Goh Ying-Xian, Anupoju Sai Manohar Balu, Nguyen Anthony, Zhang Hailong, Ponder Monica, Krometis Leigh-Anne, Pruden Amy, Liao Jingqiu
Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, VA, 24061, USA.
Nat Commun. 2024 Nov 19;15(1):10034. doi: 10.1038/s41467-024-54459-9.
Soil is an important reservoir of antibiotic resistance genes (ARGs) and understanding how corresponding environmental changes influence their emergence, evolution, and spread is crucial. The soil-dwelling bacterial genus Listeria, including L. monocytogenes, the causative agent of listeriosis, serves as a key model for establishing this understanding. Here, we characterize ARGs in 594 genomes representing 19 Listeria species that we previously isolated from soils in natural environments across the United States. Among the five putatively functional ARGs identified, lin, which confers resistance to lincomycin, is the most prevalent, followed by mprF, sul, fosX, and norB. ARGs are predominantly found in Listeria sensu stricto species, with those more closely related to L. monocytogenes tending to harbor more ARGs. Notably, phylogenetic and recombination analyses provide evidence of recent horizontal gene transfer (HGT) in all five ARGs within and/or across species, likely mediated by transformation rather than conjugation and transduction. In addition, the richness and genetic divergence of ARGs are associated with environmental conditions, particularly soil properties (e.g., aluminum and magnesium) and surrounding land use patterns (e.g., forest coverage). Collectively, our data suggest that recent HGT and environmental selection play a vital role in the acquisition and diversification of bacterial ARGs in natural environments.
土壤是抗生素抗性基因（ARGs）的重要储存库，了解相应的环境变化如何影响其出现、进化和传播至关重要。包括单核细胞增生李斯特菌（李斯特菌病的病原体）在内的土壤栖息细菌属李斯特菌，是建立这种认识的关键模型。在这里，我们对594个基因组中的ARGs进行了表征，这些基因组代表了我们之前从美国各地自然环境的土壤中分离出的19种李斯特菌。在鉴定出的五个推定功能性ARGs中，赋予对林可霉素抗性的lin最为普遍，其次是mprF、sul、fosX和norB。ARGs主要存在于狭义李斯特菌种中，那些与单核细胞增生李斯特菌关系更密切的菌种往往携带更多的ARGs。值得注意的是，系统发育和重组分析提供了证据，表明所有五个ARGs在种内和/或种间最近发生了水平基因转移（HGT），可能是由转化而非接合和转导介导的。此外，ARGs的丰富度和遗传差异与环境条件有关，特别是土壤性质（如铝和镁）和周边土地利用模式（如森林覆盖率）。总体而言，我们的数据表明，最近的HGT和环境选择在自然环境中细菌ARGs的获得和多样化中起着至关重要的作用。
