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Gheorghe-Barbu I, Surleac M, Barbu IC, Paraschiv S, Bănică LM, Rotaru LI, Vrâncianu CO, Niță Lazăr M, Oțelea D, Chifiriuc MC. Decoding the resistome, virulome and mobilome of clinical versus aquatic Acinetobacter baumannii in southern Romania. Heliyon 2024; 10:e33372. [PMID: 39035534 PMCID: PMC11259834 DOI: 10.1016/j.heliyon.2024.e33372] [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: 04/06/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024] Open
Abstract
Acinetobacter baumannii, a notorious opportunistic pathogen, presents a formidable challenge in both clinical and environmental fields due to its resilience and ability to acquire resistance. This study undertook a comprehensive analysis of 183 A. baumannii isolates collected between 2019 and 2022 from intra-hospital infections (IHI), hospital sewages (Hs), wastewater treatment plants (WWTP), and adjacent river waters from two Southern cities, focusing on their resistome, virulome, and mobilome through isolation on chromogenic media, identification by MALDI-TOF-MS and antibiotic susceptibility testing by disk diffusion) followed by genotypic characterization [Whole Genome Sequencing (WGS), 3rd generation sequencing through the MinION (ONT) platform, pangenome description, and respectively horizontal gene transfer through conjugation assays]. Our findings reveal significant genomic plasticity and the prevalence of high-risk international clones, underlining the potential of these isolates to act as reservoirs for antibiotic resistance genes (ARGs) that could be dynamically exchanged between clinical and environmental settings through mobile genetic elements (MGEs) such as the pMAL1 plasmids and the critical role of WWTPs in the persistence and spread of A. baumannii. Moreover, our study presents the first report of the co-occurrence of bla OXA-23 and bla OXA-72 in A. baumannii ST2 clone. Thus, our research underscores the necessity for integrated surveillance and targeted interventions across healthcare and environmental sectors to mitigate the risk posed by this adaptable pathogen.
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Affiliation(s)
- Irina Gheorghe-Barbu
- Department of Microbiology and Botany, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Marius Surleac
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- National Institute for Infectious Diseases, “Matei Balș’‘, Bucharest, Romania
| | - Ilda Czobor Barbu
- Department of Microbiology and Botany, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Simona Paraschiv
- National Institute for Infectious Diseases, “Matei Balș’‘, Bucharest, Romania
| | | | - Liviu-Iulian Rotaru
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Corneliu Ovidiu Vrâncianu
- Department of Microbiology and Botany, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- National Institute of Research and Development for Biological Sciences, 296 Splaiul Independentei, District 6, 060031 Bucharest, Romania
| | - Mihai Niță Lazăr
- National Institute for Research and Development for Industrial Ecology, Bucharest, Romania
| | - Dan Oțelea
- National Institute for Infectious Diseases, “Matei Balș’‘, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Department of Microbiology and Botany, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Romanian Academy, Bucharest, Romania
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Kintz E, Brainard J, Vanderes M, Vivancos R, Byrne L, Butt S, Jenkins C, Elson R, Lake I, Hunter P. Animal and environmental risk factors for sporadic Shiga toxin-producing Escherichia coli (STEC) infection in England: a case control study for O157, O26 and other STEC serotypes. Pathog Glob Health 2023; 117:655-663. [PMID: 37016510 PMCID: PMC10498794 DOI: 10.1080/20477724.2023.2197672] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Most Shiga toxin-producing E. coli (STEC) infections are sporadic. Routine enhanced surveillance questionnaires of confirmed STEC cases in England contained promising data to conduct a case-control study to identify non-food exposures linked to the risk of becoming infected with different STEC serotypes, including O157, O26 and all others; this study pulled eligible cases from the recorded enhanced surveillance data. Controls were recruited from the general population and answered a comparable postal questionnaire. Logistic regression was performed to identify risk factors associated with STEC infection for O157, O26 and other serotype cases. In adjusted models, travel outside of the U.K. and childcare occupations raised the risk of infection for all serotypes. Day trips within the UK, exposure to dogs and contact with soil were linked to lower infection risk. Resident region within England was often linked to decreased risk. Summer season was linked to O157 and O26, but not other STEC. Swimming in the sea was linked to increased risk of infection by O157, but not other types of STEC. Correlations between exposures and infection were similar when the analysis was repeated excluding participants with a history of foreign travel. As the first case-control study in England to include sporadic non-O157 STEC, the varying risk factors between O157 and non-O157 cases suggest there are potentially unique reservoirs for different serotypes.
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Affiliation(s)
- Erica Kintz
- Norwich Medical School, University of East Anglia, Norwich, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | - Julii Brainard
- Norwich Medical School, University of East Anglia, Norwich, UK
- NIHR Health Protection Research Unit in Emergency Preparedness, University of East Anglia, Norwich, UK
| | - Mike Vanderes
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Roberto Vivancos
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- Field Epidemiology Services, UK Health Security Agency, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Lisa Byrne
- Gastrointestinal Pathogens Unit, UK Health Security Agency, London, UK
| | - Saira Butt
- Gastrointestinal Pathogens Unit, UK Health Security Agency, London, UK
| | - Claire Jenkins
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- Gastrointestinal Pathogens Unit, UK Health Security Agency, London, UK
| | - Richard Elson
- Gastrointestinal Pathogens Unit, UK Health Security Agency, London, UK
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Iain Lake
- NIHR Health Protection Research Unit in Emergency Preparedness, University of East Anglia, Norwich, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Paul Hunter
- Norwich Medical School, University of East Anglia, Norwich, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emergency Preparedness, University of East Anglia, Norwich, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
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Nouws S, Verhaegen B, Denayer S, Crombé F, Piérard D, Bogaerts B, Vanneste K, Marchal K, Roosens NHC, De Keersmaecker SCJ. Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices. Front Microbiol 2023; 14:1204630. [PMID: 37520372 PMCID: PMC10381951 DOI: 10.3389/fmicb.2023.1204630] [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: 04/12/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Shiga toxin-producing Escherichia coli (STEC) is a gastrointestinal pathogen causing foodborne outbreaks. Whole Genome Sequencing (WGS) in STEC surveillance holds promise in outbreak prevention and confinement, in broadening STEC epidemiology and in contributing to risk assessment and source attribution. However, despite international recommendations, WGS is often restricted to assist outbreak investigation and is not yet fully implemented in food safety surveillance across all European countries, in contrast to for example in the United States. Methods In this study, WGS was retrospectively applied to isolates collected within the context of Belgian food safety surveillance and combined with data from clinical isolates to evaluate its benefits. A cross-sector WGS-based collection of 754 strains from 1998 to 2020 was analyzed. Results We confirmed that WGS in food safety surveillance allows accurate detection of genomic relationships between human cases and strains isolated from food samples, including those dispersed over time and geographical locations. Identifying these links can reveal new insights into outbreaks and direct epidemiological investigations to facilitate outbreak management. Complete WGS-based isolate characterization enabled expanding epidemiological insights related to circulating serotypes, virulence genes and antimicrobial resistance across different reservoirs. Moreover, associations between virulence genes and severe disease were determined by incorporating human metadata into the data analysis. Gaps in the surveillance system were identified and suggestions for optimization related to sample centralization, harmonizing isolation methods, and expanding sampling strategies were formulated. Discussion This study contributes to developing a representative WGS-based collection of circulating STEC strains and by illustrating its benefits, it aims to incite policymakers to support WGS uptake in food safety surveillance.
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Affiliation(s)
- Stéphanie Nouws
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- IDlab, Department of Information Technology, Ghent University—IMEC, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC) and for Foodborne Outbreaks (NRL FBO), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL STEC) and for Foodborne Outbreaks (NRL FBO), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Florence Crombé
- National Reference Centre for Shiga Toxin-Producing Escherichia coli (NRC STEC), Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Denis Piérard
- National Reference Centre for Shiga Toxin-Producing Escherichia coli (NRC STEC), Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- IDlab, Department of Information Technology, Ghent University—IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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Outbreak of STEC O157:H7 linked to a milk pasteurisation failure at a dairy farm in England, 2019. Epidemiol Infect 2022; 150:e114. [PMID: 35581924 PMCID: PMC9252982 DOI: 10.1017/s0950268822000929] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In November 2019, an outbreak of Shiga toxin-producing Escherichia coli O157:H7 was detected in South Yorkshire, England. Initial investigations established consumption of milk from a local dairy as a common exposure. A sample of pasteurised milk tested the next day failed the phosphatase test, indicating contamination of the pasteurised milk by unpasteurised (raw) milk. The dairy owner agreed to immediately cease production and initiate a recall. Inspection of the pasteuriser revealed a damaged seal on the flow divert valve. Ultimately, there were 21 confirmed cases linked to the outbreak, of which 11 (52%) were female, and 12/21 (57%) were either <15 or >65 years of age. Twelve (57%) patients were treated in hospital, and three cases developed haemolytic uraemic syndrome. Although the outbreak strain was not detected in the milk samples, it was detected in faecal samples from the cattle on the farm. Outbreaks of gastrointestinal disease caused by milk pasteurisation failures are rare in the UK. However, such outbreaks are a major public health concern as, unlike unpasteurised milk, pasteurised milk is marketed as ‘safe to drink’ and sold to a larger, and more dispersed, population. The rapid, co-ordinated multi-agency investigation initiated in response to this outbreak undoubtedly prevented further cases.
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Aslam B, Khurshid M, Arshad MI, Muzammil S, Rasool M, Yasmeen N, Shah T, Chaudhry TH, Rasool MH, Shahid A, Xueshan X, Baloch Z. Antibiotic Resistance: One Health One World Outlook. Front Cell Infect Microbiol 2021; 11:771510. [PMID: 34900756 PMCID: PMC8656695 DOI: 10.3389/fcimb.2021.771510] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/29/2021] [Indexed: 01/07/2023] Open
Abstract
Antibiotic resistance (ABR) is a growing public health concern worldwide, and it is now regarded as a critical One Health issue. One Health’s interconnected domains contribute to the emergence, evolution, and spread of antibiotic-resistant microorganisms on a local and global scale, which is a significant risk factor for global health. The persistence and spread of resistant microbial species, and the association of determinants at the human-animal-environment interface can alter microbial genomes, resulting in resistant superbugs in various niches. ABR is motivated by a well-established link between three domains: human, animal, and environmental health. As a result, addressing ABR through the One Health approach makes sense. Several countries have implemented national action plans based on the One Health approach to combat antibiotic-resistant microbes, following the Tripartite’s Commitment Food and Agriculture Organization (FAO)-World Organization for Animal Health (OIE)-World Health Organization (WHO) guidelines. The ABR has been identified as a global health concern, and efforts are being made to mitigate this global health threat. To summarize, global interdisciplinary and unified approaches based on One Health principles are required to limit the ABR dissemination cycle, raise awareness and education about antibiotic use, and promote policy, advocacy, and antimicrobial stewardship.
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Affiliation(s)
- Bilal Aslam
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Saima Muzammil
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Maria Rasool
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Nafeesa Yasmeen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
| | - Tamoor Hamid Chaudhry
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan.,Public Health Laboratories Division, National Institute of Health, Islamabad, Pakistan
| | | | - Aqsa Shahid
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Faisalabad, Pakistan
| | - Xia Xueshan
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
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Evidence of on-going transmission of Shiga toxin-producing Escherichia coli O157:H7 following a foodborne outbreak. Epidemiol Infect 2021; 149:e147. [PMID: 34096488 PMCID: PMC8251666 DOI: 10.1017/s0950268821001278] [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] [Indexed: 12/02/2022] Open
Abstract
In August 2019, public health surveillance systems in Scotland and England identified seven, geographically dispersed cases infected with the same strain (defined as isolates that fell within the same five single nucleotide polymorphism single linage cluster) of Shiga toxin-producing Escherichia coli O157:H7. Epidemiological analysis of enhanced surveillance questionnaire data identified handling raw beef and shopping from the same national retailer (retailer A) as the common exposure. Concurrently, a microbiological survey of minced beef at retail identified the same strain in a sample of minced beef sold by retailer A, providing microbiological evidence of the link. Between September and November 2019, a further four primary and two secondary cases infected with the same strain were identified; two cases developed haemolytic uraemic syndrome. None of the four primary cases reported consumption of beef from retailer A and the transmission route of these subsequent cases was not identified, although all four primary cases visited the same petting farm. Generally, outbreaks of STEC O157:H7 in the UK appear to be distinct, short-lived events; however, on-going transmission linked to contaminated food, animals or environmental exposures and person-to-person contact do occur. Although outbreaks of STEC caused by contaminated fresh produce are increasingly common, undercooked meat products remain a risk of infection.
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7
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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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Wee BA, Muloi DM, van Bunnik BAD. Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics. Clin Microbiol Infect 2020; 26:1612-1616. [PMID: 32979568 PMCID: PMC7721588 DOI: 10.1016/j.cmi.2020.09.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/05/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Livestock have been implicated as a reservoir for antimicrobial resistance (AMR) that can spread to humans. Close proximity and ecological interfaces involving livestock have been posited as risk factors for the transmission of AMR. In spite of this, there are sparse data and limited agreement on the transmission dynamics that occur. OBJECTIVES To identify how genome sequencing approaches can be used to quantify the dynamics of AMR transmission at the human-livestock interface, and where current knowledge can be improved to better understand the impact of transmission on the spread of AMR. SOURCES Key articles investigating various aspects of AMR transmission at the human-livestock interface are discussed, with a focus on Escherichia coli. CONTENT We recapitulate the current understanding of the transmission of AMR between humans and livestock based on current genomic and epidemiological approaches. We discuss how the use of well-designed, high-resolution genome sequencing studies can improve our understanding of the human-livestock interface. IMPLICATIONS A better understanding of the human-livestock interface will aid in the development of evidence-based and effective One Health interventions that can ultimately reduce the burden of AMR in humans.
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Affiliation(s)
- Bryan A Wee
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Dishon M Muloi
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom; International Livestock Research Institute, Nairobi, Kenya
| | - Bram A D van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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9
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Nouws S, Bogaerts B, Verhaegen B, Denayer S, Crombé F, De Rauw K, Piérard D, Marchal K, Vanneste K, Roosens NHC, De Keersmaecker SCJ. The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country. Foods 2020; 9:E1030. [PMID: 32752159 PMCID: PMC7466227 DOI: 10.3390/foods9081030] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022] Open
Abstract
Gradually, conventional methods for foodborne pathogen typing are replaced by whole genome sequencing (WGS). Despite studies describing the overall benefits, National Reference Laboratories of smaller countries often show slower uptake of WGS, mainly because of significant investments required to generate and analyze data of a limited amount of samples. To facilitate this process and incite policy makers to support its implementation, a Shiga toxin-producing Escherichia coli (STEC) O157:H7 (stx1+, stx2+, eae+) outbreak (2012) and a STEC O157:H7 (stx2+, eae+) outbreak (2013) were retrospectively analyzed using WGS and compared with their conventional investigations. The corresponding results were obtained, with WGS delivering even more information, e.g., on virulence and antimicrobial resistance genotypes. Besides a universal, all-in-one workflow with less hands-on-time (five versus seven actual working days for WGS versus conventional), WGS-based cgMLST-typing demonstrated increased resolution. This enabled an accurate cluster definition, which remained unsolved for the 2013 outbreak, partly due to scarce epidemiological linking with the suspect source. Moreover, it allowed detecting two and one earlier circulating STEC O157:H7 (stx1+, stx2+, eae+) and STEC O157:H7 (stx2+, eae+) strains as closely related to the 2012 and 2013 outbreaks, respectively, which might have further directed epidemiological investigation initially. Although some bottlenecks concerning centralized data-sharing, sampling strategies, and perceived costs should be considered, we delivered a proof-of-concept that even in smaller countries, WGS offers benefits for outbreak investigation, if a sufficient budget is available to ensure its implementation in surveillance. Indeed, applying a database with background isolates is critical in interpreting isolate relationships to outbreaks, and leveraging the true benefit of WGS in outbreak investigation and/or prevention.
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Affiliation(s)
- Stéphanie Nouws
- Department of Expertise and service provision, Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.N.); (B.B.); (K.V.); (N.H.C.R.)
- Department of Information Technology, IDLab, imec, Ghent University, 9052 Ghent, Belgium;
| | - Bert Bogaerts
- Department of Expertise and service provision, Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.N.); (B.B.); (K.V.); (N.H.C.R.)
- Department of Information Technology, IDLab, imec, Ghent University, 9052 Ghent, Belgium;
| | - Bavo Verhaegen
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL-STEC), National Reference Laboratory for Foodborne Outbreaks (NRL-FBO), Department of Infectious diseases in humans, Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium; (B.V.); (S.D.)
| | - Sarah Denayer
- National Reference Laboratory for Shiga Toxin-Producing Escherichia coli (NRL-STEC), National Reference Laboratory for Foodborne Outbreaks (NRL-FBO), Department of Infectious diseases in humans, Foodborne Pathogens, Sciensano, 1050 Brussels, Belgium; (B.V.); (S.D.)
| | - Florence Crombé
- Department of Microbiology and Infection Control, National Reference Center for Shiga Toxin-Producing Escherichia coli (NRC-STEC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium; (F.C.); (K.D.R.); (D.P.)
| | - Klara De Rauw
- Department of Microbiology and Infection Control, National Reference Center for Shiga Toxin-Producing Escherichia coli (NRC-STEC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium; (F.C.); (K.D.R.); (D.P.)
| | - Denis Piérard
- Department of Microbiology and Infection Control, National Reference Center for Shiga Toxin-Producing Escherichia coli (NRC-STEC), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium; (F.C.); (K.D.R.); (D.P.)
| | - Kathleen Marchal
- Department of Information Technology, IDLab, imec, Ghent University, 9052 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria 0083, South Africa
| | - Kevin Vanneste
- Department of Expertise and service provision, Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.N.); (B.B.); (K.V.); (N.H.C.R.)
| | - Nancy H. C. Roosens
- Department of Expertise and service provision, Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.N.); (B.B.); (K.V.); (N.H.C.R.)
| | - Sigrid C. J. De Keersmaecker
- Department of Expertise and service provision, Transversal activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (S.N.); (B.B.); (K.V.); (N.H.C.R.)
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Jenkins C, Dallman TJ, Grant KA. Impact of whole genome sequencing on the investigation of food-borne outbreaks of Shiga toxin-producing Escherichia coli serogroup O157:H7, England, 2013 to 2017. ACTA ACUST UNITED AC 2020; 24. [PMID: 30696532 PMCID: PMC6352002 DOI: 10.2807/1560-7917.es.2019.24.4.1800346] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We aim to provide insight and guidance on the utility of whole genome sequencing (WGS) data for investigating food-borne outbreaks of Shiga toxin-producing Escherichia coli (STEC) O157:H7 in England between 2013 and 2017. Analysis of WGS data delivered an unprecedented level of strain discrimination when compared with multilocus variable number tandem repeat analysis. The robustness of the WGS method ensured confidence in the microbiological identification of linked cases, even when epidemiological links were obscured. There was evidence that phylogeny derived from WGS data can be used to trace the geographical origin of an isolate. Further analysis of the phylogenetic data provided insight on the evolutionary context of emerging pathogenic strains. Publically available WGS data linked to the clinical, epidemiological and environmental context of the sequenced strain has improved trace back investigations during outbreaks. Expanding the use of WGS-based typing analysis globally will ensure the rapid implementation of interventions to protect public health, inform risk assessment and facilitate the management of national and international food-borne outbreaks of STEC O157:H7.
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Affiliation(s)
- Claire Jenkins
- National Infection Service, Public Health England, United Kingdom
| | | | - Kathie A Grant
- National Infection Service, Public Health England, United Kingdom
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Treacy J, Jenkins C, Paranthaman K, Jorgensen F, Mueller-Doblies D, Anjum M, Kaindama L, Hartman H, Kirchner M, Carson T, Kar-Purkayastha I. Outbreak of Shiga toxin-producing Escherichia coli O157:H7 linked to raw drinking milk resolved by rapid application of advanced pathogen characterisation methods, England, August to October 2017. ACTA ACUST UNITED AC 2020; 24. [PMID: 31014418 PMCID: PMC6826345 DOI: 10.2807/1560-7917.es.2019.24.16.1800191] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An outbreak of Shiga toxin-producing Escherichia coli (STEC) O157:H7 occurred on the Isle of Wight between August and October 2017. Of the seven cases linked to the outbreak, five were identified through the statutory notification process and two were identified through national surveillance of whole genome sequencing data. Enhanced surveillance questionnaires established a common link to a farm, and link to the likely food vehicle, raw drinking milk (RDM). Microbiological investigations, including PCR, identified the presence of STEC O157:H7 in samples of RDM. Analysis of core genome single nucleotide polymorphism (SNP) data of STEC O157:H7 from human stool specimens, animal faecal samples and RDM demonstrated a one SNP difference between isolates, and therefore close genetic relatedness. Control measures that were put in place included suspension of sales and recall of RDM, as well as restrictions on public access to parts of the farm. Successful integration of traditional epidemiological surveillance and advanced laboratory methods for the detection and characterisation of STEC O157:H7 from human, animal and environmental samples enabled prompt identification of the outbreak vehicle and provided evidence to support the outbreak control team’s decision-making, leading to implementation of effective control measures in a timely manner.
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Affiliation(s)
- Juli Treacy
- Public Health England South East, Hampshire and Isle of Wight Health Protection Team, Fareham, United Kingdom
| | - Claire Jenkins
- National Infection Service, Public Health England, London, United Kingdom
| | - Karthik Paranthaman
- National Infection Service, Field Epidemiology Service, Public Health England, London, United Kingdom
| | - Frieda Jorgensen
- National Infection Service, Food Water and Environmental Microbiology Laboratory, Public Health England, Porton, United Kingdom
| | | | - Muna Anjum
- Animal and Plant Health Agency, Surrey, United Kingdom
| | - Lukeki Kaindama
- Gastrointestinal Emerging and Zoonoses Infections, Public Health England, London, United Kingdom
| | - Hassan Hartman
- Public Health England South East, Hampshire and Isle of Wight Health Protection Team, Fareham, United Kingdom
| | | | | | - Ishani Kar-Purkayastha
- Public Health England South East, Hampshire and Isle of Wight Health Protection Team, Fareham, United Kingdom
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12
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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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13
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Fusco V, Chieffi D, Fanelli F, Logrieco AF, Cho G, Kabisch J, Böhnlein C, Franz CMAP. Microbial quality and safety of milk and milk products in the 21st century. Compr Rev Food Sci Food Saf 2020; 19:2013-2049. [DOI: 10.1111/1541-4337.12568] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Vincenzina Fusco
- Institute of Sciences of Food Production National Research Council of Italy (CNR‐ISPA) Bari Italy
| | - Daniele Chieffi
- Institute of Sciences of Food Production National Research Council of Italy (CNR‐ISPA) Bari Italy
| | - Francesca Fanelli
- Institute of Sciences of Food Production National Research Council of Italy (CNR‐ISPA) Bari Italy
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production National Research Council of Italy (CNR‐ISPA) Bari Italy
| | - Gyu‐Sung Cho
- Department of Microbiology and BiotechnologyMax‐Rubner Institut Kiel Germany
| | - Jan Kabisch
- Department of Microbiology and BiotechnologyMax‐Rubner Institut Kiel Germany
| | - Christina Böhnlein
- Department of Microbiology and BiotechnologyMax‐Rubner Institut Kiel Germany
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14
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McLauchlin J, Aird H, Elliott A, Forester E, Jørgensen F, Willis C. Microbiological quality of raw drinking milk and unpasteurised dairy products: results from England 2013-2019. Epidemiol Infect 2020; 148:e135. [PMID: 32406346 PMCID: PMC7374804 DOI: 10.1017/s0950268820001016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/21/2020] [Accepted: 05/11/2020] [Indexed: 11/06/2022] Open
Abstract
The aim of this study was to review microbiology results from testing >2500 raw drinking milk and dairy products made with unpasteurised milk examined in England between 2013 and 2019. Samples were collected as part of incidents of contamination, investigation of infections or as part of routine monitoring and were tested using standard methods for a range of both pathogens and hygiene indicators. Results from testing samples of raw cow's milk or cheese made from unpasteurised milk for routine monitoring purposes were overall of better microbiological quality than those collected during incident or investigations of infections. Results from routine monitoring were satisfactory for 62% of milks, 82% of cream, 100% of ice-cream, 51% of butter, 63% of kefir and 79% of cheeses, with 5% of all samples being considered potentially hazardous. Analysis of data from cheese demonstrated a significant association between increasing levels of indicator Escherichia coli with elevated levels of coagulase positive staphylococci and decreased probability of isolation of Shiga toxin-producing E. coli. These data highlight the public health risk associated with these products and provide further justification for controls applied to raw drinking milk and dairy products made with unpasteurised milk.
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Affiliation(s)
- J. McLauchlin
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Services, Colindale, London, UK
| | - H. Aird
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Laboratory York, National Agri-Food Innovation Campus, York, UK
| | - A. Elliott
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Laboratory Porton, Porton Down, Salisbury, UK
- Public Health England, National Infection Service, Field Services, South West, Bristol, UK
| | - E. Forester
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Laboratory York, National Agri-Food Innovation Campus, York, UK
- Public Health England, National Infection Service, Field Services, North West Office, Liverpool, UK
| | - F. Jørgensen
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Laboratory Porton, Porton Down, Salisbury, UK
| | - C. Willis
- Public Health England, National Infection Service, Food Water and Environmental Microbiology Laboratory Porton, Porton Down, Salisbury, UK
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15
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Kenyon J, Inns T, Aird H, Swift C, Astbury J, Forester E, Decraene V. Campylobacter outbreak associated with raw drinking milk, North West England, 2016. Epidemiol Infect 2020; 148:e13. [PMID: 32000879 PMCID: PMC7019543 DOI: 10.1017/s0950268820000096] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/17/2019] [Accepted: 01/08/2020] [Indexed: 12/03/2022] Open
Abstract
In December 2016, Public Health England investigated an outbreak of campylobacteriosis in North West England, with 69 cases in total. Epidemiological, microbiological and environmental investigations associated the illness with the consumption of unpasteurised cows' milk from Farm X, where milk was predominantly sold from a vending machine. Campylobacter was detected in milk samples which, when sequenced, were identical in sequence type as pathogens isolated from cases (Clonal Complex ST-403, Sequence Type 7432). The farm was served with a Hygiene Emergency Prohibition Order to prevent further cases. To our knowledge, this is the first outbreak of campylobacter associated with unpasteurised milk in England since 1996. Our findings highlighted several important lessons, including that the current testing regime in England for unpasteurised milk is not fit for purpose and that the required warning label should include additional wording, underscoring the risk to vulnerable groups. There has been a substantial increase in both the volume of unpasteurised milk consumed in England and the use of vending machines to sell unpasteurised milk over the last 10 years, making unpasteurised milk more readily accessible to a wider population. The evidence generated from outbreaks like this is therefore critical and should be used to influence policy development.
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Affiliation(s)
- J. Kenyon
- Public Health England North West Centre, Preston, UK
| | - T. Inns
- Field Service, National Infection Service, Public Health England, London, UK
| | - H. Aird
- Food, Water & Environmental Microbiology Laboratory, Public Health England, York, UK
| | - C. Swift
- Gastrointestinal Bacterial Reference Unit, Public Health England, London, UK
| | - J. Astbury
- Public Health England North West Centre, Preston, UK
| | - E. Forester
- Food, Water & Environmental Microbiology Laboratory, Public Health England, York, UK
| | - V. Decraene
- Field Service, National Infection Service, Public Health England, London, UK
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16
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Kintz E, Byrne L, Jenkins C, McCARTHY N, Vivancos R, Hunter P. Outbreaks of Shiga Toxin-Producing Escherichia coli Linked to Sprouted Seeds, Salad, and Leafy Greens: A Systematic Review. J Food Prot 2019; 82:1950-1958. [PMID: 31638410 DOI: 10.4315/0362-028x.jfp-19-014] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) outbreaks involving ready-to-eat salad products have been described in the scientific literature since 1995. These products typically do not undergo a definitive control step such as cooking to eliminate pathogens. To reduce the number of STEC infections from salad products, efforts will need to focus on preventing and reducing contamination throughout the food chain. We performed a systematic review of STEC outbreaks involving sprouted seeds, salad, or leafy green products to determine whether there were recurrent features, such as availability of microbiological evidence or identification of the contamination event, which may inform future investigations and prevention and control strategies. Thirty-five STEC outbreaks linked to contaminated leafy greens were identified for inclusion. The outbreaks occurred from 1995 to 2018 and ranged from 8 to more than 8,500 cases. Detection of STEC in the food product was rare (4 of 35 outbreaks). For the remaining outbreaks, the determination of leafy greens as the source of the outbreak mainly relied on analytical epidemiology (20 of 35) or descriptive evidence (11 of 35). The traceback investigation in 21 of 32 outbreaks was not able to identify possible routes leading to where the STEC bacteria came from or how the leaves were contaminated. Investigations in eight outbreaks found poor practice during processing that may have contributed to the outbreak, such as insufficient postharvest disinfection of the product. Six outbreak investigations were able to identify the outbreak strain in animal feces near the growing fields; two of these were also able to find it in irrigation water on the farms, providing a likely route of contamination. These results highlight the limitations of relying on microbiological confirmation as a basis to initiate investigations of upstream production to understand the source of contamination. This review also demonstrates the importance of, and difficulties associated with, food-chain traceback studies to inform control measures and future prevention.
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Affiliation(s)
- Erica Kintz
- Norwich Medical School, University of East Anglia, Norwich, Norfolk NR4 7TJ, UK (ORCID: https://orcid.org/0000-0002-6829-5701 [E.K.]).,NIHR Health Protection Research Unit in Gastrointestinal Infections, UK
| | - Lisa Byrne
- National Infection Service, Public Health England, London NW9 5EQ, UK
| | - Claire Jenkins
- National Infection Service, Public Health England, London NW9 5EQ, UK
| | - Noel McCARTHY
- NIHR Health Protection Research Unit in Gastrointestinal Infections, UK.,Department of Zoology, University of Oxford, UK.,Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Roberto Vivancos
- NIHR Health Protection Research Unit in Gastrointestinal Infections, UK.,National Infection Service, Public Health England, London NW9 5EQ, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, UK
| | - Paul Hunter
- NIHR Health Protection Research Unit in Gastrointestinal Infections, UK.,Department of Environmental Health, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa
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Elson R, Davies TM, Jenkins C, Vivancos R, O'Brien SJ, Lake IR. Application of kernel smoothing to estimate the spatio-temporal variation in risk of STEC O157 in England. Spat Spatiotemporal Epidemiol 2019; 32:100305. [PMID: 32007279 DOI: 10.1016/j.sste.2019.100305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 01/27/2023]
Abstract
Identifying geographical areas with significantly higher or lower rates of infectious diseases can provide important aetiological clues to inform the development of public health policy and interventions designed to reduce morbidity. We applied kernel smoothing to estimate the spatial and spatio-temporal variation in risk of STEC O157 infection in England between 2009 and 2015, and to explore differences between the residential locations of cases reporting travel and those not reporting travel. We provide evidence that the distribution of STEC O157 infection in England is non-uniform with respect to the distribution of the at-risk population; that the spatial distribution of the three main genetic lineages infecting humans (I, II and I/II) differs significantly and that the spatio-temporal risk is highly dynamic. Our results also indicate that cases of STEC O157 reporting travel within or outside the UK are more likely to live in the south/south-east of the country, meaning that their residential location may not reflect the location of exposure that led to their infection. We suggest that the observed variation in risk reflects exposure to sources of STEC O157 that are geographically prescribed. These differences may be related to a combination of changes in the strains circulating in the ruminant reservoir, animal movements (livestock, birds or wildlife) or the behavior of individuals prior to infection. Further work to identify the importance of behaviours and exposures reported by cases relative to residential location is needed.
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Affiliation(s)
- Richard Elson
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; School of Environmental Sciences, University of East Anglia, United Kingdom.
| | - Tilman M Davies
- Department of Mathematics & Statistics, University of Otago, Dunedin, New Zealand
| | - Claire Jenkins
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom
| | - Roberto Vivancos
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Emerging and Zoonotic Infections, United Kingdom
| | - Sarah J O'Brien
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; Institute of Population Health Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Iain R Lake
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; School of Environmental Sciences, University of East Anglia, United Kingdom
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18
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Gastrointestinal infections caused by consumption of raw drinking milk in England & Wales, 1992-2017. Epidemiol Infect 2019; 147:e281. [PMID: 34596012 PMCID: PMC6805749 DOI: 10.1017/s095026881900164x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Systematic, national surveillance of outbreaks of intestinal infectious disease has been undertaken by Public Health England (PHE) since 1992. Between 1992 and 2002, there were 19 outbreaks linked to raw drinking milk (RDM) or products made using raw milk, involving 229 people; 36 of these were hospitalised. There followed an eleven-year period (2003–2013) where no outbreaks linked to RDM were reported. However, since 2014 seven outbreaks of Escherichia coli O157:H7 (n = 3) or Campylobacter jejuni (n = 4) caused by contaminated RDM were investigated and reported. Between 2014 and 2017, there were 114 cases, five reported hospitalisations and one death. The data presented within this review indicated that the risk of RDM has increased since 2014. Despite the labelling requirements and recommendations that children should not consume RDM, almost a third of outbreak cases were children. In addition, there has been an increase in consumer popularity and in registered RDM producers in the UK. The Food Standards Agency (FSA) continue to provide advice on RDM to consumers and have recently made additional recommendations to enhance existing controls around registration and hygiene of RDM producers.
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19
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Van Goethem N, Descamps T, Devleesschauwer B, Roosens NHC, Boon NAM, Van Oyen H, Robert A. Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79. [PMID: 31409417 PMCID: PMC6692930 DOI: 10.1186/s13012-019-0930-2] [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] [Received: 10/22/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist's perspective. METHODS In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. RESULTS Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. CONCLUSIONS For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist's perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.
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Affiliation(s)
- Nina Van Goethem
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
| | - Tine Descamps
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Brecht Devleesschauwer
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Nele A. M. Boon
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Herman Van Oyen
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Public Health and Primary Care, Faculty of Medicine, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
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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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21
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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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22
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Lund BM. Provision of microbiologically safe food for vulnerable people in hospitals, care homes and in the community. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.09.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Elson R, Awofisayo-Okuyelu A, Greener T, Swift C, Painset A, Amar CFL, Newton A, Aird H, Swindlehurst M, Elviss N, Foster K, Dallman TJ, Ruggles R, Grant K. Utility of Whole Genome Sequencing To Describe the Persistence and Evolution of Listeria monocytogenes Strains within Crabmeat Processing Environments Linked to Two Outbreaks of Listeriosis. J Food Prot 2019; 82:30-38. [PMID: 30702931 DOI: 10.4315/0362-028x.jfp-18-206] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This article describes the identification and investigation of two extended outbreaks of listeriosis in which crabmeat was identified as the vehicle of infection. Comparing contemporary and retrospective typing data of Listeria monocytogenes isolates from clinical cases and from food and food processing environments allowed the detection of cases going back several years. This information, combined with the analysis of routinely collected enhanced surveillance data, helped to direct the investigation and identify the vehicle of infection. Retrospective whole genome sequencing (WGS) analysis of isolates provided robust microbiological evidence of links between cases, foods, and the environments in which they were produced and demonstrated that for some cases and foods, identified by fluorescent amplified fragment length polymorphism, the molecular typing method in routine use at the time, were not part of the outbreak. WGS analysis also showed that the strains causing illness had persisted in two food production environments for many years and in one producer had evolved into two strains over a period of around 8 years. This article demonstrates the value of reviewing L. monocytogenes typing data from clinical cases together with that from foods as a means of identifying potential vehicles and sources of infection in outbreaks of listeriosis. It illustrates the importance of reviewing retrospective L. monocytogenes typing alongside enhanced surveillance data to characterize extended outbreaks and inform control measures. Also, this article highlights the advantages of WGS analysis for strain discrimination and clarification of evolutionary relationships that refine outbreak investigations and improve our understanding of L. monocytogenes in the food chain.
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Affiliation(s)
- Richard Elson
- 1 Public Health England, National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.,2 National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, University of Liverpool, Liverpool L3 5TR, UK
| | - Adedoyin Awofisayo-Okuyelu
- 2 National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, University of Liverpool, Liverpool L3 5TR, UK
| | - Trevor Greener
- 3 North Tyneside Council, Public Protection Services, The Silverlink North, Cobalt Business Park, North Tyneside NE27 0BY, UK
| | - Craig Swift
- 1 Public Health England, National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Anaïs Painset
- 1 Public Health England, National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.,2 National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, University of Liverpool, Liverpool L3 5TR, UK
| | | | - Autilia Newton
- 4 Public Health England UKOT Program IHR, 133-135, Wellington Road, London SE1 8UG, UK
| | - Heather Aird
- 5 Public Health England, National Infection Service, Food, Water and Environmental Microbiology Laboratory, National Agri-Food Innovation Campus, Block 10, Sand Hutton, York YO41 1LZ, UK
| | - Mark Swindlehurst
- 5 Public Health England, National Infection Service, Food, Water and Environmental Microbiology Laboratory, National Agri-Food Innovation Campus, Block 10, Sand Hutton, York YO41 1LZ, UK
| | - Nicola Elviss
- 5 Public Health England, National Infection Service, Food, Water and Environmental Microbiology Laboratory, National Agri-Food Innovation Campus, Block 10, Sand Hutton, York YO41 1LZ, UK
| | - Kirsty Foster
- 6 Public Health England, North East PHE Centre, Floor 2 Citygate, Gallowgate, Newcastle-upon-Tyne NE1 4WH, UK
| | - Timothy J Dallman
- 1 Public Health England, National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.,2 National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, University of Liverpool, Liverpool L3 5TR, UK
| | - Ruth Ruggles
- 1 Public Health England, National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Kathie Grant
- 1 Public Health England, National Infection Service, 61 Colindale Avenue, London NW9 5EQ, UK.,2 National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, University of Liverpool, Liverpool L3 5TR, UK
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24
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Bogaty C, Mataseje L, Gray A, Lefebvre B, Lévesque S, Mulvey M, Longtin Y. Investigation of a Carbapenemase-producing Acinetobacter baumannii outbreak using whole genome sequencing versus a standard epidemiologic investigation. Antimicrob Resist Infect Control 2018; 7:140. [PMID: 30479753 PMCID: PMC6249735 DOI: 10.1186/s13756-018-0437-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/12/2018] [Indexed: 11/11/2022] Open
Abstract
Background The standard epidemiologic investigation of outbreaks typically relies on spatiotemporal data and pulsed-field gel electrophoresis (PFGE), but whole genome sequencing (WGS) is becoming increasingly used. This investigation aimed to characterize a carbapenemase-producing Acinetobacter baumannii (CPAb) nosocomial outbreak using WGS compared to a standard outbreak investigation. Methods The CPAb outbreak occurred in a single center between 2012 and 2014. The standard investigation used spatiotemporal data and PFGE to generate a chain of transmission. A separate WGS investigation generated a chain of transmission based solely on WGS and date of sampling and was blinded to all other spatiotemporal data and PFGE. Core single nucleotide variant (SNV) phylogenetic analysis was performed on WGS data generated using the Illumina MiSeq platform. The chains of transmission were compared quantitatively and qualitatively to assess the concordance between both methods. Results 28 colonized and infected cases were included. Of the 27 transmission events identified using the standard investigation, 12 (44%) were identical to the transmission events using WGS. WGS identified several transmission events that had not been detected by traditional method, and numerous transmission events that had occurred on different hospital wards than suspected by standard methods. The average number (standard deviation [SD]) of SNVs per transmission events was 1.63 (SD, 1.31) by traditional method and 0.63 (SD, 0.79) by WGS (p = 0.001) All isolates harbored the rare carbapenemase blaOXA-237. Conclusions The traditional and WGS investigations had moderate concordance. When used alongside epidemiologic data and clinical information, WGS could help improve the mapping of transmission events.
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Affiliation(s)
| | | | | | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC Canada
| | - Simon Lévesque
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC Canada
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25
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Rokney A, Valinsky L, Moran-Gilad J, Vranckx K, Agmon V, Weinberger M. Genomic Epidemiology of Campylobacter jejuni Transmission in Israel. Front Microbiol 2018; 9:2432. [PMID: 30386311 PMCID: PMC6198274 DOI: 10.3389/fmicb.2018.02432] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/21/2018] [Indexed: 01/22/2023] Open
Abstract
Objectives: Campylobacter jejuni is responsible for 80% of Campylobacter infections in Israel, a country with a high incidence reaching 91/100,000 population. We studied the phylogeny, diversity and prevalence of virulence factors using whole genome sequencing (WGS) of a national sample of C. jejuni clinical, food, and animal isolates collected over a 10-year period (2003-2012). Methods: C. jejuni isolates (n = 263) were subject to WGS using Illumina sequencing (PE 250bpx2). Raw reads and de novo assemblies were analyzed with the BioNumerics whole genome MLST (wgMLST) pipeline. Reads were screened for 71 virulence genes by the SRST2 script. Allelic profiles were analyzed to create minimum spanning trees and allelic core distances were investigated to determine a reliable cutoff for strain determination. Results: wgMLST analysis of 263 C. jejuni isolates indicated significant diversity among the prevalent clonal complexes (CCs) with CC-21 and CC-353 being the most diverse, and CC-574 the most clonal. Within CC-21, sequence type (ST)-1359 created a separate clade. Human, poultry and bovine isolates clustered together across the different STs. Forty four percent of studied isolates were assigned to 29 genetic clusters. Temporal and geographical relatedness were found among the minority of clusters, while most phylogenetically associated cases appeared diffuse and unassociated epidemiologically. The majority of virulence factors were highly prevalent across the dataset and not associated with genotype, source of isolation or invasiveness. Conversely, all 13 genes associated with type VI secretion system (T6SS) were lineage-related and identified in only 18% of the isolates. T6SS was detected in 95.2% of ST-1359, a common type in Israel. Conclusions: wgMLST supported the assessment that poultry and cattle are likely food sources of infection in Israel. Substantial genetic clustering among C. jejuni isolates suggested multiple point source and diffuse outbreaks that were previously unreported in Israel. The high prevalence of T6SS among ST-1359 isolates is unique to Israel, and requires further investigation. This study exemplifies the importance of studying foodborne pathogens using advanced genomic approaches across the entire spectrum of One Health.
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Affiliation(s)
- Assaf Rokney
- Central Government Laboratories, Israel Ministry of Health, Jerusalem, Israel
| | - Lea Valinsky
- Central Government Laboratories, Israel Ministry of Health, Jerusalem, Israel
| | - Jacob Moran-Gilad
- Public Health Services, Israel Ministry of Health, Jerusalem, Israel.,Department of Health Policy and Management, Faculty of Health Sciences, School of Public Health, Ben-Gurion University of the Negev, Be'er-Sheva, Israel.,ESCMID Study Group for Genomic and Molecular Diagnostics, Basel, Switzerland
| | | | - Vered Agmon
- Central Government Laboratories, Israel Ministry of Health, Jerusalem, Israel
| | - Miriam Weinberger
- Infectious Diseases Unit, Assaf Harofeh Medical Center, Zerifin, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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26
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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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27
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Setup, Validation, and Quality Control of a Centralized Whole-Genome-Sequencing Laboratory: Lessons Learned. J Clin Microbiol 2018; 56:JCM.00261-18. [PMID: 29695528 DOI: 10.1128/jcm.00261-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Routine use of whole-genome analysis for infectious diseases can be used to enlighten various scenarios pertaining to public health, including identification of microbial pathogens, relating individual cases to an outbreak of infectious disease, establishing an association between an outbreak of food poisoning and a specific food vehicle, inferring drug susceptibility, source tracing of contaminants, and study of variations in the genome that affect pathogenicity/virulence. We describe the setup, validation, and ongoing verification of a centralized whole-genome-sequencing (WGS) laboratory to carry out sequencing for these public health functions for the National Infection Services, Public Health England, in the United Kingdom. The performance characteristics and quality control metrics measured during validation and verification of the entire end-to-end process (accuracy, precision, reproducibility, and repeatability) are described and include information regarding the automated pass and release of data to service users without intervention.
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28
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McLauchlin J, Aird H, Charlett A, Chattaway M, Elviss N, Hartman H, Jenkins C, Jørgensen F, Larkin L, Sadler-Reeves L, Willis C. Imported edible leaves collected at retail sale in England during 2017 with an emphasis on betel and curry leaves: microbiological quality with respect toSalmonella, Shiga-toxin-producingE. coli(STEC) and levels ofEscherichia coli. J Appl Microbiol 2018; 125:1175-1185. [DOI: 10.1111/jam.13931] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 11/29/2022]
Affiliation(s)
- J. McLauchlin
- Public Health England Food Water and Environmental Microbiology Services; National Infection Service; London UK
- Institute of Infection and Global Health; University of Liverpool; Liverpool UK
| | - H. Aird
- Public Health England Food Water and Environmental Microbiology Laboratory York; National Infection Service; York UK
| | - A. Charlett
- Public Health England Statistics, Modelling and Economics Department; National Infection Service; London UK
| | - M. Chattaway
- Public Health England Gastrointestinal Bacteria Reference Unit; National Infection Service; London UK
| | - N. Elviss
- Public Health England Food Water and Environmental Microbiology Laboratory London; National Infection Service; London UK
| | - H. Hartman
- Public Health England Gastrointestinal Bacteria Reference Unit; National Infection Service; London UK
| | - C. Jenkins
- Public Health England Gastrointestinal Bacteria Reference Unit; National Infection Service; London UK
| | - F. Jørgensen
- Public Health England Food Water and Environmental Microbiology Laboratory Porton; National Infection Service; Salisbury UK
| | - L. Larkin
- Public Health England; Gastrointestinal Infections Department; National Infection Service; London UK
| | - L. Sadler-Reeves
- Public Health England Food Water and Environmental Microbiology Laboratory Porton; National Infection Service; Salisbury UK
| | - C. Willis
- Public Health England Food Water and Environmental Microbiology Laboratory Porton; National Infection Service; Salisbury UK
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29
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Kiel M, Sagory-Zalkind P, Miganeh C, Stork C, Leimbach A, Sekse C, Mellmann A, Rechenmann F, Dobrindt U. Identification of Novel Biomarkers for Priority Serotypes of Shiga Toxin-Producing Escherichia coli and the Development of Multiplex PCR for Their Detection. Front Microbiol 2018; 9:1321. [PMID: 29997582 PMCID: PMC6028524 DOI: 10.3389/fmicb.2018.01321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/30/2018] [Indexed: 12/22/2022] Open
Abstract
It would be desirable to have an unambiguous scheme for the typing of Shiga toxin-producing Escherichia coli (STEC) isolates to subpopulations. Such a scheme should take the high genomic plasticity of E. coli into account and utilize the stratification of STEC into subgroups, based on serotype or phylogeny. Therefore, our goal was to identify specific marker combinations for improved classification of STEC subtypes. We developed and evaluated two bioinformatic pipelines for genomic marker identification from larger sets of bacterial genome sequences. Pipeline A performed all-against-all BLASTp analyses of gene products predicted in STEC genome test sets against a set of control genomes. Pipeline B identified STEC marker genes by comparing the STEC core proteome and the "pan proteome" of a non-STEC control group. Both pipelines defined an overlapping, but not identical set of discriminative markers for different STEC subgroups. Differential marker prediction resulted from differences in genome assembly, ORF finding and inclusion cut-offs in both workflows. Based on the output of the pipelines, we defined new specific markers for STEC serogroups and phylogenetic groups frequently associated with outbreaks and cases of foodborne illnesses. These included STEC serogroups O157, O26, O45, O103, O111, O121, and O145, Shiga toxin-positive enteroaggregative E. coli O104:H4, and HUS-associated sequence type (ST)306. We evaluated these STEC marker genes for their presence in whole genome sequence data sets. Based on the identified discriminative markers, we developed a multiplex PCR (mPCR) approach for detection and typing of the targeted STEC. The specificity of the mPCR primer pairs was verified using well-defined clinical STEC isolates as well as isolates from the ECOR, DEC, and HUSEC collections. The application of the STEC mPCR for food analysis was tested with inoculated milk. In summary, we evaluated two different strategies to screen large genome sequence data sets for discriminative markers and implemented novel marker genes found in this genome-wide approach into a DNA-based typing tool for STEC that can be used for the characterization of STEC from clinical and food samples.
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Affiliation(s)
- Matthias Kiel
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | - Céline Miganeh
- Genostar Bioinformatics, Montbonnot-Saint-Martin, France
| | - Christoph Stork
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | | | | | | | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
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30
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Willis C, Jørgensen F, Aird H, Elviss N, Fox A, Jenkins C, Fenelon D, Sadler-Reeves L, McLauchlin J. An assessment of the microbiological quality and safety of raw drinking milk on retail sale in England. J Appl Microbiol 2018; 124:535-546. [PMID: 29215775 DOI: 10.1111/jam.13660] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 01/02/2023]
Abstract
AIMS This study aimed to review the microbiological results for raw drinking milk (RDM) samples submitted to Public Health England laboratories between 2014 and 2016 in order to produce up-to-date data on the microbiological safety of RDM and inform future risk assessments on its sale. METHODS AND RESULTS A total of 902 samples of RDM were collected from retail sale in England for microbiological examination. Overall, 454 of 770 samples (59·0%) taken for routine monitoring were of a satisfactory quality, whilst eight (1·0%) were 'unsatisfactory and potentially injurious to health' due to the presence of Shiga toxin-producing Escherichia coli, Campylobacter or elevated levels of Listeria monocytogenes or coagulase-positive staphylococci. In contrast, 16 of 114 (14·0%) of samples taken in follow-up to a previous unsatisfactory result and 5 of 18 (27·8%) of samples related to illness were potentially injurious. A total of 229 of 902 samples (25·4%) gave unsatisfactory results due to elevated aerobic colony counts and/or coliforms, whilst 139 of 902 samples (15·4%) were of borderline quality due to coagulase-positive staphylococci. Listeria monocytogenes was detected at levels of <100 CFU per ml in 66 of 902 samples (7·3%) and other Listeria species in 44 of 902 samples (4·9%). CONCLUSIONS Pathogens and/or indicators of poor hygiene were present in almost half of samples examined. Cows' milk samples gave a significantly greater proportion of unsatisfactory results compared to milk from other species (i.e. goat, sheep, buffalo, camel). SIGNIFICANCE AND IMPACT OF THE STUDY These results demonstrate the importance of maintaining strict controls on the production and sale of this product.
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Affiliation(s)
- C Willis
- Public Health England Food Water and Environmental Microbiology Laboratory Porton, Salisbury, UK
| | - F Jørgensen
- Public Health England Food Water and Environmental Microbiology Laboratory Porton, Salisbury, UK
| | - H Aird
- Public Health England Food Water and Environmental Microbiology Laboratory York, York, UK
| | - N Elviss
- Public Health England Food Water and Environmental Microbiology Laboratory London, Colindale, London, UK
| | - A Fox
- Public Health England Food Water and Environmental Microbiology Laboratory York, York, UK
| | - C Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - D Fenelon
- Public Health England Food Water and Environmental Microbiology Laboratory London, Colindale, London, UK
| | - L Sadler-Reeves
- Public Health England Food Water and Environmental Microbiology Laboratory Porton, Salisbury, UK
| | - J McLauchlin
- Public Health England Food Water and Environmental Microbiology Services, Colindale, London, UK.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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31
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Gobin M, Hawker J, Cleary P, Inns T, Gardiner D, Mikhail A, McCormick J, Elson R, Ready D, Dallman T, Roddick I, Hall I, Willis C, Crook P, Godbole G, Tubin-Delic D, Oliver I. National outbreak of Shiga toxin-producing Escherichia coli O157:H7 linked to mixed salad leaves, United Kingdom, 2016. Euro Surveill 2018; 23:17-00197. [PMID: 29741151 PMCID: PMC6053625 DOI: 10.2807/1560-7917.es.2018.23.18.17-00197] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/21/2017] [Indexed: 11/20/2022] Open
Abstract
We investigated a large outbreak of Escherichia coli O157 in the United Kingdom (UK) with 165 cases between 31 May and 29 July 2016. No linked cases were reported in other countries. Cases were predominately female (n = 128) and adult (n = 150), 66 attended hospital and nine had features of haemorrhagic uraemic syndrome. A series of epidemiological studies (case-control, case-case, ingredients-based and venue-based studies) and supply chain investigations implicated mixed salad leaves from Supplier A as the likely outbreak vehicle. Whole genome sequencing (WGS) indicated a link with strains from the Mediterranean and informed the outbreak control team to request that Supplier A cease distributing salad leaves imported from Italy. Microbiological tests of samples of salad leaves from Supplier A were negative. We were unable to confirm the source of contamination or the contaminated constituent leaf although our evidence pointed to red batavia received from Italy as the most likely vehicle. Variations in Shiga toxin-producing E.coli surveillance and diagnosis may have prevented detection of cases outside the UK and highlights a need for greater standardisation. WGS was useful in targeting investigations, but greater coverage across Europe is needed to maximise its potential.
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Affiliation(s)
- Maya Gobin
- Field Epidemiology Services, Public Health England, London, United Kingdom
| | - Jeremy Hawker
- Field Epidemiology Services, Public Health England, London, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
| | - Paul Cleary
- Field Epidemiology Services, Public Health England, London, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
| | - Thomas Inns
- Field Epidemiology Services, Public Health England, London, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
| | - Daniel Gardiner
- Field Epidemiology Services, Public Health England, London, United Kingdom
- Field Epidemiology Training Programme, Public Health England, London, United Kingdom
| | - Amy Mikhail
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
| | - Jacquelyn McCormick
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
| | - Richard Elson
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
| | - Derren Ready
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
| | - Tim Dallman
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
| | - Iain Roddick
- Field Epidemiology Services, Public Health England, London, United Kingdom
| | - Ian Hall
- Emergency Response Department Science and Technology, Public Health England, Salisbury, United Kingdom
| | - Caroline Willis
- Food Water and Environmental Microbiology Laboratory Porton, Public Health England, Salisbury, United Kingdom
| | - Paul Crook
- Field Epidemiology Services, Public Health England, London, United Kingdom
| | - Gauri Godbole
- Field Epidemiology Training Programme, Public Health England, London, United Kingdom
| | | | - Isabel Oliver
- Field Epidemiology Services, Public Health England, London, United Kingdom
- NIHR Health Protection Research Unit in Evaluation of Interventions at the University of Bristol, Bristol, England
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32
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Yahata Y, Ohshima N, Odaira F, Nakamura N, Ichikawa H, Ichikawa H, Matsuno K, Shuri J, Toyozawa T, Terajima J, Watanabe H, Nakashima K, Sunagawa T, Taniguchi K, Okabe N. Web survey-based selection of controls for epidemiological analyses of a multi-prefectural outbreak of enterohaemorrhagic Escherichia coli O157 in Japan associated with consumption of self-grilled beef hanging tender. Epidemiol Infect 2018; 146:450-457. [PMID: 29397049 PMCID: PMC9134521 DOI: 10.1017/s0950268817003132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 12/03/2017] [Accepted: 12/08/2017] [Indexed: 11/06/2022] Open
Abstract
An outbreak of enterohaemorrhagic Escherichia coli O157 occurred in multiple prefectures of Japan in November 2009. We conducted two case-control studies with trace-back and trace-forward investigations to determine the source. The case definition was met by 21 individuals; 14 (66.7%) were hospitalised, but no haemolytic uraemic syndrome, acute encephalopathy or deaths occurred. Median age was 23 (range 12-48) years and 14 cases were male (66.7%). No significant associations with food were found in a case-control study by local public health centres, but our matched case-control study using Internet surveys found that beef hanging tender (or hanger steak), derived from the diaphragm of the cattle, was significantly associated with illness (odds ratio = 15.77; 95% confidence interval, 2.00-124.11). Pulsed-field gel electrophoresis analysis of isolates from patients and the suspected food showed five different patterns: two in faecal and food samples, and another three in patient faecal samples only, although there were epidemiological links to the meat consumed at the restaurants. Trace-back investigation implicated a common food processing company from outside Japan. Examination of the logistics of the meat processing company suggested that contamination did not occur in Japan. We concluded that the source of the outbreak was imported hanging tender. This investigation revealed that Internet surveys could be useful for outbreak investigations.
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Affiliation(s)
- Y. Yahata
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - N. Ohshima
- Public Health Center, Medical Care Bureau, City of Yokohama, Kanagawa 231-0015, Japan
| | - F. Odaira
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- Osaka Psychiatric Medical Center, Osaka 573-0022, Japan
| | - N. Nakamura
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- Medical Corporations ARCWELL, Kanagawa 213-0001, Japan
| | - H. Ichikawa
- Public Health Center, Medical Care Bureau, City of Yokohama, Kanagawa 231-0015, Japan
| | - H. Ichikawa
- Public Health Center, Medical Care Bureau, City of Yokohama, Kanagawa 231-0015, Japan
| | - K. Matsuno
- Public Health Center, Medical Care Bureau, City of Yokohama, Kanagawa 231-0015, Japan
| | - J. Shuri
- Public Health Center, Medical Care Bureau, City of Yokohama, Kanagawa 231-0015, Japan
| | - T. Toyozawa
- Public Health Center, Medical Care Bureau, City of Yokohama, Kanagawa 231-0015, Japan
| | - J. Terajima
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- Iwate University, Iwate 020-8550, Japan
| | - H. Watanabe
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- International University of Health and Welfare, Akasaka, Tokyo 107-8402, Japan
| | - K. Nakashima
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- Daito Bunka University, Saitama 355-0054, Japan
| | - T. Sunagawa
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - K. Taniguchi
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- National Hospital Organization Mie National Hospital, Mie 514-0125, Japan
| | - N. Okabe
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
- Kawasaki City Institute for Public Health, Kanagawa 201-0821, Japan
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33
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MIKHAIL AFW, JENKINS C, DALLMAN TJ, INNS T, DOUGLAS A, MARTÍN AIC, FOX A, CLEARY P, ELSON R, HAWKER J. An outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with contaminated salad leaves: epidemiological, genomic and food trace back investigations. Epidemiol Infect 2018; 146:187-196. [PMID: 29248018 PMCID: PMC9134740 DOI: 10.1017/s0950268817002874] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 11/06/2022] Open
Abstract
In August 2015, Public Health England detected an outbreak of Shiga toxin-producing Escherichia coli (STEC) serotype O157:H7 caused by contaminated salad leaves in a mixed leaf prepacked salad product from a national retailer. The implicated leaves were cultivated at five different farms and the zoonotic source of the outbreak strain was not determined. In March 2016, additional isolates from new cases were identified that shared a recent common ancestor with the outbreak strain. A case-case study involving the cases identified in 2016 revealed that ovine exposures were associated with illness (n = 16; AOR 8·24; 95% CI 1·55-39·74). By mapping the recent movement of sheep and lambs across the United Kingdom, epidemiological links were established between the cases reporting ovine exposures. Given the close phylogenetic relationship between the outbreak strain and the isolates from cases with ovine exposures, it is plausible that ovine faeces may have contaminated the salad leaves via untreated irrigation water or run-off from fields nearby. Timely and targeted veterinary and environmental sampling should be considered during foodborne outbreaks of STEC, particularly where ready to eat vegetables and salads are implicated.
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Affiliation(s)
| | - C. JENKINS
- National Infection Service, Public Health England, London, UK
| | - T. J. DALLMAN
- National Infection Service, Public Health England, London, UK
| | - T. INNS
- Field Epidemiology Services, Public Health England, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, London, UK
| | - A. DOUGLAS
- National Infection Service, Public Health England, London, UK
| | - A. I. C. MARTÍN
- European Program for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - A. FOX
- National Infection Service, Public Health England, London, UK
| | - P. CLEARY
- Field Epidemiology Services, Public Health England, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, London, UK
| | - R. ELSON
- National Infection Service, Public Health England, London, UK
| | - J. HAWKER
- Field Epidemiology Services, Public Health England, London, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, London, UK
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34
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Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I, Concepcion-Acevedo J, Gilpin B, Smith AM, Man Kam K, Perez E, Trees E, Kubota K, Takkinen J, Nielsen EM, Carleton H. PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. ACTA ACUST UNITED AC 2017; 22:30544. [PMID: 28662764 PMCID: PMC5479977 DOI: 10.2807/1560-7917.es.2017.22.23.30544] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/11/2017] [Indexed: 11/21/2022]
Abstract
PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies. WGS data are suitable for surveillance and outbreak purposes and for answering scientific questions pertaining to source attribution, antimicrobial resistance, transmission patterns, and virulence, which will further enable the protection and improvement of public health with respect to food-borne disease.
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Affiliation(s)
- Celine Nadon
- Public Health Agency of Canada, National Microbiology Laboratory, Canada.,These authors contributed equally to this work
| | - Ivo Van Walle
- These authors contributed equally to this work.,European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Josefina Campos
- National Institute of Infectious Diseases "Dr Carlos G. Malbran", Argentina
| | - Isabel Chinen
- National Institute of Infectious Diseases "Dr Carlos G. Malbran", Argentina
| | | | - Brent Gilpin
- Institute of Environmental Science and Research Limited; Christchurch, New Zealand
| | | | - Kai Man Kam
- Chinese University of Hong Kong, Hong Kong Special Adminstrative Region, China
| | - Enrique Perez
- Pan American Health Organization/World Health Organization, Washington, DC, United States
| | - Eija Trees
- Centers for Disease Control and Prevention, United States
| | - Kristy Kubota
- Association of Public Health Laboratories, United States
| | - Johanna Takkinen
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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- The members of the FWD-NEXT Expert Panel are listed at the end of the article
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35
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Rantsiou K, Kathariou S, Winkler A, Skandamis P, Saint-Cyr MJ, Rouzeau-Szynalski K, Amézquita A. Next generation microbiological risk assessment: opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment. Int J Food Microbiol 2017; 287:3-9. [PMID: 29246458 DOI: 10.1016/j.ijfoodmicro.2017.11.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/16/2017] [Accepted: 11/12/2017] [Indexed: 12/11/2022]
Abstract
Whole genome sequencing (WGS) of important foodborne pathogens is a technology under development, but is already employed in routine surveillance by public health agencies and is being increasingly exploited in tracing transmission routes and identifying contamination events (source tracking) that take place in the farm-to-fork continuum. Furthermore, data generated from WGS, complemented by other -omics data, have the potential to be integrated into and strengthen microbiological risk assessment. In this paper, we discuss the contribution of WGS in diverse areas important to food safety and public health. Additionally, an outlook of future WGS applications, which should contribute to our understanding of the ecology and physiology of foodborne microorganisms, is presented.
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Affiliation(s)
- Kalliopi Rantsiou
- Department of Agriculture, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy.
| | - Sophia Kathariou
- North Carolina State University, Department of Food, Bioprocessing and Nutrition Sciences, Raleigh, NC, USA
| | - Annet Winkler
- Mondelez International, Kraft Foods R&D, Unterbiberger St. 15, D-81737 Munich, Germany
| | - Panos Skandamis
- Laboratory of Food Quality Control & Hygiene, Department of Food Science & Technology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | | | | | - Alejandro Amézquita
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
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36
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Waldram A, Dolan G, Ashton PM, Jenkins C, Dallman TJ. Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, England and Wales 2014. Food Microbiol 2017; 71:39-45. [PMID: 29366467 DOI: 10.1016/j.fm.2017.02.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/30/2017] [Accepted: 02/09/2017] [Indexed: 11/18/2022]
Abstract
The unprecedented level of bacterial strain discrimination provided by whole genome sequencing (WGS) presents new challenges with respect to the utility and interpretation of the data. Whole genome sequences from 1445 isolates of Salmonella belonging to the most commonly identified serotypes in England and Wales isolated between April and August 2014 were analysed. Single linkage single nucleotide polymorphism thresholds at the 10, 5 and 0 level were explored for evidence of epidemiological links between clustered cases. Analysis of the WGS data organised 566 of the 1445 isolates into 32 clusters of five or more. A statistically significant epidemiological link was identified for 17 clusters. The clusters were associated with foreign travel (n = 8), consumption of Chinese takeaways (n = 4), chicken eaten at home (n = 2), and one each of the following; eating out, contact with another case in the home and contact with reptiles. In the same time frame, one cluster was detected using traditional outbreak detection methods. WGS can be used for the highly specific and highly sensitive detection of biologically related isolates when epidemiological links are obscured. Improvements in the collection of detailed, standardised exposure information would enhance cluster investigations.
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Affiliation(s)
- Alison Waldram
- Field Epidemiology Services, National Infection Service, Public Health England, UK; Field Epidemiology Training Programme, Public Health England, London, UK; European Programme for Intervention Epidemiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Gayle Dolan
- Field Epidemiology Services, National Infection Service, Public Health England, UK; Field Epidemiology Training Programme, Public Health England, London, UK; European Programme for Intervention Epidemiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Philip M Ashton
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, London, UK
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, London, UK.
| | - Timothy J Dallman
- Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, London, UK
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37
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ROWELL S, KING C, JENKINS C, DALLMAN TJ, DECRAENE V, LAMDEN K, HOWARD A, FEATHERSTONE CA, CLEARY P. An outbreak of Shiga toxin-producing Escherichia coli serogroup O157 linked to a lamb-feeding event. Epidemiol Infect 2016; 144:2494-500. [PMID: 27297133 PMCID: PMC9150456 DOI: 10.1017/s0950268816001229] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 04/29/2016] [Accepted: 05/25/2016] [Indexed: 11/07/2022] Open
Abstract
Fifteen confirmed cases and 15 possible cases of Shiga toxin-producing Escherichia coli (STEC) O157 phage type 21/28 were linked to direct contact with lambs at a 'Lambing Live' event in the North West of England between 29 March and 21 April 2014. Twenty-one (70%) of the cases were female, 23 (77%) were children aged <16 years, of whom 14 (46%) were in the 0-5 years age group. Five children developed haemolytic uraemic syndrome. Multilocus variable number tandem repeat analysis (MLVA) profiles on 14 human cases were indistinguishable, and 6/10 animal isolates had a MLVA profile identical to the outbreak profile. Whole-genome sequencing analysis revealed that all isolates, both human and animal, fell within a 5-single nucleotide polymorphism cluster indicating the isolates belonged to the same point source. On inspection of the premises, extensive and uncontrolled physical contact between visitors and animals was occuring within the animal pens and during bottle-feeding. Public areas were visibly contaminated with animal faeces. Information to visitors, and the infection control awareness demonstrated by staff, was inadequate. Managing the risk to visitors of STEC O157 infection at animal petting events and open farms requires implementation of stringent control measures by the operator, as outlined in the industry code of practice. Enforcement action is sometimes required to prevent high-risk activities taking place at both permanent and temporary attractions.
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Affiliation(s)
- S. ROWELL
- Cumbria and Lancashire Public Health England Centre, Chorley, Lancashire, UK
| | - C. KING
- Cumbria and Lancashire Public Health England Centre, Chorley, Lancashire, UK
| | - C. JENKINS
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - T. J. DALLMAN
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - V. DECRAENE
- Field Epidemiology Service North West, Public Health England, UK
| | - K. LAMDEN
- Cumbria and Lancashire Public Health England Centre, Chorley, Lancashire, UK
| | - A. HOWARD
- South Ribble Borough Council, Leyland, Lancashire, UK
| | - C. A. FEATHERSTONE
- Animal and Plant Health Agency, Veterinary Investigation Centre, Thirsk, North Yorkshire, UK
| | - P. CLEARY
- Field Epidemiology Service North West, Public Health England, UK
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