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
Sara Romano-Bertrand, Maxine Virieux-Petit, Florian Mauffrey, Laurence Senn, Dominique S Blanc
{"title":"定义研究铜绿假单胞菌医院暴发的基因组阈值。","authors":"Sara Romano-Bertrand, Maxine Virieux-Petit, Florian Mauffrey, Laurence Senn, Dominique S Blanc","doi":"10.1016/j.jhin.2025.04.028","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>When investigating Pseudomonas aeruginosa (PA) outbreak, the clonality of isolates should be demonstrated using molecular typing method. Whole-genome sequencing (WGS) is the new Gold Standard for bacterial genotyping, but results interpretation must be careful about considering isolates as part of the same chain of transmission.</p><p><strong>Aim: </strong>To determine genomic threshold to identify recent transmission events considering the spatiotemporal scale of the outbreak.</p><p><strong>Methods: </strong>PA outbreaks occurring in our hospital during the past 15 years were retrospectively analysed by both core-genome MLST and single-nucleotide polymorphism (SNP) in regards of epidemiological data. Our results were discussed in the light of previous published literature employing WGS to investigate hospital outbreaks of PA.</p><p><strong>Findings: </strong>14 investigations of PA outbreaks in our hospital were included, lasting a few days to 9 years. Isolates belonging to a 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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":54806,"journal":{"name":"Journal of Hospital Infection","volume":" ","pages":""},"PeriodicalIF":3.9000,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Defining a genomic threshold for investigating Pseudomonas aeruginosa hospital outbreak.\",\"authors\":\"Sara Romano-Bertrand, Maxine Virieux-Petit, Florian Mauffrey, Laurence Senn, Dominique S Blanc\",\"doi\":\"10.1016/j.jhin.2025.04.028\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>When investigating Pseudomonas aeruginosa (PA) outbreak, the clonality of isolates should be demonstrated using molecular typing method. Whole-genome sequencing (WGS) is the new Gold Standard for bacterial genotyping, but results interpretation must be careful about considering isolates as part of the same chain of transmission.</p><p><strong>Aim: </strong>To determine genomic threshold to identify recent transmission events considering the spatiotemporal scale of the outbreak.</p><p><strong>Methods: </strong>PA outbreaks occurring in our hospital during the past 15 years were retrospectively analysed by both core-genome MLST and single-nucleotide polymorphism (SNP) in regards of epidemiological data. Our results were discussed in the light of previous published literature employing WGS to investigate hospital outbreaks of PA.</p><p><strong>Findings: </strong>14 investigations of PA outbreaks in our hospital were included, lasting a few days to 9 years. Isolates belonging to a 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.</p><p><strong>Conclusions: </strong>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.</p>\",\"PeriodicalId\":54806,\"journal\":{\"name\":\"Journal of Hospital Infection\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":3.9000,\"publicationDate\":\"2025-05-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Hospital Infection\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1016/j.jhin.2025.04.028\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"INFECTIOUS DISEASES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Hospital Infection","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1016/j.jhin.2025.04.028","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}
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。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Defining a genomic threshold for investigating Pseudomonas aeruginosa hospital outbreak.

Background: When investigating Pseudomonas aeruginosa (PA) outbreak, the clonality of isolates should be demonstrated using molecular typing method. Whole-genome sequencing (WGS) is the new Gold Standard for bacterial genotyping, but results interpretation must be careful about 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) in regards of epidemiological data. Our results were discussed in the light of previous published literature employing WGS to investigate hospital outbreaks of PA.

Findings: 14 investigations of PA outbreaks in our hospital were included, lasting a few days to 9 years. Isolates belonging to a 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.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Journal of Hospital Infection
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.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信