Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis
Mycobacterium bovis is the causal agent of bovine tuberculosis, one of the most important diseases currently facing the UK cattle industry. Here, we use high-density whole genome sequencing (WGS) in a defined sub-population of M. bovis in 145 cattle across 66 herd breakdowns to gain insights into lo...
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doaj-a90fdbd7cc9f47e09f6d2497fae43d962020-11-24T23:15:14ZengElsevierEpidemics1755-43651878-00672016-03-0114C263510.1016/j.epidem.2015.08.003Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosisHannah Trewby0David Wright1Eleanor L. Breadon2Samantha J. Lycett3Tom R. Mallon4Carl McCormick5Paul Johnson6Richard J. Orton7Adrian R. Allen8Julie Galbraith9Pawel Herzyk10Robin A. Skuce11Roman Biek12Rowland R. Kao13Boyd Orr Centre for Population and Ecosystem Health, Institute for Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UKSchool of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UKVeterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland, UKThe Roslin Institute, University of Edinburgh, Edinburgh, UKVeterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland, UKVeterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland, UKBoyd Orr Centre for Population and Ecosystem Health, Institute for Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UKBoyd Orr Centre for Population and Ecosystem Health, Institute for Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UKVeterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland, UKGlasgow Polyomics, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UKGlasgow Polyomics, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UKSchool of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UKBoyd Orr Centre for Population and Ecosystem Health, Institute for Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UKBoyd Orr Centre for Population and Ecosystem Health, Institute for Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UKMycobacterium bovis is the causal agent of bovine tuberculosis, one of the most important diseases currently facing the UK cattle industry. Here, we use high-density whole genome sequencing (WGS) in a defined sub-population of M. bovis in 145 cattle across 66 herd breakdowns to gain insights into local spread and persistence. We show that despite low divergence among isolates, WGS can in principle expose contributions of under-sampled host populations to M. bovis transmission. However, we demonstrate that in our data such a signal is due to molecular type switching, which had been previously undocumented for M. bovis. Isolates from farms with a known history of direct cattle movement between them did not show a statistical signal of higher genetic similarity. Despite an overall signal of genetic isolation by distance, genetic distances also showed no apparent relationship with spatial distance among affected farms over distances <5 km. Using simulations, we find that even over the brief evolutionary timescale covered by our data, Bayesian phylogeographic approaches are feasible. Applying such approaches showed that M. bovis dispersal in this system is heterogeneous but slow overall, averaging 2 km/year. These results confirm that widespread application of WGS to M. bovis will bring novel and important insights into the dynamics of M. bovis spread and persistence, but that the current questions most pertinent to control will be best addressed using approaches that more directly integrate WGS with additional epidemiological data.http://www.sciencedirect.com/science/article/pii/S1755436515000833Bacterial evolutionLivestock diseaseMolecular epidemiologyMycobacterium bovisPhylogeography |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hannah Trewby David Wright Eleanor L. Breadon Samantha J. Lycett Tom R. Mallon Carl McCormick Paul Johnson Richard J. Orton Adrian R. Allen Julie Galbraith Pawel Herzyk Robin A. Skuce Roman Biek Rowland R. Kao |
spellingShingle |
Hannah Trewby David Wright Eleanor L. Breadon Samantha J. Lycett Tom R. Mallon Carl McCormick Paul Johnson Richard J. Orton Adrian R. Allen Julie Galbraith Pawel Herzyk Robin A. Skuce Roman Biek Rowland R. Kao Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis Epidemics Bacterial evolution Livestock disease Molecular epidemiology Mycobacterium bovis Phylogeography |
author_facet |
Hannah Trewby David Wright Eleanor L. Breadon Samantha J. Lycett Tom R. Mallon Carl McCormick Paul Johnson Richard J. Orton Adrian R. Allen Julie Galbraith Pawel Herzyk Robin A. Skuce Roman Biek Rowland R. Kao |
author_sort |
Hannah Trewby |
title |
Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis |
title_short |
Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis |
title_full |
Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis |
title_fullStr |
Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis |
title_full_unstemmed |
Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis |
title_sort |
use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis |
publisher |
Elsevier |
series |
Epidemics |
issn |
1755-4365 1878-0067 |
publishDate |
2016-03-01 |
description |
Mycobacterium bovis is the causal agent of bovine tuberculosis, one of the most important diseases currently facing the UK cattle industry. Here, we use high-density whole genome sequencing (WGS) in a defined sub-population of M. bovis in 145 cattle across 66 herd breakdowns to gain insights into local spread and persistence. We show that despite low divergence among isolates, WGS can in principle expose contributions of under-sampled host populations to M. bovis transmission. However, we demonstrate that in our data such a signal is due to molecular type switching, which had been previously undocumented for M. bovis. Isolates from farms with a known history of direct cattle movement between them did not show a statistical signal of higher genetic similarity. Despite an overall signal of genetic isolation by distance, genetic distances also showed no apparent relationship with spatial distance among affected farms over distances <5 km. Using simulations, we find that even over the brief evolutionary timescale covered by our data, Bayesian phylogeographic approaches are feasible. Applying such approaches showed that M. bovis dispersal in this system is heterogeneous but slow overall, averaging 2 km/year. These results confirm that widespread application of WGS to M. bovis will bring novel and important insights into the dynamics of M. bovis spread and persistence, but that the current questions most pertinent to control will be best addressed using approaches that more directly integrate WGS with additional epidemiological data. |
topic |
Bacterial evolution Livestock disease Molecular epidemiology Mycobacterium bovis Phylogeography |
url |
http://www.sciencedirect.com/science/article/pii/S1755436515000833 |
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