Epidemiology Unit, Laboratory for Animal Health, Paris-Est University, Anses, 94700, Maisons-Alfort, France.
Université Paris-Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France.
Vet Res. 2022 Apr 2;53(1):28. doi: 10.1186/s13567-022-01044-x.
In two "départements" in the South-West of France, bovine tuberculosis (bTB) outbreaks due to Mycobacterium bovis spoligotype SB0821 have been identified in cattle since 2002 and in wildlife since 2013. Using whole genome sequencing, the aim of our study was to clarify badger contribution to bTB transmission in this area. We used a Bayesian evolutionary model, to infer phylogenetic trees and migration rates between two pathogen populations defined by their host-species. In order to account for sampling bias, sub-population structure was inferred using the marginal approximation of the structured coalescent (Mascot) implemented in BEAST2. We included 167 SB0821 strains (21 isolated from badgers and 146 from cattle) and identified 171 single nucleotide polymorphisms. We selected a HKY model and a strict molecular clock. We estimated a badger-to-cattle transition rate (median: 2.2 transitions/lineage/year) 52 times superior to the cattle-to-badger rate (median: 0.042 transitions/lineage/year). Using the maximum clade credibility tree, we identified that over 75% of the lineages from 1989 to 2000 were present in badgers. In addition, we calculated a median of 64 transition events from badger-to-cattle (IQR: 10-91) and a median of zero transition event from cattle-to-badger (IQR: 0-3). Our model enabled us to infer inter-species transitions but not intra-population transmission as in previous epidemiological studies, where relevant units were farms and badger social groups. Thus, while we could not confirm badgers as possible intermediaries in farm-to-farm transmission, badger-to-cattle transition rate was high and we confirmed long-term presence of M. bovis in the badger population in the South-West of France.
在法国西南部的两个“départements”，自 2002 年以来，牛结核病（bTB）爆发归因于牛分枝杆菌 spoligotype SB0821，在牛中发现，自 2013 年以来在野生动物中发现。使用全基因组测序，我们的研究旨在阐明该地区獾在 bTB 传播中的作用。我们使用贝叶斯进化模型，根据宿主物种定义的两种病原体种群推断系统发育树和迁移率。为了考虑采样偏差，我们使用 BEAST2 中实现的结构化合并的边缘近似（Mascot）推断亚种群结构。我们包括 167 株 SB0821 菌株（21 株从獾中分离，146 株从牛中分离）和鉴定了 171 个单核苷酸多态性。我们选择了 HKY 模型和严格的分子钟。我们估计了獾到牛的转换率（中位数：2.2 次/谱系/年），比牛到獾的转换率（中位数：0.042 次/谱系/年）高 52 倍。使用最大枝可信树，我们确定 1989 年至 2000 年的谱系中有超过 75%存在于獾中。此外，我们计算了 64 次从獾到牛的转换事件（IQR：10-91）和零次从牛到獾的转换事件（IQR：0-3）的中位数。我们的模型使我们能够推断物种间的转换，但不能推断之前的流行病学研究中的种群内传播，在之前的研究中，相关单位是农场和獾社会群体。因此，虽然我们不能确认獾是否可能成为农场到农场传播的中介，但獾到牛的转换率很高，我们证实了 M. bovis 在法国西南部獾种群中的长期存在。
