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Greig DR, Quinn OI, Rodwell EV, Olonade I, Swift C, Douglas A, Balasegram S, Jenkins C. Genomic analysis of an outbreak of Shiga toxin-producing Escherichia coli O183:H18 in the United Kingdom, 2023. Microb Genom 2024; 10:001243. [PMID: 38771013 PMCID: PMC11165631 DOI: 10.1099/mgen.0.001243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/10/2024] [Indexed: 05/22/2024] Open
Abstract
In June 2023, UKHSA surveillance systems detected an outbreak of severe gastrointestinal symptoms caused by a rare serotype of Shiga toxin-producing Escherichia coli, STEC O183:H18. There were 26 cases aged 6 months to 74 years (42 % cases were aged 0-9 years), distributed across the UK with onset dates range between 22 May 2023 and 4 July 2023. The epidemiological and food chain investigations were inconclusive, although meat products made from beef mince were implicated as a potential vehicle. The outbreak strain belonged to sequence type (ST) 657 and harboured a Shiga toxin (stx) subtype stx2a located on a prophage that was unique in the UKHSA stx-encoding bacteriophage database. Plasmid encoded, putative virulence genes subA, ehxA, saa, iha, lpfA and iss were detected, however, the established STEC virulence genes involved in attachment to the gut mucosa (eae and aggR) were absent. The acquisition of stx across the global population structure of ST657 appeared to correspond with the presence of subA, ehxA, saa, iha, lpfA and iss. During the outbreak investigation, we used long read sequencing to characterise the plasmid and prophage content of this atypical STEC, to look for evidence to explain its recent emergence. Although we were unable to determine source and transmission route of the outbreak strain, the genomic analysis revealed potential clues as to how novel strains for STEC evolve. With the implementation of PCR capable of detecting all STEC, and genome sequencing for typing and virulence profiling, we have the tools to enable us to monitor the changing landscape of STEC. Improvements in the standardised collection of epidemiological data and trace-back strategies within the food industry, will ensure we have a surveillance system capable of alerting us to emerging threats to public health.
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Affiliation(s)
- David R. Greig
- Gastrointestinal Bacteria Reference Unit, Public Health Microbiology, UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Orlagh I. Quinn
- Gastrointestinal Infections & Food Safety (One Health), Clinical & Public Health, UK Health Security Agency, London, UK
| | - Ella V. Rodwell
- Gastrointestinal Bacteria Reference Unit, Public Health Microbiology, UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Israel Olonade
- Gastrointestinal Bacteria Reference Unit, Public Health Microbiology, UK Health Security Agency, London, UK
| | - Craig Swift
- Gastrointestinal Bacteria Reference Unit, Public Health Microbiology, UK Health Security Agency, London, UK
| | - Amy Douglas
- Gastrointestinal Infections & Food Safety (One Health), Clinical & Public Health, UK Health Security Agency, London, UK
| | - Sooria Balasegram
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- Gastrointestinal Infections & Food Safety (One Health), Clinical & Public Health, UK Health Security Agency, London, UK
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health Microbiology, UK Health Security Agency, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
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Chase-Topping M, Dallman TJ, Allison L, Lupolova N, Matthews L, Mitchell S, Banks CJ, Prentice J, Brown H, Tongue S, Henry M, Evans J, Gunn G, Hoyle D, McNeilly TN, Fitzgerald S, Smith-Palmer A, Shaaban S, Holmes A, Hanson M, Woolhouse M, Didelot X, Jenkins C, Gally DL. Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health. Microb Genom 2023; 9:001090. [PMID: 37672388 PMCID: PMC10569735 DOI: 10.1099/mgen.0.001090] [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: 01/17/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
For the last two decades, the human infection frequency of Escherichia coli O157 (O157) in Scotland has been 2.5-fold higher than in England and Wales. Results from national cattle surveys conducted in Scotland and England and Wales in 2014/2015 were combined with data on reported human clinical cases from the same time frame to determine if strain differences in national populations of O157 in cattle could be associated with higher human infection rates in Scotland. Shiga toxin subtype (Stx) and phage type (PT) were examined within and between host (cattle vs human) and nation (Scotland vs England and Wales). For a subset of the strains, whole genome sequencing (WGS) provided further insights into geographical and host association. All three major O157 lineages (I, II, I/II) and most sub-lineages (Ia, Ib, Ic, IIa, IIb, IIc) were represented in cattle and humans in both nations. While the relative contribution of different reservoir hosts to human infection is unknown, WGS analysis indicated that the majority of O157 diversity in human cases was captured by isolates from cattle. Despite comparable cattle O157 prevalence between nations, strain types were localized. PT21/28 (sub-lineage Ic, Stx2a+) was significantly more prevalent in Scottish cattle [odds ratio (OR) 8.7 (2.3-33.7; P<0.001] and humans [OR 2.2 (1.5-3.2); P<0.001]. In England and Wales, cattle had a significantly higher association with sub-lineage IIa strains [PT54, Stx2c; OR 5.6 (1.27-33.3); P=0.011] while humans were significantly more closely associated with sub-lineage IIb [PT8, Stx1 and Stx2c; OR 29 (4.9-1161); P<0.001]. Therefore, cattle farms in Scotland were more likely to harbour Stx2a+O157 strains compared to farms in E and W (P<0.001). There was evidence of limited cattle strain migration between nations and clinical isolates from one nation were more similar to cattle isolates from the same nation, with sub-lineage Ic (mainly PT21/28) exhibiting clear national association and evidence of local transmission in Scotland. While we propose the higher rate of O157 clinical cases in Scotland, compared to England and Wales, is a consequence of the nationally higher level of Stx2a+O157 strains in Scottish cattle, we discuss the multiple additional factors that may also contribute to the different infection rates between these nations.
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Affiliation(s)
- Margo Chase-Topping
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Timothy J. Dallman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5HT, UK
| | - Lesley Allison
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Nadejda Lupolova
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Louise Matthews
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sonia Mitchell
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Christopher J. Banks
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Jamie Prentice
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Helen Brown
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Sue Tongue
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Madeleine Henry
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Judith Evans
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - George Gunn
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Deborah Hoyle
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | - Stephen Fitzgerald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | | | - Sharif Shaaban
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Anne Holmes
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Mary Hanson
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh EH9 3DL, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Warwick CV4 7AL, UK
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5HT, UK
| | - David L. Gally
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
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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] [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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Okuno M, Arimizu Y, Miyahara S, Wakabayashi Y, Gotoh Y, Yoshino S, Harada T, Seto K, Yamamoto T, Nakamura K, Hayashi T, Ogura Y. Escherichia cryptic clade I is an emerging source of human intestinal pathogens. BMC Biol 2023; 21:81. [PMID: 37055811 PMCID: PMC10100065 DOI: 10.1186/s12915-023-01584-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/30/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Within the genus Escherichia, several monophyletic clades other than the traditionally defined species have been identified. Of these, cryptic clade I (C-I) appears to represent a subspecies of E. coli, but due to the difficulty in distinguishing it from E. coli sensu stricto, the population structure and virulence potential of C-I are unclear. RESULTS We defined a set of true C-I strains (n = 465), including a Shiga toxin 2a (Stx2a)-producing isolate from a patient with bloody diarrhoea identified by the retrospective analyses using a C-I-specific detection system. Through genomic analysis of 804 isolates from the cryptic clades, including these C-I strains, we revealed their global population structures and the marked accumulation of virulence genes and antimicrobial resistance genes in C-I. In particular, half of the C-I strains contained hallmark virulence genes of Stx-producing E. coli (STEC) and/or enterotoxigenic E. coli (ETEC). We also found the host-specific distributions of virulence genes, which suggests bovines as the potential source of human infections caused by STEC- and STEC/ETEC hybrid-type C-I strains, as is known in STEC. CONCLUSIONS Our findings demonstrate the emergence of human intestinal pathogens in C-I lineage. To better understand the features of C-I strains and their infections, extensive surveillance and larger population studies of C-I strains are needed. The C-I-specific detection system developed in this study will be a powerful tool for screening and identifying C-I strains.
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Affiliation(s)
- Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Yoko Arimizu
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
- Department of Infectious Disease, National Hospital Organization Kyushu Medical Center, Fukuoka, 810-0065, Japan
| | - Seina Miyahara
- Department of Microbiology, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, 889-2155, Japan
| | - Yuki Wakabayashi
- Division of Microbiology, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shuji Yoshino
- Department of Microbiology, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, 889-2155, Japan
| | - Tetsuya Harada
- Division of Microbiology, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Kazuko Seto
- Division of Planning, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Takeshi Yamamoto
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan.
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Miyata T, Taniguchi I, Nakamura K, Gotoh Y, Yoshimura D, Itoh T, Hirai S, Yokoyama E, Ohnishi M, Iyoda S, Ogura Y, Hayashi T. Alteration of a Shiga toxin-encoding phage associated with a change in toxin production level and disease severity in Escherichia coli. Microb Genom 2023; 9:mgen000935. [PMID: 36821793 PMCID: PMC9997748 DOI: 10.1099/mgen.0.000935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Among the nine clades of Shiga toxin (Stx)-producing Escherichia coli O157:H7, clade 8 is thought to be highly pathogenic, as it causes severe disease more often than other clades. Two subclades have been proposed, but there are conflicting reports on intersubclade differences in Stx2 levels, although Stx2 production is a risk factor for severe disease development. The global population structure of clade 8 has also yet to be fully elucidated. Here, we present genome analyses of a global clade 8 strain set (n=510), including 147 Japanese strains sequenced in this study. The complete genome sequences of 18 of the 147 strains were determined to perform detailed clade-wide genome analyses together with 17 publicly available closed genomes. Intraclade variations in Stx2 production level and disease severity were also re-evaluated within the phylogenetic context. Based on phylogenomic analysis, clade 8 was divided into four lineages corresponding to the previously proposed SNP genotypes (SGs): SG8_30, SG8_31A, SG8_31B and SG8_32. SG8_30 and the common ancestor of the other SGs were first separated, with SG8_31A and SG8_31B emerging from the latter and SG8_32 emerging from SG8_31B. Comparison of 35 closed genomes revealed the overall structure of chromosomes and pO157 virulence plasmids and the prophage contents to be well conserved. However, Stx2a phages exhibit notable genomic diversity, even though all are integrated into the argW locus, indicating that subtype changes in Stx2a phage occurred from the γ subtype to its variant (γ_v1) in SG8_31A and from γ to δ in SG8_31B and SG8_32 via replacement of parts or almost entire phage genomes, respectively. We further show that SG8_30 strains (all carrying γ Stx2a phages) produce significantly higher levels of Stx2 and cause severe disease more frequently than SG8_32 strains (all carrying δ Stx2a phages). Clear conclusions on SG8_31A and SG8_31B cannot be made due to the small number of strains available, but as SG8_31A (carrying γ_v1 Stx2a phages) contains strains that produce much more Stx2 than SG8_30 strains, attention should also be paid to this SG.
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Affiliation(s)
- Tatsuya Miyata
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba 260-8715, Japan.,Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo 208-0011, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba 260-8715, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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6
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Weinroth MD, Clawson ML, Arthur TM, Wells JE, Brichta-Harhay DM, Strachan N, Bono JL. Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche. BMC Genomics 2022; 23:275. [PMID: 35392797 PMCID: PMC8991562 DOI: 10.1186/s12864-022-08497-6] [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: 09/21/2021] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
Background Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feedlot. All strains were subjected to short-read sequencing, with a subset of 36 also subjected to long-read sequencing. Results Over 96% of the strains fell into four phylogenetically distinct clades. Clade membership was associated with multiple factors including stx composition and the alleles of a well-characterized polymorphism (tir 255 T > A). Small plasmids (2.7 to 40 kb) were found to be primarily clade specific. Within each clade, chromosomal rearrangements were observed along with a core phageome and clade specific phages. Across both core and mobile elements of the genome, multiple SNP alleles were in complete linkage disequilibrium across all strains within specific clades. Clade evolutionary rates varied between 0.9 and 2.8 SNP/genome/year with two tir A allele clades having the lowest evolutionary rates. Investigation into possible causes of the differing rates was not conclusive but revealed a synonymous based mutation in the DNA polymerase III of the fastest evolving clade. Phylogenetic trees generated through our bioinformatic pipeline versus the NCBI’s pathogen detection project were similar, with the two tir A allele clades matching individual NCBI SNP clusters, and the two tir T allele clades assigned to multiple closely-related SNP clusters. Conclusions In one ecological niche, a diverse STEC O157:H7 population exhibited different rates of evolution that associated with SNP alleles in linkage disequilibrium in the core genome and mobile elements, including tir 255 T > A. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08497-6.
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Affiliation(s)
- Margaret D Weinroth
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.,Present address: U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, 30605, USA
| | - Michael L Clawson
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Terrance M Arthur
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - James E Wells
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Dayna M Brichta-Harhay
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Norval Strachan
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, Scotland, AB24 3UU, UK
| | - James L Bono
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.
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The epidemiology of Shiga toxin-producing Escherichia coli serogroup O157 in England, 2009-2019. Epidemiol Infect 2022; 150:e52. [PMID: 35241189 PMCID: PMC8915195 DOI: 10.1017/s0950268822000206] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) serogroup O157 is a zoonotic, foodborne gastrointestinal pathogen of major public health concern. We describe the epidemiology of STEC O157 infection in England by exploring the microbiological and clinical characteristics, the demographic and geographical distribution of cases, and examining changes in environmental exposures over 11 years of enhanced surveillance. Enhanced surveillance data including microbiological subtyping, clinical presentations and exposures were extracted for all cases resident in England with evidence of STEC O157 infection, either due to faecal culture or serology detection. Incidence rates were calculated based on mid-year population estimates from the Office of National Statistics (ONS). Demographics, geography, severity and environmental exposures were compared across the time periods 2009–2014 and 2015–2019. The number of cases reported to national surveillance decreased, with the mean cases per year dropping from 887 for the period 2009–2014 to 595 for the period 2015–2019. The decline in STEC O157 infections appears to be mirrored by the decrease in cases infected with phage type 21/28. Although the percentage of cases that developed HUS decreased, the percentage of cases reporting bloody diarrhoea and hospitalisation remained stable. The number of outbreaks declined over time, although more refined typing methods linked more cases to each outbreak. Integration of epidemiological data with microbiological typing data is essential to understanding the changes in the burden of STEC infection, assessment of the risks to public health, and the prediction and mitigation of emerging threats.
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8
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Guo Y, Ryan U, Feng Y, Xiao L. Association of Common Zoonotic Pathogens With Concentrated Animal Feeding Operations. Front Microbiol 2022; 12:810142. [PMID: 35082774 PMCID: PMC8784678 DOI: 10.3389/fmicb.2021.810142] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/17/2021] [Indexed: 12/24/2022] Open
Abstract
Animal farming has intensified significantly in recent decades, with the emergence of concentrated animal feeding operations (CAFOs) in industrialized nations. The congregation of susceptible animals in CAFOs can lead to heavy environmental contamination with pathogens, promoting the emergence of hyper-transmissible, and virulent pathogens. As a result, CAFOs have been associated with emergence of highly pathogenic avian influenza viruses, hepatitis E virus, Escherichia coli O157:H7, Streptococcus suis, livestock-associated methicillin-resistant Staphylococcus aureus, and Cryptosporidium parvum in farm animals. This has led to increased transmission of zoonotic pathogens in humans and changes in disease patterns in general communities. They are exemplified by the common occurrence of outbreaks of illnesses through direct and indirect contact with farm animals, and wide occurrence of similar serotypes or subtypes in both humans and farm animals in industrialized nations. Therefore, control measures should be developed to slow down the dispersal of zoonotic pathogens associated with CAFOs and prevent the emergence of new pathogens of epidemic and pandemic potential.
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Affiliation(s)
- Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Una Ryan
- Vector- and Water-Borne Pathogen Research Group, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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9
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AB 5 Enterotoxin-Mediated Pathogenesis: Perspectives Gleaned from Shiga Toxins. Toxins (Basel) 2022; 14:toxins14010062. [PMID: 35051039 PMCID: PMC8779504 DOI: 10.3390/toxins14010062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Foodborne diseases affect an estimated 600 million people worldwide annually, with the majority of these illnesses caused by Norovirus, Vibrio, Listeria, Campylobacter, Salmonella, and Escherichia coli. To elicit infections in humans, bacterial pathogens express a combination of virulence factors and toxins. AB5 toxins are an example of such toxins that can cause various clinical manifestations, including dehydration, diarrhea, kidney damage, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Treatment of most bacterial foodborne illnesses consists of fluid replacement and antibiotics. However, antibiotics are not recommended for infections caused by Shiga toxin-producing E. coli (STEC) because of the increased risk of HUS development, although there are conflicting views and results in this regard. Lack of effective treatment strategies for STEC infections pose a public health threat during outbreaks; therefore, the debate on antibiotic use for STEC infections could be further explored, along with investigations into antibiotic alternatives. The overall goal of this review is to provide a succinct summary on the mechanisms of action and the pathogenesis of AB5 and related toxins, as expressed by bacterial foodborne pathogens, with a primary focus on Shiga toxins (Stx). The role of Stx in human STEC disease, detection methodologies, and available treatment options are also briefly discussed.
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Phylogeny and potential virulence of cryptic clade Escherichia coli species complex isolates derived from an arable field trial. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100093. [PMID: 35005658 PMCID: PMC8718834 DOI: 10.1016/j.crmicr.2021.100093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 11/22/2022] Open
Abstract
Analysis of Escherichia coli taxonomy has expanded into a species-complex with the identification of divergent cryptic clades. A key question is the evolutionary trajectory of these clades and their relationship to isolates of clinical or veterinary importance. Since they have some environmental association, we screened a collection of E. coli isolated from a long-term spring barley field trial for their presence. While most isolates clustered into the enteric-clade, four of them clustered into Clade-V, and one in Clade-IV. The Clade -V isolates shared >96% intra-clade average nucleotide sequence identity but <91% with other clades. Although pan-genomics analysis confirmed their taxonomy as Clade -V (E. marmotae), retrospective phylogroup PCR did not discriminate them correctly. Differences in metabolic and adherence gene alleles occurred in the Clade -V isolates compared to E. coli sensu scricto. They also encoded the bacteriophage phage-associated cyto-lethal distending toxin (CDT) and antimicrobial resistance (AMR) genes, including an ESBL, blaOXA-453. Thus, the isolate collection encompassed a genetic diversity, and included cryptic clade isolates that encode potential virulence factors. The analysis has determined the phylogenetic relationship of cryptic clade isolates with E. coli sensu scricto and indicates a potential for horizontal transfer of virulence factors.
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11
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Eppinger M, Almería S, Allué-Guardia A, Bagi LK, Kalalah AA, Gurtler JB, Fratamico PM. Genome Sequence Analysis and Characterization of Shiga Toxin 2 Production by Escherichia coli O157:H7 Strains Associated With a Laboratory Infection. Front Cell Infect Microbiol 2022; 12:888568. [PMID: 35770066 PMCID: PMC9234449 DOI: 10.3389/fcimb.2022.888568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/03/2022] [Indexed: 11/21/2022] Open
Abstract
A laboratory-acquired E. coli O157:H7 infection with associated severe sequelae including hemolytic uremic syndrome occurred in an individual working in the laboratory with a mixture of nalidixic acid-resistant (NalR) O157:H7 mutant strains in a soil-biochar blend. The patient was hospitalized and treated with an intravenous combination of metronidazole and levofloxacin. The present study investigated the source of this severe laboratory acquired infection and further examined the influence of the antibiotics used during treatment on the expression and production of Shiga toxin. Genomes of two Stx2a-and eae-positive O157:H7 strains isolated from the patient's stool were sequenced along with two pairs of the wt strains and their derived NalR mutants used in the laboratory experiments. High-resolution SNP typing determined the strains' individual genetic relatedness and unambiguously identified the two laboratory-derived NalR mutant strains as the source of the researcher's life-threatening disease, rather than a conceivable ingestion of unrelated O157:H7 isolates circulating at the same time. It was further confirmed that in sublethal doses, the antibiotics increased toxin expression and production. Our results support a simultaneous co-infection with clinical strains in the laboratory, which were the causative agents of previous O157:H7 outbreaks, and further that the administration of antibiotics may have impacted the outcome of the infection.
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Affiliation(s)
- Mark Eppinger
- Department of Molecular Microbiology and Immunology (MMI), University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Sonia Almería
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
| | - Anna Allué-Guardia
- Department of Molecular Microbiology and Immunology (MMI), University of Texas at San Antonio, San Antonio, TX, United States
| | - Lori K Bagi
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
| | - Anwar A Kalalah
- Department of Molecular Microbiology and Immunology (MMI), University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Joshua B Gurtler
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
| | - Pina M Fratamico
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
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Fitzgerald SF, Lupolova N, Shaaban S, Dallman TJ, Greig D, Allison L, Tongue SC, Evans J, Henry MK, McNeilly TN, Bono JL, Gally DL. Genome structural variation in Escherichia coli O157:H7. Microb Genom 2021; 7. [PMID: 34751643 PMCID: PMC8743559 DOI: 10.1099/mgen.0.000682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human zoonotic pathogen Escherichia coli O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype. We demonstrate that LCRs are a major source of genomic variation across all lineages of E. coli O157:H7 and by using both optical mapping and Oxford Nanopore long-read sequencing prove that LCRs are generated in laboratory cultures started from a single colony and that these variants can be recovered from colonized cattle. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga-toxin production, type-3 secretion and motility can be affected by LCRs. In summary, E. coli O157:H7 has acquired multiple prophage regions over time that act to continually produce structural variants of the genome. These findings raise important questions about the significance of this prophage-mediated genome contingency to enhance adaptability between environments.
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Affiliation(s)
- Stephen F Fitzgerald
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Nadejda Lupolova
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Sharif Shaaban
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - David Greig
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Lesley Allison
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Sue C Tongue
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Judith Evans
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Madeleine K Henry
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 OPZ, UK
| | - James L Bono
- United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA
| | - David L Gally
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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13
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Amadio A, Bono JL, Irazoqui M, Larzábal M, Marques da Silva W, Eberhardt MF, Riviere NA, Gally D, Manning SD, Cataldi A. Genomic analysis of shiga toxin-containing Escherichia coli O157:H7 isolated from Argentinean cattle. PLoS One 2021; 16:e0258753. [PMID: 34710106 PMCID: PMC8553066 DOI: 10.1371/journal.pone.0258753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022] Open
Abstract
Cattle are the main reservoir of Enterohemorrhagic Escherichia coli (EHEC), with O157:H7 the distinctive serotype. EHEC is the main causative agent of a severe systemic disease, Hemolytic Uremic Syndrome (HUS). Argentina has the highest pediatric HUS incidence worldwide with 12–14 cases per 100,000 children. Herein, we assessed the genomes of EHEC O157:H7 isolates recovered from cattle in the humid Pampas of Argentina. According to phylogenetic studies, EHEC O157 can be divided into clades. Clade 8 strains that were classified as hypervirulent. Most of the strains of this clade have a Shiga toxin stx2a-stx2c genotype. To better understand the molecular bases related to virulence, pathogenicity and evolution of EHEC O157:H7, we performed a comparative genomic analysis of these isolates through whole genome sequencing. The isolates classified as clade 8 (four strains) and clade 6 (four strains) contained 13 to 16 lambdoid prophages per genome, and the observed variability of prophages was analysed. An inter strain comparison show that while some prophages are highly related and can be grouped into families, other are unique. Prophages encoding for stx2a were highly diverse, while those encoding for stx2c were conserved. A cluster of genes exclusively found in clade 8 contained 13 genes that mostly encoded for DNA binding proteins. In the studied strains, polymorphisms in Q antiterminator, the Q-stx2A intergenic region and the O and P γ alleles of prophage replication proteins are associated with different levels of Stx2a production. As expected, all strains had the pO157 plasmid that was highly conserved, although one strain displayed a transposon interruption in the protease EspP gene. This genomic analysis may contribute to the understanding of the genetic basis of the hypervirulence of EHEC O157:H7 strains circulating in Argentine cattle. This work aligns with other studies of O157 strain variation in other populations that shows key differences in Stx2a-encoding prophages.
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Affiliation(s)
- Ariel Amadio
- Instituto de Investigación de la Cadena Láctea IDICaL (INTA-CONICET), Rafaela, Argentina
| | - James L. Bono
- U.S Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, United States of America
| | - Matías Irazoqui
- Instituto de Investigación de la Cadena Láctea IDICaL (INTA-CONICET), Rafaela, Argentina
| | - Mariano Larzábal
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | - Wanderson Marques da Silva
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | | | - Nahuel A. Riviere
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
| | - David Gally
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Shannon D. Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Angel Cataldi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO)-CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de investigaciones Científicas y Tecnológicas (CONICET), Hurlingham, Argentina
- * E-mail:
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Nakamura K, Tokuda C, Arimitsu H, Etoh Y, Hamasaki M, Deguchi Y, Taniguchi I, Gotoh Y, Ogura Y, Hayashi T. Development of a homogeneous time-resolved FRET (HTRF) assay for the quantification of Shiga toxin 2 produced by E. coli. PeerJ 2021; 9:e11871. [PMID: 34395095 PMCID: PMC8325423 DOI: 10.7717/peerj.11871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a major intestinal pathogen and causes serious gastrointestinal illness, which includes diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome. The major virulence factors of STEC are Shiga toxins (Stx1 and Stx2), which belong to the AB-type toxin family. Among several subtypes of Stx1 and Stx2, the production of Stx2a is thought to be a risk factor for severe STEC infections, but Stx2a production levels vary markedly between STEC strains, even strains with the same serotype. Therefore, quantitative analyses of Stx2 production by STEC strains are important to understand the virulence potential of specific lineages or sublineages. In this study, we developed a novel Stx2 quantification method by utilizing homogeneous time-resolved fluorescence resonance energy transfer (HTRF) technology. To determine suitable “sandwich” assay conditions, we tested 6 combinations of fluorescence-labeled monoclonal antibodies (mAbs) specific to Stx2 and compared the HTRF signal intensities obtained at various incubation times. Through this analysis, we selected the most suitable mAb pair, one recognizing the A subunit and the other recognizing the B subunit, thus together detecting Stx holotoxins. The optimal incubation time was also determined (18 h). Then, we optimized the concentrations of the two mAbs based on the range for linearity. The established HTRF assay detected 0.5 ng/ml of the highly purified recombinant Stx2a and Stx2e proteins and the working range was 1–64 ng/ml for both Stx2a and Stx2e. Through the quantification analysis of Stx proteins in STEC cell lysates, we confirmed that other Stx2 subtypes (Stx2b, Stx2c, Stx2d and Stx2g) can also be quantified at a certain level of accuracy, while this assay system does not detect Stx2f, which is highly divergent in sequence from other Stx2 subtypes, and Stx1. As the HTRF protocol we established is simple, this assay system should prove useful for the quantitative analysis of Stx2 production levels of a large number of STEC strains.
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Affiliation(s)
- Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Hideyuki Arimitsu
- School of Human Science and Environment, University of Hyogo, Himeji, Japan
| | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, Dazaifu, Japan
| | | | - Yuichiro Deguchi
- Production Medicine Center, Agricultural Mutual Aid Association in Miyazaki Prefecture, Koyugun-Shintomicho, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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15
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Byrne L, Adams N, Jenkins C. Association between Shiga Toxin-Producing Escherichia coli O157:H7 stx Gene Subtype and Disease Severity, England, 2009-2019. Emerg Infect Dis 2021; 26:2394-2400. [PMID: 32946720 PMCID: PMC7510717 DOI: 10.3201/eid2610.200319] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Signs and symptoms of Shiga toxin–producing Escherichia coli (STEC) serogroup O157:H7 infection range from mild gastrointestinal to bloody diarrhea and hemolytic uremic syndrome (HUS). We assessed the association between Shiga toxin gene (stx) subtype and disease severity for »3,000 patients with STEC O157:H7 in England during 2009–2019. Odds of bloody diarrhea, HUS, or both, were significantly higher for patients infected with STEC O157:H7 possessing stx2a only or stx2a combined with other stx subtypes. Odds of severe signs/symptoms were significantly higher for isolates encoding stx2a only and belonging to sublineage Ic and lineage I/II than for those encoding stx2a only and belonging to sublineage IIb, indicating that stx2a is not the only driver causing HUS. Strains of STEC O157:H7 that had stx1a were also significantly more associated with severe disease than strains with stx2c only. This finding confounds public health risk assessment algorithms based on detection of stx2 as a predictor of severe disease.
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16
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A cluster of Shiga Toxin-producing Escherichia coli O157:H7 highlights raw pet food as an emerging potential source of infection in humans. Epidemiol Infect 2021; 149:e124. [PMID: 33955833 PMCID: PMC8161292 DOI: 10.1017/s0950268821001072] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In August 2017, a cluster of four persons infected with genetically related strains of Shiga toxin-producing Escherichia coli (STEC) O157:H7 was identified. These strains possessed the Shiga toxin (stx) subtype stx2a, a toxin type known to be associated with severe clinical outcome. One person died after developing haemolytic uraemic syndrome. Interviews with cases revealed that three of the cases had been exposed to dogs fed on a raw meat-based diet (RMBD), specifically tripe. In two cases, the tripe had been purchased from the same supplier. Sampling and microbiological screening of raw pet food was undertaken and indicated the presence of STEC in the products. STEC was isolated from one sample of raw tripe but was different from the strain causing illness in humans. Nevertheless, the detection of STEC in the tripe provided evidence that raw pet food was a potential source of human STEC infection during this outbreak. This adds to the evidence of raw pet food as a risk factor for zoonotic transmission of gastrointestinal pathogens, which is widely accepted for Salmonella, Listeria and Campylobacter spp. Feeding RMBD to companion animals has recently increased in popularity due to the belief that they provide health benefits to animals. Although still rare, an increase in STEC cases reporting exposure to RMBDs was detected in 2017. There has also been an increased frequency of raw pet food incidents in 2017, suggesting an increasing trend in potential risk to humans from raw pet food. Recommendations to reduce the risk of infection included improved awareness of risk and promotion of good hygiene practices among the public when handling raw pet food.
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Nakamura K, Ogura Y, Gotoh Y, Hayashi T. Prophages integrating into prophages: A mechanism to accumulate type III secretion effector genes and duplicate Shiga toxin-encoding prophages in Escherichia coli. PLoS Pathog 2021; 17:e1009073. [PMID: 33914852 PMCID: PMC8112680 DOI: 10.1371/journal.ppat.1009073] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/11/2021] [Accepted: 04/14/2021] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages (or phages) play major roles in the evolution of bacterial pathogens via horizontal gene transfer. Multiple phages are often integrated in a host chromosome as prophages, not only carrying various novel virulence-related genetic determinants into host bacteria but also providing various possibilities for prophage-prophage interactions in bacterial cells. In particular, Escherichia coli strains such as Shiga toxin (Stx)-producing E. coli (STEC) and enteropathogenic E. coli (EPEC) strains have acquired more than 10 prophages (up to 21 prophages), many of which encode type III secretion system (T3SS) effector gene clusters. In these strains, some prophages are present at a single locus in tandem, which is usually interpreted as the integration of phages that use the same attachment (att) sequence. Here, we present phages integrating into T3SS effector gene cluster-associated loci in prophages, which are widely distributed in STEC and EPEC. Some of the phages integrated into prophages are Stx-encoding phages (Stx phages) and have induced the duplication of Stx phages in a single cell. The identified attB sequences in prophage genomes are apparently derived from host chromosomes. In addition, two or three different attB sequences are present in some prophages, which results in the generation of prophage clusters in various complex configurations. These phages integrating into prophages represent a medically and biologically important type of inter-phage interaction that promotes the accumulation of T3SS effector genes in STEC and EPEC, the duplication of Stx phages in STEC, and the conversion of EPEC to STEC and that may be distributed in other types of E. coli strains as well as other prophage-rich bacterial species. Multiple prophages are often integrated in a bacterial host chromosome and some are present at a single locus in tandem. The most striking examples are Shiga toxin (Stx)-producing and enteropathogenic Escherichia coli (STEC and EPEC) strains, which usually contain more than 10 prophages (up to 21). Many of them encode a cluster of type III secretion system (T3SS) effector genes, contributing the acquisition of a large number of effectors (>30) by STEC and EPEC. Here, we describe prophages integrating into T3SS effector gene cluster-associated loci in prophages, which are widely distributed in STEC and EPEC. Two or three different attachment sequences derived from host chromosomes are present in some prophages, generating prophage clusters in various complex configurations. Of note, some of such phages integrating into prophages are Stx-encoding phages (Stx phages) and have induced the duplication of Stx phages. Thus, “prophage-in-prophage” represents an important inter-phage interaction as they can promote not only the accumulation of T3SS effectors in STEC and EPEC but also the duplication of Stx phages and the conversion of EPEC to STEC.
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Affiliation(s)
- Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- * E-mail:
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Epidemiological investigation of recurrent outbreaks of haemolytic uraemic syndrome caused by Shiga toxin-producing Escherichia coli serotype O55:H7 in England, 2014-2018. Epidemiol Infect 2021; 149:e108. [PMID: 33866980 PMCID: PMC8161408 DOI: 10.1017/s0950268821000844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recurrent outbreaks of haemolytic uraemic syndrome (HUS) caused by Shiga toxin-producing Escherichia coli (STEC) serotype O55:H7 occurred in England between 2014 and 2018. We reviewed the epidemiological evidence to identify potential source(s) and transmission routes of the pathogen, and to assess the on-going risk to public health. Over the 5-year period, there were 43 confirmed and three probable cases of STEC O55:H7. The median age of cases was 4 years old (range 6 months to 69 years old) and over half of all cases were female (28/46, 61%). There were 36/46 (78.3%) symptomatic cases, and over half of all cases developed HUS (25/46, 54%), including two fatal cases. No common food or environmental exposures were identified, although the majority of cases lived in rural or semi-rural environments and reported contact with both wild and domestic animals. This investigation informed policy on the clinical and public health management of HUS caused by STEC other than serotype O157:H7 (non-O157 STEC) in England, including comprehensive testing of all household contacts and household pets and more widespread use of polymerase chain reaction assays for the rapid diagnosis of STEC-HUS.
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Lupolova N, Chalka A, Gally DL. Predicting Host Association for Shiga Toxin-Producing E. coli Serogroups by Machine Learning. Methods Mol Biol 2021; 2291:99-117. [PMID: 33704750 DOI: 10.1007/978-1-0716-1339-9_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Escherichia coli is a species of bacteria that can be present in a wide variety of mammalian hosts and potentially soil environments. E. coli has an open genome and can show considerable diversity in gene content between isolates. It is a reasonable assumption that gene content reflects evolution of strains in particular host environments and therefore can be used to predict the host most likely to be the source of an isolate. An extrapolation of this argument is that strains may also have gene content that favors success in multiple hosts and so the possibility of successful transmission from one host to another, for example, from cattle to human, can also be predicted based on gene content. In this methods chapter, we consider the issue of Shiga toxin (Stx)-producing E. coli (STEC) strains that are present in ruminants as the main host reservoir and for which we know that a subset causes life-threatening infections in humans. We show how the genome sequences of E. coli isolated from both cattle and humans can be used to build a classifier to predict human and cattle host association and how this can be applied to score key STEC serotypes known to be associated with human infection. With the example dataset used, serogroups O157, O26, and O111 show the highest, and O103 and O145 the lowest, predictions for human association. The long-term ambition is to combine such machine learning predictions with phylogeny to predict the zoonotic threat of an isolate based on its whole genome sequence (WGS).
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Affiliation(s)
- Nadejda Lupolova
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Antonia Chalka
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - David L Gally
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
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Dallman TJ, Greig DR, Gharbia SE, Jenkins C. Phylogenetic structure of Shiga toxin-producing Escherichia coli O157:H7 from sub-lineage to SNPs. Microb Genom 2021; 7. [PMID: 33720818 PMCID: PMC8190602 DOI: 10.1099/mgen.0.000544] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Sequence similarity of pathogen genomes can infer the relatedness between isolates as the fewer genetic differences identified between pairs of isolates, the less time since divergence from a common ancestor. Clustering based on hierarchical single linkage clustering of pairwise SNP distances has been employed to detect and investigate outbreaks. Here, we evaluated the evidence-base for the interpretation of phylogenetic clusters of Shiga toxin-producing Escherichia coli (STEC) O157:H7. Whole genome sequences of 1193 isolates of STEC O157:H7 submitted to Public Health England between July 2015 and December 2016 were mapped to the Sakai reference strain. Hierarchical single linkage clustering was performed on the pairwise SNP difference between all isolates at descending distance thresholds. Cases with known epidemiological links fell within 5-SNP single linkage clusters. Five-SNP single linkage community clusters where an epidemiological link was not identified were more likely to be temporally and/or geographically related than sporadic cases. Ten-SNP single linkage clusters occurred infrequently and were challenging to investigate as cases were few, and temporally and/or geographically dispersed. A single linkage cluster threshold of 5-SNPs has utility for the detection of outbreaks linked to both persistent and point sources. Deeper phylogenetic analysis revealed that the distinction between domestic UK and imported isolates could be inferred at the sub-lineage level. Cases associated with domestically acquired infection that fall within clusters that are predominantly travel associated are likely to be caused by contaminated imported food.
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Affiliation(s)
- Timothy J Dallman
- National Infection Services, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - David R Greig
- National Infection Services, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Saheer E Gharbia
- National Infection Services, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Claire Jenkins
- National Infection Services, Public Health England, 61 Colindale Avenue, London, NW9 5EQ, UK
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21
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Greig DR, Jenkins C, Gharbia SE, Dallman TJ. Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing. Microb Genom 2021; 7:mgen000545. [PMID: 33683192 PMCID: PMC8190617 DOI: 10.1099/mgen.0.000545] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/15/2021] [Indexed: 12/03/2022] Open
Abstract
Compared to short-read sequencing data, long-read sequencing facilitates single contiguous de novo assemblies and characterization of the prophage region of the genome. Here, we describe our methodological approach to using Oxford Nanopore Technology (ONT) sequencing data to quantify genetic relatedness and to look for microevolutionary events in the core and accessory genomes to assess the within-outbreak variation of four genetically and epidemiologically linked isolates. Analysis of both Illumina and ONT sequencing data detected one SNP between the four sequences of the outbreak isolates. The variant calling procedure highlighted the importance of masking homologous sequences in the reference genome regardless of the sequencing technology used. Variant calling also highlighted the systemic errors in ONT base-calling and ambiguous mapping of Illumina reads that results in variations in the genetic distance when comparing one technology to the other. The prophage component of the outbreak strain was analysed, and nine of the 16 prophages showed some similarity to the prophage in the Sakai reference genome, including the stx2a-encoding phage. Prophage comparison between the outbreak isolates identified minor genome rearrangements in one of the isolates, including an inversion and a deletion event. The ability to characterize the accessory genome in this way is the first step to understanding the significance of these microevolutionary events and their impact on the evolutionary history, virulence and potentially the likely source and transmission of this zoonotic, foodborne pathogen.
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Affiliation(s)
- David R. Greig
- National Infection Service, Public Health England, London, NW9 5EQ, UK
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Claire Jenkins
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Saheer E. Gharbia
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Timothy J. Dallman
- National Infection Service, Public Health England, London, NW9 5EQ, UK
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
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22
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Greig DR, Jenkins C, Dallman TJ. A Shiga Toxin-Encoding Prophage Recombination Event Confounds the Phylogenetic Relationship Between Two Isolates of Escherichia coli O157:H7 From the Same Patient. Front Microbiol 2020; 11:588769. [PMID: 33193248 PMCID: PMC7645076 DOI: 10.3389/fmicb.2020.588769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/23/2020] [Indexed: 11/24/2022] Open
Abstract
We compared genomes from multiple isolations of Shiga toxin-producing Escherichia coli (STEC) O157:H7 from the same patient, in cases notified to Public Health England (PHE) between 2015 and 2019. There were 261 cases where multiple isolates were sequenced from the same patient comprising 589 isolates. Serial isolates from the same patient fell within five single nucleotide polymorphisms (SNPs) of each other for 260/261 (99.6%) of the cases, indicating that there was little evidence of within host variation. The investigation into the 13 SNP discrepancy between one isolate pair revealed the cause to be a recombination event within a stx2a-encoding prophage resulting in the insertion/deletion of a fragment of the genome. This 50 kbp prophage fragment was homologous to a prophage in the reference genome, and the short reads from the isolate that had the 50 kbp fragment, mapped unambiguously to this region. The discrepant variants in the isolate without the 50 kbp fragment were attributed to ambiguous mapping of the short reads from other prophage regions to the 50 kbp fragment in the reference genome. Identification of such recombination events in this dataset appeared to be rare, most likely because the majority of prophage regions in the Sakai reference genome are masked during the analysis. Identification of SNPs under neutral selection, and masking recombination events, is a requirement for phylogenetic analysis used for public health surveillance, and for the detection of point source outbreaks. However, assaying the accessory genome by combining the use of short and long read technologies for public health surveillance may provide insight into how recombination events impact on the evolutionary course of STEC O157:H7.
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Affiliation(s)
- David R Greig
- National Infection Service, Public Health England, London, United Kingdom.,Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, United Kingdom
| | - Claire Jenkins
- National Infection Service, Public Health England, London, United Kingdom
| | - Timothy J Dallman
- National Infection Service, Public Health England, London, United Kingdom.,Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, United Kingdom
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23
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Greig DR, Mikhail AFW, Dallman TJ, Jenkins C. Analysis Shiga Toxin-Encoding Bacteriophage in a Rare Strain of Shiga Toxin-Producing Escherichia coli O157:H7 stx2a/stx2c. Front Microbiol 2020; 11:577658. [PMID: 33193199 PMCID: PMC7609406 DOI: 10.3389/fmicb.2020.577658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/09/2020] [Indexed: 02/05/2023] Open
Abstract
In December 2015, six cases of Shiga toxin (Stx)-producing Escherichia coli (STEC) O157:H7 stx2a/stx2c phage type (PT) 24 were identified by the national gastrointestinal disease surveillance system at Public Health England (PHE). Frozen grated coconut imported from India was implicated as the vehicle of infection. Short and long read sequencing data were interrogated for genomic markers to provide evidence that the outbreak strain was from an imported source. The outbreak strain belonged to a sub-lineage (IIa) rare in domestically acquired infection in the United Kingdom, and indicative of an imported strain. Phylogenetic analysis identified the most closely related isolates to the outbreak strain were from cases reporting recent travel not to India, but to Uganda. Phylo-geographical signals based on travel data may be confounded by the failure of local and/or global monitoring systems to capture the full diversity of strains in a given country. This may be due to low prevalence strains circulating in-country under the surveillance radar, or a recent importation event involving the migration of animals and/or people. Comparison of stx2a-encoding prophage harbored by the outbreak strain with publicly available stx2a-encoding prophage sequences revealed that it was most closely related to stx2a-encoding prophage acquired by STEC O157:H7 that caused the first outbreak of STEC-hemolytic uremic syndrome (HUS) in England in 1982–83. Animal and people migration events may facilitate the transfer of stx2a-encoding prophage from indigenous STEC O157:H7 to recently imported strains, or vice versa. Monitoring the global transmission of STEC O157:H7 and tracking the exchange of stx2a-encoding phage between imported and indigenous strains may provide an early warning of emerging threats to public health.
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Affiliation(s)
- David R Greig
- National Infection Service, Public Health England, London, United Kingdom.,Division of Infection and Immunity, The Royal (Dick) School of Veterinary Studies, The Roslin Institute, The University of Edinburgh, Easter Bush, United Kingdom
| | - Amy F W Mikhail
- National Infection Service, Public Health England, London, United Kingdom
| | - Timothy J Dallman
- National Infection Service, Public Health England, London, United Kingdom.,Division of Infection and Immunity, The Royal (Dick) School of Veterinary Studies, The Roslin Institute, The University of Edinburgh, Easter Bush, United Kingdom
| | - Claire Jenkins
- National Infection Service, Public Health England, London, United Kingdom
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24
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Gutema FD, Rasschaert G, Agga GE, Jufare A, Duguma AB, Abdi RD, Duchateau L, Crombe F, Gabriël S, De Zutter L. Occurrence, Molecular Characteristics, and Antimicrobial Resistance of Escherichia coli O157 in Cattle, Beef, and Humans in Bishoftu Town, Central Ethiopia. Foodborne Pathog Dis 2020; 18:1-7. [PMID: 32865441 DOI: 10.1089/fpd.2020.2830] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli O157 is a Shiga toxin-producing E. coli causing disease in humans. Cattle are the primary reservoir of the pathogen. Information regarding the contribution of cattle to diarrheal illnesses in humans through consumption of contaminated beef is scarce in Ethiopia. We collected samples from 240 cattle, 127 beef, and 216 diarrheic patients in Bishoftu town in Ethiopia to assess the occurrence and determine the virulence genes, genetic relatedness, and antimicrobial resistance of E. coli O157. E. coli O157 was detected in 7.1% of the rectal content samples from cattle in slaughterhouses, in 6.3% (n = 127) of the beef samples, and in 2.8% of the diarrheic patients' stool samples. All isolates were positive for eae gene, 24 (77%) of them were positive for stx2 gene (21 stx2c and 3 stx2a), whereas stx1 gene was not detected. Molecular typing grouped the isolates into eight pulsed-field gel electrophoresis pulsotypes with three pulsotypes containing isolates from all three sources, one pulsotype containing one isolate from human origin and one isolate from beef. The remaining four pulsotypes contained isolates unique either to beef or to humans. With the exception of 1 multidrug-resistant isolate from beef, which was resistant to 8 antimicrobial drugs, the remaining 30 isolates were susceptible to the 14 antimicrobials tested. In conclusion, the finding of genetically similar isolates in cattle, beef, and humans may indicate a potential transmission of E. coli O157 from cattle to humans through beef. However, more robust studies are required to confirm this epidemiological link.
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Affiliation(s)
- Fanta D Gutema
- Department of Microbiology, Immunology and Veterinary Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia.,Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Geertrui Rasschaert
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Getahun E Agga
- Food Animal Environmental Systems Research Unit, Agricultural Research Service, U. S. Department of Agriculture, Bowling Green, Kentucky, USA
| | - Alemnesh Jufare
- Department of Animal Health, Alage Agricultural Technical Vocational and Educational Training College, Alage, Ethiopia
| | - Addisu B Duguma
- Department of Internal Medicine, Bishoftu Hospital, Bishoftu, Ethiopia
| | - Reta D Abdi
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Greenvale, New York, USA
| | - Luc Duchateau
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Florence Crombe
- Department of Microbiology and Infection Control, Belgian National Reference Centre for STEC/VTEC, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Sarah Gabriël
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Lieven De Zutter
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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25
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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26
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Investigation into a national outbreak of STEC O157:H7 associated with frozen beef burgers, UK, 2017. Epidemiol Infect 2020; 148:e215. [PMID: 32669142 PMCID: PMC7522850 DOI: 10.1017/s0950268820001582] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In November 2017, Public Health England identified an outbreak of Shiga toxin-producing Escherichia coli O157:H7 in England where whole genome sequencing results indicated cases were likely to be linked to a common source, and began investigations. Hypothesis generation included a review of enhanced surveillance data, a case-case study and trawling interviews. The hypothesis of interest was tested through the administration of focussed questionnaires and review of shopping history using loyalty card data. Twelve outbreak cases were detected, eight were hospitalised and four developed haemolytic uraemic syndrome. Frozen beef burgers supplied by a national retailer were identified as the vehicle of the outbreak. Testing of two left-over burger samples obtained from the freezers of two separate (unlinked) cases and a retained sample from the production premises were tested and found to be positive for the outbreak strain. A voluntary recall of the burgers was implemented by the retailer. Investigations at the production premises identified no contraventions of food safety legislation. Cooking guidance on the product packaging was deemed to be adequate and interviews with the cases/carers who prepared the burgers revealed no deficiencies in cooking practices at home. Given the long-shelf life of frozen burgers, the product recall likely prevented more cases.
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27
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Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ. Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada. Microb Genom 2020; 6. [PMID: 32496181 PMCID: PMC7371104 DOI: 10.1099/mgen.0.000376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher’s exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.
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Affiliation(s)
- Lu Ya Ruth Wang
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
| | | | - Chad R Laing
- National Centre for Animal Disease, Canadian Food Inspection Agency, Lethbridge, Alberta, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
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28
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Nyong EC, Zaia SR, Allué-Guardia A, Rodriguez AL, Irion-Byrd Z, Koenig SSK, Feng P, Bono JL, Eppinger M. Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes. Front Microbiol 2020; 11:619. [PMID: 32351476 PMCID: PMC7175801 DOI: 10.3389/fmicb.2020.00619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
The toxigenic conversion of Escherichia coli strains by Shiga toxin-converting (Stx) bacteriophages were prominent and recurring events in the stepwise evolution of enterohemorrhagic E. coli (EHEC) O157:H7 from an enteropathogenic (EPEC) O55:H7 ancestor. Atypical, attenuated isolates have been described for both non-sorbitol fermenting (NSF) O157:H7 and SF O157:NM serotypes, which are distinguished by the absence of Stx, the characteristic virulence hallmark of Stx-producing E. coli (STEC). Such atypical isolates either never acquired Stx-phages or may have secondarily lost stx during the course of infection, isolation, or routine subculture; the latter are commonly referred to as LST (Lost Shiga Toxin)-isolates. In this study we analyzed the genomes of 15 NSF O157:H7 and SF O157:NM strains from North America, Europe, and Asia that are characterized by the absence of stx, the virulence hallmark of STEC. The individual genomic basis of the Stx (-) phenotype has remained largely undetermined as the majority of STEC genomes in public genome repositories were generated using short read technology and are in draft stage, posing a major obstacle for the high-resolution whole genome sequence typing (WGST). The application of LRT (long-read technology) sequencing provided us with closed genomes, which proved critical to put the atypical non-shigatoxigenic NSF O157:H7 and SF O157:NM strains into the phylogenomic context of the stepwise evolutionary model. Availability of closed chromosomes for representative Stx (-) NSF O157:H7 and SF O157:NM strains allowed to describe the genomic basis and individual evolutionary trajectories underlying the absence of Stx at high accuracy and resolution. The ability of LRT to recover and accurately assemble plasmids revealed a strong correlation between the strains' featured plasmid genotype and chromosomally inferred clade, which suggests the coevolution of the chromosome and accessory plasmids. The identified ancestral traits in the pSFO157 plasmid of NSF O157:H7 strain LSU-61 provided additional evidence for its intermediate status. Taken together, these observations highlight the utility of LRTs for advancing our understanding of EHEC O157:H7/NM pathogenome evolution. Insights into the genomic and phenotypic plasticity of STEC on a lineage- and genome-wide scale are foundational to improve and inform risk assessment, biosurveillance, and prevention strategies.
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Affiliation(s)
- Emmanuel C. Nyong
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Sam R. Zaia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Anna Allué-Guardia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Armando L. Rodriguez
- Research Computing Support Group, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Zaina Irion-Byrd
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Sara S. K. Koenig
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | | | - James L. Bono
- United States Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture (ARS-USDA), Clay Center, NE, United States
| | - Mark Eppinger
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
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29
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Yara DA, Greig DR, Gally DL, Dallman TJ, Jenkins C. Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157:H7 in the UK. Microb Genom 2020; 6:e000334. [PMID: 32100710 PMCID: PMC7200060 DOI: 10.1099/mgen.0.000334] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/17/2020] [Indexed: 12/18/2022] Open
Abstract
Over the last 35 years in the UK, the burden of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infection has, during different periods of time, been associated with five different sub-lineages (1983-1995, Ia, I/IIa and I/IIb; 1996-2014, Ic; and 2015-2018, IIb). The acquisition of a stx2a-encoding bacteriophage by these five sub-lineages appears to have coincided with their respective emergences. The Oxford Nanopore Technologies (ONT) system was used to sequence, characterize and compare the stx-encoding prophages harboured by each sub-lineage to investigate the integration of this key virulence factor. The stx2a-encoding prophages from each of the lineages causing clinical disease in the UK were all different, including the two UK sub-lineages (Ia and I/IIa) circulating concurrently and causing severe disease in the early 1980s. Comparisons between the stx2a-encoding prophage in sub-lineages I/IIb and IIb revealed similarity to the prophage commonly found to encode stx2c, and the same site of bacteriophage integration (sbcB) as stx2c-encoding prophage. These data suggest independent acquisition of previously unobserved stx2a-encoding phage is more likely to have contributed to the emergence of STEC O157:H7 sub-lineages in the UK than intra-UK lineage to lineage phage transmission. In contrast, the stx2c-encoding prophage showed a high level of similarity across lineages and time, consistent with the model of stx2c being present in the common ancestor to extant STEC O157:H7 and maintained by vertical inheritance in the majority of the population. Studying the nature of the stx-encoding bacteriophage contributes to our understanding of the emergence of highly pathogenic strains of STEC O157:H7.
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Affiliation(s)
- Daniel A. Yara
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - David R. Greig
- National Infection Service, Public Health England, London NW9 5EQ, UK
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - David L. Gally
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Timothy J. Dallman
- National Infection Service, Public Health England, London NW9 5EQ, UK
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Claire Jenkins
- National Infection Service, Public Health England, London NW9 5EQ, UK
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30
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Zhang Y, Liao YT, Salvador A, Sun X, Wu VCH. Prediction, Diversity, and Genomic Analysis of Temperate Phages Induced From Shiga Toxin-Producing Escherichia coli Strains. Front Microbiol 2020; 10:3093. [PMID: 32038541 PMCID: PMC6986202 DOI: 10.3389/fmicb.2019.03093] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a notorious foodborne pathogen containing stx genes located in the sequence region of Shiga toxin (Stx) prophages. Stx prophages, as one of the mobile elements, are involved in the transfer of virulence genes to other strains. However, little is known about the diversity of prophages among STEC strains. The objectives of this study were to predict various prophages from different STEC genomes and to evaluate the effect of different stress factors on Stx prophage induction. Forty bacterial whole-genome sequences of STEC strains obtained from National Center for Biotechnology Information (NCBI) were used for the prophage prediction using PHASTER webserver. Eight of the STEC strains from different serotypes were subsequently selected to quantify the induction of Stx prophages by various treatments, including antibiotics, temperature, irradiation, and antimicrobial agents. After induction, Stx1-converting phage Lys8385Vzw and Stx2-converting phage Lys12581Vzw were isolated and further confirmed for the presence of stx genes using conventional PCR. Phage morphology was observed by transmission electron microscopy. The prediction results showed an average of 8–22 prophages, with one or more encoding stx, were predicted from each STEC genome obtained in this study. Additionally, the phylogenetic analysis revealed high genetic diversity of Stx prophages among the 40 STEC genomes. However, the sequences of Stx prophages in the genomes of STEC O45, O111, and O121 strains, in general, shared higher genetic homology than those in other serotypes. Interestingly, most STEC strains with two or more stx genes carried at least one each of Stx1 and Stx2 prophages. The induction results indicated EDTA and UV were the most effective inducers of Stx1 and Stx2 prophages of the 8 selected STECs, respectively. Additionally, both Stx-converting phages could infect non-pathogenic E. coli (WG5, DH5α, and MG1655) and form new lysogens. The findings of this study confirm that Stx prophages can be induced by environmental stress, such as exposure to solar radiation, and lysogenize other commensal E. coli strains.
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Affiliation(s)
- Yujie Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Yen-Te Liao
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Alexandra Salvador
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Xiaohong Sun
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Vivian C H Wu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
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Nakamura K, Murase K, Sato MP, Toyoda A, Itoh T, Mainil JG, Piérard D, Yoshino S, Kimata K, Isobe J, Seto K, Etoh Y, Narimatsu H, Saito S, Yatsuyanagi J, Lee K, Iyoda S, Ohnishi M, Ooka T, Gotoh Y, Ogura Y, Hayashi T. Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28. Microb Genom 2020; 6:e000323. [PMID: 31935184 PMCID: PMC7067040 DOI: 10.1099/mgen.0.000323] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 12/09/2019] [Indexed: 12/20/2022] Open
Abstract
Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing Escherichia coli O145:H28, the major virulence factors of which are encoded by prophages (PPs) or plasmids. The results indicated that PPs are more stably maintained than plasmids. A set of ancestrally acquired PPs was well conserved, while various PPs, including Stx phages, were acquired by multiple sublineages. In contrast, gains and losses of a wide range of plasmids have frequently occurred across the O145:H28 lineage, and only the virulence plasmid was well conserved. The different dynamics of PPs and plasmids have differentially impacted the pangenome of O145:H28, with high proportions of PP- and plasmid-associated genes in the variably present and rare gene fractions, respectively. The dynamics of PPs and plasmids have also strongly impacted virulence gene repertoires, such as the highly variable distribution of stx genes and the high conservation of a set of type III secretion effectors, which probably represents the core effectors of O145:H28 and the genes on the virulence plasmid in the entire O145:H28 population. These results provide detailed insights into the dynamics of PPs and plasmids, and show the application of genomic analyses using a large set of draft genomes and appropriately selected complete genomes.
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Affiliation(s)
- Keiji Nakamura
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazunori Murase
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mitsuhiko P. Sato
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Tokyo, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | | | | | - Shuji Yoshino
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Japan
| | | | | | - Kazuko Seto
- Osaka Institute of Public Health, Osaka, Japan
| | - Yoshiki Etoh
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | | | - Shioko Saito
- Akita Research Center for Public Health and Environment, Akita, Japan
| | - Jun Yatsuyanagi
- Akita Research Center for Public Health and Environment, Akita, Japan
| | - Kenichi Lee
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Sunao Iyoda
- National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Tadasuke Ooka
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Yasuhiro Gotoh
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Henry MK, McCann CM, Humphry RW, Morgan M, Willett A, Evans J, Gunn GJ, Tongue SC. The British E. coli O157 in cattle study (BECS): factors associated with the occurrence of E. coli O157 from contemporaneous cross-sectional surveys. BMC Vet Res 2019; 15:444. [PMID: 31805948 PMCID: PMC6896709 DOI: 10.1186/s12917-019-2188-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Escherichia coli O157 is a bacterial pathogen associated with severe disease in humans for which cattle are an important reservoir of infection. The identification of possible risk factors for infection in cattle could facilitate the development of control strategies and interventions to mitigate the risk to human health. The purpose of this study was to utilize data collected in 2014-2015 during the two contemporaneous cross-sectional surveys of the British E. coli O157 in Cattle Study (BECS) to investigate potential risk factors for E. coli O157 status in cattle destined for the food chain. RESULTS In the England & Wales survey only one variable, herd size, was associated with the outcome farm-level E. coli O157 positive status. The odds increased for each additional animal in the herd. In the Scotland survey, as well as a measure of herd size (the number of cattle aged 12-30 months), having brought breeding females on to the farm in the last year also increased the odds, whereas farms sampled in spring were less likely to be positive compared to those sampled in autumn. On the positive farms, in both surveys, an increase in the proportion of pats positive for E. coli O157 was associated with animals being housed at the time of sampling. However, the effect of housing on pat-level prevalence within positive groups was lower on farms from England & Wales than from Scotland (OR 0.45 (95% C.I. 0.24-0.86)). CONCLUSION For the first time, factors associated with farm-level E. coli O157 status have been investigated in two contemporaneous surveys with comparable study design. Although factors associated with farm-level E. coli O157 status differed between the two surveys, one consistent factor was an association with a measure of herd size. Factors associated with the proportion of E. coli O157 positive pats within a positive farm were similar in both surveys but differed from those associated with farm-level status. These findings raise the hypothesis that measures to protect public health by reducing the risk from cattle may need to be tailored, rather than by assuming that a GB-wide protocol is the best approach.
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Affiliation(s)
- Madeleine K. Henry
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - Catherine M. McCann
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - Roger W. Humphry
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - Mair Morgan
- RSK ADAS Ltd., Spring Lodge, 172 Chester Road, Helsby, Cheshire, WA6 0AR UK
| | - Alice Willett
- RSK ADAS Ltd., Spring Lodge, 172 Chester Road, Helsby, Cheshire, WA6 0AR UK
| | - Judith Evans
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - George J. Gunn
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - Sue C. Tongue
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
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Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Malorny B, Ribeiro Duarte AS, Torpdahl M, da Silva Felício MT, Guerra B, Rossi M, Herman L. Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms. EFSA J 2019; 17:e05898. [PMID: 32626197 PMCID: PMC7008917 DOI: 10.2903/j.efsa.2019.5898] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne pathogens. WGS offers the highest level of bacterial strain discrimination for food‐borne outbreak investigation and source‐attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial‐temporal factors and the detection of multidirectional transmission and pathogen–host interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non‐culturable, difficult‐to‐culture or slow‐growing microorganisms, for tracking of hazard‐related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin‐producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGS‐based genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross‐border outbreaks and for the development of international standardised risk assessments of food‐borne microorganisms.
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Fitzgerald SF, Beckett AE, Palarea-Albaladejo J, McAteer S, Shaaban S, Morgan J, Ahmad NI, Young R, Mabbott NA, Morrison L, Bono JL, Gally DL, McNeilly TN. Shiga toxin sub-type 2a increases the efficiency of Escherichia coli O157 transmission between animals and restricts epithelial regeneration in bovine enteroids. PLoS Pathog 2019; 15:e1008003. [PMID: 31581229 PMCID: PMC6776261 DOI: 10.1371/journal.ppat.1008003] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023] Open
Abstract
Specific Escherichia coli isolates lysogenised with prophages that express Shiga toxin (Stx) can be a threat to human health, with cattle being an important natural reservoir. In many countries the most severe pathology is associated with enterohaemorrhagic E. coli (EHEC) serogroups that express Stx subtype 2a. In the United Kingdom, phage type (PT) 21/28 O157 strains have emerged as the predominant cause of life-threatening EHEC infections and this phage type commonly encodes both Stx2a and Stx2c toxin types. PT21/28 is also epidemiologically linked to super-shedding (>103 cfu/g of faeces) which is significant for inter-animal transmission and human infection as demonstrated using modelling studies. We demonstrate that Stx2a is the main toxin produced by stx2a+/stx2c+ PT21/28 strains induced with mitomycin C and this is associated with more rapid induction of gene expression from the Stx2a-encoding prophage compared to that from the Stx2c-encoding prophage. Bacterial supernatants containing either Stx2a and/or Stx2c were demonstrated to restrict growth of bovine gastrointestinal organoids with no restriction when toxin production was not induced or prevented by mutation. Isogenic strains that differed in their capacity to produce Stx2a were selected for experimental oral colonisation of calves to assess the significance of Stx2a for both super-shedding and transmission between animals. Restoration of Stx2a expression in a PT21/28 background significantly increased animal-to-animal transmission and the number of sentinel animals that became super-shedders. We propose that while both Stx2a and Stx2c can restrict regeneration of the epithelium, it is the relatively rapid and higher levels of Stx2a induction, compared to Stx2c, that have contributed to the successful emergence of Stx2a+ E. coli isolates in cattle in the last 40 years. We propose a model in which Stx2a enhances E. coli O157 colonisation of in-contact animals by restricting regeneration and turnover of the colonised gastrointestinal epithelium. Enterohaemorrhagic E. coli (EHEC) O157 strains are found in cattle where they are asymptomatic, while human exposure can lead to severe symptoms including bloody diarrhoea and kidney damage due to the activity of Shiga toxin (Stx). The most serious symptoms in humans are associated with isolates that encode Stx subtype 2a. The advantage of these toxins in the animal reservoir is still not clear, however there is experimental evidence implicating Stx with increased bacterial adherence, immune modulation and suppression of predatory protozoa. In this study, the hypothesis that Stx2a is important for super-shedding and calf-to-calf transmission was tested by comparing excretion and transmission dynamics of E. coli O157 strains with and without Stx2a. While Stx2a did not alter excretion levels when calfs were orally challenge, it enabled colonisation of more in contact ‘sentinel’ animals in our transmission model. We show that Stx2a is generally induced more rapidly than Stx2c, resulting in increased levels of Stx2a expression. Both Stx2a and Stx2c were able to restrict cellular proliferation of epithelial cells in cultured bovine enteroids. Taken together, we propose that rapid production of Stx2a and its role in establishing E. coli O157 colonisation in the bovine gastrointestinal tract facilitate effective transmission and have led to its expansion in the cattle E. coli O157 population.
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Affiliation(s)
- Stephen F. Fitzgerald
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
- Moredun Research Institute, Penicuik, United Kingdom
| | - Amy E. Beckett
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
- Moredun Research Institute, Penicuik, United Kingdom
| | | | - Sean McAteer
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
| | - Sharif Shaaban
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
| | - Jason Morgan
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
- Moredun Research Institute, Penicuik, United Kingdom
| | | | - Rachel Young
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
| | - Neil A. Mabbott
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
| | - Liam Morrison
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
| | - James L. Bono
- United States Department of Agriculture, Agricultural Research Service, Nebraska, United States of America
| | - David L. Gally
- Division of Immunity and Infection, The Roslin Institute and R(D)SVS, The University of Edinburgh, Midlothian, United Kingdom
- * E-mail: (DLG); (TNM)
| | - Tom N. McNeilly
- Moredun Research Institute, Penicuik, United Kingdom
- * E-mail: (DLG); (TNM)
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The importance of integrating genetic strain information for managing cases of Shiga toxin-producing E. coli infection. Epidemiol Infect 2019; 147:e264. [PMID: 31496452 PMCID: PMC6805796 DOI: 10.1017/s0950268819001602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Dallman TJ, Greig DR, Gharbia SE, Jenkins C. Phylogenetic context of Shiga toxin-producing Escherichia coli serotype O26:H11 in England. Microb Genom 2019; 7:000551. [PMID: 33760723 PMCID: PMC8627664 DOI: 10.1099/mgen.0.000551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/02/2021] [Indexed: 01/09/2023] Open
Abstract
The increasing use of PCR for the detection of gastrointestinal pathogens in hospital laboratories in England has improved the detection of Shiga toxin-producing Escherichia coli (STEC), and the diagnosis of haemolytic uraemic syndrome (HUS). We aimed to analyse the microbiological characteristics and phylogenetic relationships of STEC O26:H11, clonal complex (CC) 29, in England to inform surveillance, and to assess the threat to public health. There were 502 STEC belonging to CC29 isolated between 2014 and 2019, of which 416 were from individual cases. The majority of isolates belonged to one of three major sequence types (STs), ST16 (n=37), ST21 (n=350) and ST29 (n=24). ST16 and ST29 were mainly isolated from cases reporting recent travel abroad. Within ST21, there were three main clades associated with domestic acquisition. All three domestic clades had Shiga toxin subtype gene (stx) profiles associated with causing severe clinical outcomes including STEC-HUS, specifically either stx1a, stx2a or stx1a/stx2a. Isolates from the same patient, same household or same outbreak with an established source for the most part fell within 5-SNP single linkage clusters. There were 19 5-SNP community clusters, of which six were travel-associated and one was an outbreak of 16 cases caused by the consumption of contaminated salad leaves. Of the remaining 12 clusters, 9/12 were either temporally or geographically related or both. Exposure to foodborne STEC O26:H11 ST21 capable of causing severe clinical outcomes, including STEC-HUS, is an emerging risk to public health in England. The lack of comprehensive surveillance of this STEC serotype is a concern, and there is a need to expand the implementation of methods capable of detecting STEC in local hospital settings.
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Affiliation(s)
- Timothy J. Dallman
- National Infection Service, Public Health England, London, NW9 5EQ, UK
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - David R. Greig
- National Infection Service, Public Health England, London, NW9 5EQ, UK
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Saheer E. Gharbia
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Claire Jenkins
- National Infection Service, Public Health England, London, NW9 5EQ, UK
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Cowley LA, Dallman TJ, Jenkins C, Sheppard SK. Phage Predation Shapes the Population Structure of Shiga-Toxigenic Escherichia coli O157:H7 in the UK: An Evolutionary Perspective. Front Genet 2019; 10:763. [PMID: 31543896 PMCID: PMC6730009 DOI: 10.3389/fgene.2019.00763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/18/2019] [Indexed: 01/19/2023] Open
Abstract
Bacterial–host interactions are non-linear and actually threefold, involving significant selection through predatory lytic bacteriophages in the host environment. In studies of human and animal gut microbiome bacteria, it is important to consider phage in all host–pathogen interactions. We use an important zoonotic pathogen, Shiga toxigenic Escherichia coli (STEC) O157:H7, to investigate this. Our study provides evidence that phage resistance profiles are well maintained at the sub-lineage level with variation in profiles within sub-lineages uncommon. This indicates that phage resistance heterogeneity happened early on in the STEC O157:H7 natural history and that occasional “wobbles” do not often outcompete the stable lineage unless combined with a competitive advantage. We discuss an example of this in the acquisition of stx2a that, while an important virulence factor, also conveys increased phage cross-resistance. We also discuss the role of phage resistance in co-occurrence of the three stable lineages worldwide and whether differing phage resistance is maintaining diversity.
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Affiliation(s)
- Lauren A Cowley
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Timothy J Dallman
- National Infection Services, Public Health England, London, United Kingdom
| | - Claire Jenkins
- National Infection Services, Public Health England, London, United Kingdom
| | - Samuel K Sheppard
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016. J Clin Microbiol 2019; 57:JCM.00573-19. [PMID: 31315956 PMCID: PMC6711911 DOI: 10.1128/jcm.00573-19] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/08/2019] [Indexed: 12/28/2022] Open
Abstract
Carbapenemase-producing Enterobacterales (CPE) are being increasingly reported in Australia, and integrated clinical and genomic surveillance is critical to effectively manage this threat. We sought to systematically characterize CPE in Victoria, Australia, from 2012 to 2016. Carbapenemase-producing Enterobacterales (CPE) are being increasingly reported in Australia, and integrated clinical and genomic surveillance is critical to effectively manage this threat. We sought to systematically characterize CPE in Victoria, Australia, from 2012 to 2016. Suspected CPE were referred to the state public health laboratory in Victoria, Australia, from 2012 to 2016 and examined using phenotypic, multiplex PCR and whole-genome sequencing (WGS) methods and compared with epidemiological metadata. Carbapenemase genes were detected in 361 isolates from 291 patients (30.8% of suspected CPE isolates), mostly from urine (42.1%) or screening samples (34.8%). IMP-4 (28.0% of patients), KPC-2 (25.3%), NDM (24.1%), and OXA carbapenemases (22.0%) were most common. Klebsiella pneumoniae (48.8% of patients) and Escherichia coli (26.1%) were the dominant species. Carbapenemase-inactivation method (CIM) testing reliably detected carbapenemase-positive isolates (100% sensitivity, 96.9% specificity), identifying an additional five CPE among 159 PCR-negative isolates (IMI and SME carbapenemases). When epidemiologic investigations were performed, all pairs of patients designated “highly likely” or “possible” local transmission had ≤23 pairwise single-nucleotide polymorphisms (SNPs) by genomic transmission analysis; conversely, all patient pairs designated “highly unlikely” local transmission had ≥26 pairwise SNPs. Using this proposed threshold, possible local transmission was identified involving a further 16 patients for whom epidemiologic data were unavailable. Systematic application of genomics has uncovered the emergence of polyclonal CPE as a significant threat in Australia, providing important insights to inform local public health guidelines and interventions. Using our workflow, pairwise SNP distances between CPE isolates of ≤23 SNPs suggest local transmission.
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Browne AS, Biggs PJ, Wilkinson DA, Cookson AL, Midwinter AC, Bloomfield SJ, Hranac CR, Rogers LE, Marshall JC, Benschop J, Withers H, Hathaway S, George T, Jaros P, Irshad H, Fong Y, Dufour M, Karki N, Winkleman T, French NP. Use of Genomics to Investigate Historical Importation of Shiga Toxin-Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand. Emerg Infect Dis 2019; 25:489-500. [PMID: 30789138 PMCID: PMC6390770 DOI: 10.3201/eid2503.180899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Shiga toxin-producing Escherichia coli serogroup O26 is an important public health pathogen. Phylogenetic bacterial lineages in a country can be associated with the level and timing of international imports of live cattle, the main reservoir. We sequenced the genomes of 152 E. coli O26 isolates from New Zealand and compared them with 252 E. coli O26 genomes from 14 other countries. Gene variation among isolates from humans, animals, and food was strongly associated with country of origin and stx toxin profile but not isolation source. Time of origin estimates indicate serogroup O26 sequence type 21 was introduced at least 3 times into New Zealand from the 1920s to the 1980s, whereas nonvirulent O26 sequence type 29 strains were introduced during the early 2000s. New Zealand's remarkably fewer introductions of Shiga toxin-producing Escherichia coli O26 compared with other countries (such as Japan) might be related to patterns of trade in live cattle.
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40
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Greig DR, Jenkins C, Gharbia S, Dallman TJ. Comparison of single-nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga toxin-producing Escherichia coli. Gigascience 2019; 8:giz104. [PMID: 31433830 PMCID: PMC6703438 DOI: 10.1093/gigascience/giz104] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/12/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND We aimed to compare Illumina and Oxford Nanopore Technology sequencing data from the 2 isolates of Shiga toxin-producing Escherichia coli (STEC) O157:H7 to determine whether concordant single-nucleotide variants were identified and whether inference of relatedness was consistent with the 2 technologies. RESULTS For the Illumina workflow, the time from DNA extraction to availability of results was ∼40 hours, whereas with the ONT workflow serotyping and Shiga toxin subtyping variant identification were available within 7 hours. After optimization of the ONT variant filtering, on average 95% of the discrepant positions between the technologies were accounted for by methylated positions found in the described 5-methylcytosine motif sequences, CC(A/T)GG. Of the few discrepant variants (6 and 7 difference for the 2 isolates) identified by the 2 technologies, it is likely that both methodologies contain false calls. CONCLUSIONS Despite these discrepancies, Illumina and Oxford Nanopore Technology sequences from the same case were placed on the same phylogenetic location against a dense reference database of STEC O157:H7 genomes sequenced using the Illumina workflow. Robust single-nucleotide polymorphism typing using MinION-based variant calling is possible, and we provide evidence that the 2 technologies can be used interchangeably to type STEC O157:H7 in a public health setting.
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Affiliation(s)
- David R Greig
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Claire Jenkins
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Saheer Gharbia
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Timothy J Dallman
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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Stimson J, Gardy J, Mathema B, Crudu V, Cohen T, Colijn C. Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions. Mol Biol Evol 2019; 36:587-603. [PMID: 30690464 DOI: 10.1093/molbev/msy242] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Whole-genome sequencing (WGS) is increasingly used to aid the understanding of pathogen transmission. A first step in analyzing WGS data is usually to define "transmission clusters," sets of cases that are potentially linked by direct transmission. This is often done by including two cases in the same cluster if they are separated by fewer single-nucleotide polymorphisms (SNPs) than a specified threshold. However, there is little agreement as to what an appropriate threshold should be. We propose a probabilistic alternative, suggesting that the key inferential target for transmission clusters is the number of transmissions separating cases. We characterize this by combining the number of SNP differences and the length of time over which those differences have accumulated, using information about case timing, molecular clock, and transmission processes. Our framework has the advantage of allowing for variable mutation rates across the genome and can incorporate other epidemiological data. We use two tuberculosis studies to illustrate the impact of our approach: with British Columbia data by using spatial divisions; with Republic of Moldova data by incorporating antibiotic resistance. Simulation results indicate that our transmission-based method is better in identifying direct transmissions than a SNP threshold, with dissimilarity between clusterings of on average 0.27 bits compared with 0.37 bits for the SNP-threshold method and 0.84 bits for randomly permuted data. These results show that it is likely to outperform the SNP-threshold method where clock rates are variable and sample collection times are spread out. We implement the method in the R package transcluster.
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Affiliation(s)
- James Stimson
- Department of Mathematics, Imperial College London, London, UK
| | - Jennifer Gardy
- British Columbia Centre for Disease Control, Communicable Disease Prevention and Control Services, Vancouver, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Ted Cohen
- Yale University School of Public Health, New Haven
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, UK.,Department of Mathematics, Simon Fraser University, Vancouver, Canada
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42
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Byrne L, Dallman TJ, Adams N, Mikhail AFW, McCarthy N, Jenkins C. Highly Pathogenic Clone of Shiga Toxin-Producing Escherichia coli O157:H7, England and Wales. Emerg Infect Dis 2019; 24:2303-2308. [PMID: 30457532 PMCID: PMC6256402 DOI: 10.3201/eid2412.180409] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We used whole-genome sequencing to investigate the evolutionary context of an emerging highly pathogenic strain of Shiga toxin–producing Escherichia coli (STEC) O157:H7 in England and Wales. A timed phylogeny of sublineage IIb revealed that the emerging clone evolved from a STEC O157:H7 stx-negative ancestor ≈10 years ago after acquisition of a bacteriophage encoding Shiga toxin (stx) 2a, which in turn had evolved from a stx2c progenitor ≈20 years ago. Infection with the stx2a clone was a significant risk factor for bloody diarrhea (OR 4.61, 95% CI 2.24–9.48; p<0.001), compared with infection with other strains within sublineage IIb. Clinical symptoms of cases infected with sublineage IIb stx2c and stx-negative clones were comparable, despite the loss of stx2c. Our analysis highlighted the highly dynamic nature of STEC O157:H7 Stx-encoding bacteriophages and revealed the evolutionary history of a highly pathogenic clone emerging within sublineage IIb, a sublineage not previously associated with severe clinical symptoms.
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43
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Ingle DJ, Gonçalves da Silva A, Valcanis M, Ballard SA, Seemann T, Jennison AV, Bastian I, Wise R, Kirk MD, Howden BP, Williamson DA. Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia. Microb Genom 2019; 5. [PMID: 31107203 PMCID: PMC6562248 DOI: 10.1099/mgen.0.000268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Shiga-toxin-producing Escherichia coli (STEC) infection is an important global cause of foodborne disease. To date however, genomics-based studies of STEC have been predominately focused upon STEC collected in the Northern Hemisphere. Here, we demonstrate the population structure of 485 STEC isolates in Australia, and show that several clonal groups (CGs) common to Australia were infrequently detected in a representative selection of contemporary STEC genomes from around the globe. Further, phylogenetic analysis demonstrated that lineage II of the global O157:H7 STEC was most prevalent in Australia, and was characterized by a frameshift mutation in flgF, resulting in the H-non-motile phenotype. Strong concordance between in silico and phenotypic serotyping was observed, along with concordance between in silico and conventional detection of stx genes. These data represent the most comprehensive STEC analysis from the Southern Hemisphere, and provide a framework for future national genomics-based surveillance of STEC in Australia.
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Affiliation(s)
- Danielle J. Ingle
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Melbourne Bioinformatics Group, Victoria, Australia
| | - Amy V. Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Queensland, Australia
| | | | - Rolf Wise
- SA Pathology, South Australia, Australia
| | - Martyn D. Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Deborah A. Williamson
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- *Correspondence: Deborah A. Williamson,
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44
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Adams N, Byrne L, Rose T, Adak B, Jenkins C, Charlett A, Violato M, O'Brien S, Whitehead M, Barr B, Taylor-Robinson D, Hawker J. Sociodemographic and clinical risk factors for paediatric typical haemolytic uraemic syndrome: retrospective cohort study. BMJ Paediatr Open 2019; 3:e000465. [PMID: 31909217 PMCID: PMC6936988 DOI: 10.1136/bmjpo-2019-000465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/07/2019] [Accepted: 08/25/2019] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES Haemolytic uraemic syndrome (HUS) following Shiga toxin-producing Escherichia coli (STEC) infection is the the most common cause of acute renal failure among children in the UK. This study explored differential progression from STEC to HUS by social, demographic and clinical risk factors. METHODS We undertook a retrospective cohort study linking two datasets. We extracted data on paediatric STEC and HUS cases identified in the Public Health England National Enhanced Surveillance System for STEC and British Paediatric Surveillance Unit HUS surveillance from 1 October 2011 to 31 October 2014. Using logistic regression, we estimated the odds of HUS progression by risk factors. RESULTS 1059 paediatric STEC cases were included in the study, of which 207 (19.55%, 95% CI 17% to 22%) developed HUS. In the fully adjusted model, the odds of progression to HUS were highest in those aged 1-4 years (OR 4.93, 95% CI 2.30 to 10.56, compared with 10-15 years), were infected with an Shiga toxin (stx) 2-only strain (OR 5.92, 95% CI 2.49 to 14.10), were prescribed antibiotics (OR 8.46, 95% CI 4.71 to 15.18) and had bloody diarrhoea (OR 3.56, 95% CI 2.04 to 6.24) or vomiting (OR 4.47, 95% CI 2.62 to 7.63), but there was no association with progression to HUS by socioeconomic circumstances or rurality. CONCLUSION Combining data from an active clinical surveillance system for HUS with the national enhanced STEC surveillance system suggests that 20% of diagnosed paediatric STEC infections in England resulted in HUS. No relationship was found with socioeconomic status or rurality of cases, but differences were demonstrated by age, stx type and presenting symptoms.
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Affiliation(s)
- Natalie Adams
- Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, Liverpool, UK.,National Infection Service, Public Health England, London, UK
| | - Lisa Byrne
- National Infection Service, Public Health England, London, UK
| | - Tanith Rose
- Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, Liverpool, UK.,Department of Public Health and Policy, University of Liverpool, Liverpool, UK
| | - Bob Adak
- Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, Liverpool, UK
| | - Claire Jenkins
- Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, Liverpool, UK.,National Infection Service, Public Health England, London, UK
| | - Andre Charlett
- National Infection Service, Public Health England, London, UK
| | - Mara Violato
- Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, Liverpool, UK.,Health Economics Research Centre, University of Oxford, Oxford, UK
| | - Sarah O'Brien
- Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, Liverpool, UK.,Department of Public Health and Policy, University of Liverpool, Liverpool, UK
| | - Margaret Whitehead
- Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, Liverpool, UK.,Department of Public Health and Policy, University of Liverpool, Liverpool, UK
| | - Benjamin Barr
- Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, Liverpool, UK.,Department of Public Health and Policy, University of Liverpool, Liverpool, UK
| | - David Taylor-Robinson
- Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, Liverpool, UK.,Department of Public Health and Policy, University of Liverpool, Liverpool, UK
| | - Jeremy Hawker
- Health Protection Research Unit in Gastrointestinal Infections, National Institute for Health Research, Liverpool, UK.,National Infection Service, Public Health England, Birmingham, UK
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45
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Tetro JA. From hidden outbreaks to epidemic emergencies: the threat associated with neglecting emerging pathogens. Microbes Infect 2019; 21:4-9. [PMID: 29959095 PMCID: PMC7110498 DOI: 10.1016/j.micinf.2018.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 06/20/2018] [Indexed: 12/11/2022]
Abstract
Not all infectious disease outbreaks undergo full epidemiological investigations. In certain situations, the resultant lack of knowledge has led to the development of epidemics and public health emergencies. This review will examine six emerging pathogens including their history, present status, and potential to expand to epidemics. Recommendations to improve our understanding of these hidden outbreaks and others also will be provided in the context of health systems policy.
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Affiliation(s)
- Jason A Tetro
- College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
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46
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Boehmer T, Vogler AJ, Thomas A, Sauer S, Hergenroether M, Straubinger RK, Birdsell D, Keim P, Sahl JW, Williamson CHD, Riehm JM. Phenotypic characterization and whole genome analysis of extended-spectrum beta-lactamase-producing bacteria isolated from dogs in Germany. PLoS One 2018; 13:e0206252. [PMID: 30365516 PMCID: PMC6203360 DOI: 10.1371/journal.pone.0206252] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/09/2018] [Indexed: 12/30/2022] Open
Abstract
Asymptomatic colonization with extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae has been described for humans, various mammal species, and birds. Here, antimicrobial resistant bacteria were recovered from dog feces originating in Germany, Kosovo, Afghanistan, Croatia, and Ukraine, with a subset of mostly E. coli isolates obtained from a longitudinal collection over twelve months. In vitro antimicrobial resistance testing revealed various patterns of resistance against single or all investigated beta-lactam antibiotics, with none of the 101 isolates resistant against two tested carbapenem antibiotics. Whole genome sequence analysis revealed bacteria species-specific patterns for 23 antimicrobial resistance coding DNA sequences (CDS) that were unapparent from the in vitro analysis alone. Phylogenetic analysis of single nucleotide polymorphisms (SNP) revealed clonal bacterial isolates originating from different dogs, suggesting transmission between dogs in the same community. However, individual resistant E. coli clones were not detected over a period longer than seven days. Multi locus sequence typing (MLST) of 85 E. coli isolates revealed 31 different sequence types (ST) with an accumulation of ST744 (n = 9), ST10 (n = 8), and ST648 (n = 6), although the world-wide hospital-associated CTX-M beta-lactamase producing ST131 was not detected. Neither the antimicrobial resistance CDSs patterns nor the phylogenetic analysis revealed an epidemiological correlation among the longitudinal isolates collected from a period longer than seven days. No genetic linkage could be associated with the geographic origin of isolates. In conclusion, healthy dogs frequently carry ESBL-producing bacteria, independent to prior treatment, which may be transmitted between individual dogs of the same community. Otherwise, these antimicrobial resistant bacteria share few commonalities, making their presence eerily unpredictable.
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Affiliation(s)
- Tim Boehmer
- Central Institute of the Bundeswehr Medical Service Munich, Garching, Bavaria, Germany
| | - Amy J. Vogler
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Astrid Thomas
- Institute of Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilian University, Munich, Germany
| | | | - Markus Hergenroether
- Central Institute of the Bundeswehr Medical Service Munich, Garching, Bavaria, Germany
| | - Reinhard K. Straubinger
- Institute of Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilian University, Munich, Germany
| | - Dawn Birdsell
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Charles H. D. Williamson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Julia M. Riehm
- Central Institute of the Bundeswehr Medical Service Munich, Garching, Bavaria, Germany
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47
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A spatial and temporal analysis of risk factors associated with sporadic Shiga toxin-producing Escherichia coli O157 infection in England between 2009 and 2015. Epidemiol Infect 2018; 146:1928-1939. [PMID: 30205851 DOI: 10.1017/s095026881800256x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Infection with STEC O157 is relatively rare but has potentially serious sequelae, particularly for children. Large outbreaks have prompted considerable efforts designed to reduce transmission primarily from food and direct animal contact. Despite these interventions, numbers of infections have remained constant for many years and the mechanisms leading to many sporadic infections remain unclear.Here, we show that two-thirds of all cases reported in England between 2009 and 2015 were sporadic. Crude rates of infection differed geographically and were highest in rural areas during the summer months. Living in rural areas with high densities of cattle, sheep or pigs and those served by private water supplies were associated with increased risk. Living in an area of lower deprivation contributed to increased risk but this appeared to be associated with reported travel abroad. Fresh water coverage and residential proximity to the coast were not risk factors.To reduce the overall burden of infection in England, interventions designed to reduce the number of sporadic infections with STEC should focus on the residents of rural areas with high densities of livestock and the effective management of non-municipal water supplies. The role of sheep as a reservoir and potential source of infection in humans should not be overlooked.
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48
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Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections. J Clin Microbiol 2018; 56:JCM.00517-18. [PMID: 29925641 PMCID: PMC6113479 DOI: 10.1128/jcm.00517-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/09/2018] [Indexed: 02/07/2023] Open
Abstract
The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome multilocus sequence typing (cgMLST) has not been explored so far. The current study developed an allele-based cgMLST method and compared its performance to that of the genome-wide SNP approach and the traditional multilocus variable-number tandem repeat analysis (MLVA) on a defined sample collection. The data set was comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 isolates with unknown epidemiological status, composed of human and animal samples collected in Italy. The cgMLST scheme generated in this study contained 2,704 targets of the B. melitensis 16M reference genome. We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be ≤6 loci in the cgMLST and ≤7 in WGS SNP analysis. Higher phylogenetic distance resolution was achieved with cgMLST and SNP analysis than with MLVA, particularly for strains belonging to the same lineage, thereby allowing diverse and unrelated genotypes to be identified with greater confidence. The application of a cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen, and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.
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49
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Phylogenetic Groups and Antimicrobial Susceptibility Patterns of Escherichia coli from Healthy Chicken in Eastern and Central Uganda. J Vet Med 2018; 2018:9126467. [PMID: 30159337 PMCID: PMC6106960 DOI: 10.1155/2018/9126467] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/25/2018] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial resistance is an emerging problem in both humans and animals due to misuse and excessive use of drugs. Resistance in commensal E. coli isolates can be used to predict emergence of resistance in other gut microflora. The aim of this study is to determine the phylogenetic groups and antimicrobial resistance patterns of E. coli from healthy chickens in Uganda. The phylogenetic grouping of 120 fecal E. coli isolates from eastern and central Uganda was derived using the triplex PCR assay and their susceptibility patterns determined by agar disc diffusion method to 5 antimicrobial drugs. Most E. coli is segregated into phylogenetic group A comprising 84%, while 12% and 4% were in groups D and B1, respectively. Similarly most E. coli from central (87%) and eastern Uganda (82%) belonged to group A. Overall, 85 (70%) of E. coli were resistant to antimicrobial drugs, of which 72/101 (70%) are in PG A, 10 of 14 (71.4%) in PG D, and 3 of 5 (60%) in PG B1. Significantly, most of the isolates in PG A from both central (66.7%) and (60.6%) eastern Uganda were resistant to one antimicrobial. Resistance to tetracycline alone or in combination with other drugs for central and eastern Uganda in PG A is 51% and 55%, respectively. Multidrug resistance to tetracycline and ciprofloxacin or nalidixic acid was 10% and 18% in isolates from central and 10% and 12% in isolates from eastern region, respectively. Phylogenetic group A accounts for most of the E. coli in chicken from Uganda. No difference in the resistance rates between the phylogenetic groups of E. coli has been observed. The high prevalence of resistant E. coli strains from different phylogenetic groups in healthy chickens suggests antimicrobial drug selection pressure due to excessive drug in the rearing layer chickens.
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50
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Kinnula S, Hemminki K, Kotilainen H, Ruotsalainen E, Tarkka E, Salmenlinna S, Hallanvuo S, Leinonen E, Jukka O, Rimhanen-Finne R. Outbreak of multiple strains of non-O157 Shiga toxin-producing and enteropathogenic Escherichia coli associated with rocket salad, Finland, autumn 2016. Euro Surveill 2018; 23:1700666. [PMID: 30180926 PMCID: PMC6124187 DOI: 10.2807/1560-7917.es.2018.23.35.1700666] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
In August 2016, an outbreak of Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) with 237 cases occurred in the Helsinki metropolitan area, Finland. Gastroenteritis cases were reported at 11 events served by one catering company. Microbiological and epidemiological investigations suggested rocket salad as the cause of the outbreak. STEC ONT H11 and EPEC O111:H8 strains isolated from food samples containing rocket were identical to the patient isolates. In this outbreak, the reported symptoms were milder than considered before for STEC infection, and the guidelines for STEC control measures need to be updated based on the severity of the illness. Based on our experience in this outbreak, national surveillance criteria for STEC have been updated to meet the practice in reporting laboratories covering both PCR-positive and culture-confirmed findings. We suggest that EPEC could be added to the national surveillance since diagnostics for EPEC are routinely done in clinical laboratories.
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Affiliation(s)
- Sohvi Kinnula
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
| | - Kaisa Hemminki
- Environmental Health, Social and Health Services Espoo, Espoo, Finland
| | - Hannele Kotilainen
- City of Helsinki, Communicable Diseases, Epidemiology Unit, Social Services and Health Care Sector, Helsinki, Finland
| | - Eeva Ruotsalainen
- Division of Infectious Diseases, Inflammation Center, Helsinki University Central Hospital, Helsinki, Finland
| | - Eveliina Tarkka
- Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Saara Salmenlinna
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
| | - Saija Hallanvuo
- Finnish Food Safety Authority Evira, Research and Laboratory Services Department, Microbiology Research Unit, Helsinki, Finland
| | - Elina Leinonen
- Finnish Food Safety Authority Evira, Food Safety Department, Microbiological Food Safety Unit, Helsinki, Finland
| | - Ollgren Jukka
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
| | - Ruska Rimhanen-Finne
- National Institute for Health and Welfare, Health Security Department, Helsinki, Finland
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