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

Abstract

Human-to-human transmission of the melioidosis bacterium, Burkholderia pseudomallei , 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 B. pseudomallei 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 B. pseudomallei 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 B. pseudomallei 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.

Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis

“…There has only been a single report of a handful of suspected cases of human-to-human transmission of B. pseudomallei [62], and skin inoculation, the oral ingestion of B. pseudomallei- contaminated water [4, 63, 64], and the inhalation of B. pseudomallei during extreme weather events [65, 66] are considered the main routes of infection.…”

Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli sequence type (ST)131 associated with bacteraemia in Wales, United Kingdom

“…However, SPANDx was utilised for the methodology employed in this study as it has been peer reviewed (46) and is under regular development, with v4.0.1 released on 02 April 2020. Additionally, previous quality assurance analyses using SPANDx have been reported (68) to ensure; a single mixed strain does not affect tree topology and phylogenetic inference, and the importance of assessing datasets for the presence of mixed strains prior to phylogenetic analyses.…”

Pharmacodynamic Evaluation of Plasma and Epithelial Lining Fluid Exposures of Amikacin against Pseudomonas aeruginosa in a Dynamic In Vitro Hollow-Fiber Infection Model

“…Samples were periodically removed from the central compartment outlet at 0.25, 0.5, 0. 45,1,2,3,4,6,8,10,12,24,25,30,36,48,49,54,60,72,73,78,84,96,120,144,145, and 156 h to determine the amikacin concentration for pharmacokinetic analysis. As the central compartment contents rapidly equilibrate with the hollow-fiber cartridge, the concentrations obtained in the central compartment reflect that in the hollow-fiber cartridge.…”

“…The comparative genomics pipeline, SPANDx v3.2.1 (43), was used to determine genomic variation using either the isolate CTAP23 or isolate CTAP40 as the reference genome, depending on the lineage analyzed. Within-species mixtures were analyzed using the GATK v4.1.0.0 (44) to identify mutations with less than 100% allele frequency using the method outlined in Aziz et al (45).…”