Uljanovas Dainius, Gölz Greta, Fleischmann Susanne, Kudirkiene Egle, Kasetiene Neringa, Grineviciene Audrone, Tamuleviciene Egle, Aksomaitiene Jurgita, Alter Thomas, Malakauskas Mindaugas
Department of Food Safety and Quality, Faculty of Veterinary Medicine, Veterinary Academy, Lithuanian University of Health Sciences, Tilzes St. 18, LT-47181 Kaunas, Lithuania.
Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany.
Microorganisms. 2023 May 28;11(6):1425. doi: 10.3390/microorganisms11061425.
, the most widespread species within the genus , is considered as an emerging pathogen causing gastroenteritis in humans. Here, we performed a comparative genome-wide analysis of 40 strains from Lithuania to determine the genetic relationship, pangenome structure, putative virulence, and potential antimicrobial- and heavy-metal-resistance genes. Core genome single nucleotide polymorphism (cgSNP) analysis revealed low within-group variability (≤4 SNPs) between three milk strains (RCM42, RCM65, RCM80) and one human strain (H19). Regardless of the type of input (i.e., cgSNPs, accessory genome, virulome, resistome), these strains showed a recurrent phylogenetic and hierarchical grouping pattern. demonstrated a relatively large and highly variable accessory genome (comprising of 6284 genes with around 50% of them identified as singletons) that only partially correlated to the isolation source. Downstream analysis of the genomes resulted in the detection of 115 putative antimicrobial- and heavy-metal-resistance genes and 136 potential virulence factors that are associated with the induction of infection in host (e.g., , , ), survival and environmental adaptation (e.g., flagellar genes, CheA-CheY chemotaxis system, urease cluster). This study provides additional knowledge for a better -related risk assessment and highlights the need for further genomic epidemiology studies in Lithuania and other countries.
该属中分布最广的物种被认为是一种新兴的人类肠胃炎病原体。在此，我们对来自立陶宛的40株该菌株进行了全基因组比较分析，以确定其遗传关系、泛基因组结构、假定的毒力以及潜在的抗微生物和重金属抗性基因。核心基因组单核苷酸多态性（cgSNP）分析显示，三株牛奶菌株（RCM42、RCM65、RCM80）和一株人类菌株（H19）之间的组内变异性较低（≤4个SNP）。无论输入类型（即cgSNP、辅助基因组、毒力组、抗性组）如何，这些菌株都呈现出反复出现的系统发育和层次分组模式。该菌株展示了一个相对较大且高度可变的辅助基因组（由6284个基因组成，其中约50%被鉴定为单拷贝基因），其与分离源仅部分相关。对基因组的下游分析导致检测到115个假定的抗微生物和重金属抗性基因以及136个潜在的毒力因子，这些因子与宿主感染的诱导（例如， ， ， ）、生存和环境适应（例如鞭毛基因、CheA-CheY趋化系统、脲酶簇）相关。本研究为更好地进行该菌株相关风险评估提供了更多知识，并强调了在立陶宛和其他国家开展进一步基因组流行病学研究的必要性。
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