Institute of Hygiene, Cologne Merheim Medical Centre, University Hospital of Witten/Herdecke, Ostmerheimer Strasse 200, 51109, Cologne, Germany.
Division of Hygiene and Environmental Medicine, Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany.
Antimicrob Resist Infect Control. 2022 Apr 1;11(1):54. doi: 10.1186/s13756-022-01094-y.
Enterobacter cloacae complex is a group of common opportunistic pathogens on neonatal intensive care units. Active microbiological screening to guide empirical antimicrobial treatment or to detect transmission events is recommended in high-risk preterm neonates. A rise in colonization with E. cloacae complex was observed in a German perinatal centre. The aim of this study was to evaluate the performance of different typing techniques using whole genome sequencing (WGS) as a reference.
Enterobacter cloacae complex isolates from clinical and screening specimens with an epidemiological link to the neonatal intensive care units were further assessed. Identification and antibiotic susceptibility testing was performed by a combination of VITEK2 (bioMérieux) and MALDI-TOF (Bruker Daltonics), followed by RAPD/rep-PCR and PFGE (XbaI). Retrospectively, all isolates were analyzed by Fourier-transform infrared (FTIR) spectroscopy (IR Biotyper, Bruker Daltonics). Whole genome sequencing with SNP-based clustering was used as the reference method. Furthermore, resistome analysis, sequence type and species identification were derived from the WGS data. Transmission analysis was based on epidemiological and typing data.
Between September 2017 and March 2018 32 mostly preterm neonates were found to be colonized with E. cloacae complex and 32 isolates from 24 patients were available for further typing. RAPD/rep-PCR and PFGE showed good concordance with WGS whereas FTIR displayed mediocre results [adjusted rand index (ARI) = 0.436]. A polyclonal increase and two dominant and overlapping clonal clusters of two different E. hormaechei subspecies were detected. Overall, four different species were identified. Genotyping confirmed third-generation cephalosporin resistance development in isolates of the same patient. During the six-month period several infection prevention interventions were performed and no E. cloacae complex isolates were observed during the following months.
Interpretation of the microbiological results alone to detect transmission events is often challenging and bacterial typing is of utmost importance to implement targeted infection control measures in an epidemic occurrence of E. cloacae complex. WGS is the most discriminatory method. However, traditional methods such as PFGE or RAPD/rep-PCR can provide reliable and quicker results in many settings. Furthermore, research is needed to quickly identify E. cloacae complex to the species level in the microbiological laboratory.
阴沟肠杆菌复合群是新生儿重症监护病房常见的机会致病菌。建议对高危早产儿进行主动微生物筛查，以指导经验性抗菌治疗或检测传播事件。在德国围产期中心观察到阴沟肠杆菌复合群的定植率上升。本研究旨在评估不同的分型技术，以全基因组测序（WGS）为参考。
对与新生儿重症监护病房有流行病学联系的临床和筛查标本中的阴沟肠杆菌复合群分离株进行进一步评估。通过 VITEK2（生物梅里埃）和 MALDI-TOF（布鲁克·道尔顿）组合进行鉴定和药敏试验，随后进行 RAPD/rep-PCR 和 PFGE（XbaI）。回顾性地，所有分离株均采用傅里叶变换红外（FTIR）光谱法（IR Biotyper，布鲁克·道尔顿）进行分析。基于 SNP 的聚类的全基因组测序被用作参考方法。此外，从 WGS 数据中得出了抗性组分析、序列类型和物种鉴定。传播分析基于流行病学和分型数据。
2017 年 9 月至 2018 年 3 月期间，发现 32 例早产儿定植阴沟肠杆菌复合群，24 例患者中有 32 例分离株可用于进一步分型。RAPD/rep-PCR 和 PFGE 与 WGS 具有良好的一致性，而 FTIR 显示出中等的结果[调整后的兰德指数（ARI）=0.436]。检测到两种不同的埃希氏菌亚种的多克隆增加和两个主要的重叠克隆群。总的来说，鉴定出了四种不同的物种。基因分型证实了同一患者的第三代头孢菌素耐药性的发展。在六个月的时间里，进行了多次感染预防干预，在接下来的几个月里没有观察到阴沟肠杆菌复合群的分离株。
仅通过解释微生物学结果来检测传播事件通常具有挑战性，细菌分型对于在阴沟肠杆菌复合群的流行发生中实施有针对性的感染控制措施至关重要。WGS 是最具区分力的方法。然而，在许多情况下，传统方法，如 PFGE 或 RAPD/rep-PCR 可以提供可靠和快速的结果。此外，需要研究在微生物实验室中快速鉴定阴沟肠杆菌复合群到种的水平。
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