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Eze JI, Correia-Gomes C, Gunn GJ, Tongue SC. Bovine mortality: the utility of two data sources for the provision of population-level surveillance intelligence. Front Vet Sci 2024; 11:1270329. [PMID: 38384953 PMCID: PMC10880450 DOI: 10.3389/fvets.2024.1270329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction The use of existing data to provide surveillance intelligence is widely advocated but often presents considerable challenges. Two data sources could be used as proxies for the mortality experienced by the Scottish cattle population: deaths recorded in the mandatory register [Cattle Tracing System (CTS)] and fallen stock collections by the National Fallen Stock Company (NSFCo) with a nationwide voluntary membership. Methods Data for the period 2011-2016 were described and compared to establish their strengths and limitations. Similarities and differences in their temporal, seasonal and spatial patterns were examined overall, at postcode area level and for different age groups. Temporal aberration detection algorithms (TADA) were fitted. Results Broadly, similar patterns were observed in the two datasets; however, there were some notable differences. The observed seasonal, annual and spatial patterns match expectations, given knowledge of Scottish cattle production systems. The registry data provide more comprehensive coverage of all areas of Scotland, while collections data provide a more comprehensive measure of the mortality experienced in 0-1-month-old calves. Discussion Consequently, estimates of early calf mortality and their impact on the livestock sector made using CTS, or successor registers, will be under-estimates. This may apply to other registry-based systems. Fitted TADA detected points of deviations from expected norms some of which coincided in the two datasets; one with a known external event that caused increased mortality. We have demonstrated that both data sources do have the potential to be utilized to provide measures of mortality in the Scottish cattle population that could inform surveillance activities. While neither is perfect, they are complementary. Each has strengths and weaknesses, so ideally, a system where they are analyzed and interpreted in parallel would optimize the information obtained for surveillance purposes for epidemiologists, risk managers, animal health policy-makers and the wider livestock industry sector. This study provides a foundation on which to build an operational system. Further development will require improvements in the timeliness of data availability and further investment of resources.
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Affiliation(s)
- Jude I. Eze
- Centre for Epidemiology and Planetary Health, Scotland’s Rural College (SRUC), Inverness, United Kingdom
- Biomathematics and Statistics Scotland, Edinburgh, United Kingdom
| | - Carla Correia-Gomes
- Centre for Epidemiology and Planetary Health, Scotland’s Rural College (SRUC), Inverness, United Kingdom
| | - George J. Gunn
- Centre for Epidemiology and Planetary Health, Scotland’s Rural College (SRUC), Inverness, United Kingdom
| | - Sue C. Tongue
- Centre for Epidemiology and Planetary Health, Scotland’s Rural College (SRUC), Inverness, United Kingdom
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2
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Hoyle DV, Wee BA, Macleod K, Chase-Topping ME, Bease AG, Tongue SC, Gally DL, Delannoy S, Fach P, Pearce MC, Gunn GJ, Holmes A, Allison L. Phylogenetic relationship and virulence composition of Escherichia coli O26:H11 cattle and human strain collections in Scotland; 2002-2020. Front Microbiol 2023; 14:1260422. [PMID: 38029122 PMCID: PMC10657854 DOI: 10.3389/fmicb.2023.1260422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
O26 is the commonest non-O157 Shiga toxin (stx)-producing Escherichia coli serogroup reported in human infections worldwide. Ruminants, particularly cattle, are the primary reservoir source for human infection. In this study, we compared the whole genomes and virulence profiles of O26:H11 strains (n = 99) isolated from Scottish cattle with strains from human infections (n = 96) held by the Scottish Escherichia coli O157/STEC Reference Laboratory, isolated between 2002 and 2020. Bovine strains were from two national cross-sectional cattle surveys conducted between 2002-2004 and 2014-2015. A maximum likelihood phylogeny was constructed from a core-genome alignment with the O26:H11 strain 11368 reference genome. Genomes were screened against a panel of 2,710 virulence genes using the Virulence Finder Database. All stx-positive bovine O26:H11 strains belonged to the ST21 lineage and were grouped into three main clades. Bovine and human source strains were interspersed, and the stx subtype was relatively clade-specific. Highly pathogenic stx2a-only ST21 strains were identified in two herds sampled in the second cattle survey and in human clinical infections from 2010 onwards. The closest pairwise distance was 9 single-nucleotide polymorphisms (SNPs) between Scottish bovine and human strains and 69 SNPs between the two cattle surveys. Bovine O26:H11 was compared to public EnteroBase ST29 complex genomes and found to have the greatest commonality with O26:H11 strains from the rest of the UK, followed by France, Italy, and Belgium. Virulence profiles of stx-positive bovine and human strains were similar but more conserved for the stx2a subtype. O26:H11 stx-negative ST29 (n = 17) and ST396 strains (n = 5) were isolated from 19 cattle herds; all were eae-positive, and 10 of these herds yielded strains positive for ehxA, espK, and Z2098, gene markers suggestive of enterohaemorrhagic potential. There was a significant association (p < 0.001) between nucleotide sequence percent identity and stx status for the bacteriophage insertion site genes yecE for stx2 and yehV for stx1. Acquired antimicrobial resistance genes were identified in silico in 12.1% of bovine and 17.7% of human O26:H11 strains, with sul2, tet, aph(3″), and aph(6″) being most common. This study describes the diversity among Scottish bovine O26:H11 strains and investigates their relationship to human STEC infections.
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Affiliation(s)
- Deborah V. Hoyle
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Bryan A. Wee
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Kareen Macleod
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Margo E. Chase-Topping
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Andrew G. Bease
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Sue C. Tongue
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, North Faculty, Scotland’s Rural College (SRUC), Inverness, United Kingdom
| | - David L. Gally
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Sabine Delannoy
- Unité ColiPath – Plateforme IdentyPath, Laboratoire de Sécurité des Aliments, Agence Nationale De Sécurité Sanitaire de l’alimentation, de l’environnement et du travail (ANSES), Maisons-Alfort, France
| | - Patrick Fach
- Unité ColiPath – Plateforme IdentyPath, Laboratoire de Sécurité des Aliments, Agence Nationale De Sécurité Sanitaire de l’alimentation, de l’environnement et du travail (ANSES), Maisons-Alfort, France
| | - Michael C. Pearce
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, North Faculty, Scotland’s Rural College (SRUC), Inverness, United Kingdom
| | - George J. Gunn
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, North Faculty, Scotland’s Rural College (SRUC), Inverness, United Kingdom
| | - Anne Holmes
- Scottish E. coli O157/STEC Reference Laboratory (SERL), Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Lesley Allison
- Scottish E. coli O157/STEC Reference Laboratory (SERL), Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
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Duncan AJ, Eze JI, Brülisauer F, Stirling JM, Jennings A, Tongue SC. Corrigendum: Evaluations of the disease surveillance centre network in Scotland: what parts has it reached? Front Vet Sci 2023; 10:1192445. [PMID: 37124569 PMCID: PMC10130870 DOI: 10.3389/fvets.2023.1192445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fvets.2023.1099057.].
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Affiliation(s)
- Andrew J. Duncan
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Inverness, United Kingdom
- UHI Inverness, University of the Highlands and Islands, Inverness, United Kingdom
- *Correspondence: Andrew J. Duncan
| | - Jude I. Eze
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Inverness, United Kingdom
- Biomathematics and Statistics Scotland, Edinburgh, United Kingdom
| | | | - Julie M. Stirling
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Inverness, United Kingdom
| | - Amy Jennings
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Sue C. Tongue
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Inverness, United Kingdom
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Duncan AJ, Eze JI, Brülisauer F, Stirling JM, Jennings A, Tongue SC. Evaluations of the Disease Surveillance Centre network in Scotland: What parts has it reached? Front Vet Sci 2023; 10:1099057. [PMID: 36896290 PMCID: PMC9988905 DOI: 10.3389/fvets.2023.1099057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
Regular evaluation is a prerequisite for systems that provide surveillance of animal populations. Scotland's Rural College Veterinary vices' Disease Surveillance Centre (DSC) network plays an integral part in surveillance to detect new and re-emerging threats within animal populations, predominantly livestock. In ronse to surveillance reviews and proposed changes to the network, an initial evaluation of diagnostic submissions data in 2010 to mid-2012 established a baseline "footprint", while highlighting challenges with the data. In this recenaluation for the period 2013-2018, we developed a new denominator using a combination of agricultural census and movement data, to identify relevant holdings more accurately. Iterative discussions between those processing submissions data ahose involved in collection at source took place to understand the intricacies of the data, establish the most appropriate dataset, and develop the processes required to optimise the data extraction and cleansing. The subsequent descriptive analysis identifies the number of diatic submissions, the number of unique holdings making submissions to the network and shows that both the surrounding geographic region of, and maximum dise to the closest DSC vary greatly between centres. Analysis of those submissions classed as farm animal post-mortems also highlights the effect of distance to the closest DSC. Whether specific differences between the time periods are due to changes in the behavior of the submitting holdior the data extraction and cleaning processes was difficult to disentangle. However, with the improved techniques producing better data to work with, a new baseline foot prior the network has been created. This provides information that can help policy makers and surveillance providers make decisions about service provision and evaluate the impact of future changes. Additionally, thtputs of these analyses can provide feedback to those employed in the service, providing evidence of what they are achieving and why changes to data collection processes and ways of working are being made. In a different setting, er data will be available and different challenges may arise. However, the fundamental principles highlighted in these evaluations and the solutions developed should be of interest to any surveillance providers generating similar diagnostic data.
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Affiliation(s)
- Andrew J Duncan
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Inverness, United Kingdom.,UHI Inverness, University of the Highlands and Islands, Inverness, United Kingdom
| | - Jude I Eze
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Inverness, United Kingdom.,Biomathematics and Statistics Scotland, Edinburgh, United Kingdom
| | | | - Julie M Stirling
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Inverness, United Kingdom
| | - Amy Jennings
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Sue C Tongue
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Inverness, United Kingdom
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5
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Bishop H, Evans J, Eze JI, Webster C, Humphry RW, Beattie R, White J, Couper J, Allison L, Brown D, Tongue SC. Bacteriological Survey of Fresh Minced Beef on Sale at Retail Outlets in Scotland in 2019: Three Foodborne Pathogens, Hygiene Process Indicators, and Phenotypic Antimicrobial Resistance. J Food Prot 2022; 85:1370-1379. [PMID: 35653627 DOI: 10.4315/jfp-22-051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/26/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT The health and economic burden of foodborne illness is high, with approximately 2.4 million cases occurring annually in the United Kingdom. A survey to understand the baseline microbial quality and prevalence of food-related hazards of fresh beef mince on retail sale could inform risk assessment, management, and communication to ensure the safety of this commodity. In such a survey, a two-stage sampling design was used to reflect variations in population density and the market share of five categories of retail outlets in Scotland. From January to December 2019, 1,009 fresh minced beef samples were collected from 15 geographic areas. The microbial quality of each sample was assessed using aerobic colony count and Escherichia coli count. Samples were cultured for Campylobacter and Salmonella, and PCR was used to detect target genes (stx1 all variants, stx2 a to g, and rfbO157) for Shiga toxin-producing E. coli (STEC). The presence of viable E. coli O157 and STEC in samples with a positive PCR signal was confirmed via culture and isolation. Phenotypic antimicrobial sensitivity patterns of cultured pathogens and 100 E. coli isolates were determined, mostly via disk diffusion. The median aerobic colony count and E. coli counts were 6.4 × 105 (interquartile range, 6.9 × 104 to 9.6 × 106) and <10 CFU/g (interquartile range, <10 to 10) of minced beef, respectively. The prevalence was 0.1% (95% confidence interval [CI], 0 to 0.7%) for Campylobacter, 0.3% (95% CI, 0 to 1%) for Salmonella, 22% (95% CI, 20 to 25%) for PCR-positive STEC, and 4% (95% CI, 2 to 5%) for culture-positive STEC. The evidence for phenotypic antimicrobial resistance detected did not give cause for concern, mainly occurring in a few E. coli isolates as single nonsusceptibilities to first-line active substances. The low prevalence of pathogens and phenotypic antimicrobial resistance is encouraging, but ongoing consumer food safety education is necessary to mitigate the residual public health risk. HIGHLIGHTS
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Affiliation(s)
- H Bishop
- Scotland's Rural College, An Lochran, 10 Inverness Campus, Inverness IV2 5NA, UK
| | - J Evans
- Scotland's Rural College, An Lochran, 10 Inverness Campus, Inverness IV2 5NA, UK
| | - J I Eze
- Scotland's Rural College, An Lochran, 10 Inverness Campus, Inverness IV2 5NA, UK.,Biomathematics & Statistics Scotland, JCMB, The King's Buildings, Edinburgh EH9 3FD, UK
| | - C Webster
- Scotland's Rural College, An Lochran, 10 Inverness Campus, Inverness IV2 5NA, UK
| | - R W Humphry
- Scotland's Rural College, An Lochran, 10 Inverness Campus, Inverness IV2 5NA, UK
| | - R Beattie
- Scientific Services Laboratories of Edinburgh, Glasgow and Tayside Councils, 6 James Lindsay Place, Dundee, DD1 5JJ, 4 Marine Esplanade, Edinburgh EH6 7LU, and Colston Laboratories 64 Everard Drive, Glasgow G21 1XG, UK
| | - J White
- Scientific Services Laboratories of Edinburgh, Glasgow and Tayside Councils, 6 James Lindsay Place, Dundee, DD1 5JJ, 4 Marine Esplanade, Edinburgh EH6 7LU, and Colston Laboratories 64 Everard Drive, Glasgow G21 1XG, UK
| | - J Couper
- Scientific Services Laboratories of Edinburgh, Glasgow and Tayside Councils, 6 James Lindsay Place, Dundee, DD1 5JJ, 4 Marine Esplanade, Edinburgh EH6 7LU, and Colston Laboratories 64 Everard Drive, Glasgow G21 1XG, UK
| | - L Allison
- Scottish Microbiological Reference Laboratories (SMiRL) (Edinburgh and Glasgow), Scottish E. coli O157/STEC Reference Laboratory (SERL), Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Old Dalkeith Road, Edinburgh EH16 4SA, and Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G21 3ER, UK
| | - D Brown
- Scottish Microbiological Reference Laboratories (SMiRL) (Edinburgh and Glasgow), Scottish E. coli O157/STEC Reference Laboratory (SERL), Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Old Dalkeith Road, Edinburgh EH16 4SA, and Level 5, New Lister Building, Glasgow Royal Infirmary, 10-16 Alexandra Parade, Glasgow G21 3ER, UK
| | - S C Tongue
- Scotland's Rural College, An Lochran, 10 Inverness Campus, Inverness IV2 5NA, UK
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6
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Fernández Rivas C, Porphyre T, Chase-Topping ME, Knapp CW, Williamson H, Barraud O, Tongue SC, Silva N, Currie C, Elsby DT, Hoyle DV. High Prevalence and Factors Associated With the Distribution of the Integron intI1 and intI2 Genes in Scottish Cattle Herds. Front Vet Sci 2021; 8:755833. [PMID: 34778436 PMCID: PMC8585936 DOI: 10.3389/fvets.2021.755833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Integrons are genetic elements that capture and express antimicrobial resistance genes within arrays, facilitating horizontal spread of multiple drug resistance in a range of bacterial species. The aim of this study was to estimate prevalence for class 1, 2, and 3 integrons in Scottish cattle and examine whether spatial, seasonal or herd management factors influenced integron herd status. We used fecal samples collected from 108 Scottish cattle herds in a national, cross-sectional survey between 2014 and 2015, and screened fecal DNA extracts by multiplex PCR for the integrase genes intI1, intI2, and intI3. Herd-level prevalence was estimated [95% confidence interval (CI)] for intI1 as 76.9% (67.8-84.0%) and intI2 as 82.4% (73.9-88.6%). We did not detect intI3 in any of the herd samples tested. A regional effect was observed for intI1, highest in the North East (OR 11.5, 95% CI: 1.0-130.9, P = 0.05) and South East (OR 8.7, 95% CI: 1.1-20.9, P = 0.04), lowest in the Highlands. A generalized linear mixed model was used to test for potential associations between herd status and cattle management, soil type and regional livestock density variables. Within the final multivariable model, factors associated with herd positivity for intI1 included spring season of the year (OR 6.3, 95% CI: 1.1-36.4, P = 0.04) and watering cattle from a natural spring source (OR 4.4, 95% CI: 1.3-14.8, P = 0.017), and cattle being housed at the time of sampling for intI2 (OR 75.0, 95% CI: 10.4-540.5, P < 0.001). This study provides baseline estimates for integron prevalence in Scottish cattle and identifies factors that may be associated with carriage that warrant future investigation.
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Affiliation(s)
- Cristina Fernández Rivas
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom
| | - Thibaud Porphyre
- Laboratoire de Biométrie et Biologie Évolutive, UMR5558, CNRS, VetAgro Sup, Université de Lyon, Villeurbanne Cedex, France
| | - Margo E Chase-Topping
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom
| | - Charles W Knapp
- Centre for Water, Environment, Sustainability and Public Health, Department of Civil & Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom
| | - Helen Williamson
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom
| | - Olivier Barraud
- INSERM, CHU Limoges, UMR1092, Université de Limoges, Limoges, France
| | - Sue C Tongue
- Epidemiology Research Unit, Scotland's Rural College (SRUC), An Lòchran, Inverness Campus, Inverness, United Kingdom
| | - Nuno Silva
- Moredun Research Institute, Edinburgh, United Kingdom
| | - Carol Currie
- Moredun Research Institute, Edinburgh, United Kingdom
| | - Derek T Elsby
- Environmental Research Institute, University of the Highlands and Islands, Thurso, United Kingdom
| | - Deborah V Hoyle
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom
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Fitzgerald SF, Lupolova N, Shaaban S, Dallman TJ, Greig D, Allison L, Tongue SC, Evans J, Henry MK, McNeilly TN, Bono JL, Gally DL. Genome structural variation in Escherichia coli O157:H7. Microb Genom 2021; 7. [PMID: 34751643 PMCID: PMC8743559 DOI: 10.1099/mgen.0.000682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human zoonotic pathogen Escherichia coli O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype. We demonstrate that LCRs are a major source of genomic variation across all lineages of E. coli O157:H7 and by using both optical mapping and Oxford Nanopore long-read sequencing prove that LCRs are generated in laboratory cultures started from a single colony and that these variants can be recovered from colonized cattle. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga-toxin production, type-3 secretion and motility can be affected by LCRs. In summary, E. coli O157:H7 has acquired multiple prophage regions over time that act to continually produce structural variants of the genome. These findings raise important questions about the significance of this prophage-mediated genome contingency to enhance adaptability between environments.
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Affiliation(s)
- Stephen F Fitzgerald
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Nadejda Lupolova
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Sharif Shaaban
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Timothy J Dallman
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - David Greig
- Gastrointestinal Bacterial Reference Unit, 61 Colindale Avenue, Public Health England, NW9 5EQ London, UK
| | - Lesley Allison
- Scottish E. coli O157/VTEC Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, UK
| | - Sue C Tongue
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Judith Evans
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Madeleine K Henry
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, IV2 5NA, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 OPZ, UK
| | - James L Bono
- United States Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, Nebraska, USA
| | - David L Gally
- Division of Infection and Immunity, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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8
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Humphry RW, Henry MK, Reeves A, Correia-Gomes C, Innocent GT, Smith R, Mason CS, Gunn GJ, Tongue SC. Estimating antimicrobial usage based on sales to beef and dairy farms from UK veterinary practices. Vet Rec 2021; 189:e28. [PMID: 33729562 DOI: 10.1002/vetr.28] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 09/01/2020] [Accepted: 12/24/2020] [Indexed: 11/07/2022]
Abstract
BACKGROUND Accurate estimation of antimicrobial use (AMU) is important in assessing reduction of agricultural AMU. This cross-sectional study aimed to evaluate several approaches for estimating AMU at the herd level and to report on AMU for beef and dairy farms in Scotland. METHODS Pharmaceutical sales data for 75 cattle herds (2011-2015) were screened for antimicrobial products and aggregated by herd and year. Several denominators for usage estimates were calculated and compared for their suitability at the herd level. RESULTS The median total mass of active ingredient sold per kg of bovine livestock was 9.5 mg/kg for beef herds and 14.3 mg/kg for dairy herds. The 'highest priority critically important' antimicrobials (HPCIA) were by total mass of active ingredient, 10.6% of all sales; by total defined daily dose veterinary (DDDVet), 29.8% and by DCDvet, 20.0%. These are the first estimates of AMU for beef cattle in the UK, and for cattle of any kind in Scotland. Estimates of herd-level usage based on population correction unit (PCU) were sensitive to low values for PCU for specific herd-years due to their demographic composition. CONCLUSION Pharmaceutical sales data can provide useful estimates of AMU, but estimating usage per PCU is not appropriate for comparing groups of cattle with different demographic compositions or for setting herd-level targets. Total mass of active ingredient per kilogram of livestock is more stable and hence suitable than PCU-based methods for assessing AMU at the herd level.
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Affiliation(s)
- Roger William Humphry
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College, Inverness, Scotland, IV2 5NA, UK
| | - Madeleine Kate Henry
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College, Inverness, Scotland, IV2 5NA, UK
| | - Aaron Reeves
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College, Inverness, Scotland, IV2 5NA, UK.,Scottish Government's Centre of Expertise on Animal Disease Outbreaks (EPIC)
| | | | - Giles Thomas Innocent
- Scottish Government's Centre of Expertise on Animal Disease Outbreaks (EPIC).,Biomathematics & Statistics Scotland, JCMB, The King's Buildings, Edinburgh, Scotland, UK
| | - R Smith
- c/o R. W. Humphry, Epidemiology Research Unit, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Inverness Campus, Inverness, Scotland, IV2 5NA, UK
| | - Colin Stuart Mason
- SRUC Veterinary Services, St Marys Industrial Estate, Dumfries, Scotland, DG1 1DX, UK
| | - George John Gunn
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College, Inverness, Scotland, IV2 5NA, UK
| | - Sue C Tongue
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College, Inverness, Scotland, IV2 5NA, UK
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Stirling JM, Eze JI, Foster G, Reeves A, Gunn GJ, Tongue SC. The Use of Sheep Movement Data to Inform Design and Interpretation of Slaughterhouse-Based Surveillance Activities. Front Vet Sci 2020; 7:205. [PMID: 32391387 PMCID: PMC7193055 DOI: 10.3389/fvets.2020.00205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/27/2020] [Indexed: 11/17/2022] Open
Abstract
The design of surveillance strategies is often a compromise between science, feasibility, and available resources, especially when sampling is based at fixed locations, such as slaughter-houses. Advances in animal identification, movement recording and traceability should provide data that can facilitate the development, design and interpretation of surveillance activities. Here, for the first time since the introduction of electronic identification of sheep, the utility of a statutory sheep movement database to inform the design and interpretation of slaughter-house based surveillance activities has been investigated. Scottish sheep movement records for 2015–2018 were analyzed in combination with several other data sources. Patterns of off-farm movements of Scottish sheep to slaughter were described and the spatial distribution of several distinct slaughter populations, throughputs and catchment areas for Scottish slaughterhouses were determined. These were used to evaluate the coverage of a convenience-sample slaughter-house based survey for antimicrobial resistance (AMR). In addition, non-slaughter sheep movements within and between Scottish regions were described and inter-and intra-regional movement matrices were produced. There is potential at a number of levels for bias in spatially-associated factors for ovine surveillance activities based at Scottish slaughterhouses. The first is intrinsic because the slaughtered in Scotland population differs from the overall Scottish sheep slaughter population. Other levels will be survey-dependent and occur when the catchment area differs from the slaughtered in Scotland population and when the sampled sheep differ from the catchment area. These are both observed in the AMR survey. Furthermore, the Scottish non-slaughter sheep population is dynamic. Inter-regional movements vary seasonally, driven by the sheep calendar year, structure of the Scottish sheep industry and management practices. These sheep movement data provide a valuable resource for surveillance purposes, despite a number of challenges and limitations that were encountered. They can be used to identify and characterize the spatial origin of relevant populations and so inform the interpretation of existing slaughterhouse-based surveillance activities. They can be used to improve future design by exploring the feasibility and cost:benefit of alternative sampling strategies. Further development could also contribute to other surveillance activities, such as situational awareness and resource allocation, for the benefit of stakeholders.
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Affiliation(s)
- Julie M Stirling
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, United Kingdom
| | - Jude I Eze
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, United Kingdom.,Biomathematics and Statistics Scotland, JCMB, Edinburgh, United Kingdom
| | - Geoffrey Foster
- SRUC Veterinary Services (Inverness), Northern Faculty, Scotland's Rural College (SRUC), Scotland, United Kingdom
| | - Aaron Reeves
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, United Kingdom
| | - George J Gunn
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, United Kingdom
| | - Sue C Tongue
- Epidemiology Research Unit (Inverness), Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College (SRUC), Scotland, United Kingdom
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10
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Tongue SC, Eze JI, Correia-Gomes C, Brülisauer F, Gunn GJ. Improving the Utility of Voluntary Ovine Fallen Stock Collection and Laboratory Diagnostic Submission Data for Animal Health Surveillance Purposes: A Development Cycle. Front Vet Sci 2020; 6:487. [PMID: 32039248 PMCID: PMC6993589 DOI: 10.3389/fvets.2019.00487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/09/2019] [Indexed: 01/20/2023] Open
Abstract
There are calls from policy-makers and industry to use existing data sources to contribute to livestock surveillance systems, especially for syndromic surveillance. However, the practical implications of attempting to use such data sources are challenging; development often requires incremental steps in an iterative cycle. In this study the utility of business operational data from a voluntary fallen stock collection service was investigated, to determine if they could be used as a proxy for the mortality experienced by the British sheep population. Retrospectively, Scottish ovine fallen stock collection data (2011-2014) were transformed into meaningful units for analysis, temporal and spatial patterns were described, time-series methods and a temporal aberration detection algorithm applied. Distinct annual and spatial trends plus seasonal patterns were observed in the three age groups investigated. The algorithm produced an alarm at the point of an historic known departure from normal (April 2013) for two age groups, across Scotland as a whole and in specific postcode areas. The analysis was then extended. Initially, to determine if similar methods could be applied to ovine fallen stock collections from England and Wales for the same time period. Additionally, Scottish contemporaneous laboratory diagnostic submission data were analyzed to see if they could provide further insight for interpretation of statistical alarms. Collaboration was required between the primary data holders, those with industry sector knowledge, plus veterinary, epidemiological and statistical expertise, in order to turn data and analytical outcomes into potentially useful information. A number of limitations were identified and recommendations were made as to how some could be addressed in order to facilitate use of these data as surveillance "intelligence." e.g., improvements to data collection and provision. A recent update of the fallen stock collections data has enabled a longer temporal period to be analyzed, with evidence of changes made in line with the recommendations. Further development will be required before a functional system can be implemented. However, there is potential for use of these data as: a proxy measure for mortality in the sheep population; complementary components in a future surveillance system, and to inform the design of additional surveillance system components.
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Affiliation(s)
- Sue C. Tongue
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College, Inverness, United Kingdom
| | - Jude I. Eze
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College, Inverness, United Kingdom
- Biomathematics and Statistics Scotland (BioSS), JCMB, Edinburgh, United Kingdom
| | - Carla Correia-Gomes
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College, Inverness, United Kingdom
| | - Franz Brülisauer
- SRUC Veterinary Services, Scotland's Rural College, Inverness, United Kingdom
| | - George J. Gunn
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Northern Faculty, Scotland's Rural College, Inverness, United Kingdom
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11
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Henry MK, McCann CM, Humphry RW, Morgan M, Willett A, Evans J, Gunn GJ, Tongue SC. The British E. coli O157 in cattle study (BECS): factors associated with the occurrence of E. coli O157 from contemporaneous cross-sectional surveys. BMC Vet Res 2019; 15:444. [PMID: 31805948 PMCID: PMC6896709 DOI: 10.1186/s12917-019-2188-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Escherichia coli O157 is a bacterial pathogen associated with severe disease in humans for which cattle are an important reservoir of infection. The identification of possible risk factors for infection in cattle could facilitate the development of control strategies and interventions to mitigate the risk to human health. The purpose of this study was to utilize data collected in 2014-2015 during the two contemporaneous cross-sectional surveys of the British E. coli O157 in Cattle Study (BECS) to investigate potential risk factors for E. coli O157 status in cattle destined for the food chain. RESULTS In the England & Wales survey only one variable, herd size, was associated with the outcome farm-level E. coli O157 positive status. The odds increased for each additional animal in the herd. In the Scotland survey, as well as a measure of herd size (the number of cattle aged 12-30 months), having brought breeding females on to the farm in the last year also increased the odds, whereas farms sampled in spring were less likely to be positive compared to those sampled in autumn. On the positive farms, in both surveys, an increase in the proportion of pats positive for E. coli O157 was associated with animals being housed at the time of sampling. However, the effect of housing on pat-level prevalence within positive groups was lower on farms from England & Wales than from Scotland (OR 0.45 (95% C.I. 0.24-0.86)). CONCLUSION For the first time, factors associated with farm-level E. coli O157 status have been investigated in two contemporaneous surveys with comparable study design. Although factors associated with farm-level E. coli O157 status differed between the two surveys, one consistent factor was an association with a measure of herd size. Factors associated with the proportion of E. coli O157 positive pats within a positive farm were similar in both surveys but differed from those associated with farm-level status. These findings raise the hypothesis that measures to protect public health by reducing the risk from cattle may need to be tailored, rather than by assuming that a GB-wide protocol is the best approach.
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Affiliation(s)
- Madeleine K. Henry
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - Catherine M. McCann
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - Roger W. Humphry
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - Mair Morgan
- RSK ADAS Ltd., Spring Lodge, 172 Chester Road, Helsby, Cheshire, WA6 0AR UK
| | - Alice Willett
- RSK ADAS Ltd., Spring Lodge, 172 Chester Road, Helsby, Cheshire, WA6 0AR UK
| | - Judith Evans
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - George J. Gunn
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - Sue C. Tongue
- Epidemiology Research Unit (Inverness campus), Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
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12
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Tongue SC. Of sheep, sentinels and surveillance: what is the new 'normal'? Vet Rec 2019; 184:647-648. [PMID: 31123208 DOI: 10.1136/vr.l3057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Sue C Tongue
- Epidemiology Research Unit, Scotland's Rural College, Inverness, UK
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13
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Correia-Gomes C, Henry MK, Williamson S, Irvine RM, Gunn GJ, Woolfenden N, White MEC, Tongue SC. Syndromic surveillance by veterinary practitioners: a pilot study in the pig sector. Vet Rec 2019; 184:556. [PMID: 31023871 DOI: 10.1136/vr.104868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 12/12/2018] [Accepted: 01/21/2019] [Indexed: 11/04/2022]
Abstract
Traditional indicator-based livestock surveillance has been focused on case definitions, definitive diagnoses and laboratory confirmation. The use of syndromic disease surveillance would increase the population base from which animal health data are captured and facilitate earlier detection of new and re-emerging threats to animal health. Veterinary practitioners could potentially play a vital role in such activities. In a pilot study, specialist private veterinary practitioners (PVP) working in the English pig industry were asked to collect and transfer background data and disease incident reports for pig farms visited during the study period. Baseline data from 110 pig farms were received, along with 68 disease incident reports. Reports took an average of approximately 25 minutes to complete. Feedback from the PVPs indicated that they saw value in syndromic surveillance. Maintenance of anonymity in the outputs would be essential, as would timely access for the PVPs to relevant information on syndromic trends. Further guidance and standardisation would also be required. Syndromic surveillance by PVPs is possible for the pig industry. It has potential to fill current gaps in the collection of animal health data, as long as the engagement and participation of data providers can be obtained and maintained.
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Affiliation(s)
- Carla Correia-Gomes
- Epidemiology Research Unit, SRUC (Inverness Campus) Epidemiology Research Unit, Edinburgh, UK.,SRUC (Inverness Campus) Epidemiology Research Unit, An Lochran, Inverness Campus, Inverness, UK
| | - Madeleine Kate Henry
- Epidemiology Research Unit, SRUC (Inverness Campus) Epidemiology Research Unit, Edinburgh, UK.,SRUC (Inverness Campus) Epidemiology Research Unit, An Lochran, Inverness Campus, Inverness, UK
| | | | - Richard M Irvine
- Surveillance Intelligence Unit, Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - George J Gunn
- Epidemiology Research Unit, SRUC (Inverness Campus) Epidemiology Research Unit, Edinburgh, UK.,SRUC (Inverness Campus) Epidemiology Research Unit, An Lochran, Inverness Campus, Inverness, UK
| | | | - Mark E C White
- Pig Veterinary Society, Pig Veterinary Society, Thirsk, North Yorkshire, UK
| | - Sue C Tongue
- Epidemiology Research Unit, SRUC (Inverness Campus) Epidemiology Research Unit, Edinburgh, UK.,SRUC (Inverness Campus) Epidemiology Research Unit, An Lochran, Inverness Campus, Inverness, UK
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14
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Velasova M, Smith RP, Lemma F, Horton RA, Duggett NA, Evans J, Tongue SC, Anjum MF, Randall LP. Detection of extended-spectrum β-lactam, AmpC and carbapenem resistance in Enterobacteriaceae in beef cattle in Great Britain in 2015. J Appl Microbiol 2019; 126:1081-1095. [PMID: 30693606 DOI: 10.1111/jam.14211] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/02/2019] [Accepted: 01/21/2019] [Indexed: 02/06/2023]
Abstract
AIMS This study investigated the occurrence and genetic diversity of Enterobacteriaceae with extended-spectrum β-lactamase (ESBL)-, AmpC- and carbapenemase-mediated resistance in British beef cattle, and related risk factors. METHODS AND RESULTS Faecal samples (n = 776) were obtained from farms in England and Wales (n = 20) and Scotland (n = 20) in 2015. Isolates from selective agars were identified by MALDI ToF mass spectrometry. Selected isolates were characterized by multiplex PCR (blaCTX -M, blaOXA , blaSHV and blaTEM genes), whole-genome sequencing (WGS), minimum inhibitory concentrations and pulsed-field gel electrophoresis. None of the faecal samples yielded carbapenem-resistant Escherichia coli. Ten (25%) of the farms tested positive for ESBL-producing CTX-M Enterobacteriaceae, 15 (37·5%) of the farms were positive for AmpC phenotype E. coli and none were positive for carbapenem-resistant E. coli. WGS showed a total of 30 different resistance genes associated with E. coli, Citrobacter and Serratia from ESBL agars, and colocation of resistance genes with blaCTX -M1 . Buying bulls and bringing in fattening cattle from another farm were identified as significant risk factors for positive samples harbouring CTX-M Enterobacteriaceae or AmpC phenotype E. coli respectively. CONCLUSIONS Beef cattle on a proportion of farms in GB carry ESBL-producing Enterobacteriaceae. Factors, such as operating as a closed herd, may have an important role in reducing introduction and transmission of resistant Enterobacteriaceae. The results indicate management factors may play an important role in impacting ESBL prevalence. In particular, further study would be valuable to understand the impact of maintaining a closed herd on reducing the introduction of resistant Enterobacteriaceae. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study showing the presence of ESBL-producing Enterobacteriaceae in British beef cattle.
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Affiliation(s)
- M Velasova
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - R P Smith
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - F Lemma
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - R A Horton
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - N A Duggett
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - J Evans
- SRUC (Inverness Campus), Edinburgh, UK
| | | | - M F Anjum
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
| | - L P Randall
- Animal and Plant Health Agency (Weybridge), Addlestone, UK
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15
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Smith RP, Correia-Gomes C, Williamson S, Marier EA, Gilson D, Tongue SC. Review of pig health and welfare surveillance data sources in England and Wales. Vet Rec 2019; 184:349. [PMID: 30635452 DOI: 10.1136/vr.104896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 10/26/2018] [Accepted: 12/16/2018] [Indexed: 11/04/2022]
Abstract
The capability to set baselines and monitor trends of health and welfare conditions is an important requirement for livestock industries in order to maintain economic competitiveness and sustainability. Monitoring schemes evaluate the relative importance of conditions so that: appropriate actions can be determined, prioritised and implemented; new and (re)emerging conditions can be promptly detected and the effectiveness of any actions can be measured. In 2011, the national pig levy board published a strategy document highlighting health and welfare conditions of importance to the pig industry that were to be targeted for control. In this study, existing schemes that could be used to monitor or set baselines for these conditions in pigs were reviewed, in order to evaluate their suitability for this purpose, using a standardised surveillance evaluation framework (SERVAL). The schemes included: government-funded surveillance of endemic and exotic disease and pig welfare; industry surveillance of endemic diseases; regional schemes for improving pig health; national accreditation schemes and information collected by retailers, private veterinary practices and private laboratories. The evaluation of each scheme highlights its capability to monitor any of the targeted conditions. This study identifies the biases, strengths and gaps in each scheme and provides discussion of opportunities for future development.
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Affiliation(s)
- Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | | | | | | | - Daniel Gilson
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | - Sue C Tongue
- Epidemiology Research Unit, Scotland's Rural College, Edinburgh, UK
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16
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Tongue SC, Duncan AJ, Vipond J, Stocker P, Gunn GJ. Blowfly strike in sheep: self-help surveillance for shepherds is unsustainable. Vet Rec 2017; 180:280. [PMID: 28119476 DOI: 10.1136/vr.104011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2017] [Indexed: 11/03/2022]
Affiliation(s)
- S C Tongue
- Epidemiology Research Unit (Inverness), SRUC (Scotland's Rural College), West Mains Road, Edinburgh EH9 3JG, UK
| | - A J Duncan
- Epidemiology Research Unit (Inverness), SRUC (Scotland's Rural College), West Mains Road, Edinburgh EH9 3JG, UK
| | - J Vipond
- SAC Consulting, SRUC, West Mains Road, Edinburgh EH9 3JG, UK
| | - P Stocker
- National Sheep Association (NSA), The Sheep Centre, Malvern, Worcestershire WR13 6PH, UK
| | - G J Gunn
- Epidemiology Research Unit (Inverness), SRUC (Scotland's Rural College), West Mains Road, Edinburgh EH9 3JG, UK
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17
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Tongue SC, Pritchard I, Watson D, Hosie BD. Preliminary survey of lamb losses (black loss) in Highland sheep flocks. Vet Rec 2017; 180:197. [PMID: 27881696 DOI: 10.1136/vr.104010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2016] [Indexed: 11/04/2022]
Affiliation(s)
- S C Tongue
- Epidemiology Research Unit (Inverness Campus), SRUC, West Mains Road, Edinburgh EH9 3JG, UK
| | - I Pritchard
- SAC Consulting Veterinary Services, SRUC, Bush Estate, Penicuik, Midlothian EH26 0QE, UK
| | - D Watson
- SAOS Ltd, The Rural Centre, Ingliston, Newbridge EH28 8 NZ, UK
| | - B D Hosie
- SAC Consulting Veterinary Services, SRUC, Bush Estate, Penicuik, Midlothian EH26 0QE, UK
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18
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Correia-Gomes C, Smith RP, Eze JI, Henry MK, Gunn GJ, Williamson S, Tongue SC. Pig Abattoir Inspection Data: Can It Be Used for Surveillance Purposes? PLoS One 2016; 11:e0161990. [PMID: 27564417 PMCID: PMC5001630 DOI: 10.1371/journal.pone.0161990] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/16/2016] [Indexed: 11/18/2022] Open
Abstract
Statutory recording of carcass lesions at the abattoir may have significant potential as a resource for surveillance of livestock populations. Food Standards Agency (FSA) data in Great Britain are not currently used for surveillance purposes. There are concerns that the sensitivity of detection, combined with other issues, may make the outputs unreliable. In this study we postulate that FSA data could be used for surveillance purposes. To test this we compared FSA data with BPHS (a targeted surveillance system of slaughtered pigs) and laboratory diagnostic scanning surveillance (FarmFile) data, from mid-2008 to mid-2012, for respiratory conditions and tail bite lesions in pigs at population level. We also evaluated the agreement/correlation at batch level between FSA and BPHS inspections in four field trials during 2013. Temporal trends and regional differences at population level were described and compared using logistic regression models. Population temporal analysis showed an increase in respiratory disease in all datasets but with regional differences. For tail bite, the temporal trend and monthly patterns were completely different between the datasets. The field trials were run in three abattoirs and included 322 batches. Pearson’s correlation and Cohen’s kappa tests were used to assess correlation/agreement between inspections systems. It was moderate to strong for high prevalence conditions but slight for low prevalence conditions. We conclude that there is potential to use FSA data as a component of a surveillance system to monitor temporal trends and regional differences of chosen indicators at population level. At producer level and for low prevalence conditions it needs further improvement. Overall a number of issues still need to be addressed in order to provide the pig industry with the confidence to base their decisions on these FSA inspection data. Similar conclusions, at national level, may apply to other livestock sectors but require further evaluation of the inspection and data collection processes.
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Affiliation(s)
- Carla Correia-Gomes
- Epidemiology Research Unit, Future Farming Systems Research Group, Scotland’s Rural College, Kings Building, West Mains Road, Edinburgh, United Kingdom
- * E-mail:
| | - Richard P. Smith
- Animal and Plant Health Agency, New Haw, Addlestone, Weybridge, Surrey, United Kingdom
| | - Jude I. Eze
- Epidemiology Research Unit, Future Farming Systems Research Group, Scotland’s Rural College, Kings Building, West Mains Road, Edinburgh, United Kingdom
| | - Madeleine K. Henry
- Epidemiology Research Unit, Future Farming Systems Research Group, Scotland’s Rural College, Kings Building, West Mains Road, Edinburgh, United Kingdom
| | - George J. Gunn
- Epidemiology Research Unit, Future Farming Systems Research Group, Scotland’s Rural College, Kings Building, West Mains Road, Edinburgh, United Kingdom
| | - Susanna Williamson
- Animal and Plant Health Agency, Rougham Hill, Bury St Edmunds, Suffolk, United Kingdom
| | - Sue C. Tongue
- Epidemiology Research Unit, Future Farming Systems Research Group, Scotland’s Rural College, Kings Building, West Mains Road, Edinburgh, United Kingdom
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19
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Hickey GL, Diggle PJ, McNeilly TN, Tongue SC, Chase-Topping ME, Williams DJ. Corrigendum to “The feasibility of testing whether Fasciola hepatica is associated with increased risk of verocytotoxin producing Escherichia coli O157 from an existing study protocol” [Prev. Vet. Med. 119 (2015) 97–104]. Prev Vet Med 2015. [PMCID: PMC4718928 DOI: 10.1016/j.prevetmed.2015.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Hickey GL, Diggle PJ, McNeilly TN, Tongue SC, Chase-Topping ME, Williams DJL. The feasibility of testing whether Fasciola hepatica is associated with increased risk of verocytotoxin producing Escherichia coli O157 from an existing study protocol. Prev Vet Med 2015; 119:97-104. [PMID: 25779556 PMCID: PMC4401447 DOI: 10.1016/j.prevetmed.2015.02.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/19/2015] [Accepted: 02/22/2015] [Indexed: 02/04/2023]
Abstract
Interaction between Fasciola hepatica and VTEC O157 in cattle. Simulations that calculate statistical power for association between two pathogens. Simulation parameters for a study constrained by a pre-determined design. Augmenting a prospective study on VTEC O157 prevalence with a co-infection study. Results show an 87% power to detect an odds ratio of 2.
The parasite Fasciola hepatica is a major cause of economic loss to the agricultural community worldwide as a result of morbidity and mortality in livestock, including cattle. Cattle are the principle reservoir of verocytotoxigenic Escherichia coli O157 (VTEC O157), an important cause of disease in humans. To date there has been little empirical research on the interaction between F. hepatica and VTEC O157. It is hypothesised that F. hepatica, which is known to suppress type 1 immune responses and induce an anti-inflammatory or regulatory immune environment in the host, may promote colonisation of the bovine intestine with VTEC O157. Here we assess whether it is statistically feasible to augment a prospective study to quantify the prevalence of VTEC O157 in cattle in Great Britain with a pilot study to test this hypothesis. We simulate data under the framework of a mixed-effects logistic regression model in order to calculate the power to detect an association effect size (odds ratio) of 2. In order to reduce the resources required for such a study, we exploit the fact that the test results for VTEC O157 will be known in advance of testing for F. hepatica by restricting analysis to farms with a VTEC O157 sample prevalence of >0% and <100%. From a total of 270 farms (mean 27 cows per farm) that will be tested for VTEC O157, power of 87% can be achieved, whereby testing of F. hepatica would only be necessary for an expected 50 farms, thus considerably reducing costs. Pre-study sample size calculations are an important part of any study design. The framework developed here is applicable to the study of other co-infections.
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Affiliation(s)
- Graeme L Hickey
- Department of Epidemiology and Population Health, Institute of Infection and Global Heath, University of Liverpool, The Farr Institute@HeRC, Waterhouse Building, 1-5 Brownlow Street, Liverpool L69 3GL, UK.
| | - Peter J Diggle
- Department of Epidemiology and Population Health, Institute of Infection and Global Heath, University of Liverpool, The Farr Institute@HeRC, Waterhouse Building, 1-5 Brownlow Street, Liverpool L69 3GL, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands, Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, UK
| | - Sue C Tongue
- SRUC (Scotland's Rural College), West Mains Road, Edinburgh, Scotland EH9 3JG, UK
| | - Margo E Chase-Topping
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Diana J L Williams
- Department of Infection Biology, Institute of Infection and Global Heath, University of Liverpool, Liverpool L69 7ZJ, UK; School of Veterinary Science, University of Liverpool, Leahurst Campus, Chester High Road, Neston CH64 7TE, UK
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21
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Henry MK, Tongue SC, Gunn GJ. E coli prevalence study among finishing cattle in the UK. Vet Rec 2014; 175:208. [PMID: 25172654 DOI: 10.1136/vr.g5328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Madeleine K Henry
- Epidemiology Research Unit, SRUC Drummondhill, Stratherrick Road, Inverness IV2 4JZ
| | - Sue C Tongue
- Epidemiology Research Unit, SRUC Drummondhill, Stratherrick Road, Inverness IV2 4JZ
| | - George J Gunn
- Epidemiology Research Unit, SRUC Drummondhill, Stratherrick Road, Inverness IV2 4JZ
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22
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Dexter G, Tongue SC, Heasman L, Bellworthy SJ, Davis A, Moore SJ, Simmons MM, Sayers AR, Simmons HA, Matthews D. The evaluation of exposure risks for natural transmission of scrapie within an infected flock. BMC Vet Res 2009; 5:38. [PMID: 19818127 PMCID: PMC2768688 DOI: 10.1186/1746-6148-5-38] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 10/09/2009] [Indexed: 11/17/2022] Open
Abstract
Background Although the epidemiology of scrapie has been broadly understood for many years, attempts to introduce voluntary or compulsory controls to eradicate the disease have frequently failed. Lack of precision in defining the risk factors on farm has been one of the challenges to designing control strategies. This study attempted to define which parts of the annual flock management cycle represented the greatest risk of infection to naive lambs exposed to the farm environment at different times. Results In VRQ/VRQ lambs exposed to infected sheep at pasture or during lambing, and exposed to the buildings in which lambing took place, the attack rate was high and survival times were short. Where exposure was to pasture alone the number of sheep affected in each experimental group was reduced, and survival times were longer and related to length of exposure. Conclusion At the flock level, eradication and control strategies for scrapie must take into account the need to decontaminate buildings used for lambing, and to reduce (or prevent) the exposure of lambs to infected sheep, especially in the later stages of incubation, and at lambing. The potential for environmental contamination from pasture should also be considered. Genotype selection may still prove to be the only viable tool to prevent infection from contaminated pasture, reduce environmental contamination and limit direct transmission from sheep to sheep.
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Affiliation(s)
- Glenda Dexter
- Veterinary Laboratories Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK.
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23
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Tongue SC, Pfeiffer DU, Shearn PD, Wilesmith JW. PrP genotype: a flock-level risk factor for scrapie? Prev Vet Med 2009; 92:309-23. [PMID: 19783057 DOI: 10.1016/j.prevetmed.2009.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 08/07/2009] [Accepted: 08/16/2009] [Indexed: 11/26/2022]
Abstract
Previous epidemiological studies of risk factors for classical scrapie at flock level have identified a variety of management and purchase related variables, along with increased flock size and, in some cases, breed effects. Although known as a risk factor at the individual animal level, PrP genotype frequencies at flock level have not yet been studied. In an unmatched case-control study, three measures of flock-level prion protein (PrP) frequency estimates were investigated with respect to the scrapie status of the flock in 293 British sheep flocks (195 control flocks and 98 case flocks). Flocks with positive frequencies (more than 0 per cent) of two genotypes (VRQ/VRQ and AHQ/VRQ), large frequencies (more than 10 per cent) of the ARR/VRQ genotype, and large frequencies (more than 5.2 per cent) of the VRQ allele were at increased odds of being affected with clinical classical scrapie. When adjusted for flock size, breed and sampling strategy the genotype and allele effects remained, except that for flocks with positive frequencies of VRQ/VRQ. The known effect of increased risk with increased flock size was confirmed. A measure of the flock PrP genotype frequency profile should thus be included in studies of risk factors for scrapie. It could also be integrated into risk-based surveillance strategies for identification of "at-risk-of scrapie" flocks.
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Affiliation(s)
- Sue C Tongue
- Centre for Epidemiology and Risk Analysis, Veterinary Laboratories Agency - Weybridge, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, UK.
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24
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Fediaevsky A, Tongue SC, Nöremark M, Calavas D, Ru G, Hopp P. A descriptive study of the prevalence of atypical and classical scrapie in sheep in 20 European countries. BMC Vet Res 2008; 4:19. [PMID: 18544152 PMCID: PMC2442063 DOI: 10.1186/1746-6148-4-19] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Accepted: 06/10/2008] [Indexed: 12/03/2022] Open
Abstract
Background The development of active surveillance programmes for transmissible spongiform encephalopathies of small ruminants across Europe has led to the recent identification of a previously undetected form of ovine prion disease, 'atypical' scrapie. Knowledge of the epidemiology of this disease is still limited, as is whether it represents a risk for animal and/or public health. The detection of atypical scrapie has been related to the use of only some of the EU agreed rapid tests. Information about the rapid tests used is not, as yet, available from public reports on the surveillance of transmissible spongiform encephalopathies in small ruminants. We collected detailed results of active surveillance from European countries to estimate and to compare the prevalence of atypical scrapie and classical scrapie in sheep for each country stratified by each surveillance stream; healthy slaughtered and found dead adult sheep. Results From the 20 participating countries, it appeared that atypical scrapie was detected in Europe wherever the conditions necessary for its diagnosis were present. In most countries, atypical scrapie and classical scrapie occurred at low prevalence level. The classical scrapie prevalence estimates were more variable than those for atypical scrapie, which appeared remarkably homogeneous across countries, surveillance streams and calendar years of surveillance. Differences were observed in the age and genotype of atypical scrapie and classical scrapie cases that are consistent with previous published findings. Conclusion This work suggests that atypical scrapie is not rare compared to classical scrapie. The homogeneity of its prevalence, whatever the country, stream of surveillance or year of detection, contrasts with the epidemiological pattern of classical scrapie. This suggests that the aetiology of atypical scrapie differs from that of classical scrapie.
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Affiliation(s)
- Alexandre Fediaevsky
- AFSSA-Lyon, Unité Epidémiologie, 31 Avenue Tony Garnier, 69364 Lyon Cedex 07, France.
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25
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Abstract
Surveillance activities for ovine scrapie have expanded in the 21st century, following concerns about the potential for a hidden epidemic of bovine spongiform encephalopathy in European sheep populations. Large-scale surveys have been used to estimate the prevalence of scrapie infection. In this study we analyse data from the surveys in Great Britain between 2002 and 2004. When we estimate genotype-specific prevalences for each of the two screening tests used a difference is observed. One test underestimates the number of positive cases in genotypes classically considered to be at a low relative risk of developing clinical disease (ARR- and AHQ-containing genotypes). By comparison, the other test underestimates the number of positive cases in genotypes classically considered to be at an increased relative risk of developing clinical disease (VRQ-containing genotypes). These findings have implications for surveillance, disease control, and diagnostic test evaluation.
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Affiliation(s)
- S C Tongue
- Centre for Epidemiology and Risk Analysis, Veterinary Laboratories Agency, Weybridge, Surrey, UK.
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26
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Tongue SC, Pfeiffer DU, Heasman L, Simmons H, Ryder SJ. PrP genotype and lamb birth weight in a scrapie-free environment: Is there an association? Livest Sci 2006. [DOI: 10.1016/j.livsci.2006.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Tongue SC, Pfeiffer DU, Wilesmith JW. Reporting of clinical scrapie in the UK. Vet Rec 2006; 159:463. [PMID: 17012614 DOI: 10.1136/vr.159.14.463-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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28
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Tongue SC, Pfeiffer DU, Wilesmith JW. Descriptive spatial analysis of scrapie-affected flocks in Great Britain between January 1993 and December 2002. Vet Rec 2006; 159:165-70. [PMID: 16891423 DOI: 10.1136/vr.159.6.165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The spatial distribution of sheep flocks in Great Britain with confirmed clinical scrapie between January 1993 and December 2002 inclusive was investigated by using kernel density estimation and a cluster scan test statistic. Six statistically significant clusters were identified: three were lower risk, and were centred on the north-western coast of Scotland, the north-western coast of Wales and the South Yorkshire/Pennine region; three were of higher risk, and were centred in the central south, North Yorkshire and north Cumbria. General knowledge and the results of previous epidemiological studies were used to generate biologically plausible hypotheses that might explain these findings. They included aspects of flock management and disease transmission, and factors associated with the identification of cases, including their detection, recognition and, in particular, reporting levels, as well as diagnosis and animal movements.
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Affiliation(s)
- S C Tongue
- Scrapie Epidemiology Group, Centre for Epidemiology and Risk Analysis, Veterinary Laboratories Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey kt15 3nb
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Del Rio Vilas VJ, Ryan J, Elliott HG, Tongue SC, Wilesmith JW. Prevalence of scrapie in sheep: results from fallen stock surveys in Great Britain in 2002 and 2003. Vet Rec 2006; 157:744-5. [PMID: 16326969 DOI: 10.1136/vr.157.23.744] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- V J Del Rio Vilas
- Centre for Epidemiology and Risk Analysis, Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
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30
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Tongue SC, Pfeiffer DU, Warner R, Elliott H, Del Rio Vilas V. Estimation of the relative risk of developing clinical scrapie: the role of prion protein (PrP) genotype and selection bias. Vet Rec 2006; 158:43-50. [PMID: 16415231 DOI: 10.1136/vr.158.2.43] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Prion protein (PrP) genotype data from statutory confirmed cases and from three non-case datasets have been used to calculate the odds ratio (or) for the development of clinical scrapie for an individual sheep of a given PrP genotype, compared with one possessing the "wild-type" ARQ/ARQ genotype. Logistic regression has been used to estimate the ors, and a multiple-test procedure has been used to evaluate the statistical significance of each comparison. The results are similar to those observed in other studies: the VRQ/VRQ genotype has or point estimates greater than 20; the ARQ/VRQ and ARH/VRQ genotypes have or point estimates between 5 and 20; AHQ/VRQ between 0.03 and 0.1; ARR/VRQ 0.4 and 0.5; all the other PrP genotypes, excluding ARR/ARR, ARR/ARH and AHQ/ARH for which no clinical cases have been recorded have or point estimates of less than 0.3. The estimates derived from each dataset are comparable, but not identical. This can be explained by plausible biases inherent in the sampling of the non-case populations.
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Affiliation(s)
- S C Tongue
- Scrapie Epidemiology Group, Centre for Epidemiology and Risk Analysis, New Haw, Addlestone, Surrey KT15 3NB, UK
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31
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Affiliation(s)
- S C Tongue
- Scrapie Epidemiology Group, Centre for Epidemiology and Risk Analysis, Veterinary Laboratories Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB
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Tongue SC, Wilesmith JW, Cook CJ. Frequencies of prion protein (PrP) genotypes and distribution of ages in 15 scrapieaffected flocks in Great Britain. Vet Rec 2004; 154:9-16. [PMID: 14725423 DOI: 10.1136/vr.154.1.9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The frequencies of prion protein (PrP) genotypes were investigated in 15 scrapie-affected flocks in Great Britain. The flocks were heterogeneous in the frequencies of different genotypes and alleles, and in their age distributions. The median flock frequency of animals with VRQ-containing genotypes was 21 per cent (range 2 to 82 per cent, mean 25 per cent). The VRQ-containing and other non-ARR genotypes made up 11 to 82 per cent of a flock (median 46 per cent, mean 48 per cent). In comparison with data from the general population the scrapie-affected population had a lower frequency of the ARR/ARR genotype, and so of the ARR allele, and had a higher frequency of VRQ/non-ARR heterozygote genotypes, and thus of the VRQ allele.
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Affiliation(s)
- S C Tongue
- Scrapie Epidemiology Group, VLA - Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB
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