Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly.
Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly.
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DOI：
10.1371/journal.pone.0236533
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发表时间：
2020
期刊：
影响因子：
3.7
通讯作者：
Bushman FD
中科院分区：
文献类型：
--
作者：
Gu CH;Zhao C;Hofstaedter C;Tebas P;Glaser L;Baldassano R;Bittinger K;Mattei LM;Bushman FD
龟分枝杆菌是一种快速生长的非结核分枝杆菌，是医院感染的常见原因。在此，我们描述了宾夕法尼亚大学医院 (HUP) 对龟分枝杆菌可能院内传播的调查。从 2017 年 HUP 发生术后感染的两名患者身上分离出具有类似高水平抗生素耐药模式的龟分枝杆菌菌株，表明可能存在点源感染。使用 Illumina 和 Oxford Nanopore 技术对这些分离株以及其他患者的其他临床分离株进行了测序。由此产生的短读长和长读长被混合组装成基因组草案。通过量化核心基因组中的单核苷酸变异来比较基因组，并使用对照数据集进行评估，以量化相同基因组比较中的错误率。我们表明，所有测试的龟分枝杆菌分离株都高度不同，如高成对 SNV 值所示，这与环境采集一致，而不是医院点源。我们的控制数据集确定了评估菌株之间同一性的阈值，同时控制测序错误。最后，预测了我们的分离株的抗生素抗性基因，并鉴定了几种有可能调节耐药性的单核苷酸变异。
Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high-level antibiotic resistance patterns were isolated from two patients who developed post-operative infections at HUP in 2017, suggesting a possible point source infection. The isolates, along with other clinical isolates from other patients, were sequenced using the Illumina and Oxford Nanopore technologies. The resulting short and long reads were hybrid assembled into draft genomes. The genomes were compared by quantifying single nucleotide variants in the core genome and assessed using a control dataset to quantify error rates in comparisons of identical genomes. We show that all M. chelonae isolates tested were highly dissimilar, as indicated by high pairwise SNV values, consistent with environmental acquisition and not a nosocomial point source. Our control dataset determined a threshold for evaluating identity between strains while controlling for sequencing error. Finally, antibiotic resistance genes were predicted for our isolates, and several single nucleotide variants were identified that have the potential to modulated drug resistance.
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