Phylodynamic analysis of an emergent Mycobacterium bovis outbreak in an area with no previously known wildlife infections

Abstract

1. Understanding how emergent pathogens successfully establish themselves and persist in previously unaffected populations is a crucial problem in disease ecology, with important implications for disease management. In multi-host pathogen systems this problem is particularly difficult, as the importance of each host species to transmission is often poorly characterised, and the disease epidemiology is complex. Opportunities to observe and analyse such emergent scenarios are few.2. Here, we exploit a unique dataset combining densely collected data on the epidemiological and evolutionary characteristics of an outbreak of Mycobacterium bovis (the causative agent of bovine tuberculosis, bTB) in a population of cattle and badgers in an area considered low risk for bTB, with no previous record of either persistent infection in cattle, or of any infection in wildlife. We analyse the outbreak dynamics using a combination of mathematical modelling, Bayesian evolutionary analyses and machine learning.3. Comparison to M. bovis whole-genome sequences from Northern Ireland confirmed this to be a pathogen single introduction from the latter region, with evolutionary analysis supporting an introduction directly into the local cattle population 6 years prior to its first discovery in badgers.4. Once introduced, the evidence supports M. bovis epidemiological dynamics passing through two phases, the first dominated by cattle-to-cattle transmission before becoming established in the local badger population. Synthesis and applications.The Mycobacterium bovis emergent outbreak that was the object of this study was of considerable concern because of the geographical distance from previously known high-risk areas. Initial decisions about the outbreak control were supported by the whole-genome sequencing data. The further analyses described here were used to estimate the time of introduction (and This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France

“…Our results are consistent with a previous study by Crispell et al showing a badger-to-cattle transition rate (0.045 transitions/lineage/year) 10 times superior to the cattle-to-badger transition rate (0.0044 per lineage per year) on a subset of cattle ( n = 83) and badger ( n = 97) strains isolated in the UK [ 19 ]. Conversely, Rossi et al estimated a higher cattle-to-badger transition rate in a newly infected region in the North-West of England and concluded on the possible requirement of a “build-up in badger infections […] before badger-to-cattle infections become probable” [ 46 ].…”

Detection of a local Mycobacterium bovis reservoir using cattle surveillance data

“…2019; Rossi et al. 2021) and cattle have been proposed as reliable sentinels for TB in badgers elsewhere (Murphy et al., 2011). A study in New Zealand used TB surveillance data from cattle to estimate the probability of freedom from M. bovis infection in the brushtail possum (Anderson et al., 2017).…”

“…In the longer term, robust evidence should be sought from analysis of transmission pathways in areas of low and high cattle and wildlife densities. Genetic analyses of M. bovis isolates from badgers and cattle show that the level and the predominant direction of transmission between cattle and badgers vary between areas (Crispell et al., 2019; Rossi et al., 2021). Incorporation of data from other wildlife and domesticated species could provide a clearer ecological picture.…”

“…In England, the majority of evidence that the badger is a wildlife host for M. bovis comes from the south‐west, although infected badgers have also been detected in the north (Bourne et al. 2007; Delahay et al., 2000, 2001; Rossi et al., 2021). In Woodchester Park in south‐west England, the prevalence of TB in badgers monitored within a 15 km 2 area increased from 5% to over 30% between 1982 and 2005 (Delahay et al., 2013).…”

Simulating Partial Vaccine Protection: Bcg in Badgers

“…It would become increasingly important to prevent cattle-to-badger infection as vaccination progresses to avoid re-infection. Indeed cattle-to-badger infection has been shown to be more frequent than badger-to-cattle infection in both the Low Risk Area of England (Rossi et al, 2022) and in Northern Ireland (Akhmetova et al, 2021), although the reverse has been reported in endemic areas of England (Crispell et al, 2019). In terms of monitoring the effectiveness of badger vaccination, the prevalence of bTB in badgers is the easiest metric to measure in the field, through either live capture and sampling (combined with subsequent laboratory diagnostic tests) or Road Traffic Accident (RTA) post-mortem surveys.…”