Webb JR

Mayo M

Rachlin A

Woerle C

Meumann EM

Rigas V

Harrington G

Kaestli M

Currie BJ

2022-01-26

Each case of melioidosis results from a single event when a human is infected by the environmental bacterium Burkholderia pseudomallei. Darwin in tropical northern Australia has the highest incidences of melioidosis globally and the Darwin Prospective Melioidosis Study (DPMS) commenced in 1989, documenting all culture confirmed melioidosis cases. From 2000-2019 we sampled DPMS patient's environments for B. pseudomallei when a specific location was considered to have been where infection occurred. With the aim to use genomic epidemiology to understand B. pseudomallei transmission and infecting scenarios. Environmental sampling was performed at 98 DPMS patient sites, where we collected 975 environmental samples (742 soil; 233 water). Genotyping matched the clinical and epidemiologically linked environmental B. pseudomallei for 19 patients (19%), with the environmental isolates cultured from soil (n=11) or water (n=8) sources. B. pseudomallei isolates from patients and their local environments that matched on genotyping were whole genome sequenced (WGS). Of the 19 patients with a clinical-environmental genotype match, 17 pairs clustered on a Darwin core genome single-nucleotide polymorphism (SNP) phylogeny, later confirmed by single ST phylogenies and pairwise comparative genomics. When related back to patient clinical scenarios, the matched clinical and environmental B. pseudomallei pairs informed likely modes of infection: percutaneous inoculation, inhalation, and ingestion. Targeted environmental sampling for B. pseudomallei can inform infecting scenarios for melioidosis and dangerous occupational and recreational activities and identify hot spots of B. pseudomallei presence. However, WGS and careful genomics are required to avoid overcalling the relatedness between clinical and environmental isolates of B. pseudomallei.

Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia.

Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia.

Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia.

J Clin Microbiol. 2022 Jan 26:JCM0164821. doi: 10.1128/JCM.01648-21.

0000-0002-6332-039X

https://pubmed.ncbi.nlm.nih.gov/35080450/?otool=iaurydwlib

https://hdl.handle.net/10137/12106

Genomic epidemiology links Burkholderia pseudomallei from individual human cases to B. pseudomallei from targeted environmental sampling in Northern Australia.

Journal Article

Publication