Background

Meticillin-susceptible and -resistant Staphylococcus aureus (MSSA and MRSA) are responsible for outbreaks in intensive care units. MSSA infections have the same morbidity and mortality rate as MRSA infections but are studied less often. Whole-genome sequencing (WGS) is used increasingly for outbreak monitoring, but still requires specific installation and trained personnel to obtain and analyse the data.

Aim

To evaluate the workflow and benefits of EpiSeq solution (bioMérieux, Marcy l’Etoile, France) in exploring the increased incidence of S. aureus bloodstream infections in a neonatal intensive care unit (NICU).

Methods

Four S. aureus bacteraemia isolates and 27 colonization isolates obtained between January and July 2016 were submitted to the ‘all in one solution’ EpiSeq [WGS, quality data assessment, multi-locus sequence typing (MLST), spa typing, virulome and resistome characterization, and phylogenetic tree construction]. More in-depth analyses were performed (whole-genome MLST and whole-genome single nucleotide polymorphism (wgSNP)] with BioNumerics software (Applied Maths, Sint-Martens-Latem, Belgium).

Findings

Nine different sequence types and 13 different spa types were found among the 31 isolates studied. Among those isolates, 11 (seven patients) were ST146 spa type t002, five (four patients) were ST30 and four (four patients) were ST398. The 11 ST146 isolates had a maximum of seven pairwise SNP differences.

Conclusion

Use of EpiSeq solution allowed fast demonstration of the polyclonal profile of the MSSA population in neonates, and enabled the suspicion of a global outbreak to be ruled out. However, wgSNP analysis showed the transmission and persistence of one sequence type for over six months in the NICU, and enabled the infection control team to adapt its response.

中文翻译：

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在新生儿重症监护病房的金黄色葡萄球菌暴发调查中评估“全合一”七天全基因组测序解决方案

背景

易感甲氧西林的金黄色葡萄球菌（MSSA和MRSA）是导致重症监护病房暴发的原因。MSSA感染与MRSA感染具有相同的发病率和死亡率，但很少进行研究。全基因组测序（WGS）越来越多地用于爆发监测，但仍需要特定的安装和受过训练的人员来获取和分析数据。

目的

为了评估EpiSeq解决方案（bioMérieux，Marcy l'Etoile，法国）在探索新生儿重症监护病房（NICU）中金黄色葡萄球菌血流感染发生率增加方面的工作流程和益处。

方法

2016年1月至2016年7月之间获得的4株金黄色葡萄球菌菌血症分离株和27株定殖分离株已提交给“多合一解决方案” EpiSeq [WGS，质量数据评估，多位点序列分型（MLST），spa分型，毒理和抗病菌组表征和系统树的构建]。使用BioNumerics软件（比利时Sint-Martens-Latem的Applied Maths）进行了更深入的分析（全基因组MLST和全基因组单核苷酸多态性（wgSNP））。

发现

在研究的31种分离物中发现了9种不同的序列类型和13种不同的水疗类型。在这些分离株中，有11例（七例）是ST146 t002型水疗中心，五例（四例）是ST30型，四例（四例）是ST398型。11个ST146分离株最多具有七个成对的SNP差异。

结论

EpiSeq解决方案的使用可以快速证明新生儿MSSA群体的多克隆概况，并排除了对全球爆发的怀疑。然而，wgSNP分析显示了一种序列类型在重症监护病房中的传播和持续时间超过六个月，并使感染控制小组能够适应其反应。