Carter Glen P, Buultjens Andrew H, Ballard Susan A, Baines Sarah L, Tomita Takehiro, Strachan Janet, Johnson Paul D R, Ferguson John K, Seemann Torsten, Stinear Timothy P, Howden Benjamin P
Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, University of Melbourne, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3000, Australia.
J Antimicrob Chemother. 2016 Dec;71(12):3367-3371. doi: 10.1093/jac/dkw314. Epub 2016 Aug 15.
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.
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.
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.
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.
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.
屎肠球菌是一种主要的医院病原体，在全球范围内导致显著的发病率和死亡率。使用多位点序列分型（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可能不足以用于屎肠球菌监测。
使用全基因组测序（WGS）对最近鉴定出的、无法通过MLST分型的耐万古霉素屎肠球菌（VREfm）分离株进行特征分析，这些分离株似乎在澳大利亚引发了多辖区的疫情暴发。
使用Illumina NextSeq和Pacific Biosciences SMRT测序平台确定66株无法分型的屎肠球菌（NTEfm）分离株的基因组序列。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。
通过WGS从澳大利亚多个卫生辖区鉴定出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中存在大的染色体重排，这可能促进了pstS区域的缺失。对该群体的系统发育基因组分析表明，屎肠球菌中pstS的缺失至少独立发生了三次。重要的是，这些分离株中的大多数显示出耐万古霉素基因型。
我们鉴定出了似乎在澳大利亚引发多辖区疫情暴发的NTEfm分离株。鉴定这些分离株对于旨在监测VREfm传播的基于MLST的分型活动具有重要意义，并提供了进一步的证据支持使用WGS进行医院屎肠球菌监测。
