Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection

PLoS Pathogens
Talima PearsonPaul Keim

Abstract

Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314's sputum despite intensive initial therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314's airways over a >16-year period, and also sampled the patient's home environment, recovering six closely related B. pseudomallei isolates from the household water system. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a strictly clonal mode of genetic inheritance. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successf...Continue Reading

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Citations

Feb 9, 2021·Frontiers in Microbiology·Chalita ChomkatekaewClaire Chewapreecha
Mar 24, 2021·Emerging Infectious Diseases·Ella M MeumannBart J Currie

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Datasets Mentioned

BETA
CP025264.1
CP025265.1
PRJNA321854

Methods Mentioned

BETA
X-ray
PCR

Software Mentioned

Bowtie2
Tracer
GATK
Tandem Repeats Finder
MEM
BLAST
LogCombiner
FigTree
HyPHY
ISG

Related Concepts