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Volume 6, Issue 2

Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality Open Access

Abstract

Human-to-human transmission of the melioidosis bacterium, , is exceedingly rare, with only a handful of suspected cases documented to date. Here, we used whole-genome sequencing (WGS) to characterize one such unusual transmission event, which occurred between a breastfeeding mother with mastitis and her child. Two strains corresponding to multilocus sequence types (STs)-259 and -261 were identified in the mother’s sputum from both the primary culture sweep and in purified colonies, confirming an unusual polyclonal infection in this patient. In contrast, primary culture sweeps of the mother’s breast milk and the child’s cerebrospinal fluid and blood samples contained only ST-259, indicating monoclonal transmission to the child. Analysis of purified ST-259 isolates showed no genetic variation between mother and baby isolates, providing the strongest possible evidence of human-to-human transmission, probably via breastfeeding. Next, phylogenomic analysis of all isolates, including the mother’s mixed ST-259/ST-261 sputum sample, was performed to investigate the effects of mixtures on phylogenetic inference. Inclusion of this mixture caused a dramatic reduction in the number of informative SNPs, resulting in branch collapse of ST-259 and ST-261 isolates, and several instances of incorrect topology in a global phylogeny, resulting in phylogenetic incongruence. Although phylogenomics can provide clues about the presence of mixtures within WGS datasets, our results demonstrate that this methodology can lead to phylogenetic misinterpretation if mixed genomes are not correctly identified and omitted. Using current bioinformatic tools, we demonstrate a robust method for bacterial mixture identification and strain parsing that avoids these pitfalls.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): branch collapse , Burkholderia pseudomallei , human-to-human transmission , phylogenetic incongruence , phylogenomics and strain mixtures
Funding
This study was supported by the:
  • Advance Queensland (Award AQRF13016-17RD2)
    • Principle Award Recipient: Erin P. Price
  • Advance Queensland (Award AQIRF0362018)
    • Principle Award Recipient: Derek S. Sarovich
  • National Health and Medical Research Council (Award 1078557)
    • Principle Award Recipient: Ammar Aziz
  • National Health and Medical Research Council (Award 1131932)
    • Principle Award Recipient: Bart J. Currie
  • National Health and Medical Research Council (Award 1098337)
    • Principle Award Recipient: Erin P. Price
  • National Health and Medical Research Council (Award 1098337)
    • Principle Award Recipient: Derek S. Sarovich
  • National Health and Medical Research Council (Award 1098337)
    • Principle Award Recipient: Mark Mayo
  • National Health and Medical Research Council (Award 1098337)
    • Principle Award Recipient: Bart J. Currie
  • National Health and Medical Research Council (Award 1046812)
    • Principle Award Recipient: Erin P. Price
  • National Health and Medical Research Council (Award 1046812)
    • Principle Award Recipient: Derek S. Sarovich
  • National Health and Medical Research Council (Award 1046812)
    • Principle Award Recipient: Mark Mayo
  • National Health and Medical Research Council (Award 1046812)
    • Principle Award Recipient: Bart J. Currie
© 2020 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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2020-01-20
2024-04-27
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Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality
M Gen 6, e000326 (2020); https://doi.org/10.1099/mgen.0.000326
/content/journal/mgen/10.1099/mgen.0.000326
/content/journal/mgen/10.1099/mgen.0.000326
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