD, INRAE, 34000 Montpellier, France
| | - Elodie Devillers
- UMR BIPAR, Animal Health Laboratory, ANSES, INRAE, National Veterinary School of Alfort, Paris-Est University, Maisons-Alfort, 94700 Paris, France; (M.G.); (E.D.); (C.G.); (M.V.-T.)
| | - Clémence Galon
- UMR BIPAR, Animal Health Laboratory, ANSES, INRAE, National Veterinary School of Alfort, Paris-Est University, Maisons-Alfort, 94700 Paris, France; (M.G.); (E.D.); (C.G.); (M.V.-T.)
| | - Jennifer Pradel
- CIRAD, UMR ASTRE, F-97170 Petit-Bourg, 97170 Guadeloupe, France; (V.P.); (R.A.); (J.P.); (E.A.)
- ASTRE, Univ Montpellier, CIRAD, INRAE, 34000 Montpellier, France
| | - Muriel Vayssier-Taussat
- UMR BIPAR, Animal Health Laboratory, ANSES, INRAE, National Veterinary School of Alfort, Paris-Est University, Maisons-Alfort, 94700 Paris, France; (M.G.); (E.D.); (C.G.); (M.V.-T.)
| | - Emmanuel Albina
- CIRAD, UMR ASTRE, F-97170 Petit-Bourg, 97170 Guadeloupe, France; (V.P.); (R.A.); (J.P.); (E.A.)
- ASTRE, Univ Montpellier, CIRAD, INRAE, 34000 Montpellier, France
| | - Sara Moutailler
- UMR BIPAR, Animal Health Laboratory, ANSES, INRAE, National Veterinary School of Alfort, Paris-Est University, Maisons-Alfort, 94700 Paris, France; (M.G.); (E.D.); (C.G.); (M.V.-T.)
- Correspondence: ; Tel.: +33-1-49-77-46-50
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Cointe A, Birgy A, Mariani-Kurkdjian P, Liguori S, Courroux C, Blanco J, Delannoy S, Fach P, Loukiadis E, Bidet P, Bonacorsi S. Emerging Multidrug-Resistant Hybrid Pathotype Shiga Toxin-Producing Escherichia coli O80 and Related Strains of Clonal Complex 165, Europe. Emerg Infect Dis 2019; 24:2262-2269. [PMID: 30457551 PMCID: PMC6256387 DOI: 10.3201/eid2412.180272] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 12/16/2022] Open
Abstract
Enterohemorrhagic Escherichia coli serogroup O80, involved in hemolytic uremic syndrome associated with extraintestinal infections, has emerged in France. We obtained circularized sequences of the O80 strain RDEx444, responsible for hemolytic uremic syndrome with bacteremia, and noncircularized sequences of 35 O80 E. coli isolated from humans and animals in Europe with or without Shiga toxin genes. RDEx444 harbored a mosaic plasmid, pR444_A, combining extraintestinal virulence determinants and a multidrug resistance-encoding island. All strains belonged to clonal complex 165, which is distantly related to other major enterohemorrhagic E. coli lineages. All stx-positive strains contained eae-ξ, ehxA, and genes characteristic of pR444_A. Among stx-negative strains, 1 produced extended-spectrum β-lactamase, 1 harbored the colistin-resistance gene mcr1, and 2 possessed genes characteristic of enteropathogenic and pyelonephritis E. coli. Because O80-clonal complex 165 strains can integrate intestinal and extraintestinal virulence factors in combination with diverse drug-resistance genes, they constitute dangerous and versatile multidrug-resistant pathogens.
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Mahamat Abdelrahim A, Radomski N, Delannoy S, Djellal S, Le Négrate M, Hadjab K, Fach P, Hennekinne JA, Mistou MY, Firmesse O. Large-Scale Genomic Analyses and Toxinotyping of Clostridium perfringens Implicated in Foodborne Outbreaks in France. Front Microbiol 2019; 10:777. [PMID: 31057505 PMCID: PMC6481350 DOI: 10.3389/fmicb.2019.00777] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 07/30/2018] [Accepted: 03/26/2019] [Indexed: 11/13/2022] Open
Abstract
Clostridium perfringens is both an ubiquitous environmental bacterium and the fourth most common causative agent of foodborne outbreaks (FBOs) in France and Europe. These outbreaks are known to be caused by C. perfringens enterotoxin (CPE) encoded by the cpe gene. However, additional information on the toxin/virulence gene content of C. perfringens has become available in the last few years. Therefore, to understand the enteropathogenicity of this bacterium, we need to describe the toxin and virulence genes content of strains involved in FBOs. In this study, we used a new real-time PCR typing technique based on a comprehensive set of 17 genes encoding virulence factors. The analysis was performed on a collection of 141 strains involved in 42 FBOs in the Paris region. It was combined with whole genome sequence (WGS) phylogenomic reconstruction, based on the coregenome single nucleotide polymorphisms (SNPs) of 58 isolates, representatives of the identified virulence gene profiles. Two or three different virulence gene profiles were detected in 10 FBOs, demonstrating that C. perfringens FBOs may be associated with heterogeneous strains. cpe-positive strains were isolated in 23 outbreaks, confirming the prominent role of CPE in pathogenicity. However, while C. perfringens was the sole pathogen isolated from the incriminated food, the cpe gene was not detected in strains related to 13 outbreaks. This result indicates either that the standard method was not able to isolate cpe+ strains or that the cpe gene may not be the only determinant of the enterotoxigenic potential of C. perfringens strains. Using phylogenomic reconstruction, we identified two clades distinguishing chromosomal cpe-positive from cpe-negative and plasmid-borne cpe. Important epidemiological information was also garnered from this phylogenomic reconstruction that revealed unexpected links between different outbreaks associated with closely related strains (seven SNP differences) and having common virulence gene profiles. This study provides new insight into the characterization of foodborne C. perfringens and highlights the potential of WGS for the investigation of FBOs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Olivier Firmesse
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
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Gondard M, Michelet L, Nisavanh A, Devillers E, Delannoy S, Fach P, Aspan A, Ullman K, Chirico J, Hoffmann B, van der Wal FJ, de Koeijer A, van Solt-Smits C, Jahfari S, Sprong H, Mansfield KL, Fooks AR, Klitgaard K, Bødker R, Moutailler S. Prevalence of tick-borne viruses in Ixodes ricinus assessed by high-throughput real-time PCR. Pathog Dis 2018; 76:5181333. [PMID: 30423120 DOI: 10.1093/femspd/fty083] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/12/2018] [Indexed: 12/18/2022] Open
Abstract
Ticks are one of the principal arthropod vectors of human and animal infectious diseases. Whereas the prevalence of tick-borne encephalitis virus in ticks in Europe is well studied, there is less information available on the prevalence of the other tick-borne viruses (TBVs) existing worldwide. The aim of this study was to improve the epidemiological survey tools of TBVs by the development of an efficient high-throughput test to screen a wide range of viruses in ticks.In this study, we developed a new high-throughput virus-detection assay based on parallel real-time PCRs on a microfluidic system, and used it to perform a large scale epidemiological survey screening for the presence of 21 TBVs in 18 135 nymphs of Ixodes ricinus collected from five European countries. This extensive investigation has (i) evaluated the prevalence of four viruses present in the collected ticks, (ii) allowed the identification of viruses in regions where they were previously undetected.In conclusion, we have demonstrated the capabilities of this new screening method that allows the detection of numerous TBVs in a large number of ticks. This tool represents a powerful and rapid system for TBVs surveillance in Europe and could be easily customized to assess viral emergence.
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Affiliation(s)
- Mathilde Gondard
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 14 Rue P. et M. Curie, 94700 Maisons-Alfort, France
| | - Lorraine Michelet
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 14 Rue P. et M. Curie, 94700 Maisons-Alfort, France
| | - Athinna Nisavanh
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 14 Rue P. et M. Curie, 94700 Maisons-Alfort, France
| | - Elodie Devillers
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 14 Rue P. et M. Curie, 94700 Maisons-Alfort, France
| | - Sabine Delannoy
- IdentyPath Platform, Food Safety Laboratory, ANSES, 14 Rue P. et M. Curie, 94700 Maisons-Alfort, France
| | - Patrick Fach
- IdentyPath Platform, Food Safety Laboratory, ANSES, 14 Rue P. et M. Curie, 94700 Maisons-Alfort, France
| | - Anna Aspan
- Department of Microbiology, National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden
| | - Karin Ullman
- Department of Microbiology, National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden
| | - Jan Chirico
- Department of Microbiology, National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Sü dufer 10, 17493 Greifswald - Insel Riems, Germany
| | - Fimme Jan van der Wal
- Wageningen Bioveterinary Research (WBVR), Wageningen UR, Houtribweg 39, 8221 RA Lelystad, The Netherlands
| | - Aline de Koeijer
- Wageningen Bioveterinary Research (WBVR), Wageningen UR, Houtribweg 39, 8221 RA Lelystad, The Netherlands
| | - Conny van Solt-Smits
- Wageningen Bioveterinary Research (WBVR), Wageningen UR, Houtribweg 39, 8221 RA Lelystad, The Netherlands
| | - Seta Jahfari
- Laboratory for Zoonoses and Environmental Microbiology, National Institute for Public Health and Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Hein Sprong
- Laboratory for Zoonoses and Environmental Microbiology, National Institute for Public Health and Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
| | - Karen L Mansfield
- Animal and Plant Health Agency (APHA), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Anthony R Fooks
- Animal and Plant Health Agency (APHA), Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Kirstine Klitgaard
- National Veterinary Institute, DTU, Henrik Dams Allé, Building 205B, 2800 Kgs. Lyngby, Denmark
| | - Rene Bødker
- National Veterinary Institute, DTU, Henrik Dams Allé, Building 205B, 2800 Kgs. Lyngby, Denmark
| | - Sara Moutailler
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 14 Rue P. et M. Curie, 94700 Maisons-Alfort, France
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Noll LW, Chall R, Shridhar PB, Liu X, Bai J, Delannoy S, Fach P, Nagaraja TG. Validation and Application of a Real-Time PCR Assay Based on the CRISPR Array for Serotype-Specific Detection and Quantification of Enterohemorrhagic Escherichia coli O157:H7 in Cattle Feces †. J Food Prot 2018; 81:1157-1164. [PMID: 29939793 DOI: 10.4315/0362-028x.jfp-18-049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 12/27/2022]
Abstract
Several real-time quantitative PCR (qPCR) assays have been developed for detection and quantification of Escherichia coli O157:H7 in complex matrices by targeting genes for serogroup-specific O-antigen ( rfbEO157), H7 antigen, and one or more major virulence factors (Shiga toxin and intimin). A major limitation of such assays is that coamplification of H7 and virulence genes in a sample does not signal association of those genes with the O157 serogroup. Clusters of regularly interspaced short palindromic repeats (CRISPR) polymorphisms are highly correlated with certain enterohemorrhagic E. coli (EHEC) serotypes, including O157:H7, and the presence of genes for Shiga toxin ( stx1 and stx2) and intimin ( eae). Our objectives were to develop and validate a qPCR assay targeting the CRISPR array for the detection and quantification of EHEC O157:H7 in cattle feces and to evaluate the applicability of the assay for detection of and comparison with a four-plex qPCR assay targeting rfbEO157, stx1, stx2, and eae genes and a culture method. Detection limits of the CRISPRO157:H7 qPCR assay for cattle feces spiked with pure cultures were 2.1 × 103 and 2.3 × 100 CFU/g before and after enrichment, respectively. Detection of E. coli O157 in feedlot cattle fecal samples ( n = 576) was compared among the CRISPRO157:H7 qPCR assay, culture method, and four-plex qPCR assay. The CRISPRO157:H7 qPCR detected 42.2% of the samples (243 of 576 samples) as positive for E. coli O157:H7, compared with 30.4% (175 samples) by the culture method. Nearly all samples (97.2%; 560 samples) were positive for rfbEO157 by the four-plex PCR, but 21.8% (122 of 560 samples) were negative for the stx and/or eae genes, making it unlikely that EHEC O157:H7 was present in these samples. Cohen's kappa statistic indicated a fair and poor agreement beyond that due to chance between the CRISPR assay and the culture method and four-plex assay, respectively. This novel qPCR assay can detect the EHEC O157:H7 serotype in cattle feces by targeting CRISPR polymorphisms.
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Affiliation(s)
- Lance W Noll
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Rachel Chall
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Pragathi B Shridhar
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Xuming Liu
- 2 Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Jianfa Bai
- 2 Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Sabine Delannoy
- 3 Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - Patrick Fach
- 3 Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - T G Nagaraja
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
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Briet A, Helsens N, Delannoy S, Debuiche S, Brisabois A, Midelet G, Granier SA. NDM-1-producing Vibrio parahaemolyticus isolated from imported seafood. J Antimicrob Chemother 2018; 73:2578-2579. [DOI: 10.1093/jac/dky200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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)
- Arnaud Briet
- Anses, Laboratory for food safety, F-62200 Boulogne-sur-Mer, France
| | - Nicolas Helsens
- Anses, Laboratory for food safety, F-62200 Boulogne-sur-Mer, France
| | - Sabine Delannoy
- Université Paris-Est, Anses, Laboratory for food safety, F-94700 Maisons-Alfort, France
| | - Sabine Debuiche
- Anses, Laboratory for food safety, F-62200 Boulogne-sur-Mer, France
| | - Anne Brisabois
- Anses, Laboratory for food safety, F-62200 Boulogne-sur-Mer, France
- Université Paris-Est, Anses, Laboratory for food safety, F-94700 Maisons-Alfort, France
| | | | - Sophie A Granier
- Université Paris-Est, Anses, Laboratory for food safety, F-94700 Maisons-Alfort, France
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Delannoy S, Le Devendec L, Jouy E, Fach P, Drider D, Kempf I. Characterization of Colistin-Resistant Escherichia coli Isolated from Diseased Pigs in France. Front Microbiol 2017; 8:2278. [PMID: 29209292 PMCID: PMC5702452 DOI: 10.3389/fmicb.2017.02278] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 06/15/2017] [Accepted: 11/06/2017] [Indexed: 11/17/2022] Open
Abstract
We studied a collection of 79 colistin-resistant Escherichia coli isolates isolated from diseased pigs in France between 2009 and 2013. We determined a number of phenotypic and genetic characters using broth microdilution to characterize their antimicrobial susceptibility. We performed pulse field gel electrophoresis (PFGE) to assess their genetic diversity and assign them to phylogroups. High-throughput real-time PCR micro-array was used to screen for a selection of genetic markers of virulence, and PCR and sequencing of the main recognized resistance genes allowed us to investigate the mechanisms of colistin resistance. Results showed that isolates belonged to several phylogroups and most had a unique PFGE profile. More than 50% of the isolates were also resistant to sulfonamides, trimethoprim, tetracycline, ampicillin or chloramphenicol. The mcr-1 gene was detected in 70 out of 79 isolates and was transferred by conjugation in 33 of them, sometimes together with resistance to sulfonamides, trimethoprim, tetracycline, ampicillin, chloramphenicol, cefotaxime, or gentamicin. Mutations in the amino-acid sequences of proteins MgrB, PhoP, PhoQ, PmrB, but not PmrA, were detected in isolates with or without the mcr-1 gene. More than one-third of the isolates harbored the F18, F4, astA, hlyA, estI, estII, elt, stx2e, iha, orfA, orfB, paa, terE, ecs1763, or ureD virulence markers. In conclusion, although most isolates had a unique PFGE profile, a few particular combinations of phylogenetic groups, virulence genes and mutations in the sequenced genes involved in colistin resistance were identified on a number of occasions, suggesting the persistence of certain isolates over several years.
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Affiliation(s)
- Sabine Delannoy
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Food Safety Laboratory, Université Paris-Est, Maisons-Alfort, France
| | - Laetitia Le Devendec
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Eric Jouy
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Patrick Fach
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Food Safety Laboratory, Université Paris-Est, Maisons-Alfort, France
| | - Djamel Drider
- Institut Charles Viollette, Université de Lille, Lille, France
| | - Isabelle Kempf
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
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Delannoy S, Mariani-Kurkdjian P, Webb HE, Bonacorsi S, Fach P. The Mobilome; A Major Contributor to Escherichia coli stx2-Positive O26:H11 Strains Intra-Serotype Diversity. Front Microbiol 2017; 8:1625. [PMID: 28932209 PMCID: PMC5592225 DOI: 10.3389/fmicb.2017.01625] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 12/15/2016] [Accepted: 08/10/2017] [Indexed: 12/12/2022] Open
Abstract
Shiga toxin-producing Escherichia coli of serotype O26:H11/H- constitute a diverse group of strains and several clones with distinct genetic characteristics have been identified and characterized. Whole genome sequencing was performed using Illumina and PacBio technologies on eight stx2-positive O26:H11 strains circulating in France. Comparative analyses of the whole genome of the stx2-positive O26:H11 strains indicate that several clones of EHEC O26:H11 are co-circulating in France. Phylogenetic analysis of the French strains together with stx2-positive and stx-negative E. coli O26:H11 genomes obtained from Genbank indicates the existence of four clonal complexes (SNP-CCs) separated in two distinct lineages, one of which comprises the "new French clone" (SNP-CC1) that appears genetically closely related to stx-negative attaching and effacing E. coli (AEEC) strains. Interestingly, the whole genome SNP (wgSNP) phylogeny is summarized in the cas gene phylogeny, and a simple qPCR assay targeting the CRISPR array specific to SNP-CC1 (SP_O26-E) can distinguish between the two main lineages. The PacBio sequencing allowed a detailed analysis of the mobile genetic elements (MGEs) of the strains. Numerous MGEs were identified in each strain, including a large number of prophages and up to four large plasmids, representing overall 8.7-19.8% of the total genome size. Analysis of the prophage pool of the strains shows a considerable diversity with a complex history of recombination. Each clonal complex (SNP-CC) is characterized by a unique set of plasmids and phages, including stx-prophages, suggesting evolution through separate acquisition events. Overall, the MGEs appear to play a major role in O26:H11 intra-serotype clonal diversification.
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Affiliation(s)
- Sabine Delannoy
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPathMaisons-Alfort, France
| | - Patricia Mariani-Kurkdjian
- Assistance Publique Hopitaux de Paris, Hôpital Robert-Debré, Service de Microbiologie, CNR Associé Escherichia coliParis, France
- Infection, Antimicrobials, Modelling, Evolution, UMR 1137, Institut National de la Santé et de la Recherche MédicaleParis, France
- Infection, Antimicrobials, Modelling, Evolution, UMR 1137, Univ Paris Diderot, Sorbonne Paris CitéParis, France
| | - Hattie E. Webb
- Department of Animal and Food Sciences, Texas Tech UniversityLubbock, TX, United States
| | - Stephane Bonacorsi
- Assistance Publique Hopitaux de Paris, Hôpital Robert-Debré, Service de Microbiologie, CNR Associé Escherichia coliParis, France
- Infection, Antimicrobials, Modelling, Evolution, UMR 1137, Institut National de la Santé et de la Recherche MédicaleParis, France
- Infection, Antimicrobials, Modelling, Evolution, UMR 1137, Univ Paris Diderot, Sorbonne Paris CitéParis, France
| | - Patrick Fach
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPathMaisons-Alfort, France
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Douëllou T, Delannoy S, Ganet S, Fach P, Loukiadis E, Montel MC, Sergentet-Thevenot D. Molecular characterization of O157:H7, O26:H11 and O103:H2 Shiga toxin-producing Escherichia coli isolated from dairy products. Int J Food Microbiol 2017; 253:59-65. [PMID: 28499121 DOI: 10.1016/j.ijfoodmicro.2017.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 01/10/2023]
Abstract
Pathogenic Shiga toxin-producing E. coli (STEC) are recognized worldwide as environment and foodborne pathogens which can be transmitted by ingestion of ready-to-eat food such as raw milk-derived products. STEC show a prevalence rate in dairy products of 0.9%, yet comparably few outbreaks have been related to dairy products consumption. In this study, we used rt-qPCR to identify the virulence potential of O157, O26 and O103 STEC strains isolated from raw-milk dairy products by analyzing virulence-related gene frequencies and associations with O-island (OI) 44, OI-48, OI-50, OI-57, OI-71 and OI-122. Results showed that 100% of STEC strains investigated harbored genes associated with EHEC-related virulence profile patterns (eae and stx, with either espK, espV, ureD and/or Z2098). We also found similarities in virulence-related gene content between O157:H7 and O103:H2 dairy and non-dairy STEC strains, especially isolates from human cases. The O26:H11-serotype STEC strains investigated harbor the arcA-allele 2 gene associated with specific genetic markers. These profiles are associated with high-virulence seropathotype-A STEC. However, the low frequency of stx2 gene associated with absence of other virulence genes in dairy isolates of O26:H11 remains a promising avenue of investigation to estimate their real pathogenicity. All O26:H11 attaching-effacing E. coli (AEEC) strains carried CRISPRO26:H11SP_O26_E but not genetic markers espK, espV, ureD and/or Z2098 associated with the emerging potentially high-virulence "new French clone". These strains are potentially as "EHEC-like" strains because they may acquire (or have lost) stx gene. In this study, O157:H7, O103:H2 and O26:H11 STEC strains isolated from dairy products were assigned as potential pathogens. However, research now needs to investigate the impact of dairy product environment and dairy processing on the expression of their pathogenicity.
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Affiliation(s)
- T Douëllou
- Institute National de Recherche Agronomique, Unité de Recherches Fromagères, 15000 Aurillac, France; Université de Lyon, Research Group "Bacterial Opportunistic Pathogens and Environment", UMR5557 Ecologie Microbienne Lyon, Université Lyon 1, CNRS, VetAgro Sup, 69280 Marcy l'Etoile, France.
| | - S Delannoy
- Université Paris-Est, ANSES, Laboratoire de Sécurité des Aliments, Plateforme IdentyPath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - S Ganet
- Université de Lyon, Research Group "Bacterial Opportunistic Pathogens and Environment", UMR5557 Ecologie Microbienne Lyon, Université Lyon 1, CNRS, VetAgro Sup, 69280 Marcy l'Etoile, France; Université de Lyon, VetAgro Sup Campus Vétérinaire, Laboratoire d'Etudes des Microorganismes Alimentaires Pathogènes-French National Reference laboratory for Escherichia coli including Shiga toxin-producing E. coli (NRL-STEC), 69280 Marcy l'Etoile, France
| | - P Fach
- Université Paris-Est, ANSES, Laboratoire de Sécurité des Aliments, Plateforme IdentyPath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - E Loukiadis
- Université de Lyon, Research Group "Bacterial Opportunistic Pathogens and Environment", UMR5557 Ecologie Microbienne Lyon, Université Lyon 1, CNRS, VetAgro Sup, 69280 Marcy l'Etoile, France; Université de Lyon, VetAgro Sup Campus Vétérinaire, Laboratoire d'Etudes des Microorganismes Alimentaires Pathogènes-French National Reference laboratory for Escherichia coli including Shiga toxin-producing E. coli (NRL-STEC), 69280 Marcy l'Etoile, France
| | - M-C Montel
- Institute National de Recherche Agronomique, Unité de Recherches Fromagères, 15000 Aurillac, France
| | - D Sergentet-Thevenot
- Université de Lyon, Research Group "Bacterial Opportunistic Pathogens and Environment", UMR5557 Ecologie Microbienne Lyon, Université Lyon 1, CNRS, VetAgro Sup, 69280 Marcy l'Etoile, France; Université de Lyon, VetAgro Sup Campus Vétérinaire, Laboratoire d'Etudes des Microorganismes Alimentaires Pathogènes-French National Reference laboratory for Escherichia coli including Shiga toxin-producing E. coli (NRL-STEC), 69280 Marcy l'Etoile, France
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Petit F, Clermont O, Delannoy S, Servais P, Gourmelon M, Fach P, Oberlé K, Fournier M, Denamur E, Berthe T. Change in the Structure of Escherichia coli Population and the Pattern of Virulence Genes along a Rural Aquatic Continuum. Front Microbiol 2017; 8:609. [PMID: 28458656 PMCID: PMC5394106 DOI: 10.3389/fmicb.2017.00609] [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: 11/09/2016] [Accepted: 03/24/2017] [Indexed: 12/15/2022] Open
Abstract
The aim of this study was to investigate the diversity of the Escherichia coli population, focusing on the occurrence of pathogenic E. coli, in surface water draining a rural catchment. Two sampling campaigns were carried out in similar hydrological conditions (wet period, low flow) along a river continuum, characterized by two opposite density gradients of animals (cattle and wild animals) and human populations. While the abundance of E. coli slightly increased along the river continuum, the abundance of both human and ruminant-associated Bacteroidales markers, as well as the number of E. coli multi-resistant to antibiotics, evidenced a fecal contamination originating from animals at upstream rural sites, and from humans at downstream urban sites. A strong spatial modification of the structure of the E. coli population was observed. At the upstream site close to a forest, a higher abundance of the B2 phylogroup and Escherichia clade strains were observed. At the pasture upstream site, a greater proportion of both E and B1 phylogroups was detected, therefore suggesting a fecal contamination of mainly bovine origin. Conversely, in downstream urban sites, A, D, and F phylogroups were more abundant. To assess the occurrence of intestinal pathogenic strains, virulence factors [afaD, stx1, stx2, eltB (LT), estA (ST), ipaH, bfpA, eae, aaiC and aatA] were screened among 651 E. coli isolates. Intestinal pathogenic strains STEC O174:H21 (stx2) and EHEC O26:H11 (eae, stx1) were isolated in water and sediments close to the pasture site. In contrast, in the downstream urban site aEPEC/EAEC and DAEC of human origin, as well as extra-intestinal pathogenic E. coli belonging to clonal group A of D phylogroup, were sampled. Even if the estimated input of STEC (Shiga toxin-producing E. coli) - released in water at the upstream pasture site - at the downstream site was low, we show that STEC could persist in sediment. These results show that, the run-off of small cattle farms contributed, as much as the wastewater effluent, in the dissemination of pathogenic E. coli in both water and sediments, even if the microbiological quality of the water was good or to average quality according to the French water index.
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Affiliation(s)
- Fabienne Petit
- Normandie Université, UniRouen, UniCaen, CNRS UMR M2CRouen, France.,Sorbonne Universités, UPMC, CNRS, EPHE, UMR 7619 METISParis, France
| | - Olivier Clermont
- INSERM UMR1137, IAME, Université Paris Diderot, Sorbonne Paris CitéParis, France
| | - Sabine Delannoy
- Université Paris-Est, Anses, Food Safety Laboratory, IdentyPath Platform, Maisons-AlfortFrance
| | - Pierre Servais
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la PlaineBruxelles, Belgium
| | - Michèle Gourmelon
- Institut Français de Recherche pour l'Exploitation de la Mer, RBE-SG2M-LSEMPlouzané, France
| | - Patrick Fach
- Université Paris-Est, Anses, Food Safety Laboratory, IdentyPath Platform, Maisons-AlfortFrance
| | - Kenny Oberlé
- Normandie Université, UniRouen, UniCaen, CNRS UMR M2CRouen, France
| | | | - Erick Denamur
- INSERM UMR1137, IAME, Université Paris Diderot, Sorbonne Paris CitéParis, France
| | - Thierry Berthe
- Normandie Université, UniRouen, UniCaen, CNRS UMR M2CRouen, France
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Feng P, Delannoy S, Lacher DW, Bosilevac JM, Fach P. Characterization and Virulence Potential of Serogroup O113 Shiga Toxin-Producing Escherichia coli Strains Isolated from Beef and Cattle in the United States. J Food Prot 2017; 80:383-391. [PMID: 28199145 DOI: 10.4315/0362-028x.jfp-16-325] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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
Shiga toxin-producing Escherichia coli (STEC) of serotype O113:H21 have caused severe diseases but are unusual in that they do not produce the intimin protein required for adherence to intestinal epithelial cells. Strains of serogroup O113 are one of the most common STEC found in ground beef and beef products in the United States, but their virulence potential is unknown. We used a microarray to characterize 65 O113 strains isolated in the United States from ground beef, beef trim, cattle feces, and fresh spinach. Most were O113:H21 strains, but there were also nine strains of O113:H4 serotype. Although strains within the same serotype had similar profiles for the genes that were tested on the array, the profiles were distinct between the two serotypes, and the strains belonged to different clonal groups. Analysis by clustered regularly interspaced short palindromic repeat analysis showed that O113:H4 strains are conserved genetically, but the O113:H21 strains showed considerable polymorphism and genetic diversity. In comparison to the O113:H21 strains from Australia that were implicated in severe disease, the U.S. isolates showed similar genetic profiles to the known pathogens from Australia, suggesting that these may also have the potential to cause infections.
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Affiliation(s)
- Peter Feng
- Division of Microbiology, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, Maryland 20740, USA
| | - Sabine Delannoy
- French Agency for Food, Environmental and Occupational Health and Safety, 27-31 Avenue du General Leclerc, 94701 Maisons-Alfort, France
| | - David W Lacher
- Division of Molecular Biology, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708, USA
| | - Joseph M Bosilevac
- U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933, USA
| | - Patrick Fach
- French Agency for Food, Environmental and Occupational Health and Safety, 27-31 Avenue du General Leclerc, 94701 Maisons-Alfort, France
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Delannoy S, Beutin L, Mariani-Kurkdjian P, Fleiss A, Bonacorsi S, Fach P. The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters. Front Cell Infect Microbiol 2017; 7:30. [PMID: 28224115 PMCID: PMC5293828 DOI: 10.3389/fcimb.2017.00030] [Citation(s) in RCA: 14] [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] [Received: 11/21/2016] [Accepted: 01/23/2017] [Indexed: 01/10/2023] Open
Abstract
Escherichia coli strains belonging to serogroups O1 and O2 are frequently associated with human infections, especially extra-intestinal infections such as bloodstream infections or urinary tract infections. These strains can be associated with a large array of flagellar antigens. Because of their frequency and clinical importance, a reliable detection of E. coli O1 and O2 strains and also the frequently associated K1 capsule is important for diagnosis and source attribution of E. coli infections in humans and animals. By sequencing the O-antigen clusters of various O1 and O2 strains we showed that the serogroups O1 and O2 are encoded by different sets of O-antigen encoding genes and identified potentially new O-groups. We developed qPCR-assays to detect the various O1 and O2 variants and the K1-encoding gene. These qPCR assays proved to be 100% sensitive and 100% specific and could be valuable tools for the investigations of zoonotic and food-borne infection of humans with O1 and O2 extra-intestinal (ExPEC) or Shiga toxin-producing E. coli (STEC) strains.
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Affiliation(s)
- Sabine Delannoy
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
| | - Lothar Beutin
- National Reference Laboratory for Escherichia coli, Federal Institute for Risk Assessment (BfR)Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Institute for Biology - Microbiology, Freie Universität BerlinBerlin, Germany
| | - Patricia Mariani-Kurkdjian
- CNR Associé Escherichia coli, Service de Microbiologie, Hôpital Robert-DebréParis, France; IAME, UMR 1137, INSERMParis, France; IAME, UMR 1137, University Paris Diderot, Sorbonne Paris CitéParis, France
| | - Aubin Fleiss
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
| | - Stéphane Bonacorsi
- CNR Associé Escherichia coli, Service de Microbiologie, Hôpital Robert-DebréParis, France; IAME, UMR 1137, INSERMParis, France; IAME, UMR 1137, University Paris Diderot, Sorbonne Paris CitéParis, France
| | - Patrick Fach
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
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35
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Fraisse A, Coudray-Meunier C, Martin-Latil S, Hennechart-Collette C, Delannoy S, Fach P, Perelle S. Digital RT-PCR method for hepatitis A virus and norovirus quantification in soft berries. Int J Food Microbiol 2017; 243:36-45. [DOI: 10.1016/j.ijfoodmicro.2016.11.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 11/16/2022]
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36
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Mondani L, Delannoy S, Mathey R, Piat F, Mercey T, Slimani S, Fach P, Livache T, Roupioz Y. Fast detection of both O157 and non-O157 shiga-toxin producing Escherichia coli by real-time optical immunoassay. Lett Appl Microbiol 2016; 62:39-46. [PMID: 26432989 DOI: 10.1111/lam.12503] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 05/29/2015] [Revised: 09/04/2015] [Accepted: 09/24/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED Among bacterial pathogens involved in food-illnesses, seven serogroups (O26, O45, O103, O111, O121, O145 and O157) of Shiga-toxin producing Escherichia coli (STEC), are frequently identified. During such outbreak, and due to the perishable property of most foodstuff, the time laps for the identification of contaminated products and pathogens is thus critical to better circumvent their spread. Traditional detection methods using PCR or culture plating are time consuming and may present some limitations. In this study, we present a multiplexed immunoassay for the optical detection of most commonly enterohemorrhagic E. coli serogroups: O26, O45, O103, O111, O121, O145 and O157:H7 in a single device. The use of Surface Plasmon Resonance imaging not only enabled the label-free analysis of the samples but gave results in a real-time manner. A dedicated protocol was set up for the detection of both low contaminating bacterial concentrations of food samples (5 CFU per 25 g) and postenrichment aliquots. By combining one single device for the detection of O157 and non-O157 STEC in a label-free manner, this rapid approach may have an important economic and societal impact. SIGNIFICANCE AND IMPACT OF THE STUDY This article presents a simple-to-operate immunoassay for the specific detection of Shiga-toxin producing Escherichia coli (STEC). This approach consists in the on-chip assay detection of viable cells on a specifically designed antibody microarray. By skipping any enrichment step and avoiding the use of labelling agent, this approach based on the Surface Plasmon Resonance imaging of the microarrays turns out to be much faster and more cost effective by comparison with standardized methods.
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Affiliation(s)
- L Mondani
- University of Grenoble Alpes, INAC-SPRAM, Grenoble, France.,CEA, INAC-SPrAM, Grenoble, France.,CNRS, INAC-SPrAM, Grenoble, France
| | - S Delannoy
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, Maisons-Alfort, France
| | - R Mathey
- University of Grenoble Alpes, INAC-SPRAM, Grenoble, France.,CEA, INAC-SPrAM, Grenoble, France.,CNRS, INAC-SPrAM, Grenoble, France
| | - F Piat
- Prestodiag, Villejuif, France
| | | | | | - P Fach
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, Maisons-Alfort, France
| | - T Livache
- University of Grenoble Alpes, INAC-SPRAM, Grenoble, France.,CEA, INAC-SPrAM, Grenoble, France.,CNRS, INAC-SPrAM, Grenoble, France
| | - Y Roupioz
- University of Grenoble Alpes, INAC-SPRAM, Grenoble, France.,CEA, INAC-SPrAM, Grenoble, France.,CNRS, INAC-SPrAM, Grenoble, France
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37
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Martin-Latil S, Hennechart-Collette C, Delannoy S, Guillier L, Fach P, Perelle S. Quantification of Hepatitis E Virus in Naturally-Contaminated Pig Liver Products. Front Microbiol 2016; 7:1183. [PMID: 27536278 PMCID: PMC4971014 DOI: 10.3389/fmicb.2016.01183] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 04/14/2016] [Accepted: 07/18/2016] [Indexed: 11/26/2022] Open
Abstract
Hepatitis E virus (HEV), the cause of self-limiting acute hepatitis in humans, is widespread and endemic in many parts of the world. The foodborne transmission of HEV has become of concern due to the identification of undercooked pork products as a risk factor for infection. Foodborne enteric viruses are conventionally processed by quantitative RT-PCR (RT-qPCR), which gives sensitive and quantitative detection results. Recently, digital PCR (dPCR) has been described as a novel approach to genome quantification with no need for a standard curve. The performance of microfluidic digital RT-PCR (RT-dPCR) was compared to RT-qPCR when detecting HEV in pig liver products. The sensitivity of the RT-dPCR assay was similar to that of RT-qPCR, and quantitative data obtained by both detection methods were not significantly different for almost all samples. This absolute quantification approach may be useful for standardizing quantification of HEV in food samples and may be extended to quantifying other human pathogens in food samples.
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Affiliation(s)
- Sandra Martin-Latil
- Université Paris Est (ANSES), Laboratory for Food Safety Maisons-Alfort, France
| | | | - Sabine Delannoy
- Université Paris Est (ANSES), Laboratory for Food Safety Maisons-Alfort, France
| | - Laurent Guillier
- Université Paris Est (ANSES), Laboratory for Food Safety Maisons-Alfort, France
| | - Patrick Fach
- Université Paris Est (ANSES), Laboratory for Food Safety Maisons-Alfort, France
| | - Sylvie Perelle
- Université Paris Est (ANSES), Laboratory for Food Safety Maisons-Alfort, France
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38
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Kerangart S, Douëllou T, Delannoy S, Fach P, Beutin L, Sergentet-Thévenot D, Cournoyer B, Loukiadis E. Variable tellurite resistance profiles of clinically-relevant Shiga toxin-producing Escherichia coli (STEC) influence their recovery from foodstuffs. Food Microbiol 2016; 59:32-42. [PMID: 27375242 DOI: 10.1016/j.fm.2016.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 11/20/2015] [Revised: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 01/08/2023]
Abstract
Tellurite (Tel)-amended selective media and resistance (Tel-R) are widely used for detecting Shiga toxin-producing Escherichia coli (STEC) from foodstuffs. Tel-R of 81 O157 and non-O157 STEC strains isolated from animal, food and human was thus investigated. Variations of STEC tellurite minimal inhibitory concentration (MIC) values have been observed and suggest a multifactorial and variable tellurite resistome between strains. Some clinically-relevant STEC were found highly susceptible and could not be recovered using a tellurite-based detection scheme. The ter operon was highly prevalent among highly Tel-R STEC but was not always detected among intermediately-resistant strains. Many STEC serogroup strains were found to harbor sublines showing a gradient of MIC values. These Tel-R sublines showed statistically significant log negative correlations with increasing tellurite concentration. Whatever the tellurite concentration, the highest number of resistant sublines was observed for STEC belonging to the O26 serogroup. Variations in the number of these Tel-R sublines could explain the poor recovery of some STEC serogroups on tellurite-amended media especially from food products with low levels of contamination. Comparison of tellurite MIC values and distribution of virulence-related genes showed Tel-R and virulence to be related.
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Affiliation(s)
- Stéphane Kerangart
- University of Lyon, Research Group on «Bacterial Opportunistic Pathogens and Environment», UMR5557 Microbial Ecology, University Lyon 1, CNRS, VetAgro Sup, 69622 Villeurbanne Cedex, France
| | - Thomas Douëllou
- University of Lyon, Research Group on «Bacterial Opportunistic Pathogens and Environment», UMR5557 Microbial Ecology, University Lyon 1, CNRS, VetAgro Sup, 69622 Villeurbanne Cedex, France; Institut National de Recherche Agronomique, Unité de Recherches Fromagères, 15000 Aurillac, France
| | - Sabine Delannoy
- Université Paris-Est, ANSES, Laboratoire de Sécurité des Aliments, Plateforme IdentyPath, 14 Rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - Patrick Fach
- Université Paris-Est, ANSES, Laboratoire de Sécurité des Aliments, Plateforme IdentyPath, 14 Rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - Lothar Beutin
- National Reference Laboratory for Escherichia coli (Including VTEC), Department of Biological Safety, Federal Institute for Risk Assessment (BfR), D-12277 Berlin, Germany
| | - Delphine Sergentet-Thévenot
- University of Lyon, Research Group on «Bacterial Opportunistic Pathogens and Environment», UMR5557 Microbial Ecology, University Lyon 1, CNRS, VetAgro Sup, 69622 Villeurbanne Cedex, France; University of Lyon, VetAgro Sup, LMAP Laboratory, National Reference Laboratory for Escherichia coli (Including VTEC), Marcy L'Etoile, France
| | - Benoit Cournoyer
- University of Lyon, Research Group on «Bacterial Opportunistic Pathogens and Environment», UMR5557 Microbial Ecology, University Lyon 1, CNRS, VetAgro Sup, 69622 Villeurbanne Cedex, France
| | - Estelle Loukiadis
- University of Lyon, Research Group on «Bacterial Opportunistic Pathogens and Environment», UMR5557 Microbial Ecology, University Lyon 1, CNRS, VetAgro Sup, 69622 Villeurbanne Cedex, France; University of Lyon, VetAgro Sup, LMAP Laboratory, National Reference Laboratory for Escherichia coli (Including VTEC), Marcy L'Etoile, France.
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39
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Douëllou T, Delannoy S, Ganet S, Mariani-Kurkdjian P, Fach P, Loukiadis E, Montel M, Thevenot-Sergentet D. Shiga toxin-producing Escherichia coli strains isolated from dairy products - Genetic diversity and virulence gene profiles. Int J Food Microbiol 2016; 232:52-62. [PMID: 27257743 DOI: 10.1016/j.ijfoodmicro.2016.04.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 10/28/2015] [Revised: 04/27/2016] [Accepted: 04/29/2016] [Indexed: 01/01/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) are widely recognized as pathogens causing food borne disease. Here we evaluate the genetic diversity of 197 strains, mainly STEC, from serotypes O157:H7, O26:H11, O103:H2, O111:H8 and O145:28 and compared strains recovered in dairy products against strains from human, meat and environment cases. For this purpose, we characterized a set of reference-collection STEC isolates from dairy products by PFGE DNA fingerprinting and a subset of these by virulence-gene profiling. PFGE profiles of restricted STEC total DNA showed high genomic variability (0.9976 on Simpson's discriminatory index), enabling all dairy isolates to be differentiated. High-throughput real-time PCR screening of STEC virulence genes were applied on the O157:H7 and O26:H11 STEC isolates from dairy products and human cases. The virulence gene profiles of dairy and human STEC strains were similar. Nevertheless, frequency-wise, stx1 was more prevalent among dairy O26:H11 isolates than in human cases ones (87% vs. 44%) while stx2 was more prevalent among O26:H11 human isolates (23% vs. 81%). For O157:H7 isolates, stx1 (0% vs. 39%), nleF (40% vs 94%) and Z6065 (40% vs 100%) were more prevalent among human than dairy strains. Our data point to differences between human and dairy strains but these differences were not sufficient to associate PFGE and virulence gene profiles to a putative lower pathogenicity of dairy strains based on their lower incidence in disease. Further comparison of whole-genome expression and virulence gene profiles should be investigated in cheese and intestinal tract samples.
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Affiliation(s)
- T Douëllou
- INRA UR Fromagères 545, 20 Cote de Reyne, 15000 Aurillac, France; Université de Lyon, "Bacterial Opportunistic Pathogens and Environment" Research Group, UMR5557 Ecologie Microbienne Lyon, Université Lyon 1, CNRS, VetAgro Sup, 69280 Marcy l'Etoile, France
| | - S Delannoy
- Université Paris-Est, ANSES, Laboratoire de Sécurité des Aliments, Plateforme IdentyPath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - S Ganet
- Université de Lyon, "Bacterial Opportunistic Pathogens and Environment" Research Group, UMR5557 Ecologie Microbienne Lyon, Université Lyon 1, CNRS, VetAgro Sup, 69280 Marcy l'Etoile, France; Université de Lyon, VetAgro Sup Campus Vétérinaire, Laboratoire d'études des Microorganismes Alimentaires Pathogènes, French National Reference Laboratory for Escherichia coli including Shiga-like toxin-producing E. coli (NRL-STEC), 69280 Marcy-l'Etoile, France
| | - P Mariani-Kurkdjian
- Centre National de Référence Associé des Escherichia coli, AP-HP, Service de Microbiologie, Hôpital Robert-Debré, 75019 Paris, France
| | - P Fach
- Université Paris-Est, ANSES, Laboratoire de Sécurité des Aliments, Plateforme IdentyPath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort, France
| | - E Loukiadis
- Université de Lyon, "Bacterial Opportunistic Pathogens and Environment" Research Group, UMR5557 Ecologie Microbienne Lyon, Université Lyon 1, CNRS, VetAgro Sup, 69280 Marcy l'Etoile, France; Université de Lyon, VetAgro Sup Campus Vétérinaire, Laboratoire d'études des Microorganismes Alimentaires Pathogènes, French National Reference Laboratory for Escherichia coli including Shiga-like toxin-producing E. coli (NRL-STEC), 69280 Marcy-l'Etoile, France
| | - Mc Montel
- INRA UR Fromagères 545, 20 Cote de Reyne, 15000 Aurillac, France
| | - D Thevenot-Sergentet
- Université de Lyon, "Bacterial Opportunistic Pathogens and Environment" Research Group, UMR5557 Ecologie Microbienne Lyon, Université Lyon 1, CNRS, VetAgro Sup, 69280 Marcy l'Etoile, France; Université de Lyon, VetAgro Sup Campus Vétérinaire, Laboratoire d'études des Microorganismes Alimentaires Pathogènes, French National Reference Laboratory for Escherichia coli including Shiga-like toxin-producing E. coli (NRL-STEC), 69280 Marcy-l'Etoile, France.
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Delannoy S, Beutin L, Fach P. Improved traceability of Shiga-toxin-producing Escherichia coli using CRISPRs for detection and typing. Environ Sci Pollut Res Int 2016; 23:8163-8174. [PMID: 26449676 DOI: 10.1007/s11356-015-5446-y] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/16/2015] [Indexed: 06/05/2023]
Abstract
Among strains of Shiga-toxin-producing Escherichia coli (STEC), seven serogroups (O26, O45, O103, O111, O121, O145, and O157) are frequently associated with severe clinical illness in humans. The development of methods for their reliable detection from complex samples such as food has been challenging thus far, and is currently based on the PCR detection of the major virulence genes stx1, stx2, and eae, and O-serogroup-specific genes. However, this approach lacks resolution. Moreover, new STEC serotypes are continuously emerging worldwide. For example, in May 2011, strains belonging to the hitherto rarely detected STEC serotype O104:H4 were identified as causative agents of one of the world's largest outbreak of disease with a high incidence of hemorrhagic colitis and hemolytic uremic syndrome in the infected patients. Discriminant typing of pathogens is crucial for epidemiological surveillance and investigations of outbreaks, and especially for tracking and tracing in case of accidental and deliberate contamination of food and water samples. Clustered regularly interspaced short palindromic repeats (CRISPRs) are composed of short, highly conserved DNA repeats separated by unique sequences of similar length. This distinctive sequence signature of CRISPRs can be used for strain typing in several bacterial species including STEC. This review discusses how CRISPRs have recently been used for STEC identification and typing.
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Affiliation(s)
- Sabine Delannoy
- ANSES, Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France.
| | - Lothar Beutin
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Patrick Fach
- ANSES, Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
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Baranzoni GM, Fratamico PM, Gangiredla J, Patel I, Bagi LK, Delannoy S, Fach P, Boccia F, Anastasio A, Pepe T. Characterization of Shiga Toxin Subtypes and Virulence Genes in Porcine Shiga Toxin-Producing Escherichia coli. Front Microbiol 2016; 7:574. [PMID: 27148249 PMCID: PMC4838603 DOI: 10.3389/fmicb.2016.00574] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [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: 02/26/2016] [Accepted: 04/07/2016] [Indexed: 11/18/2022] Open
Abstract
Similar to ruminants, swine have been shown to be a reservoir for Shiga toxin-producing Escherichia coli (STEC), and pork products have been linked with outbreaks associated with STEC O157 and O111:H-. STEC strains, isolated in a previous study from fecal samples of late-finisher pigs, belonged to a total of 56 serotypes, including O15:H27, O91:H14, and other serogroups previously associated with human illness. The isolates were tested by polymerase chain reaction (PCR) and a high-throughput real-time PCR system to determine the Shiga toxin (Stx) subtype and virulence-associated and putative virulence-associated genes they carried. Select STEC strains were further analyzed using a Minimal Signature E. coli Array Strip. As expected, stx2e (81%) was the most common Stx variant, followed by stx1a (14%), stx2d (3%), and stx1c (1%). The STEC serogroups that carried stx2d were O15:H27, O159:H16 and O159:H-. Similar to stx2a and stx2c, the stx2d variant is associated with development of hemorrhagic colitis and hemolytic uremic syndrome, and reports on the presence of this variant in STEC strains isolated from swine are lacking. Moreover, the genes encoding heat stable toxin (estIa) and enteroaggregative E. coli heat stable enterotoxin-1 (astA) were commonly found in 50 and 44% of isolates, respectively. The hemolysin genes, hlyA and ehxA, were both detected in 7% of the swine STEC strains. Although the eae gene was not found, other genes involved in host cell adhesion, including lpfAO113 and paa were detected in more than 50% of swine STEC strains, and a number of strains also carried iha, lpfAO26, lpfAO157, fedA, orfA, and orfB. The present work provides new insights on the distribution of virulence factors among swine STEC strains and shows that swine may carry Stx1a-, Stx2e-, or Stx2d-producing E. coli with virulence gene profiles associated with human infections.
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Affiliation(s)
- Gian Marco Baranzoni
- Eastern Regional Research Center, United States Department of Agriculture - Agricultural Research Service Wyndmoor, PA, USA
| | - Pina M Fratamico
- Eastern Regional Research Center, United States Department of Agriculture - Agricultural Research Service Wyndmoor, PA, USA
| | - Jayanthi Gangiredla
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration Laurel, MD, USA
| | - Isha Patel
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration Laurel, MD, USA
| | - Lori K Bagi
- Eastern Regional Research Center, United States Department of Agriculture - Agricultural Research Service Wyndmoor, PA, USA
| | - Sabine Delannoy
- Food Safety Laboratory, University of Paris-Est, Anses, Maisons-Alfort France
| | - Patrick Fach
- Food Safety Laboratory, University of Paris-Est, Anses, Maisons-Alfort France
| | - Federica Boccia
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples Italy
| | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples Italy
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples Italy
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Berenger BM, Berry C, Peterson T, Fach P, Delannoy S, Li V, Tschetter L, Nadon C, Honish L, Louie M, Chui L. The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks. ACTA ACUST UNITED AC 2016; 20:30073. [PMID: 26625187 DOI: 10.2807/1560-7917.es.2015.20.47.30073] [Citation(s) in RCA: 17] [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: 05/05/2015] [Accepted: 10/19/2015] [Indexed: 11/20/2022]
Abstract
A standardised method for determining Escherichia coli O157:H7 strain relatedness using whole genome sequencing or virulence gene profiling is not yet established. We sought to assess the capacity of either high-throughput polymerase chain reaction (PCR) of 49 virulence genes, core-genome single nt variants (SNVs) or k-mer clustering to discriminate between outbreak-associated and sporadic E. coli O157:H7 isolates. Three outbreaks and multiple sporadic isolates from the province of Alberta, Canada were included in the study. Two of the outbreaks occurred concurrently in 2014 and one occurred in 2012. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA) were employed as comparator typing methods. The virulence gene profiles of isolates from the 2012 and 2014 Alberta outbreak events and contemporary sporadic isolates were mostly identical; therefore the set of virulence genes chosen in this study were not discriminatory enough to distinguish between outbreak clusters. Concordant with PFGE and MLVA results, core genome SNV and k-mer phylogenies clustered isolates from the 2012 and 2014 outbreaks as distinct events. k-mer phylogenies demonstrated increased discriminatory power compared with core SNV phylogenies. Prior to the widespread implementation of whole genome sequencing for routine public health use, issues surrounding cost, technical expertise, software standardisation, and data sharing/comparisons must be addressed.
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Affiliation(s)
- Byron M Berenger
- Alberta Provincial Laboratory for Public Health, Alberta, Canada
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Michelacci V, Orsini M, Knijn A, Delannoy S, Fach P, Caprioli A, Morabito S. Development of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC). Front Microbiol 2016; 7:202. [PMID: 26941726 PMCID: PMC4763077 DOI: 10.3389/fmicb.2016.00202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Received: 11/26/2015] [Accepted: 02/05/2016] [Indexed: 11/13/2022] Open
Abstract
Shiga-toxin producing Escherichia coli (STEC) strains possess a large accessory genome composed of virulence genes existing in multiple allelic variants, which sometimes segregate with specific STEC subpopulations. We analyzed the allelic variability of 91 virulence genes of STEC by Real Time PCR followed by melting curves analysis in 713 E. coli strains including 358 STEC. The 91 genes investigated were located on the locus of enterocyte effacement (LEE), OI-57, and OI-122 pathogenicity islands and displayed a total of 476 alleles in the study population. The combinations of the 91 alleles of each strain were termed allelic signatures and used to perform cluster analyses. We termed such an approach High Resolution Virulence Allelic Profiling (HReVAP) and used it to investigate the phylogeny of STEC of multiple serogroups. The dendrograms obtained identified groups of STEC segregating approximately with the serogroups and allowed the identification of subpopulations within the single groups. The study of the allelic signatures provided further evidence of the coevolution of the LEE and OI-122, reflecting the occurrence of their acquisition through a single event. The HReVAP analysis represents a sensitive tool for studying the evolution of LEE-positive STEC.
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Affiliation(s)
- Valeria Michelacci
- European Reference Laboratory for Escherichia coli, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità Rome, Italy
| | - Massimiliano Orsini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale Teramo, Italy
| | - Arnold Knijn
- Servizio Informatico, Documentazione, Biblioteca e Attività Editoriali, Istituto Superiore di Sanità Rome, Italy
| | - Sabine Delannoy
- Platform IdentyPath, Food Safety Laboratory, ANSES, Université Paris-Est Maisons-Alfort, France
| | - Patrick Fach
- Platform IdentyPath, Food Safety Laboratory, ANSES, Université Paris-Est Maisons-Alfort, France
| | - Alfredo Caprioli
- European Reference Laboratory for Escherichia coli, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità Rome, Italy
| | - Stefano Morabito
- European Reference Laboratory for Escherichia coli, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità Rome, Italy
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44
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Beutin L, Delannoy S, Fach P. Genetic Analysis and Detection of fliC H1 and fliC H12 Genes Coding for Serologically Closely Related Flagellar Antigens in Human and Animal Pathogenic Escherichia coli. Front Microbiol 2016; 7:135. [PMID: 26913025 PMCID: PMC4753304 DOI: 10.3389/fmicb.2016.00135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 11/26/2015] [Accepted: 01/25/2016] [Indexed: 01/29/2023] Open
Abstract
The E. coli flagellar types H1 and H12 show a high serological cross-reactivity and molecular serotyping appears an advantageous method to establish a clear discrimination between these flagellar types. Analysis of fliCH1 and fliCH12 gene sequences showed that they were 97.5% identical at the nucleotide level. Because of this high degree of homology we developed a two-step real-time PCR detection procedure for reliable discrimination of H1 and H12 flagellar types in E. coli. In the first step, a real-time PCR assay for common detection of both fliCH1 and fliCH12 genes is used, followed in a second step by real-time PCR assays for specific detection of fliCH1 and fliCH12, respectively. The real-time PCR for common detection of fliCH1 and fliCH12 demonstrated 100% sensitivity and specificity as it reacted with all tested E. coli H1 and H12 strains and not with any of the reference strains encoding all the other 51 flagellar antigens. The fliCH1 and fliCH12 gene specific assays detected all E. coli H1 and all E. coli H12 strains, respectively (100% sensitivity). However, both assays showed cross-reactions with some flagellar type reference strains different from H1 and H12. The real-time PCR assays developed in this study can be used in combination for the detection and identification of E. coli H1 and H12 strains isolated from different sources.
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Affiliation(s)
- Lothar Beutin
- Department of Biology, Chemistry, Pharmacy, Institute for Biology - Microbiology, Freie Universität Berlin Berlin, Germany
| | - Sabine Delannoy
- Université Paris-Est, Anses, Food Safety Laboratory, IdentyPath Maisons-Alfort, France
| | - Patrick Fach
- Université Paris-Est, Anses, Food Safety Laboratory, IdentyPath Maisons-Alfort, France
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Coudray-Meunier C, Fraisse A, Martin-Latil S, Delannoy S, Fach P, Perelle S. A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System. PLoS One 2016; 11:e0147832. [PMID: 26824897 PMCID: PMC4732599 DOI: 10.1371/journal.pone.0147832] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/08/2016] [Indexed: 12/23/2022] Open
Abstract
Human enteric viruses are recognized as the main causes of food- and waterborne diseases worldwide. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR). A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The performance of high-throughput PCR methods was investigated for detecting 19 human pathogenic viruses and two main process controls used in food virology. The conventional real-time PCR system was compared to the RT-dPCR and RT-qPCR array. Based on the number of genome copies calculated by spectrophotometry, sensitivity was found to be slightly better with RT-qPCR than with RT-dPCR for 14 viruses by a factor range of from 0.3 to 1.6 log10. Conversely, sensitivity was better with RT-dPCR than with RT-qPCR for seven viruses by a factor range of from 0.10 to 1.40 log10. Interestingly, the number of genome copies determined by RT-dPCR was always from 1 to 2 log10 lower than the expected copy number calculated by RT-qPCR standard curve. The sensitivity of the RT-qPCR and RT-qPCR array assays was found to be similar for two viruses, and better with RT-qPCR than with RT-qPCR array for eighteen viruses by a factor range of from 0.7 to 3.0 log10. Conversely, sensitivity was only 0.30 log10 better with the RT-qPCR array than with conventional RT-qPCR assays for norovirus GIV detection. Finally, the RT-qPCR array and RT-dPCR assays were successfully used together to screen clinical samples and quantify pathogenic viruses. Additionally, this method made it possible to identify co-infection in clinical samples. In conclusion, given the rapidity and potential for large numbers of viral targets, this nanofluidic RT-qPCR assay should have a major impact on human pathogenic virus surveillance and outbreak investigations and is likely to be of benefit to public health.
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Affiliation(s)
- Coralie Coudray-Meunier
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Audrey Fraisse
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sandra Martin-Latil
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sabine Delannoy
- Université Paris-Est, ANSES, Food Safety Laboratory, Identypath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Patrick Fach
- Université Paris-Est, ANSES, Food Safety Laboratory, Identypath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
| | - Sylvie Perelle
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort Cedex, France
- * E-mail:
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46
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Delannoy S, Chaves BD, Ison SA, Webb HE, Beutin L, Delaval J, Billet I, Fach P. Revisiting the STEC Testing Approach: Using espK and espV to Make Enterohemorrhagic Escherichia coli (EHEC) Detection More Reliable in Beef. Front Microbiol 2016; 7:1. [PMID: 26834723 PMCID: PMC4722105 DOI: 10.3389/fmicb.2016.00001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [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: 10/30/2015] [Accepted: 01/05/2016] [Indexed: 11/29/2022] Open
Abstract
Current methods for screening Enterohemorrhagic Escherichia coli (EHEC) O157 and non-O157 in beef enrichments typically rely on the molecular detection of stx, eae, and serogroup-specific wzx or wzy gene fragments. As these genetic markers can also be found in some non-EHEC strains, a number of "false positive" results are obtained. Here, we explore the suitability of five novel molecular markers, espK, espV, ureD, Z2098, and CRISPRO26:H11 as candidates for a more accurate screening of EHEC strains of greater clinical significance in industrialized countries. Of the 1739 beef enrichments tested, 180 were positive for both stx and eae genes. Ninety (50%) of these tested negative for espK, espV, ureD, and Z2098, but 12 out of these negative samples were positive for the CRISPRO26:H11 gene marker specific for a newly emerging virulent EHEC O26:H11 French clone. We show that screening for stx, eae, espK, and espV, in association with the CRISPRO26:H11 marker is a better approach to narrow down the EHEC screening step in beef enrichments. The number of potentially positive samples was reduced by 48.88% by means of this alternative strategy compared to the European and American reference methods, thus substantially improving the discriminatory power of EHEC screening systems. This approach is in line with the EFSA (European Food Safety Authority) opinion on pathogenic STEC published in 2013.
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Affiliation(s)
- Sabine Delannoy
- Food Safety Laboratory, Université Paris-Est, Anses (French Agency for Food, Environmental and Occupational Health and Safety), Platform IdentyPathMaisons-Alfort, France
| | - Byron D. Chaves
- Department of Animal and Food Sciences, Texas Tech UniversityLubbock, TX, USA
| | - Sarah A. Ison
- Department of Animal and Food Sciences, Texas Tech UniversityLubbock, TX, USA
| | - Hattie E. Webb
- Department of Animal and Food Sciences, Texas Tech UniversityLubbock, TX, USA
| | - Lothar Beutin
- Division of Microbial Toxins, National Reference Laboratory for Escherichia coli, Federal Institute for Risk AssessmentBerlin, Germany
| | - José Delaval
- Laboratoire de Touraine, (LDA37) Conseil DépartementalTours, France
| | | | - Patrick Fach
- Food Safety Laboratory, Université Paris-Est, Anses (French Agency for Food, Environmental and Occupational Health and Safety), Platform IdentyPathMaisons-Alfort, France
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47
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Ison SA, Delannoy S, Bugarel M, Nagaraja TG, Renter DG, den Bakker HC, Nightingale KK, Fach P, Loneragan GH. Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique. Appl Environ Microbiol 2016; 82:640-9. [PMID: 26567298 PMCID: PMC4711113 DOI: 10.1128/aem.03182-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 10/04/2015] [Accepted: 11/04/2015] [Indexed: 12/31/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O26:H11, a serotype within Shiga toxin-producing E. coli (STEC) that causes severe human disease, has been considered to have evolved from attaching and effacing E. coli (AEEC) O26:H11 through the acquisition of a Shiga toxin-encoding gene. Targeted amplicon sequencing using next-generation sequencing technology of 48 phylogenetically informative single-nucleotide polymorphisms (SNPs) and three SNPs differentiating Shiga toxin-positive (stx-positive) strains from Shiga toxin-negative (stx-negative) strains were used to infer the phylogenetic relationships of 178 E. coli O26:H11 strains (6 stx-positive strains and 172 stx-negative AEEC strains) from cattle feces to 7 publically available genomes of human clinical strains. The AEEC cattle strains displayed synonymous SNP genotypes with stx2-positive sequence type 29 (ST29) human O26:H11 strains, while stx1 ST21 human and cattle strains clustered separately, demonstrating the close phylogenetic relatedness of these Shiga toxin-negative AEEC cattle strains and human clinical strains. With the exception of seven stx-negative strains, five of which contained espK, three stx-related SNPs differentiated the STEC strains from non-STEC strains, supporting the hypothesis that these AEEC cattle strains could serve as a potential reservoir for new or existing pathogenic human strains. Our results support the idea that targeted amplicon sequencing for SNP genotyping expedites strain identification and genetic characterization of E. coli O26:H11, which is important for food safety and public health.
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Affiliation(s)
- Sarah A Ison
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Sabine Delannoy
- ANSES Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - Marie Bugarel
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Tiruvoor G Nagaraja
- Department of Diagnostic Medicine Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - David G Renter
- Department of Diagnostic Medicine Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - Henk C den Bakker
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Kendra K Nightingale
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Patrick Fach
- ANSES Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - Guy H Loneragan
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
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Ison SA, Delannoy S, Bugarel M, Nightingale KK, Webb HE, Renter DG, Nagaraja TG, Loneragan GH, Fach P. Genetic Diversity and Pathogenic Potential of Attaching and Effacing Escherichia coli O26:H11 Strains Recovered from Bovine Feces in the United States. Appl Environ Microbiol 2015; 81:3671-8. [PMID: 25795673 PMCID: PMC4421050 DOI: 10.1128/aem.00397-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/15/2015] [Indexed: 12/28/2022] Open
Abstract
Escherichia coli O26 has been identified as the most common non-O157 Shiga toxin-producing E. coli (STEC) serogroup to cause human illnesses in the United States and has been implicated in outbreaks around the world. E. coli has high genomic plasticity, which facilitates the loss or acquisition of virulence genes. Attaching and effacing E. coli (AEEC) O26 strains have frequently been isolated from bovine feces, and there is a need to better characterize the relatedness of these strains to defined molecular pathotypes and to describe the extent of their genetic diversity. High-throughput real-time PCR was used to screen 178 E. coli O26 isolates from a single U.S. cattle feedlot, collected from May to July 2011, for the presence or absence of 25 O26 serogroup-specific and virulence-associated markers. The selected markers were capable of distinguishing these strains into molecularly defined groups (yielding 18 unique marker combinations). Analysis of the clustered regularly interspaced short palindromic repeat 1 (CRISPR1) and CRISPR2a loci further discriminated isolates into 24 CRISPR types. The combination of molecular markers and CRISPR typing provided 20.8% diversity. The recent CRISPR PCR target SP_O26-E, which was previously identified only in stx2-positive O26:H11 human clinical strains, was identified in 96.4% (161/167 [95% confidence interval, 99.2 to 93.6%]) of the stx-negative AEEC O26:H11 bovine fecal strains. This supports that these stx-negative strains may have previously contained a prophage carrying stx or could acquire this prophage, thus possibly giving them the potential to become pathogenic to humans. These results show that investigation of specific genetic markers may further elucidate our understanding of the genetic diversity of AEEC O26 strains in bovine feces.
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Affiliation(s)
- Sarah A Ison
- Texas Tech University, Department of Animal and Food Sciences, Lubbock, Texas, USA
| | - Sabine Delannoy
- French Agency for Food, Environmental and Occupational Health and Safety, Food Safety Laboratory, Platform IdentyPath, Maisons-Alfort, France
| | - Marie Bugarel
- Texas Tech University, Department of Animal and Food Sciences, Lubbock, Texas, USA
| | - Kendra K Nightingale
- Texas Tech University, Department of Animal and Food Sciences, Lubbock, Texas, USA
| | - Hattie E Webb
- Texas Tech University, Department of Animal and Food Sciences, Lubbock, Texas, USA
| | - David G Renter
- Kansas State University, Department of Diagnostic Medicine Pathobiology, Manhattan, Kansas, USA
| | - Tiruvoor G Nagaraja
- Kansas State University, Department of Diagnostic Medicine Pathobiology, Manhattan, Kansas, USA
| | - Guy H Loneragan
- Texas Tech University, Department of Animal and Food Sciences, Lubbock, Texas, USA
| | - Patrick Fach
- French Agency for Food, Environmental and Occupational Health and Safety, Food Safety Laboratory, Platform IdentyPath, Maisons-Alfort, France
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49
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Beutin L, Delannoy S, Fach P. Sequence Variations in the Flagellar Antigen Genes fliCH25 and fliCH28 of Escherichia coli and Their Use in Identification and Characterization of Enterohemorrhagic E. coli (EHEC) O145:H25 and O145:H28. PLoS One 2015; 10:e0126749. [PMID: 26000885 PMCID: PMC4441469 DOI: 10.1371/journal.pone.0126749] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 01/30/2015] [Accepted: 04/07/2015] [Indexed: 11/19/2022] Open
Abstract
Enterohemorrhagic E. coli (EHEC) serogroup O145 is regarded as one of the major EHEC serogroups involved in severe infections in humans. EHEC O145 encompasses motile and non-motile strains of serotypes O145:H25 and O145:H28. Sequencing the fliC-genes associated with the flagellar antigens H25 and H28 revealed the genetic diversity of the fliCH25 and fliCH28 gene sequences in E. coli. Based on allele discrimination of these fliC-genes real-time PCR tests were designed for identification of EHEC O145:H25 and O145:H28. The fliCH25 genes present in O145:H25 were found to be very similar to those present in E. coli serogroups O2, O100, O165, O172 and O177 pointing to their common evolution but were different from fliCH25 genes of a multiple number of other E. coli serotypes. In a similar way, EHEC O145:H28 harbor a characteristic fliCH28 allele which, apart from EHEC O145:H28, was only found in enteropathogenic (EPEC) O28:H28 strains that shared some common traits with EHEC O145:H28. The real time PCR-assays targeting these fliCH25[O145] and fliCH28[O145] alleles allow better characterization of EHEC O145:H25 and EHEC O145:H28. Evaluation of these PCR assays in spiked ready-to eat salad samples resulted in specific detection of both types of EHEC O145 strains even when low spiking levels of 1-10 cfu/g were used. Furthermore these PCR assays allowed identification of non-motile E. coli strains which are serologically not typable for their H-antigens. The combined use of O-antigen genotyping (O145wzy) and detection of the respective fliCH25[O145] and fliCH28[O145] allele types contributes to improve identification and molecular serotyping of E. coli O145 isolates.
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Affiliation(s)
- Lothar Beutin
- National Reference Laboratory for Escherichia coli, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277, Berlin, Germany
| | - Sabine Delannoy
- Université Paris-Est, Anses (French Agency for Food, Environmental and Occupational Health and Safety), Food Safety Laboratory, IdentyPath platform, 14 rue Pierre et Marie Curie, Fr-94700, Maisons-Alfort, France
| | - Patrick Fach
- Université Paris-Est, Anses (French Agency for Food, Environmental and Occupational Health and Safety), Food Safety Laboratory, IdentyPath platform, 14 rue Pierre et Marie Curie, Fr-94700, Maisons-Alfort, France
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Coudray-Meunier C, Fraisse A, Martin-Latil S, Guillier L, Delannoy S, Fach P, Perelle S. A comparative study of digital RT-PCR and RT-qPCR for quantification of Hepatitis A virus and Norovirus in lettuce and water samples. Int J Food Microbiol 2015; 201:17-26. [PMID: 25725459 DOI: 10.1016/j.ijfoodmicro.2015.02.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 01/26/2015] [Accepted: 02/04/2015] [Indexed: 10/24/2022]
Abstract
Sensitive and quantitative detection of foodborne enteric viruses is classically achieved by quantitative RT-PCR (RT-qPCR). Recently, digital PCR (dPCR) was described as a novel approach to genome quantification without need for a standard curve. The performance of microfluidic digital RT-PCR (RT-dPCR) was compared to RT-qPCR for detecting the main viruses responsible for foodborne outbreaks (human Noroviruses (NoV) and Hepatitis A virus (HAV)) in spiked lettuce and bottled water. Two process controls (Mengovirus and Murine Norovirus) were used and external amplification controls (EAC) were added to examine inhibition of RT-qPCR and RT-dPCR. For detecting viral RNA and cDNA, the sensitivity of the RT-dPCR assays was either comparable to that of RT-qPCR (RNA of HAV, NoV GI, Mengovirus) or slightly (around 1 log10) decreased (NoV GII and MNV-1 RNA and of HAV, NoV GI, NoV GII cDNA). The number of genomic copies determined by dPCR was always from 0.4 to 1.7 log10 lower than the expected numbers of copies calculated by using the standard qPCR curve. Viral recoveries calculated by RT-dPCR were found to be significantly higher than by RT-qPCR for NoV GI, HAV and Mengovirus in water, and for NoV GII and HAV in lettuce samples. The RT-dPCR assay proved to be more tolerant to inhibitory substances present in lettuce samples. This absolute quantitation approach may be useful to standardize quantification of enteric viruses in bottled water and lettuce samples and may be extended to quantifying other human pathogens in food samples.
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Affiliation(s)
- Coralie Coudray-Meunier
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric Viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France
| | - Audrey Fraisse
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric Viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France
| | - Sandra Martin-Latil
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric Viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France
| | - Laurent Guillier
- Université Paris-Est, ANSES, Food Safety Laboratory, Modelling of Bacterial Behaviour Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France
| | - Sabine Delannoy
- Université Paris-Est, ANSES, Food Safety Laboratory, IdentyPath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France
| | - Patrick Fach
- Université Paris-Est, ANSES, Food Safety Laboratory, IdentyPath, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France
| | - Sylvie Perelle
- Université Paris-Est, ANSES, Food Safety Laboratory, Enteric Viruses Unit, 14 rue Pierre et Marie Curie, 94701 Maisons-Alfort cedex, France.
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