Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality
Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality
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DOI：
10.1099/mgen.0.000326
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发表时间：
2020-02-01
影响因子：
3.9
通讯作者：
Price, Erin P.
中科院分区：
文献类型：
--
作者：
Aziz, Ammar;Currie, Bart J.;Price, Erin P.
类鼻疽杆菌（Burkholderia pseudomallei）的人际传播极为罕见，迄今为止只有少数疑似病例。在这里，我们使用全基因组测序（WGS）来表征这样一个不寻常的B。假鼻疽传播事件，发生在患有乳腺炎的哺乳母亲与其孩子之间。在来自原代培养物扫描和纯化菌落的母亲痰液中鉴定出对应于多位点序列类型（ST）-259和-261的两种菌株，证实该患者存在不寻常的多克隆感染。相比之下，母亲母乳和儿童脑脊液和血液样本的原代培养扫描仅含有ST-259，表明单克隆传播给儿童。对纯化ST-259分离株的分析表明，母亲和婴儿分离株之间没有遗传变异，这为B提供了最有力的证据。类鼻疽人传人，可能是通过母乳喂养。接下来，对所有分离株（包括母亲的ST-259/ST-261混合痰样品）进行PCR基因组分析，以研究混合物对系统发育推断的影响。包含该混合物导致信息SNP的数量急剧减少，导致ST-259和5 T-261分离株的分支崩溃，以及全局B中的几个不正确拓扑结构的实例。pseudomallei系统发育，导致系统发育不一致。虽然混合基因组学可以提供有关WGS数据集内混合物存在的线索，但我们的研究结果表明，如果混合基因组没有被正确识别和省略，这种方法可能会导致系统发育误解。使用目前的生物信息学工具，我们展示了一个强大的方法，细菌混合物的识别和菌株解析，避免这些陷阱。
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 5T-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.