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Chase-Topping M, Dallman TJ, Allison L, Lupolova N, Matthews L, Mitchell S, Banks CJ, Prentice J, Brown H, Tongue S, Henry M, Evans J, Gunn G, Hoyle D, McNeilly TN, Fitzgerald S, Smith-Palmer A, Shaaban S, Holmes A, Hanson M, Woolhouse M, Didelot X, Jenkins C, Gally DL. Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health. Microb Genom 2023; 9:001090. [PMID: 37672388 PMCID: PMC10569735 DOI: 10.1099/mgen.0.001090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023] Open
Abstract
For the last two decades, the human infection frequency of Escherichia coli O157 (O157) in Scotland has been 2.5-fold higher than in England and Wales. Results from national cattle surveys conducted in Scotland and England and Wales in 2014/2015 were combined with data on reported human clinical cases from the same time frame to determine if strain differences in national populations of O157 in cattle could be associated with higher human infection rates in Scotland. Shiga toxin subtype (Stx) and phage type (PT) were examined within and between host (cattle vs human) and nation (Scotland vs England and Wales). For a subset of the strains, whole genome sequencing (WGS) provided further insights into geographical and host association. All three major O157 lineages (I, II, I/II) and most sub-lineages (Ia, Ib, Ic, IIa, IIb, IIc) were represented in cattle and humans in both nations. While the relative contribution of different reservoir hosts to human infection is unknown, WGS analysis indicated that the majority of O157 diversity in human cases was captured by isolates from cattle. Despite comparable cattle O157 prevalence between nations, strain types were localized. PT21/28 (sub-lineage Ic, Stx2a+) was significantly more prevalent in Scottish cattle [odds ratio (OR) 8.7 (2.3-33.7; P<0.001] and humans [OR 2.2 (1.5-3.2); P<0.001]. In England and Wales, cattle had a significantly higher association with sub-lineage IIa strains [PT54, Stx2c; OR 5.6 (1.27-33.3); P=0.011] while humans were significantly more closely associated with sub-lineage IIb [PT8, Stx1 and Stx2c; OR 29 (4.9-1161); P<0.001]. Therefore, cattle farms in Scotland were more likely to harbour Stx2a+O157 strains compared to farms in E and W (P<0.001). There was evidence of limited cattle strain migration between nations and clinical isolates from one nation were more similar to cattle isolates from the same nation, with sub-lineage Ic (mainly PT21/28) exhibiting clear national association and evidence of local transmission in Scotland. While we propose the higher rate of O157 clinical cases in Scotland, compared to England and Wales, is a consequence of the nationally higher level of Stx2a+O157 strains in Scottish cattle, we discuss the multiple additional factors that may also contribute to the different infection rates between these nations.
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Affiliation(s)
- Margo Chase-Topping
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Timothy J. Dallman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5HT, UK
| | - Lesley Allison
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Nadejda Lupolova
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Louise Matthews
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sonia Mitchell
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Christopher J. Banks
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Jamie Prentice
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Helen Brown
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Sue Tongue
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Madeleine Henry
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Judith Evans
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - George Gunn
- Epidemiology Research Unit, Scotland’s Rural College, Inverness IV2 5NA, UK
| | - Deborah Hoyle
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | - Stephen Fitzgerald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | | | - Sharif Shaaban
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Anne Holmes
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Mary Hanson
- Scottish E. coli O157/STEC Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh EH9 3DL, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Warwick CV4 7AL, UK
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, London NW9 5HT, UK
| | - David L. Gally
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
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Greig DR, Jenkins C, Gharbia SE, Dallman TJ. Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing. Microb Genom 2021; 7:mgen000545. [PMID: 33683192 PMCID: PMC8190617 DOI: 10.1099/mgen.0.000545] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/15/2021] [Indexed: 12/03/2022] Open
Abstract
Compared to short-read sequencing data, long-read sequencing facilitates single contiguous de novo assemblies and characterization of the prophage region of the genome. Here, we describe our methodological approach to using Oxford Nanopore Technology (ONT) sequencing data to quantify genetic relatedness and to look for microevolutionary events in the core and accessory genomes to assess the within-outbreak variation of four genetically and epidemiologically linked isolates. Analysis of both Illumina and ONT sequencing data detected one SNP between the four sequences of the outbreak isolates. The variant calling procedure highlighted the importance of masking homologous sequences in the reference genome regardless of the sequencing technology used. Variant calling also highlighted the systemic errors in ONT base-calling and ambiguous mapping of Illumina reads that results in variations in the genetic distance when comparing one technology to the other. The prophage component of the outbreak strain was analysed, and nine of the 16 prophages showed some similarity to the prophage in the Sakai reference genome, including the stx2a-encoding phage. Prophage comparison between the outbreak isolates identified minor genome rearrangements in one of the isolates, including an inversion and a deletion event. The ability to characterize the accessory genome in this way is the first step to understanding the significance of these microevolutionary events and their impact on the evolutionary history, virulence and potentially the likely source and transmission of this zoonotic, foodborne pathogen.
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Affiliation(s)
- David R. Greig
- National Infection Service, Public Health England, London, NW9 5EQ, UK
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Claire Jenkins
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Saheer E. Gharbia
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Timothy J. Dallman
- National Infection Service, Public Health England, London, NW9 5EQ, UK
- Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
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3
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Tamminen LM, Söderlund R, Wilkinson DA, Torsein M, Eriksson E, Churakov M, Dicksved J, Keeling LJ, Emanuelson U. Risk factors and dynamics of verotoxigenic Escherichia coli O157:H7 on cattle farms: An observational study combining information from questionnaires, spatial data and molecular analyses. Prev Vet Med 2019; 170:104726. [PMID: 31421496 DOI: 10.1016/j.prevetmed.2019.104726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/02/2019] [Indexed: 01/29/2023]
Abstract
The increasing number of human cases infected with a highly virulent type of verotoxigenic Escherichia coli (VTEC) O157:H7 in Sweden is the result of domestic transmission originating in regional clusters of infected cattle farms. To control the spread of the bacteria a comprehensive picture of infection dynamics, routes of transmission between farms and risk factors for persistence is urgently needed. The aim of the study was to investigate different aspects of the epidemiology of VTEC O157:H7 on the Swedish island of Öland by combining information from environmental sampling of VTEC O157:H7 from 80 farms with information from farmer questionnaires, spatial and molecular analyses. The farms were sampled in the spring and fall of 2014 and on four of them additional samples were collected during summer and winter. The results show a high prevalence of VTEC O157:H7 and a high proportion of strains belonging to the virulent clade 8. Farms that became infected between samplings were all located in an area with high cattle density. The most important risk factors identified are generally associated with biosecurity and indicate that visitors travelling between farms may be important for transmission. In addition, whole genome sequencing of a subset of isolates from the four farms where additional sampling was performed revealed ongoing local transmission that cannot be observed with a lower resolution typing method. Our observations also show that VTEC O157:H7 may persist in the farm environment for extended periods of time, suggesting that specific on-farm measures to reduce environmental prevalence and spread between groups of animals may be required in these cases.
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Affiliation(s)
- Lena-Mari Tamminen
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-75007, Uppsala, Sweden.
| | | | - David A Wilkinson
- Molecular Epidemiology and Public Health Laboratory (mEpilab), Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand; New Zealand Food Safety Science and Research Centre, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Maria Torsein
- Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Box 234, SE-53223, Skara, Sweden
| | - Erik Eriksson
- National Veterinary Institute (SVA), SE-75189, Uppsala, Sweden
| | - Mikhail Churakov
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Box 7024, SE-75007, Uppsala, Sweden
| | - Johan Dicksved
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Box 7024, SE-75007, Uppsala, Sweden
| | - Linda J Keeling
- Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Box 7068, SE-75007, Uppsala, Sweden
| | - Ulf Emanuelson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-75007, Uppsala, Sweden
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4
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Nyberg K, Andersson G, Elving J. Long-term survival ofEscherichia coliO157:H7 andSalmonellaTyphimurium in cowpats on pasture. J Appl Microbiol 2018; 126:651-660. [DOI: 10.1111/jam.14148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 10/15/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Affiliation(s)
- K.A. Nyberg
- Department of Chemistry, Environment and Feed Hygiene; National Veterinary Institute; Uppsala Sweden
- Risk Benefit Assessment Department; National Food Agency; Uppsala Sweden
| | - G.M. Andersson
- Department of Chemistry, Environment and Feed Hygiene; National Veterinary Institute; Uppsala Sweden
| | - J. Elving
- Department of Chemistry, Environment and Feed Hygiene; National Veterinary Institute; Uppsala Sweden
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5
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Widgren S, Engblom S, Emanuelson U, Lindberg A. Spatio-temporal modelling of verotoxigenic Escherichia coli O157 in cattle in Sweden: exploring options for control. Vet Res 2018; 49:78. [PMID: 30068384 PMCID: PMC6071428 DOI: 10.1186/s13567-018-0574-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/20/2018] [Indexed: 01/21/2023] Open
Abstract
A spatial data-driven stochastic model was developed to explore the spread of verotoxigenic Escherichia coli O157 (VTEC O157) by livestock movements and local transmission among neighbouring holdings in the complete Swedish cattle population. Livestock data were incorporated to model the time-varying contact network between holdings and population demographics. Furthermore, meteorological data with the average temperature at the geographical location of each holding was used to incorporate season. The model was fitted against observed data and extensive numerical experiments were conducted to investigate the model’s response to control strategies aimed at reducing shedding and susceptibility, as well as interventions informed by network measures. The results showed that including local spread and season improved agreement with prevalence studies. Also, control strategies aimed at reducing the average shedding rate were more efficient in reducing the VTEC O157 prevalence than strategies based on network measures. The methodology presented in this study could provide a basis for developing disease surveillance on regional and national scales, where observed data are combined with readily available high-resolution data in simulations to get an overview of potential disease spread in unobserved regions.
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Affiliation(s)
- Stefan Widgren
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89, Uppsala, Sweden. .,Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05, Uppsala, Sweden.
| | - Stefan Engblom
- Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05, Uppsala, Sweden
| | - Ulf Emanuelson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden
| | - Ann Lindberg
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89, Uppsala, Sweden
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6
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Tarr GAM, Shringi S, Phipps AI, Besser TE, Mayer J, Oltean HN, Wakefield J, Tarr PI, Rabinowitz P. Geogenomic Segregation and Temporal Trends of Human Pathogenic Escherichia coli O157:H7, Washington, USA, 2005-2014 1. Emerg Infect Dis 2018; 24:32-39. [PMID: 29260688 PMCID: PMC5749469 DOI: 10.3201/eid2401.170851] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The often-noted and persistent increased incidence of Escherichia
coli O157:H7 infections in rural areas is not well understood. We
used a cohort of E. coli O157:H7 cases reported in Washington,
USA, during 2005–2014, along with phylogenomic characterization of the
infecting isolates, to identify geographic segregation of and temporal trends in
specific phylogenetic lineages of E. coli O157:H7. Kernel
estimation and generalized additive models demonstrated that pathogen lineages
were spatially segregated during the period of analysis and identified a focus
of segregation spanning multiple, predominantly rural, counties for each of the
main clinical lineages, Ib, IIa, and IIb. These results suggest the existence of
local reservoirs from which humans are infected. We also noted a secular
increase in the proportion of lineage IIa and IIb isolates. Spatial segregation
by phylogenetic lineage offers the potential to identify local reservoirs and
intervene to prevent continued transmission.
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7
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Tamminen LM, Fransson H, Tråvén M, Aspán A, Alenius S, Emanuelson U, Dreimanis I, Törnquist M, Eriksson E. Effect of on-farm interventions in the aftermath of an outbreak of hypervirulent verocytotoxin-producing Escherichia coli
O157:H7 in Sweden. Vet Rec 2018; 182:516. [DOI: 10.1136/vr.104223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 11/13/2017] [Accepted: 01/21/2018] [Indexed: 11/04/2022]
Affiliation(s)
- Lena-Mari Tamminen
- Section of Ruminant Medicine and Epidemiology, Department of Clinical Sciences; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Helena Fransson
- Section of Ruminant Medicine and Epidemiology, Department of Clinical Sciences; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Madeleine Tråvén
- Section of Ruminant Medicine and Epidemiology, Department of Clinical Sciences; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Anna Aspán
- Department of Microbiology; National Veterinary Institute; Uppsala Sweden
| | - Stefan Alenius
- Section of Ruminant Medicine and Epidemiology, Department of Clinical Sciences; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Ulf Emanuelson
- Section of Ruminant Medicine and Epidemiology, Department of Clinical Sciences; Swedish University of Agricultural Sciences; Uppsala Sweden
| | | | | | - Erik Eriksson
- Department of Microbiology; National Veterinary Institute; Uppsala Sweden
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8
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British Escherichia coli O157 in Cattle Study (BECS): to determine the prevalence of E. coli O157 in herds with cattle destined for the food chain. Epidemiol Infect 2017; 145:3168-3179. [PMID: 28925340 PMCID: PMC9148770 DOI: 10.1017/s0950268817002151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Escherichia coli O157 are zoonotic bacteria for which cattle are an important reservoir. Prevalence estimates for E. coli O157 in British cattle for human consumption are over 10 years old. A new baseline is needed to inform current human health risk. The British E. coli O157 in Cattle Study (BECS) ran between September 2014 and November 2015 on 270 farms across Scotland and England & Wales. This is the first study to be conducted contemporaneously across Great Britain, thus enabling comparison between Scotland and England & Wales. Herd-level prevalence estimates for E. coli O157 did not differ significantly for Scotland (0·236, 95% CI 0·166-0·325) and England & Wales (0·213, 95% CI 0·156-0·283) (P = 0·65). The majority of isolates were verocytotoxin positive. A higher proportion of samples from Scotland were in the super-shedder category, though there was no difference between the surveys in the likelihood of a positive farm having at least one super-shedder sample. E. coli O157 continues to be common in British beef cattle, reaffirming public health policy that contact with cattle and their environments is a potential infection source.
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9
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Worley JN, Flores KA, Yang X, Chase JA, Cao G, Tang S, Meng J, Atwill ER. Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California. Appl Environ Microbiol 2017; 83:e00734-17. [PMID: 28550057 PMCID: PMC5541215 DOI: 10.1128/aem.00734-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/17/2017] [Indexed: 01/12/2023] Open
Abstract
Escherichia coli serotype O157:H7 is a zoonotic food- and waterborne bacterial pathogen that causes a high hospitalization rate and can cause life-threatening complications. Increasingly, E. coli O157:H7 infections appear to originate from fresh produce. Ruminants, such as cattle, are a prominent reservoir of E. coli O157:H7 in the United States. California is one of the most agriculturally productive regions in the world for fresh produce, beef, and milk. The close proximity of fresh produce and cattle presents food safety challenges on a uniquely large scale. We performed a survey of E. coli O157:H7 on 20 farms in California to observe the regional diversity and prevalence of E. coli O157:H7. Isolates were obtained from enrichment cultures of cow feces. Some farms were sampled on two dates. Genomes from isolates were sequenced to determine their relatedness and pathogenic potential. E. coli O157:H7 was isolated from approximately half of the farms. The point prevalence of E. coli O157:H7 on farms was highly variable, ranging from zero to nearly 90%. Within farms, generally one or a few lineages were found, even when the rate of isolation was high. On farms with high isolation rates, a single clonal lineage accounted for most of the isolates. Farms that were visited months after the first visit might have had the same lineages of E. coli O157:H7. Strains of E. coli O157:H7 may be persistent for months on farms.IMPORTANCE This survey of 20 cow-calf operations from different regions of California provides an in depth look at resident Escherichia coli O157:H7 populations at the molecular level. E. coli O157:H7 is found to have a highly variable prevalence, and with whole-genome sequencing, high prevalences in herds were found to be due to a single lineage shed from multiple cows. Few repeat lineages were found between farms in this area; therefore, we predict that E. coli O157:H7 has significant diversity in this area beyond what is detected in this survey. All isolates from this study were found to have pathogenic potential based on the presence of key virulence gene sequences. This represents a novel insight into pathogen diversity within a single subtype and will inform future attempts to survey regional pathogen populations.
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Affiliation(s)
- Jay N Worley
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, USA
| | - Kristopher A Flores
- Western Center for Food Safety, University of California, Davis, Davis, California, USA
| | - Xun Yang
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Jennifer A Chase
- Western Center for Food Safety, University of California, Davis, Davis, California, USA
| | - Guojie Cao
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, USA
| | - Shuai Tang
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, USA
| | - Edward R Atwill
- Western Center for Food Safety, University of California, Davis, Davis, California, USA
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10
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Reducing Foodborne Pathogen Persistence and Transmission in Animal Production Environments: Challenges and Opportunities. Microbiol Spectr 2017; 4. [PMID: 27726803 DOI: 10.1128/microbiolspec.pfs-0006-2014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Preharvest strategies to reduce zoonotic pathogens in food animals are important components of the farm-to-table food safety continuum. The problem is complex; there are multiple pathogens of concern, multiple animal species under different production and management systems, and a variety of sources of pathogens, including other livestock and domestic animals, wild animals and birds, insects, water, and feed. Preharvest food safety research has identified a number of intervention strategies, including probiotics, direct-fed microbials, competitive exclusion cultures, vaccines, and bacteriophages, in addition to factors that can impact pathogens on-farm, such as seasonality, production systems, diet, and dietary additives. Moreover, this work has revealed both challenges and opportunities for reducing pathogens in food animals. Animals that shed high levels of pathogens and predominant pathogen strains that exhibit long-term persistence appear to play significant roles in maintaining the prevalence of pathogens in animals and their production environment. Continued investigation and advancements in sequencing and other technologies are expected to reveal the mechanisms that result in super-shedding and persistence, in addition to increasing the prospects for selection of pathogen-resistant food animals and understanding of the microbial ecology of the gastrointestinal tract with regard to zoonotic pathogen colonization. It is likely that this continued research will reveal other challenges, which may further indicate potential targets or critical control points for pathogen reduction in livestock. Additional benefits of the preharvest reduction of pathogens in food animals are the reduction of produce, water, and environmental contamination, and thereby lower risk for human illnesses linked to these sources.
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11
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Chen S, Sanderson MW, Lee C, Cernicchiaro N, Renter DG, Lanzas C. Basic Reproduction Number and Transmission Dynamics of Common Serogroups of Enterohemorrhagic Escherichia coli. Appl Environ Microbiol 2016; 82:5612-20. [PMID: 27401976 PMCID: PMC5007764 DOI: 10.1128/aem.00815-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/01/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Understanding the transmission dynamics of pathogens is essential to determine the epidemiology, ecology, and ways of controlling enterohemorrhagic Escherichia coli (EHEC) in animals and their environments. Our objective was to estimate the epidemiological fitness of common EHEC strains in cattle populations. For that purpose, we developed a Markov chain model to characterize the dynamics of 7 serogroups of enterohemorrhagic Escherichia coli (O26, O45, O103, O111, O121, O145, and O157) in cattle production environments based on a set of cross-sectional data on infection prevalence in 2 years in two U.S. states. The basic reproduction number (R0) was estimated using a Bayesian framework for each serogroup based on two criteria (using serogroup alone [the O-group data] and using O serogroup, Shiga toxin gene[s], and intimin [eae] gene together [the EHEC data]). In addition, correlations between external covariates (e.g., location, ambient temperature, dietary, and probiotic usage) and prevalence/R0 were quantified. R0 estimates varied substantially among different EHEC serogroups, with EHEC O157 having an R0 of >1 (∼1.5) and all six other EHEC serogroups having an R0 of less than 1. Using the O-group data substantially increased R0 estimates for the O26, O45, and O103 serogroups (R0 > 1) but not for the others. Different covariates had distinct influences on different serogroups: the coefficients for each covariate were different among serogroups. Our modeling and analysis of this system can be readily expanded to other pathogen systems in order to estimate the pathogen and external factors that influence spread of infectious agents. IMPORTANCE In this paper we describe a Bayesian modeling framework to estimate basic reproduction numbers of multiple serotypes of Shiga toxin-producing Escherichia coli according to a cross-sectional study. We then coupled a compartmental model to reconstruct the infection dynamics of these serotypes and quantify their risk in the population. We incorporated different sensitivity levels of detecting different serotypes and evaluated their potential influence on the estimation of basic reproduction numbers.
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Affiliation(s)
- Shi Chen
- Department of Public Health Sciences, University of North Carolina Charlotte, Charlotte, North Carolina, USA Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael W Sanderson
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - Chihoon Lee
- School of Business, Stevens Institute of Technology, Hoboken, New Jersey, USA Department of Statistics, Colorado State University, Fort Collins, Colorado, USA
| | - Natalia Cernicchiaro
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - David G Renter
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - Cristina Lanzas
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA
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12
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Widgren S, Engblom S, Bauer P, Frössling J, Emanuelson U, Lindberg A. Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle. Vet Res 2016; 47:81. [PMID: 27515697 PMCID: PMC4982012 DOI: 10.1186/s13567-016-0366-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 07/18/2016] [Indexed: 11/10/2022] Open
Abstract
European Union legislation requires member states to keep national databases of all bovine animals. This allows for disease spread models that includes the time-varying contact network and population demographic. However, performing data-driven simulations with a high degree of detail are computationally challenging. We have developed an efficient and flexible discrete-event simulator SimInf for stochastic disease spread modelling that divides work among multiple processors to accelerate the computations. The model integrates disease dynamics as continuous-time Markov chains and livestock data as events. In this study, all Swedish livestock data (births, movements and slaughter) from July 1st 2005 to December 31st 2013 were included in the simulations. Verotoxigenic Escherichia coli O157:H7 (VTEC O157) are capable of causing serious illness in humans. Cattle are considered to be the main reservoir of the bacteria. A better understanding of the epidemiology in the cattle population is necessary to be able to design and deploy targeted measures to reduce the VTEC O157 prevalence and, subsequently, human exposure. To explore the spread of VTEC O157 in the entire Swedish cattle population during the period under study, a within- and between-herd disease spread model was used. Real livestock data was incorporated to model demographics of the population. Cattle were moved between herds according to real movement data. The results showed that the spatial pattern in prevalence may be due to regional differences in livestock movements. However, the movements, births and slaughter of cattle could not explain the temporal pattern of VTEC O157 prevalence in cattle, despite their inherently distinct seasonality.
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Affiliation(s)
- Stefan Widgren
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89 Uppsala, Sweden
| | - Stefan Engblom
- Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05 Uppsala, Sweden
| | - Pavol Bauer
- Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05 Uppsala, Sweden
| | - Jenny Frössling
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89 Uppsala, Sweden
- Department of Animal Environment and Health, Swedish University of Agricultural Sciences, Box 234, 532 23 Skara, Sweden
| | - Ulf Emanuelson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Ann Lindberg
- Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89 Uppsala, Sweden
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Widgren S, Söderlund R, Eriksson E, Fasth C, Aspan A, Emanuelson U, Alenius S, Lindberg A. Longitudinal observational study over 38 months of verotoxigenic Escherichia coli O157:H7 status in 126 cattle herds. Prev Vet Med 2015; 121:343-52. [PMID: 26321656 DOI: 10.1016/j.prevetmed.2015.08.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 06/26/2015] [Accepted: 08/14/2015] [Indexed: 10/23/2022]
Abstract
Verotoxigenic Escherichia coli O157:H7 (VTEC O157:H7) is an important zoonotic pathogen capable of causing infections in humans, sometimes with severe symptoms such as hemorrhagic colitis and hemolytic uremic syndrome (HUS). It has been reported that a subgroup of VTEC O157:H7, referred to as clade 8, is overrepresented among HUS cases. Cattle are considered to be the main reservoir of VTEC O157:H7 and infected animals shed the bacteria in feces without showing clinical signs of disease. The aims of the present study were: (1) to better understand how the presence of VTEC O157:H7 in the farm environment changes over an extended period of time, (2) to investigate potential risk factors for the presence of the bacteria, and (3) describe the distribution of MLVA types and specifically the occurrence of the hypervirulent strains (clade 8 strains) of VTEC O157:H7. The farm environment of 126 cattle herds in Sweden were sampled from October 2009 to December 2012 (38 months) using pooled pat and overshoe sampling. Each herd was sampled, on average, on 17 occasions (range=1-20; median=19), at intervals of 64 days (range=7-205; median=58). Verotoxigenic E. coli O157:H7 were detected on one or more occasions in 53% of the herds (n=67). In these herds, the percentage of positive sampling occasions ranged from 6% to 72% (mean=19%; median=17%). Multi-locus variable number tandem repeat analysis (MLVA) typing was performed on isolates from infected herds to identify hypervirulent strains (clade 8). Clustering of MLVA profiles yielded 35 clusters and hypervirulent strains were found in 18 herds; the same cluster was often identified on consecutive samplings and in nearby farms. Using generalized estimating equations, an association was found between the probability of detecting VTEC O157:H7 and status at the preceding sampling, season, herd size, infected neighboring farms and recent introduction of animals. This study showed that the bacteria VTEC O157:H7 were spontaneously cleared from the farm environment in most infected herds over time, and key factors were identified to prevent the spread of VTEC O157:H7 between cattle herds.
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Affiliation(s)
| | | | - Erik Eriksson
- National Veterinary Institute (SVA), Uppsala, Sweden
| | | | - Anna Aspan
- National Veterinary Institute (SVA), Uppsala, Sweden
| | | | | | - Ann Lindberg
- National Veterinary Institute (SVA), Uppsala, Sweden
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