Minotti Chiara, Robinson Elena, Schlaepfer Pascal, Pohl Christian, Goldenberger Daniel, Schulzke Sven M, Keller Peter Michael, Bielicki Julia Anna
Infectious Disease and Vaccinology Unit and Paediatric Research Centre, University Children's Hospital Basel UKBB, Spitalstrasse 33, Basel, 4031, Switzerland.
Department of Clinical Research DKF, Faculty of Medicine, University of Basel, Basel, Switzerland.
Antimicrob Resist Infect Control. 2025 Jul 1;14(1):76. doi: 10.1186/s13756-025-01595-6.
K. oxytoca generally has a benign susceptibility profile and low virulence but can cause invasive infections in vulnerable populations, like preterm infants. We aim to describe how whole-genome sequencing (WGS) was used to inform management of a prolonged K. oxytoca outbreak on a neonatal intensive care unit (NICU) and implications for outbreak response involving similar organisms.
We retrospectively reviewed outbreak-associated clinical and environmental isolates from a Swiss NICU. WGS was used to track evolution of resistance and highlighted multiple concurrent outbreaks. WGS was performed using a MiSeq or NextSeq 500 Illumina sequencer. The resulting genome sequences were analysed using Ridom SeqSphere. The current report conforms to ORION reporting guidelines.
Of 152 Klebsiella spp. patient-derived isolates, 83 were genotyped using WGS, along with six environmental isolates. This confirmed two outbreak waves (November 2021-February 2022, ST18 wildtype; July 2022-June 2023, main cluster ST18 KI β-lactamase hyperproducer), with multiple genotypically connected clusters during the second wave. Confirmed sepsis (K. oxytoca ST18 wildtype) occurred in four preterm or low birthweight infants. Twins presented a genotypically identical ST with a different susceptibility phenotype (ST18 wildtype vs. K1 OXY-hyperproducer). WGS combined with epidemiological investigation and environmental sampling identified an environmental source. There was a second outbreak wave after source removal, presumably due to the prolonged presence of colonised infants with typically long NICU stays and insufficient standard infection prevention and control measures to prevent transmission.
WGS use in NICU outbreaks involving low-virulence bacteria can support identification and removal of potentiating environmental sources. These measures, however, will often be insufficient to contain the outbreak, and ongoing WGS surveillance of ubiquitous species may uncover multiple concurrent outbreaks, presumably driven by continuing transfer-transmission between different sources and infants in the NICU. Maximising standard infection prevention and control (IPC) measures is appropriate in this context.
产酸克雷伯菌通常具有良性的药敏谱和低毒力，但可在脆弱人群中引起侵袭性感染，如早产儿。我们旨在描述全基因组测序（WGS）如何用于指导新生儿重症监护病房（NICU）中产酸克雷伯菌长时间暴发的管理，以及对涉及类似病原体的暴发应对措施的影响。
我们回顾性分析了瑞士一家NICU中与暴发相关的临床和环境分离株。WGS用于追踪耐药性的演变，并突出显示了多个同时发生的暴发。使用MiSeq或NextSeq 500 Illumina测序仪进行WGS。使用Ridom SeqSphere分析所得的基因组序列。本报告符合ORION报告指南。
在152株肺炎克雷伯菌患者来源的分离株中，83株使用WGS进行了基因分型，另有6株环境分离株。这证实了两个暴发波（2021年11月至2022年2月，ST18野生型；2022年7月至2023年6月，主要簇为ST18 KI β-内酰胺酶高产株），在第二波期间有多个基因连接的簇。4例早产儿或低体重儿确诊为败血症（产酸克雷伯菌ST18野生型）。双胞胎呈现出基因相同的ST，但药敏表型不同（ST18野生型与K1 OXY高产株）。WGS结合流行病学调查和环境采样确定了一个环境来源。在去除污染源后出现了第二波暴发，可能是由于定植婴儿长期存在，NICU住院时间通常较长，且标准感染预防和控制措施不足以防止传播。
在涉及低毒力细菌的NICU暴发中使用WGS可以支持识别和去除潜在的环境来源。然而，这些措施往往不足以控制暴发，对常见菌种进行持续的WGS监测可能会发现多个同时发生的暴发，推测是由NICU中不同来源与婴儿之间持续的传播-传染驱动的。在这种情况下，最大限度地采取标准感染预防和控制（IPC）措施是合适的。
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