定义研究铜绿假单胞菌医院暴发的基因组阈值。

IF 3.9 3区医学 Q1 INFECTIOUS DISEASES

Journal of Hospital Infection Pub Date : 2025-05-10 DOI:10.1016/j.jhin.2025.04.028

S. Romano-Bertrand , M. Virieux-Petit , F. Mauffrey , L. Senn , D.S. Blanc

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引用次数: 0

摘要

背景：在调查铜绿假单胞菌（PA）暴发时，应采用分子分型方法证实分离株的克隆性。全基因组测序（WGS）是细菌基因分型的新金标准，但结果解释必须谨慎考虑分离株作为同一传播链的一部分。目的：考虑到疫情的时空规模，确定基因组阈值以识别最近的传播事件。方法：采用核心基因组MLST和单核苷酸多态性（SNP）对我院近15年来发生的PA暴发进行回顾性分析。我们的结果是根据先前发表的文献，使用WGS调查医院爆发的PA进行讨论。结果：纳入我院14例PA暴发调查，时间从数天到9年不等。属于同一传播链的分离株存在多达13个位点差异和25个snp。这些结果与已发表的19次暴发一致，这些暴发大多报告流行病学上相关的分离株在15-25个snp以下具有相似性。时间和空间对符合条件的snp阈值或位点差异的影响可能被其他因素所掩盖，包括基因型、WGS分析中包含的分离株数量、传播途径和环境水库的存在。结论：我们的研究强调需要将基因组阈值与流行病学数据相结合，特别是当涉及环境宿主或超突变体时，以准确评估传播动力学和暴发起源。

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Defining a genomic threshold for investigating Pseudomonas aeruginosa hospital outbreak

Background

When investigating Pseudomonas aeruginosa (PA) outbreaks, the clonality of isolates should be demonstrated using a molecular typing method. Whole-genome sequencing (WGS) is the new gold standard for bacterial genotyping, but care should be taken in the interpretation of results regarding considering isolates as part of the same chain of transmission.

Aim

To determine genomic threshold to identify recent transmission events considering the spatiotemporal scale of the outbreak.

Methods

PA outbreaks occurring in our hospital during the past 15 years were retrospectively analysed by both core-genome MLST and single-nucleotide polymorphism (SNP) with regard to epidemiological data. Our results were discussed in the light of previous published literature employing WGS to investigate hospital outbreaks of PA.

Findings

Fourteen investigations of PA outbreaks in our hospital were included, lasting a few days to nine years. Isolates belonging to the same chain of transmission presented up to 13 loci differences and 25 SNPs. These results were in accordance with the 19 published outbreaks that mostly reported a similarity among epidemiologically related isolates below 15–25 SNPs. The impact of time and space on the threshold of eligible SNPs or loci differences was possibly masked by other factors including the genotype, the number of isolates included in the WGS analysis, the path of transmission and the presence of environmental reservoir.

Conclusions

Our study emphasizes the need to integrate genomic thresholds with epidemiological data, especially when environmental reservoirs or hypermutators are involved, to accurately assess transmission dynamics and outbreak origins.

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来源期刊

Journal of Hospital Infection 医学-传染病学

CiteScore

12.70

自引率

5.80%

发文量

271

审稿时长

19 days

期刊介绍： The Journal of Hospital Infection is the editorially independent scientific publication of the Healthcare Infection Society. The aim of the Journal is to publish high quality research and information relating to infection prevention and control that is relevant to an international audience. The Journal welcomes submissions that relate to all aspects of infection prevention and control in healthcare settings. This includes submissions that: provide new insight into the epidemiology, surveillance, or prevention and control of healthcare-associated infections and antimicrobial resistance in healthcare settings; provide new insight into cleaning, disinfection and decontamination; provide new insight into the design of healthcare premises; describe novel aspects of outbreaks of infection; throw light on techniques for effective antimicrobial stewardship; describe novel techniques (laboratory-based or point of care) for the detection of infection or antimicrobial resistance in the healthcare setting, particularly if these can be used to facilitate infection prevention and control; improve understanding of the motivations of safe healthcare behaviour, or describe techniques for achieving behavioural and cultural change; improve understanding of the use of IT systems in infection surveillance and prevention and control.