耐万古霉素肠球菌,主要是屎肠球菌(VREfm),导致医院感染和爆发。细菌分型方法用于协助疫情调查。他们中的大多数,特别是基因型方法,如多基因座序列分型(MLST),全基因组测序(WGS),或脉冲场凝胶电泳,非常昂贵和耗时。傅里叶变换红外(FT-IR)光谱评估细菌的生化成分,如多糖中的羧基。这是一种负担得起的技术,并且具有更快的周转时间。因此,本研究的目的是评估FT-IR光谱技术在VREfm暴发调查中的应用.在不同的样品组中评估基本性能要求,如再现性和孵育时间的影响。在确定FT-IR光谱截止范围之后,在回顾性(n:92个分离株)和前瞻性爆发(n:15个分离株)中,调查了FT-IR和WGS之间的聚集一致性.对于WGS,使用0.999的平均核苷酸同一性(ANI)截止评分。基本性能分析显示出可重现的结果。此外,FT-IR光谱读数显示与临床暴发调查中的WGS-ANI分析高度吻合(回顾性分析为V-measure0.772,前瞻性暴发为1.000)。在疫情调查中,FT-IR光谱比MLST具有更高的辨别能力。在确定截止值以达到最佳分辨率之后,FT-IR光谱法是一种有前途的技术,可以帮助疫情调查,易于使用的工具,周转时间少于一天。重要性耐万古霉素肠球菌,主要是屎肠球菌(VREfm),是医院爆发的常见原因。几种细菌分型方法用于追踪传播和调查疫情,基于基因组的技术被用作黄金标准。目前的方法要么昂贵,耗时,或者两者兼而有之。此外,经常,需要有经过专门培训的工作人员。这项研究提供了深入的傅里叶变换红外(FT-IR)光谱的使用,一个负担得起的,易于使用的工具,具有较短的周转时间,作为VREfm的打字方法。通过评估临床样本,这项工作证明了物种辨别和可重复性的有希望的结果。与基于全基因组测序的方法相比,FT-IR光谱在分析VREfm爆发方面显示出高度的一致性。
Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are causing nosocomial infections and outbreaks. Bacterial typing methods are used to assist in outbreak investigations. Most of them, especially genotypic methods like multi-locus sequence typing (MLST), whole genome sequencing (WGS), or pulsed-field gel electrophoresis, are quite expensive and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy assesses the biochemical composition of bacteria, such as carboxyl groups in polysaccharides. It is an affordable technique and has a faster turnaround time. Thus, the aim of this study was to evaluate FT-IR spectroscopy for VREfm outbreak investigations. Basic performance requirements like reproducibility and the effects of incubation time were assessed in distinct sample sets. After determining a FT-IR spectroscopy cut-off range, the clustering agreement between FT-IR and WGS within a retrospective (n: 92 isolates) and a prospective outbreak (n: 15 isolates) was investigated. For WGS an average nucleotide identity (ANI) cut-off score of 0.999 was used. Basic performance analysis showed reproducible results. Moreover, FT-IR spectroscopy readouts showed a high agreement with WGS-ANI analysis in clinical outbreak investigations (V-measure 0.772 for the retrospective and 1.000 for the prospective outbreak). FT-IR spectroscopy had a higher discriminatory power than MLST in the outbreak investigations. After determining cut-off values to achieve optimal resolution, FT-IR spectroscopy is a promising technique to assist in outbreak investigation as an affordable, easy-to-use tool with a turnaround time of less than one day. IMPORTANCE Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are a frequent cause of nosocomial outbreaks. Several bacterial typing methods are used to track transmissions and investigate outbreaks, whereby genome-based techniques are used as a gold standard. Current methods are either expensive, time-consuming, or both. Additionally, often, specifically trained staff needs to be available. This study provides insight into the use of Fourier-transform infrared (FT-IR) spectroscopy, an affordable, easy-to-use tool with a short turnaround time as a typing method for VREfm. By assessing clinical samples, this work demonstrates promising results for species discrimination and reproducibility. FT-IR spectrosopy shows a high level of agreement in the analysis of VREfm outbreaks in comparison with whole genome sequencing-based methods.