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Kalalah AA, Koenig SSK, Feng P, Bosilevac JM, Bono JL, Eppinger M. Pathogenomes of Shiga Toxin Positive and Negative Escherichia coli O157:H7 Strains TT12A and TT12B: Comprehensive Phylogenomic Analysis Using Closed Genomes. Microorganisms 2024; 12:699. [PMID: 38674643 PMCID: PMC11052207 DOI: 10.3390/microorganisms12040699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/18/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Shiga toxin-producing Escherichia coli are zoonotic pathogens that cause food-borne human disease. Among these, the O157:H7 serotype has evolved from an enteropathogenic O55:H7 ancestor through the displacement of the somatic gene cluster and recurrent toxigenic conversion by Shiga toxin-converting bacteriophages. However, atypical strains that lack the Shiga toxin, the characteristic virulence hallmark, are circulating in this lineage. For this study, we analyzed the pathogenome and virulence inventories of the stx+ strain, TT12A, isolated from a patient with hemorrhagic colitis, and its respective co-isolated stx- strain, TT12B. Sequencing the genomes to closure proved critical to the cataloguing of subtle strain differentiating sequence and structural polymorphisms at a high-level of phylogenetic accuracy and resolution. Phylogenomic profiling revealed SNP and MLST profiles similar to the near clonal outbreak isolates. Their prophage inventories, however, were notably different. The attenuated atypical non-shigatoxigenic status of TT12B is explained by the absence of both the ΦStx1a- and ΦStx2a-prophages carried by TT12A, and we also recorded further alterations in the non-Stx prophage complement. Phenotypic characterization indicated that culture growth was directly impacted by the strains' distinct lytic phage complement. Altogether, our phylogenomic and phenotypic analyses show that these intimately related isogenic strains are on divergent Stx(+/stx-) evolutionary paths.
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Affiliation(s)
- Anwar A. Kalalah
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
| | - Peter Feng
- U.S. Food and Drug Administration (FDA), College Park, MD 20740, USA
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - James L. Bono
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
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Abafogi AT, Lee J, Kim J, Lee SW, Jang S, Park S. Automated sepsis detection with vancomycin- and allantoin-polydopamine magnetic nanoparticles. Sci Rep 2024; 14:3693. [PMID: 38355732 PMCID: PMC10867076 DOI: 10.1038/s41598-024-54236-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/10/2024] [Indexed: 02/16/2024] Open
Abstract
Rapid and accurate identification of the bacteria responsible for sepsis is paramount for effective patient care. Molecular diagnostic methods, such as polymerase chain reaction (PCR), encounter challenges in sepsis due to inhibitory compounds in the blood, necessitating their removal for precise analysis. In this study we present an innovative approach that utilizes vancomycin (Van) and allantoin (Al)-conjugated polydopamine (PDA)-coated magnetic nanoparticles (MNPs) for the rapid and automated enrichment of bacteria and their DNA extraction from blood without inducing clumping and aggregation of blood. Al/Van-PDA-MNPs, facilitated by IMS, eliminate the need for preliminary sample treatments, providing a swift and efficient method for bacterial concentration and DNA extraction within an hour. Employing Al/Van-PDA-MNPs within an automated framework has markedly improved our ability to pre-concentrate various Gram-negative and Gram-positive bacteria directly from blood samples. This advancement has effectively reduced the detection threshold to 102 colony-forming unit/mL by both PCR and quantitative PCR. The method's expedited processing time, combined with its precision, positions it as a feasible diagnostic tool for diverse healthcare settings, ranging from small clinics to large hospitals. Furthermore, the innovative application of nanoparticles for DNA extraction holds promising potential for advancing sepsis diagnostics, enabling earlier interventions and improving patient outcomes.
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Affiliation(s)
| | - Jinyeop Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
- KingoBio Inc., Seoul, 08390, Korea
| | - Joochan Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Sei Won Lee
- Department of Pulmonology and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Seongsoo Jang
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Sungsu Park
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea.
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3
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Habets A, Touzain F, Lucas P, Huong NTT, Iguchi A, Crombé F, Korsak N, Piérard D, Saulmont M, Cox E, Engelen F, Mainil J, Thiry D. Identification of Five Serotypes of Enteropathogenic Escherichia coli from Diarrheic Calves and Healthy Cattle in Belgium and Comparative Genomics with Shigatoxigenic E. coli. Vet Sci 2022; 9:vetsci9090492. [PMID: 36136709 PMCID: PMC9505469 DOI: 10.3390/vetsci9090492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/17/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Enteropathogenic Escherichia coli (EPEC) from cattle receive little attention, although some belong to the most notorious O serotypes of attaching/effacing Shigatoxigenic Escherichia coli (AE-STEC) responsible for the uremic and hemolytic syndrome in humans, such as O26. Nevertheless, the O serotypes and virulotypes of the large majority of bovine EPEC remain unidentified. This study aimed to identify five non-classical O serotypes (O123/186, O156, O177, O182, and O183) by a polymerase chain reaction (PCR) among three collections of bovine EPEC from young diarrheic calves, healthy cattle at slaughterhouses, and healthy calves in dairy farms. The virulotypes and sequence types (STs) obtained after the whole genome sequencing of several O156, O177, and O182 bovine EPEC were closely related or identical to the virulotypes and STs of ten bovine and the human AE-STEC of the same O:H serotype. This study allows us to identify more EPEC O serotypes from cattle and to speculate on their evolution. Abstract Enteropathogenic Escherichia coli (EPEC) produce attaching/effacing (AE) lesions and cause non-bloody diarrhea in mammals. A minority of bovine EPEC belong to one of the ten classical serotypes of human and bovine AE-STEC. The purpose of this study was to identify five non-classical O serotypes (O123/186, O156, O177, O182, and O183) among bovine EPEC and to characterize their virulence repertoires by whole genome sequencing. Around 40% of the 307 EPEC from 307 diarrheic calves, 368 EPEC from 47 healthy cattle, and 131 EPEC from 36 healthy calves in dairy farms were analyzed. Serotype O177 was the most frequent among EPEC from diarrheic and healthy calves, while the O156 was the most frequent in healthy cattle. The genomic analysis identified different H serotypes, MLSTypes, and/or eae gene subtypes among the O156 and O177 EPEC, while the O182 was homogeneous. The virulence gene profiles of bovine EPEC were closely related to each other and to the profiles of ten bovine and human AE-STEC. These results emphasize the need for additional studies to identify more O:H serotypes of bovine EPEC and to elucidate their origin and evolution of EPEC with regard to AE-STEC belonging to the same O:H serotypes.
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Affiliation(s)
- Audrey Habets
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, Centre for Fundamental and Applied Research in Animals and Heath (FARAH), University of Liège, Quartier Vallée II, Cureghem Avenue 6, B-4000 Liège, Belgium
| | - Fabrice Touzain
- Viral Genetics and Bio-Security Unit, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 22440 Ploufragan, France
| | - Pierrick Lucas
- Viral Genetics and Bio-Security Unit, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 22440 Ploufragan, France
| | - Nguyen Thi Thu Huong
- Department of Environment and Resource Sciences, University of Miyazaki (UoM), Miyazaki 889-2192, Japan
| | - Atsushi Iguchi
- Department of Environment and Resource Sciences, University of Miyazaki (UoM), Miyazaki 889-2192, Japan
| | - Florence Crombé
- Belgian National Reference Center STEC, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), B-1090 Brussels, Belgium
| | - Nicolas Korsak
- Food Microbiology, Department of Food Sciences, Faculty of Veterinary Medicine, Centre for Fundamental and Applied Research in Animals and Heath (FARAH), University of Liège (ULiège), B-4000 Liège, Belgium
| | - Denis Piérard
- Belgian National Reference Center STEC, Universitair Ziekenhuis Brussel (UZ Brussel), Vrije Universiteit Brussel (VUB), B-1090 Brussels, Belgium
| | - Marc Saulmont
- Regional Agency for Animal Health and Identification (ARSIA), B-5590 Ciney, Belgium
| | - Eric Cox
- Laboratory of Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Frederik Engelen
- Laboratory of Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - Jacques Mainil
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, Centre for Fundamental and Applied Research in Animals and Heath (FARAH), University of Liège, Quartier Vallée II, Cureghem Avenue 6, B-4000 Liège, Belgium
| | - Damien Thiry
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, Centre for Fundamental and Applied Research in Animals and Heath (FARAH), University of Liège, Quartier Vallée II, Cureghem Avenue 6, B-4000 Liège, Belgium
- Correspondence:
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Bibbal D, Ruiz P, Sapountzis P, Mazuy-Cruchaudet C, Loukiadis E, Auvray F, Forano E, Brugère H. Persistent Circulation of Enterohemorrhagic Escherichia coli (EHEC) O157:H7 in Cattle Farms: Characterization of Enterohemorrhagic Escherichia coli O157:H7 Strains and Fecal Microbial Communities of Bovine Shedders and Non-shedders. Front Vet Sci 2022; 9:852475. [PMID: 35411306 PMCID: PMC8994043 DOI: 10.3389/fvets.2022.852475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/09/2022] [Indexed: 12/24/2022] Open
Abstract
Cattle are carriers, without clinical manifestations, of enterohemorrhagic Escherichia coli (EHEC) O157:H7 responsible for life-threatening infections in humans. A better identification of factors playing a role in maintaining persistence of such strains in cattle is required to develop more effective control measures. Hence, we conducted a study to identify farms with a persistent circulation of EHEC O157:H7. The EHEC O157:H7 herd status of 13 farms, which had previously provided bovine EHEC O157:H7 carriers at slaughter was investigated. Two farms were still housing positive young bulls, and this was true over a 1-year period. Only one fecal sample could be considered from a supershedder, and 60% of the carriers shed concentrations below 10 MPN/g. Moreover, EHEC O157:H7 represented minor subpopulations of E. coli. PFGE analysis of the EHEC O157:H7 strains showed that persistent circulation was due either to the persistence of a few predominant strains or to the repeated exposure of cattle to various strains. Finally, we compared fecal microbial communities of shedders (S) (n = 24) and non-shedders (NS) (n = 28), including 43 young bulls and nine cows, from one farm. Regarding alpha diversity, no significant difference between S vs. NS young bulls (n = 43) was observed. At the genus level, we identified 10 amplicon sequence variant (ASV) indicators of the S or NS groups. The bacterial indicators of S belonged to the family XIII UCG-001, Slackia, and Campylobacter genera, and Ruminococcaceae NK4A21A, Lachnospiraceae-UGC-010, and Lachnospiraceae-GCA-900066575 groups. The NS group indicator ASVs were affiliated to Pirellulaceae-1088-a5 gut group, Anaerovibrio, Victivallis, and Sellimonas genera. In conclusion, the characteristics enhancing the persistence of some predominant strains observed here should be explored further, and studies focused on mechanisms of competition among E. coli strains are also needed.
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Affiliation(s)
- Delphine Bibbal
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Philippe Ruiz
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Clermont-Ferrand, France
| | | | - Christine Mazuy-Cruchaudet
- Université de Lyon, VetAgro Sup, National Reference Laboratory for E. coli (including VTEC), Marcy l'Etoile, France.,Université de Lyon, Laboratoire d'Ecologie Microbienne de Lyon, CNRS, INRAE, Université de Lyon 1, VetAgro Sup, Microbial Ecology Laboratory, Research Group on Bacterial Opportunistic Pathogens and Environment, Villeurbanne, France
| | - Estelle Loukiadis
- Université de Lyon, VetAgro Sup, National Reference Laboratory for E. coli (including VTEC), Marcy l'Etoile, France.,Université de Lyon, Laboratoire d'Ecologie Microbienne de Lyon, CNRS, INRAE, Université de Lyon 1, VetAgro Sup, Microbial Ecology Laboratory, Research Group on Bacterial Opportunistic Pathogens and Environment, Villeurbanne, France
| | - Frédéric Auvray
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
| | - Evelyne Forano
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Clermont-Ferrand, France
| | - Hubert Brugère
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, France
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5
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Projahn M, Lamparter MC, Ganas P, Goehler A, Lorenz-Wright SC, Maede D, Fruth A, Lang C, Schuh E. Genetic diversity and pathogenic potential of Shiga toxin-producing Escherichia coli (STEC) derived from German flour. Int J Food Microbiol 2021; 347:109197. [PMID: 33895597 DOI: 10.1016/j.ijfoodmicro.2021.109197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) can cause severe human illness, which are frequently linked to the consumption of contaminated beef or dairy products. However, recent outbreaks associated with contaminated flour and undercooked dough in the United States and Canada, highlight the potential of plant based food as transmission routes for STEC. In Germany STEC has been isolated from flour, but no cases of illness have been linked to flour. In this study, we characterized 123 STEC strains isolated from flour and flour products collected between 2015 and 2019 across Germany. In addition to determination of serotype and Shiga toxin subtype, whole genome sequencing (WGS) was used for isolates collected in 2018 to determine phylogenetic relationships, sequence type (ST), and virulence-associated genes (VAGs). We found a high diversity of serotypes including those frequently associated with human illness and outbreaks, such as O157:H7 (stx2c/d, eae), O145:H28 (stx2a, eae), O146:H28 (stx2b), and O103:H2 (stx1a, eae). Serotypes O187:H28 (ST200, stx2g) and O154:H31 (ST1892, stx1d) were most prevalent, but are rarely linked to human cases. However, WGS analysis revealed that these strains, as well as, O156:H25 (ST300, stx1a) harbour high numbers of VAGs, including eae, nleB and est1a/sta1. Although STEC-contaminated flour products have yet not been epidemiologically linked to human clinical cases in Germany, this study revealed that flour can serve as a vector for STEC strains with a high pathogenic potential. Further investigation is needed to determine the sources of STEC contamination in flour and flour products particularly in regards to these rare serotypes.
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Affiliation(s)
- Michaela Projahn
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Escherichia coli including VTEC, Berlin, Germany
| | - Marina C Lamparter
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Escherichia coli including VTEC, Berlin, Germany
| | - Petra Ganas
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Escherichia coli including VTEC, Berlin, Germany
| | - André Goehler
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Escherichia coli including VTEC, Berlin, Germany
| | - Sandra C Lorenz-Wright
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Escherichia coli including VTEC, Berlin, Germany
| | - Dietrich Maede
- Institute for Consumer Protection Saxony-Anhalt, Halle, Germany
| | - Angelika Fruth
- Robert Koch Institute, Division of Enteropathogenic Bacteria and Legionella, National Reference Centre for Salmonella and other Bacterial Enterics, Wernigerode, Germany
| | - Christina Lang
- Robert Koch Institute, Division of Enteropathogenic Bacteria and Legionella, National Reference Centre for Salmonella and other Bacterial Enterics, Wernigerode, Germany
| | - Elisabeth Schuh
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Escherichia coli including VTEC, Berlin, Germany.
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6
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Jung Y, Porto-Fett ACS, Parveen S, Meredith J, Shoyer BA, Henry E, Trauger Z, Shane LE, Osoria M, Schwarz J, Rupert C, Chapman B, Moxley RA, Luchansky JB. Recovery Rate of Cells of the Seven Regulated Serogroups of Shiga Toxin-Producing Escherichia coli from Raw Veal Cutlets, Ground Veal, and Ground Beef from Retail Stores in the Mid-Atlantic Region of the United States. J Food Prot 2021; 84:220-232. [PMID: 32977344 DOI: 10.4315/jfp-20-290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/19/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT A total of 482 veal cutlet, 555 ground veal, and 540 ground beef samples were purchased from retail establishments in the mid-Atlantic region of the United States over a noncontiguous 2-year period between 2014 and 2017. Samples (325 g each) were individually enriched and screened via real-time PCR for all seven regulated serogroups of Shiga toxin-producing Escherichia coli (STEC). Presumptive STEC-positive samples were subjected to serogroup-specific immunomagnetic separation and plated onto selective media. Up to five isolates typical for STEC from each sample were analyzed via multiplex PCR for both the virulence genes (i.e., eae, stx1 and/or stx2, and ehxA) and serogroup-specific gene(s) for the seven regulated STEC serogroups. The recovery rates of non-O157 STEC from veal cutlets (3.94%, 19 of 482 samples) and ground veal (7.03%, 39 of 555 samples) were significantly higher (P < 0.05) than that from ground beef (0.93%, 5 of 540 samples). In contrast, only a single isolate of STEC O157:H7 was recovered; this isolate originated from 1 (0.18%) of 555 samples of ground veal. Recovery rates for STEC were not associated with state, season, packaging type, or store type (P > 0.05) but were associated with brand and fat content (P < 0.05). Pulsed-field subtyping of the 270 viable and confirmed STEC isolates from the 64 total samples testing positive revealed 78 pulsotypes (50 to 80% similarity) belonging to 39 pulsogroups, with ≥90% similarity among pulsotypes within pulsogroups. Multiple isolates from 43 (67.7%) of 64 samples testing positive had an indistinguishable pulsotype. STEC serotypes O26 and O103 were the most prevalent serogroups in beef and veal, respectively. These findings support related findings from regulatory sampling studies over the past decade and confirm that recovery rates for the regulated STEC serogroups are higher for raw veal than for raw beef samples, as was observed in the present study of meat purchased at food retailers in the mid-Atlantic region of the United States. HIGHLIGHTS
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Affiliation(s)
- Yangjin Jung
- U.S. Department of Agriculture, Agricultural Research Service, Wyndmoor, Pennsylvania 19038
| | - Anna C S Porto-Fett
- U.S. Department of Agriculture, Agricultural Research Service, Wyndmoor, Pennsylvania 19038.,(ORCID: https://orcid.org/0000-0002-2689-6402 [A.C.S.P.F.])
| | - Salina Parveen
- University of Maryland Eastern Shore, Princess Anne, Maryland 21853
| | - Joan Meredith
- University of Maryland Eastern Shore, Princess Anne, Maryland 21853
| | - Bradley A Shoyer
- U.S. Department of Agriculture, Agricultural Research Service, Wyndmoor, Pennsylvania 19038
| | - Elizabeth Henry
- U.S. Department of Agriculture, Agricultural Research Service, Wyndmoor, Pennsylvania 19038
| | - Zachary Trauger
- U.S. Department of Agriculture, Agricultural Research Service, Wyndmoor, Pennsylvania 19038
| | - Laura E Shane
- U.S. Department of Agriculture, Agricultural Research Service, Wyndmoor, Pennsylvania 19038
| | - Manuela Osoria
- U.S. Department of Agriculture, Agricultural Research Service, Wyndmoor, Pennsylvania 19038
| | - Jurgen Schwarz
- University of Maryland Eastern Shore, Princess Anne, Maryland 21853
| | | | | | - Rodney A Moxley
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68583, USA
| | - John B Luchansky
- U.S. Department of Agriculture, Agricultural Research Service, Wyndmoor, Pennsylvania 19038
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Collis RM, Biggs PJ, Midwinter AC, Browne AS, Wilkinson DA, Irshad H, French NP, Brightwell G, Cookson AL. Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies. PLoS One 2020; 15:e0235066. [PMID: 32584859 PMCID: PMC7316241 DOI: 10.1371/journal.pone.0235066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/08/2020] [Indexed: 11/18/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are a leading cause of foodborne outbreaks of human disease, but they reside harmlessly as an asymptomatic commensal in the ruminant gut. STEC serogroup O145 are difficult to isolate as routine diagnostic methods are unable to distinguish non-O157 serogroups due to their heterogeneous metabolic characteristics, resulting in under-reporting which is likely to conceal their true prevalence. In light of these deficiencies, the purpose of this study was a twofold approach to investigate enhanced STEC O145 diagnostic culture-based methods: firstly, to use a genomic epidemiology approach to understand the genetic diversity and population structure of serogroup O145 at both a local (New Zealand) (n = 47) and global scale (n = 75) and, secondly, to identify metabolic characteristics that will help the development of a differential media for this serogroup. Analysis of a subset of E. coli serogroup O145 strains demonstrated considerable diversity in carbon utilisation, which varied in association with eae subtype and sequence type. Several carbon substrates, such as D-serine and D-malic acid, were utilised by the majority of serogroup O145 strains, which, when coupled with current molecular and culture-based methods, could aid in the identification of presumptive E. coli serogroup O145 isolates. These carbon substrates warrant subsequent testing with additional serogroup O145 strains and non-O145 strains. Serogroup O145 strains displayed extensive genetic heterogeneity that was correlated with sequence type and eae subtype, suggesting these genetic markers are good indicators for distinct E. coli phylogenetic lineages. Pangenome analysis identified a core of 3,036 genes and an open pangenome of >14,000 genes, which is consistent with the identification of distinct phylogenetic lineages. Overall, this study highlighted the phenotypic and genotypic heterogeneity within E. coli serogroup O145, suggesting that the development of a differential media targeting this serogroup will be challenging.
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Affiliation(s)
- Rose M. Collis
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J. Biggs
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Anne C. Midwinter
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - A. Springer Browne
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A. Wilkinson
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Hamid Irshad
- Animal Health Programme, National Agricultural Research Centre, Islamabad, Pakistan
| | - Nigel P. French
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Gale Brightwell
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Adrian L. Cookson
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
- Molecular Epidemiology and Veterinary Public Health Laboratory (EpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- * E-mail:
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8
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Genetic diversity of the intimin gene (eae) in non-O157 Shiga toxin-producing Escherichia coli strains in China. Sci Rep 2020; 10:3275. [PMID: 32094410 PMCID: PMC7040016 DOI: 10.1038/s41598-020-60225-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/05/2020] [Indexed: 12/24/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen. The increasing incidence of non-O157 STEC has posed a great risk to public health. Besides the Shiga toxin (Stx), the adherence factor, intimin, coded by eae gene plays a critical role in STEC pathogenesis. In this study, we investigated the prevalence and polymorphisms of eae gene in non-O157 STEC strains isolated from different sources in China. Among 735 non-O157 STEC strains, eae was present in 70 (9.5%) strains. Eighteen different eae genotypes were identified in 62 eae-positive STEC strains with the nucleotide identities ranging from 86.01% to 99.97%. Among which, seven genotypes were newly identified in this study. The eighteen eae genotypes can be categorized into five eae subtypes, namely β1, γ1, ε1, ζ3 and θ. Associations between eae subtypes/genotypes and serotypes as well as origins of strains were observed in this study. Strains belonging to serotypes O26:H11, O103:H2, O111:H8 are associated with particular eae subtypes, i.e., β1, ε1, θ, respectively. Most strains from diarrheal patients (7/9, 77.8%) carried eae-β1 subtype, while most isolates from cattle (23/26, 88.5%) carried eae-ζ3 subtype. This study demonstrated a genetic diversity of eae gene in non-O157 STEC strains from different sources in China.
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Abafogi AT, Kim J, Lee J, Mohammed MO, van Noort D, Park S. 3D-Printed Modular Microfluidic Device Enabling Preconcentrating Bacteria and Purifying Bacterial DNA in Blood for Improving the Sensitivity of Molecular Diagnostics. SENSORS 2020; 20:s20041202. [PMID: 32098268 PMCID: PMC7070462 DOI: 10.3390/s20041202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 01/22/2023]
Abstract
Molecular diagnostics for sepsis is still a challenge due to the presence of compounds that interfere with gene amplification and bacteria at concentrations lower than the limit of detection (LOD). Here, we report on the development of a 3D printed modular microfluidic device (3DpmμFD) that preconcentrates bacteria of interest in whole blood and purifies their genomic DNA (gDNA). It is composed of a W-shaped microchannel and a conical microchamber. Bacteria of interest are magnetically captured from blood in the device with antibody conjugated magnetic nanoparticles (Ab-MNPs) at 5 mL/min in the W-shaped microchannel, while purified gDNA of the preconcentrated bacteria is obtained with magnetic silica beads (MSBs) at 2 mL/min in the conical microchamber. The conical microchamber was designed to be connected to the microchannel after the capturing process using a 3D-printed rotary valve to minimize the exposure of the MSBs to interfering compounds in blood. The pretreatment process of spiked blood (2.5 mL) can be effectively completed within about 50 min. With the 3DpmμFD, the LOD for the target microorganism Escherichia coli O157:H7 measured by both polymerase chain reaction (PCR) with electrophoresis and quantitative PCR was 10 colony forming unit (CFU) per mL of whole blood. The results suggest that our method lowers the LOD of molecular diagnostics for pathogens in blood by providing bacterial gDNA at high purity and concentration.
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Affiliation(s)
- Abdurhaman Teyib Abafogi
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
| | - Jaewon Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
| | - Jinyeop Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
| | - Merem Omer Mohammed
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea;
| | - Danny van Noort
- Division of Biotechnology, IFM, Linkoping University, 58183 Linkoping, Sweden;
- Chair of Micro Process Engineering and Technology (COMPETE), University of Ljubljana, 1000 Ljubljana, Slovenia
- Centro de Investigación en Bioingeniería -BIO, Universidad de Ingenieria y Tecnologia—UTEC, Barranco 15036, Peru
| | - Sungsu Park
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea; (A.T.A.); (J.K.); (J.L.)
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Korea;
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Korea
- Correspondence: ; Tel.: +82-31-290-7431; Fax: +82-31-290-5889
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10
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Tostes R, Goji N, Amoako K, Chui L, Kastelic J, DeVinney R, Stanford K, Reuter T. Subtyping Escherichia coli Virulence Genes Isolated from Feces of Beef Cattle and Clinical Cases in Alberta. Foodborne Pathog Dis 2016; 14:35-42. [PMID: 27854514 DOI: 10.1089/fpd.2016.2199] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clinical outcomes of Shiga toxin (stx)-producing Escherichia coli infection are largely determined by virulence gene subtypes. This study used a polymerase chain reaction (PCR)-pyrosequencing assay to analyze single-nucleotide polymorphisms for subtyping three major virulence genes (stx1, stx2, eae) of pathogenic E. coli (O157, O26, O111, and O103) isolated from cattle over a 2-year interval (n = 465) and human clinical cases (n = 42) in western Canada. Most bovine isolates were PCR positive for at least one target virulence gene (367/465), whereas 100% of human isolates harbored eae in combination with at least one stx gene. Four Shiga toxin (1a, 2a, 2c, and 2e) and four eae (λ/γ1-eae, ɛ-eae, θ/γ2-eae, and β-eae) subtypes were identified in over 25 distinct virulence genotypes. Among cattle isolates, every serogroup, but O103, presented a dominant genotype (O157: stx1a+stx2a+λ/γ1-eae, O26: β-eae alone, and O111: stx1a+θ/γ2-eae). Similar patterns were found in human isolates, although it was not possible to establish a clear genotypic association between the two sources. Many O157 and non-O157 cattle isolates lacked stx genes; the absence was greater in non-O157 (75/258) and O157:non-H7 (19/40) than in O157:H7 strains (1/164). In addition, there was a greater diversity of virulence genotypes of E. coli isolated from cattle than those of human diseases, which could be due to sample characteristics (e.g., source and clinical condition). However, the majority of cattle strains had virulence profiles identical to those of clinical cases. Consequently, determining the presence of certain stx (stx1a and stx2a) and eae (λ/γ1-eae) subtypes known to cause human disease would be a valuable tool for risk assessment and prediction of disease outcome along the farm-to-fork continuum.
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Affiliation(s)
- Renata Tostes
- 1 Department of Microbiology, Immunology and Infectious Diseases, University of Calgary , Calgary, Canada
| | - Noriko Goji
- 2 Lethbridge Laboratory, National Centres for Animal Disease, Canadian Food Inspection Agency , Lethbridge, Canada
| | - Kingsley Amoako
- 2 Lethbridge Laboratory, National Centres for Animal Disease, Canadian Food Inspection Agency , Lethbridge, Canada
| | - Linda Chui
- 3 Alberta Provincial Laboratory for Public Health , Edmonton, Canada
| | - John Kastelic
- 4 Faculty of Veterinary Medicine, Production Animal Health, University of Calgary, Calgary, Canada
| | - Rebekah DeVinney
- 1 Department of Microbiology, Immunology and Infectious Diseases, University of Calgary , Calgary, Canada
| | - Kim Stanford
- 5 Alberta Agriculture and Forestry , Lethbridge, Canada
| | - Tim Reuter
- 5 Alberta Agriculture and Forestry , Lethbridge, Canada
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11
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Mellor GE, Fegan N, Duffy LL, McMILLAN KE, Jordan D, Barlow RS. National Survey of Shiga Toxin-Producing Escherichia coli Serotypes O26, O45, O103, O111, O121, O145, and O157 in Australian Beef Cattle Feces. J Food Prot 2016; 79:1868-1874. [PMID: 28221921 DOI: 10.4315/0362-028x.jfp-15-507] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Escherichia coli O157 and six non-O157 Shiga toxin-producing E. coli (STEC) serotypes (O26, O45, O103, O111, O121, and O145, colloquially referred to as the "big 6") have been classified as adulterants of raw nonintact beef products in the United States. While beef cattle are a known reservoir for the prototype STEC serotype, E. coli O157, less is known about the dissemination of non-O157 STEC serotypes in Australian cattle. In the present study, 1,500 fecal samples were collected at slaughter from adult (n =628) and young (n =286) beef cattle, adult (n =128) and young (n =143) dairy cattle, and veal calves (n = 315) across 31 Australian export-registered processing establishments. Fecal samples were enriched and tested for E. coli O157 and the big 6 STEC serotypes using BAX System PCR and immunomagnetic separation methods. Pathogenic STEC (pSTEC; isolates that possess stx, eae, and an O antigen marker for O157 or a big 6 serotype) were isolated from 115 samples (7.7%), of which 100 (6.7%) contained E. coli O157 and 19 (1.3%) contained a big 6 serotype. Four of the 115 samples contained multiple pSTEC serotypes. Among samples confirmed for big 6 pSTEC, 15 (1%) contained E. coli O26 and 4 (0.3%) contained E. coli O111. pSTEC of serotypes O45, O103, O121, and O145 were not isolated from any sample, even though genes indicative of E. coli belonging to these serotypes were detected by PCR. Analysis of animal classes revealed a higher pSTEC prevalence in younger animals, including veal (12.7%), young beef (9.8%), and young dairy (7.0%), than in adult animals, including adult beef (5.1%) and adult dairy (3.9%). This study is the largest of its kind undertaken in Australia. In contrast to E. coli O157 and consistent with previous findings, this study reports a relatively low prevalence of big 6 pSTEC serotypes in Australian cattle populations.
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Affiliation(s)
- Glen E Mellor
- CSIRO Agriculture and Food, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
| | - Narelle Fegan
- CSIRO Agriculture and Food, 671 Sneydes Road, Werribee, Victoria 3030, Australia
| | - Lesley L Duffy
- CSIRO Agriculture and Food, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
| | - Kate E McMILLAN
- CSIRO Agriculture and Food, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
| | - David Jordan
- Department of Primary Industries, 1243 Bruxner Highway, Wollongbar, New South Wales 2477, Australia
| | - Robert S Barlow
- CSIRO Agriculture and Food, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
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12
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Molecular Profiling of Shiga Toxin-Producing Escherichia coli and Enteropathogenic E. coli Strains Isolated from French Coastal Environments. Appl Environ Microbiol 2016; 82:3913-3927. [PMID: 27107119 DOI: 10.1128/aem.00271-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/17/2016] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) strains may be responsible for food-borne infections in humans. Twenty-eight STEC and 75 EPEC strains previously isolated from French shellfish-harvesting areas and their watersheds and belonging to 68 distinguishable serotypes were characterized in this study. High-throughput real-time PCR was used to search for the presence of 75 E. coli virulence-associated gene targets, and genes encoding Shiga toxin (stx) and intimin (eae) were subtyped using PCR tests and DNA sequencing, respectively. The results showed a high level of diversity between strains, with 17 unique virulence gene profiles for STEC and 56 for EPEC. Seven STEC and 15 EPEC strains were found to display a large number or a particular combination of genetic markers of virulence and the presence of stx and/or eae variants, suggesting their potential pathogenicity for humans. Among these, an O26:H11 stx1a eae-β1 strain was associated with a large number of virulence-associated genes (n = 47), including genes carried on the locus of enterocyte effacement (LEE) or other pathogenicity islands, such as OI-122, OI-71, OI-43/48, OI-50, OI-57, and the high-pathogenicity island (HPI). One O91:H21 STEC strain containing 4 stx variants (stx1a, stx2a, stx2c, and stx2d) was found to possess genes associated with pathogenicity islands OI-122, OI-43/48, and OI-15. Among EPEC strains harboring a large number of virulence genes (n, 34 to 50), eight belonged to serotype O26:H11, O103:H2, O103:H25, O145:H28, O157:H7, or O153:H2. IMPORTANCE The species E. coli includes a wide variety of strains, some of which may be responsible for severe infections. This study, a molecular risk assessment study of E. coli strains isolated from the coastal environment, was conducted to evaluate the potential risk for shellfish consumers. This report describes the characterization of virulence gene profiles and stx/eae polymorphisms of E. coli isolates and clearly highlights the finding that the majority of strains isolated from coastal environment are potentially weakly pathogenic, while some are likely to be more pathogenic.
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13
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Luedtke BE, Bosilevac JM, Harhay DM, Arthur TM. Effect of Direct-Fed Microbial Dosage on the Fecal Concentrations of EnterohemorrhagicEscherichia coliin Feedlot Cattle. Foodborne Pathog Dis 2016; 13:190-5. [DOI: 10.1089/fpd.2015.2063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Brandon E. Luedtke
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska
- Department of Biology, University of Nebraska at Kearney, Kearney, Nebraska
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska
| | - Dayna M. Harhay
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska
| | - Terrance M. Arthur
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska
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14
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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: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [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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15
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Um MM, Barraud O, Kérourédan M, Gaschet M, Stalder T, Oswald E, Dagot C, Ploy MC, Brugère H, Bibbal D. Comparison of the incidence of pathogenic and antibiotic-resistant Escherichia coli strains in adult cattle and veal calf slaughterhouse effluents highlighted different risks for public health. WATER RESEARCH 2016; 88:30-38. [PMID: 26460853 DOI: 10.1016/j.watres.2015.09.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 09/09/2015] [Accepted: 09/15/2015] [Indexed: 06/05/2023]
Abstract
The goal of this study was to investigate the involvement of bovine slaughterhouse effluents and biosolids in the risk of environmental dissemination of pathogenic and antibiotic-resistant Escherichia coli. Several samples were collected from one adult cattle and one veal calf slaughterhouse wastewater treatment plant (WWTP). The treatment process had no impact on the percentage of Shiga toxin-producing E. coli (STEC) and on the percentage of atypical enteropathogenic E. coli (aEPEC). A STEC O157:H7 was isolated from the thickened sludge of the adult cattle slaughterhouse. As thickened sludge is intended to be spread on agricultural lands, the detection of this pathogenic strain is a public health issue. The percentage of antibiotic-resistant E. coli was 5.0% and 87.5% in wastewater from the adult cattle and the veal calf slaughterhouse, respectively. These percentages were not significantly different after treatment. Integron-bearing E. coli isolates were only detected in the veal calf slaughterhouse WWTP with percentages above 50.0% for all sampling points whatever the step of the treatment process. Taken together, these findings highlighted the fact that different public health risks might be associated with adult cattle or veal calf slaughterhouses regarding the dissemination of pathogenic and antibiotic-resistant E. coli isolates into the environment.
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Affiliation(s)
- Maryse Michèle Um
- INSERM UMR1043, INRA USC1360, INP-ENVT, Université de Toulouse, Toulouse, France
| | - Olivier Barraud
- Université de Limoges, UMR1092, Limoges, France; INSERM, UMR1092, Limoges, France; CHU Limoges, laboratoire de Bactériologie-Virologie-Hygiène, Limoges, France
| | - Monique Kérourédan
- INSERM UMR1043, INRA USC1360, INP-ENVT, Université de Toulouse, Toulouse, France
| | - Margaux Gaschet
- Université de Limoges, UMR1092, Limoges, France; INSERM, UMR1092, Limoges, France; CHU Limoges, laboratoire de Bactériologie-Virologie-Hygiène, Limoges, France
| | | | - Eric Oswald
- INSERM UMR1043, INRA USC1360, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | | | - Marie-Cecile Ploy
- Université de Limoges, UMR1092, Limoges, France; INSERM, UMR1092, Limoges, France; CHU Limoges, laboratoire de Bactériologie-Virologie-Hygiène, Limoges, France
| | - Hubert Brugère
- INSERM UMR1043, INRA USC1360, INP-ENVT, Université de Toulouse, Toulouse, France
| | - Delphine Bibbal
- INSERM UMR1043, INRA USC1360, INP-ENVT, Université de Toulouse, Toulouse, France.
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16
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Microbiological analysis of pre-packed sweet basil (Ocimum basilicum) and coriander (Coriandrum sativum) leaves for the presence of Salmonella spp. and Shiga toxin-producing E. coli. Int J Food Microbiol 2015; 208:11-8. [DOI: 10.1016/j.ijfoodmicro.2015.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/03/2015] [Accepted: 05/16/2015] [Indexed: 11/21/2022]
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17
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Bettelheim KA, Goldwater PN. Escherichia coli and Sudden Infant Death Syndrome. Front Immunol 2015; 6:343. [PMID: 26191064 PMCID: PMC4490240 DOI: 10.3389/fimmu.2015.00343] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/19/2015] [Indexed: 01/02/2023] Open
Abstract
This review examines the association of strains of Escherichia coli with sudden infant death syndrome (SIDS) and the possible role these bacteria play in this enigmatic condition. The review addresses evidence for E. coli in SIDS infants, potential sources of E. coli in the environment, colonization by commensal and pathogenic strains, the variety of currently accepted pathotypes, and how these pathotypes could compromise intestinal integrity and induce inflammation. Both intestinal and extraintestinal pathotypes are compared in relation to the apparent liability in which virulence traits can be gained or lost by strains of E. coli. The way in which E. coli infections fit with current views on infant sleeping position and other SIDS risk factors is highlighted.
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Affiliation(s)
- Karl A Bettelheim
- Discipline of Paediatrics, School of Paediatrics and Reproductive Health, University of Adelaide , North Adelaide, SA , Australia
| | - Paul N Goldwater
- Discipline of Paediatrics, School of Paediatrics and Reproductive Health, University of Adelaide , North Adelaide, SA , Australia
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18
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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] [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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19
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A new pyrosequencing assay for rapid detection and genotyping of Shiga toxin, intimin and O157-specific rfbE genes of Escherichia coli. J Microbiol Methods 2015; 109:167-79. [DOI: 10.1016/j.mimet.2014.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/03/2014] [Accepted: 12/04/2014] [Indexed: 01/02/2023]
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20
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Bibbal D, Loukiadis E, Kérourédan M, Ferré F, Dilasser F, Peytavin de Garam C, Cartier P, Oswald E, Gay E, Auvray F, Brugère H. Prevalence of carriage of Shiga toxin-producing Escherichia coli serotypes O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28 among slaughtered adult cattle in France. Appl Environ Microbiol 2015; 81:1397-1405. [PMID: 25527532 PMCID: PMC4309698 DOI: 10.1128/aem.03315-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/10/2014] [Indexed: 11/20/2022] Open
Abstract
The main pathogenic enterohemorrhagic Escherichia coli (EHEC) strains are defined as Shiga toxin (Stx)-producing E. coli (STEC) belonging to one of the following serotypes: O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28. Each of these five serotypes is known to be associated with a specific subtype of the intimin-encoding gene (eae). The objective of this study was to evaluate the prevalence of bovine carriers of these “top five” STEC in the four adult cattle categories slaughtered in France. Fecal samples were collected from 1,318 cattle, including 291 young dairy bulls, 296 young beef bulls, 337 dairy cows, and 394 beef cows. A total of 96 E. coli isolates, including 33 top five STEC and 63 atypical enteropathogenic E. coli (aEPEC) isolates, with the same genetic characteristics as the top five STEC strains except that they lacked an stx gene, were recovered from these samples.O157:H7 was the most frequently isolated STEC serotype. The prevalence of top five STEC (all serotypes included) was 4.5% in young dairy bulls, 2.4% in young beef bulls, 1.8% in dairy cows, and 1.0% in beef cows. It was significantly higher in young dairy bulls (P<0.05) than in the other 3 categories. The basis for these differences between categories remains to be elucidated. Moreover,simultaneous carriage of STEC O26:H11 and STEC O103:H2 was detected in one young dairy bull. Lastly, the prevalence of bovine carriers of the top five STEC, evaluated through a weighted arithmetic mean of the prevalence by categories, was estimated to 1.8% in slaughtered adult cattle in France.
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Affiliation(s)
- Delphine Bibbal
- INSERM UMR1043, INRA USC1360, INP-ENVT ESC, Université de Toulouse, Toulouse, France
| | - Estelle Loukiadis
- Université de Lyon, VetAgro Sup, LMAP Laboratory, National Reference Laboratory for E. coli (Including VTEC), Marcy l'Etoile, France
- Université de Lyon, UMR 5557 Microbial Ecology, Université de Lyon 1, CNRS, VetAgro Sup, Research Group on Bacterial Opportunistic Pathogens and Environment, Villeurbanne, France
| | - Monique Kérourédan
- INSERM UMR1043, INRA USC1360, INP-ENVT ESC, Université de Toulouse, Toulouse, France
| | - Franck Ferré
- Université de Lyon, VetAgro Sup, LMAP Laboratory, National Reference Laboratory for E. coli (Including VTEC), Marcy l'Etoile, France
| | - Françoise Dilasser
- Université Paris-Est, Anses, Laboratory for Food Safety, Maisons-Alfort, France
| | | | | | - Eric Oswald
- INSERM UMR1043, INRA USC1360, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | - Emilie Gay
- Anses, Lyon Laboratory, Epidemiology Unit, Lyon, France
| | - Frédéric Auvray
- Université Paris-Est, Anses, Laboratory for Food Safety, Maisons-Alfort, France
| | - Hubert Brugère
- INSERM UMR1043, INRA USC1360, INP-ENVT ESC, Université de Toulouse, Toulouse, France
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21
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Microbial safety and sanitary quality of strawberry primary production in Belgium: risk factors for Salmonella and Shiga toxin-producing Escherichia coli contamination. Appl Environ Microbiol 2015; 81:2562-70. [PMID: 25636845 DOI: 10.1128/aem.03930-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Strawberries are an important fruit in Belgium in both production and consumption, but little information is available about the presence of Salmonella and Shiga toxin-producing Escherichia coli (STEC) in these berries, the risk factors in agricultural production, and possible specific mitigation options. In 2012, a survey was undertaken of three soil and three soilless cultivation systems in Belgium. No Salmonella spp. were isolated. No STEC was detected in the strawberry samples (0 of 72), but STEC was detected by PCR in 11 of 78 irrigation water and 2 of 24 substrate samples. Culture isolates were obtained for 2 of 11 PCR-positive irrigation water samples and 2 of 2 substrate samples. Multivariable logistic regression analysis revealed elevated generic E. coli numbers (the odds ratio [OR] for a 1 log increase being 4.6) as the most important risk factor for STEC, together with the berry-picking season (elevated risk in summer). The presence of generic E. coli in the irrigation water (≥1 CFU per 100 ml) was mainly influenced by the type of irrigation water (collected rainfall water stored in ponds was more often contaminated than groundwater pumped from boreholes [OR = 5.8]) and the lack of prior treatment (untreated water versus water subjected to sand filtration prior to use [OR = 19.2]). The follow-up study in 2013 at one of the producer locations indicated cattle to be the most likely source of STEC contamination of the irrigation water.
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Balière C, Rincé A, Thevenot D, Gourmelon M. Successful detection of pathogenic Shiga-toxin-producing Escherichia coli
in shellfish, environmental waters and sediment using the ISO/TS-13136 method. Lett Appl Microbiol 2015; 60:315-20. [DOI: 10.1111/lam.12386] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/18/2014] [Accepted: 01/04/2015] [Indexed: 11/29/2022]
Affiliation(s)
- C. Balière
- Unité SG2M, Département RBE; Laboratoire Santé Environnement et Microbiologie; IFREMER; Plouzané France
| | - A. Rincé
- UCBN; U2RM Stress/Virulence EA4655; Normandie-Université; Caen France
| | - D. Thevenot
- Laboratoire LMAP-LNR; UMR5557/Equipe 6; Marcy-L'Etoile France
| | - M. Gourmelon
- Unité SG2M, Département RBE; Laboratoire Santé Environnement et Microbiologie; IFREMER; Plouzané France
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Improving detection of Shiga toxin-producing Escherichia coli by molecular methods by reducing the interference of free Shiga toxin-encoding bacteriophages. Appl Environ Microbiol 2014; 81:415-21. [PMID: 25362055 DOI: 10.1128/aem.02941-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Detection of Shiga toxin-producing Escherichia coli (STEC) by culture methods is advisable to identify the pathogen, but recovery of the strain responsible for the disease is not always possible. The use of DNA-based methods (PCR, quantitative PCR [qPCR], or genomics) targeting virulence genes offers fast and robust alternatives. However, detection of stx is not always indicative of STEC because stx can be located in the genome of temperate phages found in the samples as free particles; this could explain the numerous reports of positive stx detection without successful STEC isolation. An approach based on filtration through low-protein-binding membranes and additional washing steps was applied to reduce free Stx phages without reducing detection of STEC bacteria. River water, food, and stool samples were spiked with suspensions of phage 933W and, as a STEC surrogate, a lysogen harboring a recombinant Stx phage in which stx was replaced by gfp. Bacteria were tested either by culture or by qPCR for gfp while phages were tested using qPCR targeting stx in phage DNA. The procedure reduces phage particles by 3.3 log10 units without affecting the recovery of the STEC population (culturable or assessed by qPCR). The method is applicable regardless of phage and bacteria densities and is useful in different matrices (liquid or solid). This approach eliminates or considerably reduces the interference of Stx phages in the detection of STEC by molecular methods. The reduction of possible interference would increase the efficiency and reliability of genomics for STEC detection when the method is applied routinely in diagnosis and food analysis.
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Martínez-Castillo A, Muniesa M. Implications of free Shiga toxin-converting bacteriophages occurring outside bacteria for the evolution and the detection of Shiga toxin-producing Escherichia coli. Front Cell Infect Microbiol 2014; 4:46. [PMID: 24795866 PMCID: PMC3997033 DOI: 10.3389/fcimb.2014.00046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 03/27/2014] [Indexed: 11/13/2022] Open
Abstract
In this review we highlight recent work that has increased our understanding of the distribution of Shiga toxin-converting phages that can be detected as free phage particles, independently of Shiga toxin-producing bacteria (STEC). Stx phages are a quite diverse group of temperate phages that can be found in their prophage state inserted within the STEC chromosome, but can also be found as phages released from the cell after activation of their lytic cycle. They have been detected in extraintestinal environments such as water polluted with feces from humans or animals, food samples or even in stool samples of healthy individuals. The high persistence of phages to several inactivation conditions makes them suitable candidates for the successful mobilization of stx genes, possibly resulting in the genes reaching a new bacterial genomic background by means of transduction, where ultimately they may be expressed, leading to Stx production. Besides the obvious fact that Stx phages circulating between bacteria can be, and probably are, involved in the emergence of new STEC strains, we review here other possible ways in which free Stx phages could interfere with the detection of STEC in a given sample by current laboratory methods and how to avoid such interference.
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Affiliation(s)
| | - Maite Muniesa
- Department of Microbiology, Faculty of Biology, University of BarcelonaBarcelona, Spain
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