Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Palackeho Trida 1946/1, 612 42, Brno, Czech Republic.
Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute Brno, Brno, Czech Republic.
BMC Microbiol. 2024 Sep 18;24(1):352. doi: 10.1186/s12866-024-03490-3.
The salmonid pathogen Flavobacterium psychrophilum poses a significant economic threat to global aquaculture, yet our understanding of its genetic and phenotypic diversity remains incomplete across much of its geographic range. In this study, we characterise the genetic and phenotypic diversity of 70 isolates collected from rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta m. fario) from fish farms in the Czech Republic between 2012 and 2019 to compare their genomic content with all draft or complete genomes present in the NCBI database (n = 187).
The Czech isolates underwent comprehensive evaluation, including multiplex PCR-based serotyping, genetic analysis, antimicrobial resistance testing, and assessment of selected virulence factors. Multiplex PCR serotyping revealed 43 isolates as Type 1, 23 as Type 2, with sporadic cases of Types 3 and 4. Multi-locus sequence typing unveiled 12 sequence types (ST), including seven newly described ones. Notably, 24 isolates were identified as ST329, a novel sequence type, while 22 were classified as the globally-distributed ST2. Phylogenetic analysis demonstrated clonal distribution of ST329 in the Czech Republic, with these isolates lacking a phage sequence in their genomes. Antimicrobial susceptibility testing revealed a high proportion of isolates classified as non-wild type with reduced susceptibility to oxolinic acid, oxytetracycline, flumequine, and enrofloxacin, while most isolates were classified as wild type for florfenicol, sulfamethoxazole-trimethoprim, and erythromycin. However, 31 isolates classified as wild type for florfenicol exhibited minimum inhibitory concentrations at the susceptibility breakpoint.
The prevalence of the Czech F. psychrophilum serotypes has evolved over time, likely influenced by the introduction of new isolates through international trade. Thus, it is crucial to monitor F. psychrophilum clones within and across countries using advanced methods such as MLST, serotyping, and genome sequencing. Given the open nature of the pan-genome, further sequencing of strains promises exciting discoveries in F. psychrophilum genomics.
鱼类病原体嗜冷性气单胞菌对全球水产养殖业构成了重大的经济威胁，但在其大部分地理范围内，我们对其遗传和表型多样性的了解仍不完整。在这项研究中，我们对 2012 年至 2019 年间从捷克共和国的鱼类养殖场收集的 70 株虹鳟鱼（Oncorhynchus mykiss）和褐鳟（Salmo trutta m. fario）分离株进行了遗传和表型多样性分析，将其基因组内容与 NCBI 数据库中存在的所有草案或完整基因组（n=187）进行了比较。
对捷克分离株进行了综合评估，包括基于多重 PCR 的血清型鉴定、遗传分析、抗微生物药物敏感性测试和选择的毒力因子评估。多重 PCR 血清型鉴定显示 43 株为 1 型，23 株为 2 型，少数为 3 型和 4 型。多位点序列分型揭示了 12 个序列型（ST），包括 7 个新描述的序列型。值得注意的是，24 株被鉴定为 ST329，这是一个新的序列型，而 22 株被归类为全球分布的 ST2。系统发育分析表明，ST329 在捷克共和国呈克隆分布，这些分离株的基因组中没有噬菌体序列。抗微生物药物敏感性测试显示，大多数分离株对氟苯尼考、磺胺甲恶唑-甲氧苄啶和红霉素的敏感性为野生型，而对氧氟沙星、恩诺沙星、氟甲喹和土霉素的敏感性为非野生型的比例较高。然而，31 株被归类为氟苯尼考野生型的分离株的最小抑菌浓度在敏感性折点处。
随着时间的推移，捷克嗜冷性气单胞菌血清型的流行情况发生了演变，这可能是由于通过国际贸易引入了新的分离株所致。因此，使用 MLST、血清型鉴定和基因组测序等先进方法监测国内和跨国的嗜冷性气单胞菌克隆至关重要。鉴于泛基因组的开放性，对菌株的进一步测序有望在嗜冷性气单胞菌基因组学方面有令人兴奋的发现。
