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Allen A, Magee R, Devaney R, Ardis T, McNally C, McCormick C, Presho E, Doyle M, Ranasinghe P, Johnston P, Kirke R, Harwood R, Farrell D, Kenny K, Smith J, Gordon S, Ford T, Thompson S, Wright L, Jones K, Prodohl P, Skuce R. Whole-Genome sequencing in routine Mycobacterium bovis epidemiology - scoping the potential. Microb Genom 2024; 10:001185. [PMID: 38354031 PMCID: PMC10926703 DOI: 10.1099/mgen.0.001185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Mycobacterium bovis the main agent of bovine tuberculosis (bTB), presents as a series of spatially-localised micro-epidemics across landscapes. Classical molecular typing methods applied to these micro-epidemics, based on genotyping a few variable loci, have significantly improved our understanding of potential epidemiological links between outbreaks. However, they have limited utility owing to low resolution. Conversely, whole-genome sequencing (WGS) provides the highest resolution data available for molecular epidemiology, producing richer outbreak tracing, insights into phylogeography and epidemic evolutionary history. We illustrate these advantages by focusing on a common single lineage of M. bovis (1.140) from Northern Ireland. Specifically, we investigate the spatial sub-structure of 20 years of herd-level multi locus VNTR analysis (MLVA) surveillance data and WGS data from a down sampled subset of isolates of this MLVA type over the same time frame. We mapped 2108 isolate locations of MLVA type 1.140 over the years 2000-2022. We also mapped the locations of 148 contemporary WGS isolates from this lineage, over a similar geographic range, stratifying by single nucleotide polymorphism (SNP) relatedness cut-offs of 15 SNPs. We determined a putative core range for the 1.140 MLVA type and SNP-defined sequence clusters using a 50 % kernel density estimate, using cattle movement data to inform on likely sources of WGS isolates found outside of core ranges. Finally, we applied Bayesian phylogenetic methods to investigate past population history and reproductive number of the 1.140 M. bovis lineage. We demonstrate that WGS SNP-defined clusters exhibit smaller core ranges than the established MLVA type - facilitating superior disease tracing. We also demonstrate the superior functionality of WGS data in determining how this lineage was disseminated across the landscape, likely via cattle movement and to infer how its effective population size and reproductive number has been in flux since its emergence. These initial findings highlight the potential of WGS data for routine monitoring of bTB outbreaks.
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Affiliation(s)
- Adrian Allen
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Ryan Magee
- Queen’s University Belfast, school of Biological Sciences, UK
| | - Ryan Devaney
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Tara Ardis
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Caitlín McNally
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Carl McCormick
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Eleanor Presho
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Michael Doyle
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Purnika Ranasinghe
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Philip Johnston
- Department of Agriculture, Environment and Rural Affairs for Northern Ireland, Belfast, UK
| | - Raymond Kirke
- Department of Agriculture, Environment and Rural Affairs for Northern Ireland, Belfast, UK
| | - Roland Harwood
- Department of Agriculture, Environment and Rural Affairs for Northern Ireland, Belfast, UK
| | - Damien Farrell
- Central Veterinary Research Laboratory, Kildare, Ireland
- University College Dublin, Dublin, Ireland
| | - Kevin Kenny
- Central Veterinary Research Laboratory, Kildare, Ireland
| | | | | | - Tom Ford
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Suzan Thompson
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Lorraine Wright
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Kerri Jones
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
| | - Paulo Prodohl
- Queen’s University Belfast, school of Biological Sciences, UK
| | - Robin Skuce
- Agrifood and Biosciences Institute, Veterinary Sciences Division, Belfast, UK
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Chang Y, Hartemink N, Byrne AW, Gormley E, McGrath G, Tratalos JA, Breslin P, More SJ, de Jong MCM. Inferring bovine tuberculosis transmission between cattle and badgers via the environment and risk mapping. Front Vet Sci 2023; 10:1233173. [PMID: 37841461 PMCID: PMC10572351 DOI: 10.3389/fvets.2023.1233173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/29/2023] [Indexed: 10/17/2023] Open
Abstract
Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is one of the most challenging and persistent health issues in many countries worldwide. In several countries, bTB control is complicated due to the presence of wildlife reservoirs of infection, i.e. European badger (Meles meles) in Ireland and the UK, which can transmit infection to cattle. However, a quantitative understanding of the role of cattle and badgers in bTB transmission is elusive, especially where there is spatial variation in relative density between badgers and cattle. Moreover, as these two species have infrequent direct contact, environmental transmission is likely to play a role, but the quantitative importance of the environment has not been assessed. Therefore, the objective of this study is to better understand bTB transmission between cattle and badgers via the environment in a spatially explicit context and to identify high-risk areas. We developed an environmental transmission model that incorporates both within-herd/territory transmission and between-species transmission, with the latter facilitated by badger territories overlapping with herd areas. Model parameters such as transmission rate parameters and the decay rate parameter of M. bovis were estimated by maximum likelihood estimation using infection data from badgers and cattle collected during a 4-year badger vaccination trial. Our estimation showed that the environment can play an important role in the transmission of bTB, with a half-life of M. bovis in the environment of around 177 days. Based on the estimated transmission rate parameters, we calculate the basic reproduction ratio (R) within a herd, which reveals how relative badger density dictates transmission. In addition, we simulated transmission in each small local area to generate a first between-herd R map that identifies high-risk areas.
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Affiliation(s)
- You Chang
- Quantitative Veterinary Epidemiology Group, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Nienke Hartemink
- Quantitative Veterinary Epidemiology Group, Wageningen University and Research Centre, Wageningen, Netherlands
- Biometris, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Andrew W. Byrne
- One-Health and Welfare Scientific Support Unit, Department of Agriculture, Food and the Marine, National Disease Control Centre, Dublin, Ireland
| | - Eamonn Gormley
- Tuberculosis Diagnostics and Immunology Research Centre, School of Agriculture, Food Science, and Veterinary Medicine, College of Life Sciences, University College Dublin, Dublin, Ireland
| | - Guy McGrath
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Jamie A. Tratalos
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Philip Breslin
- Ruminant Animal Health Division, Department of Agriculture, Food and the Marine, Dublin, Ireland
| | - Simon J. More
- Centre for Veterinary Epidemiology and Risk Analysis, School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Mart C. M. de Jong
- Quantitative Veterinary Epidemiology Group, Wageningen University and Research Centre, Wageningen, Netherlands
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Disturbance Ecology Meets Bovine Tuberculosis (bTB) Epidemiology: A Before-and-After Study on the Association between Forest Clearfelling and bTB Herd Risk in Cattle Herds. Pathogens 2022; 11:pathogens11070807. [PMID: 35890051 PMCID: PMC9321662 DOI: 10.3390/pathogens11070807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Disturbance ecology refers to the study of discrete processes that disrupt the structure or dynamics of an ecosystem. Such processes can, therefore, affect wildlife species ecology, including those that are important pathogen hosts. We report on an observational before-and-after study on the association between forest clearfelling and bovine tuberculosis (bTB) herd risk in cattle herds, an episystem where badgers (Meles meles) are the primary wildlife spillover host. The study design compared herd bTB breakdown risk for a period of 1 year prior to and after exposure to clearfelling across Ireland at sites cut in 2015–2017. The percent of herds positive rose from 3.47% prior to clearfelling to 4.08% after exposure. After controlling for confounders (e.g., herd size, herd type), we found that cattle herds significantly increased their odds of experiencing a bTB breakdown by 1.2-times (95%CIs: 1.07–1.36) up to 1 year after a clearfell risk period. Disturbance ecology of wildlife reservoirs is an understudied area with regards to shared endemic pathogens. Epidemiological observational studies are the first step in building an evidence base to assess the impact of such disturbance events; however, such studies are limited in inferring the mechanism for any changes in risk observed. The current cohort study suggested an association between clearfelling and bTB risk, which we speculate could relate to wildlife disturbance affecting pathogen spillback to cattle, though the study design precludes causal inference. Further studies are required. However, ultimately, integration of epidemiology with wildlife ecology will be important for understanding the underlying mechanisms involved, and to derive suitable effective management proposals, if required.
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