Gutiérrez Ana Victoria, Matthews Michaela, Diaz Maria, Le Viet Thanh, de Oliveira Martins Leonardo, Jørgensen Frieda, Aird Heather, Painset Anaïs, Som Nicolle, Omelchenko Oleksii, Adriaenssens Evelien M, Kingsley Robert A, Gilmour Matthew W
Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
UK Health Security Agency, Food, Water and Environmental Microbiology Laboratories and the Gastrointestinal Bacteria Reference Unit, London, UK.
Microb Genom. 2025 Apr;11(4). doi: 10.1099/mgen.0.001397.
is a bacterial pathogen found in an increasing number of food categories, potentially reflecting an expanding niche and food safety risk profile. In the UK, sequence type (ST) 121 is more frequently isolated from foods and food environments than from cases of clinical listeriosis, consistent with a relatively low pathogenicity. In this study, we determined the evolution associated with the environmental persistence of a clone by investigating clone-specific genome features in the context of the ST121 population structure from international sources. To enable unambiguous comparative genomic analysis of ST121 strains, we constructed 16 new high-quality genome assemblies from isolated from foods, food environments and human clinical sources in the UK from 1987 to 2019. Our dataset was supplemented with additional UK and international genomes from databases held by the Institut Pasteur and the UK Health Security Agency. Time-scaled phylogenetic reconstruction revealed that clade-specific microevolution correlated with key characteristics that may confer adaptations important for success in the environmental niche. For example, a prophage designated LP-13-6 unique to a clade is associated with multi-year persistence in a food production setting. This prophage, observed in a strain that persisted for over a decade, may encode mechanisms facilitating environmental persistence, including the exclusion of other bacteriophages. Pangenome analysis provided insights into other candidate genetic elements associated with persistence and biocide tolerance. The comparative genomic dataset compiled in this study includes an international collection of 482 genome sequences that serve as a valuable resource for future studies to explore conserved genes, regulatory regions, mutations and variations associated with particular traits, such as environmental persistence, pathogenicity or biocide tolerance.
是一种在越来越多的食品类别中被发现的细菌病原体，这可能反映了其生态位的扩大和食品安全风险状况。在英国，序列类型（ST）121从食品和食品环境中分离出来的频率高于从临床李斯特菌病病例中分离出来的频率，这与相对较低的致病性一致。在本研究中，我们通过在来自国际来源的ST121种群结构背景下研究克隆特异性基因组特征，确定了一个克隆的环境持久性相关的进化。为了能够对ST121菌株进行明确的比较基因组分析，我们从1987年至2019年在英国的食品、食品环境和人类临床来源中分离出的菌株构建了16个新的高质量基因组组装。我们的数据集补充了来自巴斯德研究所和英国卫生安全局数据库的其他英国和国际基因组。时间尺度的系统发育重建表明，特定分支的微观进化与可能赋予在环境生态位中取得成功的重要适应性的关键特征相关。例如，一个特定分支特有的原噬菌体LP - 13 - 6与在食品生产环境中的多年持久性相关。在一株持续了十多年的菌株中观察到的这种原噬菌体可能编码促进环境持久性的机制，包括排除其他噬菌体。泛基因组分析提供了对与持久性和杀生物剂耐受性相关的其他候选遗传元件的见解。本研究中汇编的比较基因组数据集包括482个基因组序列的国际集合，这些序列是未来研究探索与特定性状（如环境持久性、致病性或杀生物剂耐受性）相关的保守基因、调控区域、突变和变异的宝贵资源。
