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

Forde, T. L. et al. (2022) Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity. Microbial Genomics, 8(2), 000759. (doi: 10.1099/mgen.0.000759) (PMID:35188453) (PMCID:PMC8942019)

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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 Bacillus anthracis , remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of B. anthracis 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 B. anthracis 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 B. anthracis 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 B. anthracis , with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of B. anthracis from genomic data will require analytical approaches that account for extended and variable environmental persistence, as well as co-infection.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:MMBAGA, Professor Blandina Theoph and Lembo, Dr Tiziana and Zadoks, Professor Ruth and Harvey, Dr William and Aminu, Ms Olubunmi Rhoda and Vogel, Ms Adeline and Forde, Dr Taya and Biek, Professor Roman and Dennis, Dr Tristan
Creator Roles:
Forde, T. L.Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Visualization, Writing – original draft
Dennis, T. P.W.Conceptualization, Formal analysis, Methodology, Software, Visualization, Writing – review and editing
Aminu, O. R.Investigation, Writing – review and editing
Harvey, W. T.Formal analysis, Methodology, Software, Visualization, Writing – review and editing
Vogel, A.Formal analysis, Visualization
Zadoks, R. N.Writing – review and editing
Mmbaga, B. T.Funding acquisition, Project administration
Lembo, T.Conceptualization, Funding acquisition, Investigation, Project administration, Supervision, Writing – review and editing
Biek, R.Conceptualization, Formal analysis, Funding acquisition, Methodology, Supervision, Visualization, Writing – review and editing
Authors: Forde, T. L., Dennis, T. P.W., Aminu, O. R., Harvey, W. T., Hassim, A., Kiwelu, I., Medvecky, M., Mshanga, D., Van Heerden, H., Vogel, A., Zadoks, R. N., Mmbaga, B. T., Lembo, T., and Biek, R.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity
College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
Journal Name:Microbial Genomics
Publisher:Microbiology Society
ISSN:2057-5858
ISSN (Online):2057-5858
Published Online:21 February 2022
Copyright Holders:Copyright © 2022 The Authors
First Published:First published in Microbial Genomics 8(2): 000759
Publisher Policy:Reproduced under a Creative Commons License
Data DOI:10.5525/gla.researchdata.1217

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
171848Molecular epidemiology of Bacillus anthracis: novel data and techniques for local surveillance in TanzaniaRoman BiekEuropean Commission (EC)659223Institute of Biodiversity, Animal Health and Comparative Medicine
300423Novel molecular approaches for understanding the epidemiology of endemic anthraxTaya FordeBiotechnology and Biological Sciences Research Council (BBSRC)BB/R012075/1Institute of Biodiversity, Animal Health and Comparative Medicine
190437Impact, ecology and social determinants of bacterial zoonoses in northern TanzaniaSarah CleavelandBiotechnology and Biological Sciences Research Council (BBSRC)BB/J010367/1Institute of Biodiversity, Animal Health and Comparative Medicine
190821Hazards associated with zoonotic enteric pathogens in emerging livestock meat pathways (HAZEL)Ruth ZadoksBiotechnology and Biological Sciences Research Council (BBSRC)BB/L017679/1Institute of Biodiversity, Animal Health and Comparative Medicine
190825Social, economic and environmental drivers of zoonoses in Tanzania (SEEDZ)Sarah CleavelandBiotechnology and Biological Sciences Research Council (BBSRC)BB/L018926/1Institute of Biodiversity, Animal Health and Comparative Medicine
190785Molecular epidemology of brucellosis in northern TanzaniaDaniel HaydonBiotechnology and Biological Sciences Research Council (BBSRC)BB/L018845/1Institute of Biodiversity, Animal Health and Comparative Medicine
165842Leptospirosis in Tanzania; a study of the role of rodents in an emerging public health problem.Sarah CleavelandWellcome Trust (WELLCOTR)096400/Z/11/ZInstitute of Biodiversity, Animal Health and Comparative Medicine