1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Evaluation of the sensitivity of faecal sampling for detection of monophasic Salmonella Typhimurium and other Salmonella in cattle and pigs. Epidemiol Infect 2014; 143:1681-91. [PMID: 25266772 DOI: 10.1017/s0950268814002453] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
There has been a rapid rise in the prevalence of cases of monophasic Salmonella Typhimurium (mST) in both humans and farm animals, and it has been found in pigs, cattle and poultry. It is therefore vital to have a good understanding of how to efficiently detect infected farms. The objective of this project was to determine sample type sensitivity in the detection of Salmonella to detect infected groups of animals on both pig (breeder, grower and finisher sites) and cattle (beef and dairy) farms, using data collected from a study investigating farms that were positive for mST, and to explore any variation between different age groups and management practices. A Bayesian approach in the absence of a gold standard was adopted to analyse the individual and pooled faecal sample data collected from each epidemiological group on each of the farms. The sensitivity of pooled sampling depended on the prevalence of infection in the group being sampled, with a higher prevalence leading to higher sensitivity. Pooled sampling was found to be more efficient at detecting positive groups of animals than individual sampling, with the probability of a random sample from a group of animals with 5% prevalence testing positive being equal to 15·5% for immature pigs (3·6% for an individual faecal sample, taking into account the sensitivity and infection prevalence), 7·1% for adult pigs (1·2% for individual sampling), 30% for outdoor cattle (2% for individual sampling) and 34% for indoor cattle (1% for individual sampling). The mean prevalence of each epidemiological group was higher in outdoor farms than indoor for both pigs and cattle (mean within-farm prevalence of 29·4% and 38·7% for outdoor pigs and cattle, respectively, compared to 19·8% and 22·1% for indoor pigs and cattle).
Collapse
|
4
|
Arnold ME, Slomka MJ, Coward VJ, Mahmood S, Raleigh PJ, Brown IH. Evaluation of the pooling of swabs for real-time PCR detection of low titre shedding of low pathogenicity avian influenza in turkeys. Epidemiol Infect 2013; 141:1286-97. [PMID: 22939242 PMCID: PMC9151896 DOI: 10.1017/s0950268812001811] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 06/15/2012] [Accepted: 07/25/2012] [Indexed: 11/07/2022] Open
Abstract
The purpose of this study was to determine whether pooling avian influenza (AI)-positive swabs with negative swabs has a detrimental effect on the sensitivity of AI real-time reverse transcription-polymerase chain reactions (rRT-PCRs). Cloacal and buccal swabs were sampled daily from 12 turkeys infected with A/goose/England/07(H2N2). For half the turkeys, each swab was mixed with four swabs from known AI-negative turkeys, and for the other half the swabs were tested individually. Bayesian modelling was used to (i) determine whether pooling the positive swabs compromised the cycle threshold (C(t)) value obtained from the rRT-PCRs, and (ii) estimate the likelihood of detection of an H2N2 infected turkey flock via rRT-PCR for pooled and individually tested swabs (cloacal and buccal) vs. the number of days post-infection of the flock. Results indicated that there was no significant effect of compromising AI rRT-PCR sensitivity by pooling a weak positive swab with negative swabs on the Ct values which were obtained. Pooled sampling was able to widen the detection window compared to individual sampling, for the same number of rRT-PCR tests. This indicates that pooled sampling would be an effective method of reducing the number of tests to be performed to determine flock status during an AI outbreak and for surveillance.
Collapse
Affiliation(s)
- M E Arnold
- Animal Health Veterinary Laboratories Agency (AHVLA) Weybridge, Addlestone, Surrey, UK.
| | | | | | | | | | | |
Collapse
|
5
|
Widgren S, Eriksson E, Aspan A, Emanuelson U, Alenius S, Lindberg A. Environmental sampling for evaluating verotoxigenic Escherichia coli O157: H7 status in dairy cattle herds. J Vet Diagn Invest 2013; 25:189-98. [PMID: 23404479 DOI: 10.1177/1040638712474814] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Verotoxigenic Escherichia coli O157:H7 is a zoonotic bacterial pathogen capable of causing severe disease in human beings. Cattle are considered to be the main reservoir of the bacterium. The objective of the current study was to compare environmental sampling (consisting of dust, overshoe, and pooled pat samples) with pooled, individual fecal sampling for determining the cattle herd status under field conditions in naturally infected dairy herds. Thirty-one dairy cattle farms in Sweden, where verotoxigenic E. coli O157:H7 had been previously detected, were visited. On each farm, dust, overshoe, and pooled pat sampling were performed in each of 3 different age categories: calves, young stock, and adults. In addition, up to 140 individual fecal samples were collected and analyzed as pooled samples. In total, 3,763 individual fecal and 270 environmental samples were collected and analyzed for the presence of verotoxigenic E. coli O157:H7. Overshoe sampling, alone or in combination with dust and pooled pat sampling, correctly classified 20 of the 24 (0.83, 95% CI: 0.63-0.95) herds detected with at least 1 positive pool. On 1 farm, a dust sample was positive although all other samples were negative. In 6 of the 31 farms, the bacteria could not be detected in any of the individual fecal samples or in the environmental samples. The results establish that environmental sampling is a reliable method for identifying cattle herds with animals shedding verotoxigenic E. coli O157:H7.
Collapse
Affiliation(s)
- Stefan Widgren
- National Veterinary Institute, Zoonoscenter, Uppsala, Sweden.
| | | | | | | | | | | |
Collapse
|
6
|
Vidal AB, Rodgers J, Arnold M, Clifton-Hadley F. Comparison of Different Sampling Strategies and Laboratory Methods for the Detection ofC. jejuniandC. colifrom Broiler Flocks at Primary Production. Zoonoses Public Health 2012; 60:412-25. [DOI: 10.1111/zph.12009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
7
|
Arnold M, Carrique-Mas J, McLaren I, Davies R. A comparison of pooled and individual bird sampling for detection of Salmonella in commercial egg laying flocks. Prev Vet Med 2011; 99:176-84. [DOI: 10.1016/j.prevetmed.2010.12.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 12/21/2010] [Accepted: 12/22/2010] [Indexed: 11/26/2022]
|
8
|
Estimation of sample sizes for pooled faecal sampling for detection of Salmonella in pigs. Epidemiol Infect 2009; 137:1734-41. [DOI: 10.1017/s0950268809002702] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SUMMARYSalmonella infection in breeding pigs was the subject of a European survey in 2008. The prevalence of pig-breeding holdings infected with Salmonella was determined by microbiological culture of pooled pen faecal samples. The objective of this study was to estimate the sensitivity of pooled faecal sampling and to calculate the required sample sizes. To do this, individual and pooled faecal samples were collected from a sample of pens from nine farms. Bayesian methods were used to estimate the sensitivity of individual and pooled faecal sampling, and the degree of clustering of Salmonella at the pen level. Sample sizes were then calculated for various values of design prevalence, taking into account the clustering. Pooling was highly efficient compared to individual sampling, e.g. with 18 pooled samples required to detect a 10% prevalence with 95% certainty, compared to 35 individual rectal samples. We recommend that pooled sampling is used for detection of Salmonella in pigs. Results were influenced by the degree of clustering at pen level, and it is important to take this into account both in the estimation of appropriate sample sizes and the estimation of prevalence from pooled sample data.
Collapse
|
9
|
Pritchard GC, Smith R, Ellis-Iversen J, Cheasty T, Willshaw GA. Verocytotoxigenic Escherichia coli
O157 in animals on public amenity premises in England and Wales, 1997 to 2007. Vet Rec 2009; 164:545-9. [DOI: 10.1136/vr.164.18.545] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- G. C. Pritchard
- Veterinary Laboratories Agency (VLA) - Bury St Edmunds; Rougham Hill Bury St Edmunds Suffolk IP33 2RX
| | - R. Smith
- VLA - Weybridge; Woodham Lane, New Haw Addlestone Surrey KT15 3NB
| | - J. Ellis-Iversen
- VLA - Weybridge; Woodham Lane, New Haw Addlestone Surrey KT15 3NB
| | - T. Cheasty
- Laboratory of Enteric Pathogens; Centre for Infections; Health Protection Agency; 61 Colindale Avenue London NW9 5HT
| | - G. A. Willshaw
- Laboratory of Enteric Pathogens; Centre for Infections; Health Protection Agency; 61 Colindale Avenue London NW9 5HT
| |
Collapse
|
10
|
Mueller-Doblies D, Sayers AR, Carrique-Mas JJ, Davies RH. Comparison of sampling methods to detect Salmonella infection of turkey flocks. J Appl Microbiol 2009; 107:635-45. [PMID: 19302307 DOI: 10.1111/j.1365-2672.2009.04230.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To compare the efficiency of various sampling methods for detection of Salmonella in turkey flocks. METHODS AND RESULTS In a field study that compared various sampling methods one pair of boot swabs taken from the whole turkey house provided suitably sensitive results for fattening and rearing flocks and was no less sensitive than two pairs, each from half the house, tested as a pooled sample. The sensitivity was further enhanced by adding a dust sample. The dust sample appeared to be particularly useful in flocks with a low prevalence, especially in breeding flocks, and was more sensitive than a method which used five pairs of boot swabs per flock. Combined incubation of a boot swab and a dust sample showed no interference between the two sample types and a maximum sensitivity of detection. Litter samples and commercial sponge drag swabs provided a lower level of detection. CONCLUSIONS A single pair of boot swabs taken from the whole house is recommended for routine sampling of commercial rearing or fattening flocks. An additional dust sample could be added to increase detection in flocks with a low prevalence or in breeding flocks, but adding an additional pair of boot swabs would not increase detection compared with a single pair. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrates that significant efficiencies can be made in sampling programmes for detection of Salmonella in turkey flocks without detracting from the sensitivity. Similar studies are recommended for other poultry sectors, particularly in chicken breeding flocks.
Collapse
Affiliation(s)
- D Mueller-Doblies
- Food and Environmental Safety Department, Veterinary Laboratories Agency Weybridge, New Haw, Addlestone, Surrey, UK
| | | | | | | |
Collapse
|