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 characterise 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 mothers 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 mothers breast milk and the childs 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 transmission, probably via breastfeeding. Next, phylogenomic analysis of all isolates, including the mothers mixed ST-259/261 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.\n\nImpact StatementBurkholderia pseudomallei is the causative agent of melioidosis, a tropical disease of high mortality. B. pseudomallei infections occur almost exclusively through contact with contaminated soil and water. Using whole-genome sequencing (WGS), we investigated a rare case of suspected B. pseudomallei transmission from mother to child. The mothers sputum, breast milk and the babys blood and cerebrospinal fluid (CSF) specimens were collected, and DNA was extracted from both pure colonies and primary culture sweeps to capture potential strain mixtures. In-depth analysis of genetic variants identified two strains in the mothers sputum belonging to multilocus sequence types ST-259 and ST-261, whereas the child was infected with only ST-259. Comparative genomics revealed no genetic differences between mother and child ST-259 isolates, providing the strongest possible evidence of transmission to the child via breast milk. The sputum strain mixture was subsequently used to develop a bioinformatic method for identification and quantification of mixtures from WGS data. Using this method, we found ST-259 and ST-261 at an 87%:13% ratio, respectively. Finally, we demonstrate the negative impact that even a single strain mixture event can have on both within-ST and global phylogenomic inferences. Our findings highlight the need for bioinformatic quality control to avoid unintended consequences of phylogenomic incongruence and branch collapse.\n\nData SummaryO_LIWhole-genome sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) and GenBank under BioProject accession number PRJNA559002.\nC_LIO_LIThe GenBank accession number for MSHR0643 assembly is VXLH00000000.1.\nC_LIO_LIThe SRA accession numbers for all raw sequence data are listed in Table 1.\nC_LI\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@c3b580org.highwire.dtl.DTLVardef@c11407org.highwire.dtl.DTLVardef@9e443org.highwire.dtl.DTLVardef@169014borg.highwire.dtl.DTLVardef@d4026c_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONSummary of ST-259 and ST-261 Burkholderia pseudomallei isolates.\n\nC_TABLECAPTION C_TBL RepositoriesAll sequencing data generated as part of this study can be found under the NCBI BioProject PRJNA559002 with accession numbers listed in Table 1.