弗氏柠檬酸杆菌核心基因组多位点序列分型方案的开发和验证:在柠檬酸杆菌属暴发调查和比较分析中的应用。

IF 5.4 2区 医学 Q1 MICROBIOLOGY
Bärbel Kieninger, Gabriel E Wagner, Anca Rath, Anja Eichner, Jürgen Fritsch, Aila Caplunik-Pratsch, Jasmine Alikhani, Parham Heydarzadeh-Ghamsary, Adriana Cabal-Rosel, Werner Ruppitsch, Dag Harmsen, Mohammed R Abdulla, Lena Ulm, Karsten Becker, Wulf Schneider-Brachert, Christian Kohler
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引用次数: 0

摘要

弗氏柠檬酸杆菌是一种院内病原菌,与多药耐药和医院暴发日益相关。尽管其临床相关性日益增强,但目前还没有标准化的核心基因组多位点序列分型(cgMLST)方案可用于高分辨率流行病学分析。在这里,我们基于825个全球分布的基因组数据集开发并验证了一个强大的弗氏弓形虫cgMLST方案,该方案包含3250个目标位点,代表了广泛的序列类型和地理多样性。针对芬兰和比利时医院公布的疫情数据集,以及来自两所德国大学医院的环境和患者分离株进行验证,证明该方案具有较高的靶基因覆盖率(中位数为99.6%)和很强的歧视性。此外,我们基于2307个共享的靶基因位点和≥99.7%的靶基因覆盖率,开发了弗氏弓形虫、葡氏弓形虫、布拉基弓形虫和欧氏弓形虫的联合cgMLST方案。该方案被证明适用于跨物种爆发分析。我们的分析显示,水槽、淋浴排水管和厕所等环境可能是医院环境中柠檬酸杆菌物种持续存在的水库。这些发现表明,环境源可能在涉及患者的传播事件中发挥重要作用,而基于等位基因的聚类分析表明,患者之间的直接传播很少。鉴于多药耐药(MDR)柠檬酸杆菌菌株的日益流行,这些新开发的cgMLST方案所实现的区分水平强调了准确的物种鉴定和环境筛选对于了解机会性医疗保健相关病原体传播动力学的重要性。最终,这使它们成为基因组监测、疫情调查和感染预防的宝贵工具。重要性:多药耐药细菌的准确鉴定和高分辨率分型对于了解其在医院中的传播动态至关重要,特别是考虑到耐药菌株的全球传播和环境宿主的作用。本文提出的新开发的cgMLST方案为本地和全球科学和临床社区提供了标准化的便携式工具,可以对四种柠檬酸杆菌进行精细的基因组流行病学研究。这些计划支持详细的疫情重建、来源归属和跨医院比较,这些能力在抗菌素耐药性日益增加和国际患者流动的时代至关重要。通过实现一致的、特定物种的监测和比较分析,cgMLST加强了感染控制和公共卫生应对,促进了早期发现和有针对性的干预。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Development and validation of a core genome multilocus sequence typing scheme for Citrobacter freundii: application in outbreak investigations and comparative analysis across the Citrobacter genus.

Citrobacter freundii is a nosocomial pathogen increasingly associated with multidrug resistance and hospital outbreaks. Despite its growing clinical relevance, no standardized core genome multilocus sequence typing (cgMLST) scheme has been available for high-resolution epidemiological analyses. Here, we developed and validated a robust cgMLST scheme for C. freundii comprising 3,250 target loci based on a curated data set of 825 globally distributed genomes representing extensive sequence type and geographic diversity. Validation against published outbreak data sets from hospitals in Finland and Belgium, as well as environmental and patient isolates from two German university hospitals, proved that the scheme possesses high target gene coverage (median 99.6%) and strong discriminatory power. Additionally, we developed a combined cgMLST scheme for C. freundii, C. portucalensis, C. braakii, and C. europaeus, based on 2,307 shared target loci and target gene coverages of ≥99.7%. This scheme proved suitable for cross-species outbreak analysis. Our analyses revealed environments, such as sinks, shower drains, and toilets, as likely reservoirs where Citrobacter species may persist in hospital settings. These findings suggest that environmental sources could play a significant role in transmission events involving patients, while allele-based cluster analyses indicated that direct patient-to-patient transmission was rare. Given the increasing prevalence of multidrug-resistant (MDR) Citrobacter strains, the level of discrimination achieved by these newly developed cgMLST schemes underscores the importance of accurate species identification and environmental screening in understanding the transmission dynamics of opportunistic healthcare-associated pathogens. Ultimately, this makes them valuable tools for genomic surveillance, outbreak investigation, and infection prevention.

Importance: Accurate identification and high-resolution typing of multidrug-resistant bacteria are essential for understanding their transmission dynamics in hospitals, particularly in light of the global spread of resistant strains and the role of environmental reservoirs. The newly developed cgMLST schemes presented here provide standardized, portable tools for both local and global scientific and clinical communities to conduct fine-scale genomic epidemiology across four Citrobacter species. These schemes support detailed outbreak reconstruction, source attribution, and cross-hospital comparisons, capabilities that are critical in an era of increasing antimicrobial resistance and international patient movement. By enabling consistent, species-specific surveillance and comparative analyses, cgMLST enhances infection control and public health responses, facilitating early detection and targeted intervention.

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来源期刊
Journal of Clinical Microbiology
Journal of Clinical Microbiology 医学-微生物学
CiteScore
17.10
自引率
4.30%
发文量
347
审稿时长
3 months
期刊介绍: The Journal of Clinical Microbiology® disseminates the latest research concerning the laboratory diagnosis of human and animal infections, along with the laboratory's role in epidemiology and the management of infectious diseases.
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