@article{5c80316632e64080bee23a5af7faa503,
title = "Combining genomics and epidemiology to analyse bi-directional transmission of mycobacterium bovis in a multi-host system",
abstract = "Quantifying pathogen transmission in multi-host systems is difficult, as exemplified in bovine tuberculosis (bTB) systems, but is crucial for control. The agent of bTB, Mycobacterium bovis, persists in cattle populations worldwide, often where potential wildlife reservoirs exist. However, the relative contribution of different host species to bTB persistence is generally unknown. In Britain, the role of badgers in infection persistence in cattle is highly contentious, despite decades of research and control efforts. We applied Bayesian phylogenetic and machine-learning approaches to bacterial genome data to quantify the roles of badgers and cattle in M. bovis infection dynamics in the presence of data biases. Our results suggest that transmission occurs more frequently from badgers to cattle than vice versa (10.4x in the most likely model) and that within-species transmission occurs at higher rates than between-species transmission for both. If representative, our results suggest that control operations should target both cattle and badgers.",
keywords = "Animals, Animals, Wild/microbiology, Bayes Theorem, Cattle, Disease Reservoirs/microbiology, Genome, Bacterial/genetics, Genomics/methods, Host-Pathogen Interactions, Mustelidae/microbiology, Mycobacterium bovis/classification, Phylogeny, Tuberculosis, Bovine/epidemiology",
author = "Joseph Crispell and Benton, {Clare H.} and Daniel Balaz and {De Maio}, Nicola and Assel Ahkmetova and Adrian Allen and Roman Biek and Presho, {Eleanor L.} and James Dale and Glyn Hewinson and Lycett, {Samantha J.} and Javier Nunez-Garcia and Skuce, {Robin A.} and Hannah Trewby and Wilson, {Daniel J.} and Zadoks, {Ruth N.} and Delahay, {Richard J.} and Kao, {Rowland Raymond}",
note = "Funding Information: We thank APHA and DEFRA staff for providing valuable comments on the manuscript, particularly James McCormack and Eleftheria Palkopoulou. Thanks to Stephen Gordon for providing access to a high-performance computing cluster maintained at the University College Dublin and advice during the generation of the manuscript. Glyn Hewinson holds a Ser Cymru II Research Chair. Daniel J Wilson is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and Royal Society. Samantha Lycett was supported by BBSRC Institute Strategic Programme Grant to the Roslin Institute, University of Edinburgh: Control of Infectious Diseases and by a University of Edinburgh Chancellor{\textquoteright}s Fellowship. Joseph Crispell conducted the analyses as part of his BBSRC funded PhD studentship and post-doctoral position at the University of Glasgow and continued the research at his current position as a Post-Doctoral Research Fellow at University College Dublin funded on an SFI grant. Daniel Balaz is funded by the BBSRC as a post-doctoral researcher. Rowland Kao was initially supported by a Wellcome Trust Senior Research Fellowship. The long-term study of badgers at Woodchester Park is funded by DEFRA. Thanks to the reviewers and editors for advising on manuscript revisions. Funding Information: We thank APHA and DEFRA staff for providing valuable comments on the manuscript, particularly James McCormack and Eleftheria Palkopoulou. Thanks to Stephen Gordon for providing access to a high-performance computing cluster maintained at the University College Dublin and advice during the generation of the manuscript. Glyn Hewinson holds a Ser Cymru II Research Chair. Daniel J Wilson is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and Royal Society. Samantha Lycett was supported by BBSRC Institute Strategic Programme Grant to the Roslin Institute, University of Edinburgh: Control of Infectious Diseases and by a University of Edinburgh Chancellor?s Fellowship. Joseph Crispell conducted the analyses as part of his BBSRC funded PhD studentship and post-doctoral position at the University of Glasgow and continued the research at his current position as a Post-Doctoral Research Fellow at University College Dublin funded on an SFI grant. Daniel Balaz is funded by the BBSRC as a post-doctoral researcher. Rowland Kao was initially supported by a Wellcome Trust Senior Research Fellowship. The long-term study of badgers at Woodchester Park is funded by DEFRA. Thanks to the reviewers and editors for advising on manuscript revisions. Science Foundation Ireland 16/BBSRC/3390 Joseph Crispell Wellcome Trust 714 101237/Z/13/Z Daniel J Wilson Biotechnology and Biological Sciences Research Council BBS/E/D/20002173 Samantha J Lycett Biotechnology and Biological Sciences Research Council BB/L010569/1 Joseph Crispell Daniel Balaz Rowland Raymond Kao Biotechnology and Biological Sciences Research Council BB/L010569/2 Daniel Balaz Rowland Raymond Kao Wellcome Trust 081696/Z/06/Z Rowland Raymond Kao Biotechnology and Biological Sciences Research Council BB/P010598/1 Samantha J Lycett Rowland Raymond Kao. Publisher Copyright: {\textcopyright} 2019, eLife Sciences Publications Ltd. All rights reserved.",
year = "2019",
month = dec,
day = "17",
doi = "10.7554/eLife.45833",
language = "English",
volume = "8",
journal = "eLife",
issn = "2050-084X",
publisher = "eLife Sciences Publications",
}
