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Volume 9, Issue 7

Genome-wide phylodynamic approach reveals the epidemic dynamics of the main subtype circulating in France Open Access

Abstract

is a major aetiological agent of bovine respiratory disease worldwide. Genome-based analyses are increasingly being used to monitor the genetic diversity and global distribution of , complementing existing subtyping schemes based on locus sequencing. However, these analyses have so far provided limited information on the spatiotemporal and population dynamics of circulating subtypes. Here we applied a genome-wide phylodynamic approach to explore the epidemic dynamics of 88 French strains collected between 2000 and 2019 in France and belonging to the currently dominant subtype 2 (st2). A strong molecular clock signal detected in the genomic data enabled robust phylodynamic inferences, which estimated that the st2 population in France is composed of two lineages that successively emerged from independent introductions of international strains. The first lineage appeared around 2000 and supplanted the previously established antimicrobial-susceptible subtype 1. The second lineage, which is likely more transmissible, progressively replaced the first st2 lineage population from 2005 onward and became predominant after 2010. Analyses also showed a brief decline in this second st2 lineage population in around 2011, possibly due to the challenge from the concurrent emergence of subtype 3 in France. Finally, we identified non-synonymous mutations in genes associated with lineages, which raises prospects for identifying new surveillance molecular markers. A genome-wide phylodynamic approach provides valuable resources for monitoring the evolution and epidemic dynamics of circulating subtypes, and may prove critical for developing more effective surveillance systems and disease control strategies.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bacteria , cattle , fitness , lineage replacement , respiratory disease and surveillance
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-07-24
2024-04-28
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Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France
M Gen 9, 001067 (2023); https://doi.org/10.1099/mgen.0.001067
/content/journal/mgen/10.1099/mgen.0.001067
/content/journal/mgen/10.1099/mgen.0.001067
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