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Volume 8, Issue 2

Population genomics of from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity Open Access

Abstract

Genomic sequencing has revolutionized our understanding of bacterial disease epidemiology, but remains underutilized for zoonotic pathogens in remote endemic settings. Anthrax, caused by the spore-forming bacterium , remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of has been well-characterized, there is limited information on how its populations are genetically structured at the scale at which transmission occurs, critical for understanding the pathogen’s evolution and transmission dynamics. Using a uniquely rich dataset, we quantified genome-wide SNPs among 73 isolates derived from 33 livestock carcasses sampled over 1 year throughout the Ngorongoro Conservation Area, Tanzania, a region hyperendemic for anthrax. Genome-wide SNPs distinguished 22 unique genotypes (i.e. SNP profiles) within the study area. However, phylogeographical structure was lacking, as identical SNP profiles were found throughout the study area, likely the result of the long and variable periods of spore dormancy and long-distance livestock movements. Significantly, divergent genotypes were obtained from spatio-temporally linked cases and even individual carcasses. The high number of SNPs distinguishing isolates from the same host is unlikely to have arisen during infection, as supported by our simulation models. This points to an unexpectedly wide transmission bottleneck for , with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of from genomic data will require analytical approaches that account for extended and variable environmental persistence, as well as co-infection.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacillus anthracis endemic anthrax , phylogenomics , simulation modelling and within-host diversity
Funding
This study was supported by the:
  • Bill and Melinda Gates Foundation (Award 1083453)
    • Principle Award Recipient: O.Rhoda Aminu
  • Biotechnology and Biological Sciences Research Council (Award FORDE/BB/R012075/1)
    • Principle Award Recipient: TayaL. Forde
  • Academy of Medical Sciences (Award SBF002\1168)
    • Principle Award Recipient: TizianaLembo
  • Natural Sciences and Engineering Research Council of Canada (Award PDF-471750-2015)
    • Principle Award Recipient: TayaL. Forde
  • H2020 Marie Skłodowska-Curie Actions (Award 659223)
    • Principle Award Recipient: TayaL. Forde
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2022-02-21
2024-04-18
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Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity
M Gen 8, 000759 (2022); https://doi.org/10.1099/mgen.0.000759
/content/journal/mgen/10.1099/mgen.0.000759
/content/journal/mgen/10.1099/mgen.0.000759
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