A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France
Abstract 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 t...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | Veterinary Research |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13567-022-01044-x |
| _version_ | 1819025959741816832 |
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| author | Hélène Duault Lorraine Michelet Maria-Laura Boschiroli Benoit Durand Laetitia Canini |
| author_facet | Hélène Duault Lorraine Michelet Maria-Laura Boschiroli Benoit Durand Laetitia Canini |
| author_sort | Hélène Duault |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-21T05:18:58Z |
| format | Article |
| id | doaj.art-1dd4e19afe374ae0af3ac2d7bf0e57b8 |
| institution | Directory Open Access Journal |
| issn | 1297-9716 |
| language | English |
| last_indexed | 2024-12-21T05:18:58Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Veterinary Research |
| spelling | doaj.art-1dd4e19afe374ae0af3ac2d7bf0e57b82022-12-21T19:14:51ZengBMCVeterinary Research1297-97162022-04-0153111210.1186/s13567-022-01044-xA Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of FranceHélène Duault0Lorraine Michelet1Maria-Laura Boschiroli2Benoit Durand3Laetitia Canini4Epidemiology Unit, Laboratory for Animal Health, Paris-Est University, AnsesTuberculosis Reference Laboratory, Bacterial Zoonosis Unit, Laboratory for Animal Health, Paris-Est University, AnsesTuberculosis Reference Laboratory, Bacterial Zoonosis Unit, Laboratory for Animal Health, Paris-Est University, AnsesEpidemiology Unit, Laboratory for Animal Health, Paris-Est University, AnsesEpidemiology Unit, Laboratory for Animal Health, Paris-Est University, AnsesAbstract 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.https://doi.org/10.1186/s13567-022-01044-xMulti-host systembovine tuberculosisgenomic epidemiology |
| spellingShingle | Hélène Duault Lorraine Michelet Maria-Laura Boschiroli Benoit Durand Laetitia Canini A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France Veterinary Research Multi-host system bovine tuberculosis genomic epidemiology |
| title | A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France |
| title_full | A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France |
| title_fullStr | A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France |
| title_full_unstemmed | A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France |
| title_short | A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France |
| title_sort | bayesian evolutionary model towards understanding wildlife contribution to f4 family mycobacterium bovis transmission in the south west of france |
| topic | Multi-host system bovine tuberculosis genomic epidemiology |
| url | https://doi.org/10.1186/s13567-022-01044-x |
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