Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium
Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium
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DOI：
10.1093/jac/dkw314
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发表时间：
2016-12-01
影响因子：
5.2
通讯作者：
Howden, Benjamin P.
中科院分区：
文献类型：
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作者：
Carter, Glen P.;Buultjens, Andrew H.;Howden, Benjamin P.
背景：屎肠球菌是一种主要的医院病原体，在全世界范围内引起显着的发病率和死亡率。使用 MLST 评估屎肠球菌以了解该微生物的传播是医院感染控制措施的重要组成部分。然而，最近的研究表明 MLST 可能不足以监测屎肠球菌。 目标：使用 WGS 来表征最近发现的 MLST 无法分型的耐万古霉素屎肠球菌 (VREfm) 分离株，这些分离株似乎在澳大利亚引起多辖区疫情。方法：使用 Illumina NextSeq 和 Pacific Biosciences SMRT 测序平台来确定 66 种无法分型的屎肠球菌的基因组序列(NTEfm) 分离株。随后使用多种计算机工具进行系统发育和生物信息学分析。结果：通过 WGS 从澳大利亚多个卫生管辖区鉴定出 66 株屎肠球菌分离株，由于缺少 pstS 等位基因，这些分离株无法通过 MLST 进行分型。 SMRT 测序和完整基因组组装揭示了代表性菌株 DMG1500801 中存在大量染色体重排，这可能促进了 pstS 区域的删除。对该种群的系统发育分析表明，屎肠球菌中 pstS 的缺失至少在 3 次情况下独立发生。重要的是，这些分离株中的大多数都表现出万古霉素抗性基因型。结论：我们已经确定了 NTEfm 分离株，它们似乎在澳大利亚引起了多辖区的疫情爆发。这些分离株的鉴定对于旨在监测 VREfm 传播的基于 MLST 的分型活动具有重要意义，并为支持使用 WGS 进行医院粪肠球菌监测提供了进一步的证据。
Background: Enterococcus faecium is a major nosocomial pathogen causing significant morbidity and mortality worldwide. Assessment of E. faecium using MLST to understand the spread of this organism is an important component of hospital infection control measures. Recent studies, however, suggest that MLST might be inadequate for E. faecium surveillance.Objectives: To use WGS to characterize recently identified vancomycin-resistant E. faecium (VREfm) isolates non-typeable by MLST that appear to be causing a multi-jurisdictional outbreak in Australia.Methods: Illumina NextSeq and Pacific Biosciences SMRT sequencing platforms were used to determine the genome sequences of 66 non-typeable E. faecium (NTEfm) isolates. Phylogenetic and bioinformatics analyses were subsequently performed using a number of in silico tools.Results: Sixty-six E. faecium isolates were identified by WGS from multiple health jurisdictions in Australia that could not be typed by MLST due to a missing pstS allele. SMRT sequencing and complete genome assembly revealed a large chromosomal rearrangement in representative strain DMG1500801, which likely facilitated the deletion of the pstS region. Phylogenomic analysis of this population suggests that deletion of pstS within E. faecium has arisen independently on at least three occasions. Importantly, the majority of these isolates displayed a vancomycin-resistant genotype.Conclusions: We have identified NTEfm isolates that appear to be causing a multi-jurisdictional outbreak in Australia. Identification of these isolates has important implications for MLST-based typing activities designed to monitor the spread of VREfm and provides further evidence supporting the use of WGS for hospital surveillance of E. faecium.