通过比较基因组分析揭示的O3b血清型和高风险克隆ST37的鉴定。
Identification of serotype O3b and high-risk clone ST37 of revealed by comparative genomic analysis.
作者信息
Krishnan Sivaraman Gopalan, Sajeev Sudha, Sivam Visnuvinayagam, T Raja Swaminathan, Ojha Rakshit, Shome Bibek Ranjan, Holmes Mark, Sundaram Thanigaivel, M D Ramesh, Vinayagam Saranya, Meesala Suseela, Malik Tabarak, Dara Pavan Kumar
机构信息
Microbiology Fermentation and Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Institute of Fisheries Technology, Kochi, Kerala, India.
Department of Disease Investigation, Indian Council of Agricultural Research (ICAR)-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, Karnataka, India.
出版信息
Front Cell Infect Microbiol. 2025 Jan 20;14:1517125. doi: 10.3389/fcimb.2024.1517125. eCollection 2024.
BACKGROUND
Epidemiological risk factors such as the demography of a place, environment, food, livestock, and companion animals are known sources of infection. Whole-genome sequencing (WGS) has become a powerful tool to complement traditional microbiological characterization of foodborne pathogens. Moreover, has several species complexes (KpSC) and is very difficult to differentiate using routine microbiological methods. The present study aims to investigate the prevalence of in fish available in the retail market using WGS.
METHODS
Isolation of , identification of isolates, and determination of the minimum inhibitory concentration (MIC) were performed. Whole-genome sequencing of genomes and phylogenomic analysis were conducted for visual comparison of the genomes. Furthermore, genomes of non-human origin that were submitted from India to the NCBI database were downloaded and included in the comparative analysis.
RESULTS
The findings showed that many antibiotic-resistant genes (ARGs) are prominent, including , and . Four fish-sourced isolates had different blaSHV resistance gene variants. The presence of ARGs for aminoglycosides [aac(3)-IId], fluoroquinolones (oqxA, oqxB), and fosfomycin (fosA5, fosA6) in these isolates from fish sources was found. One of the CIFT-K6 isolates had the uncommon serotype of O3b with the high-risk clone "ST37." The ST515 sequence type was present in two isolates (CIFT-K7 and CIFT-K8), but the O3b serotype and ST192 allele type were present in the CIFT-K10 isolate.
CONCLUSION
To the best of our knowledge, this research study represents the first Indian report of linked to fish, specifically the high-risk clone 'ST37' and two other STs, 515 and 192. The most common plasmid type detected in all four isolates was IncFIB, and 75% of the isolates were IncFII and IncHI1B. The prevalence of ARGs linked to efflux pump resistance mechanisms is highlighted by the analysis of genome sequence data.
背景
诸如某地的人口统计学、环境、食物、家畜和伴侣动物等流行病学风险因素是已知的感染源。全基因组测序（WGS）已成为补充食源性病原体传统微生物学特征的有力工具。此外，有几个种复合体（KpSC），使用常规微生物学方法很难区分。本研究旨在利用WGS调查零售市场上鱼类中该菌的流行情况。
方法
进行该菌的分离、分离株鉴定以及最低抑菌浓度（MIC）测定。对该菌基因组进行全基因组测序并开展系统发育基因组分析，以便对基因组进行直观比较。此外，下载从印度提交至NCBI数据库的非人类来源基因组，并纳入比较分析。
结果
研究结果显示，许多抗生素抗性基因（ARG）很突出，包括 blaSHV、blaCTX-M 和 blaOXA。4株鱼类来源的分离株具有不同的 blaSHV 抗性基因变体。在这些鱼类来源的分离株中发现了氨基糖苷类（aac(3)-IId）、氟喹诺酮类（oqxA、oqxB）和磷霉素（fosA5、fosA6）的ARG。CIFT-K6分离株之一具有罕见的O3b血清型以及高风险克隆“ST37”。ST515序列型存在于2株该菌分离株（CIFT-K7和CIFT-K8）中，但CIFT-K10分离株中存在O3b血清型和ST192等位基因类型。
结论
据我们所知，本研究是印度关于该菌与鱼类相关的首次报告，特别是高风险克隆“ST37”以及另外两个序列型，515和192。在所有4株分离株中检测到的最常见质粒类型是IncFIB，75%的分离株为IncFII和IncHI1B。基因组序列数据分析突出了与外排泵抗性机制相关的ARG的流行情况。
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