Schmitz-Esser Stephan, Anast Justin M, Cortes Bienvenido W
Department of Animal Science, Iowa State University, Ames, IA, United States.
Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States.
Front Microbiol. 2021 Mar 12;12:653155. doi: 10.3389/fmicb.2021.653155. eCollection 2021.
The food-borne pathogen is known for its capacity to cope with multiple stress conditions occurring in food and food production environments (FPEs). Plasmids can provide benefits to their host strains, and it is known that various strains contain plasmids. However, the current understanding of plasmid frequency and function in strains remains rather limited. To determine the presence of plasmids among strains and their potential contribution to stress survival, a comprehensive dataset was established based on 1,921 published genomes from strains representing 14 sequence types (STs). Our results show that an average of 54% of all strains in the dataset contained a putative plasmid. The presence of plasmids was highly variable between different STs. While some STs, such as ST1, ST2, and ST4, contained few plasmid-bearing strains (<15% of the strains per ST), other STs, such as ST121, ST5, ST8, ST3, and ST204, possessed a higher proportion of plasmid-bearing strains with plasmids found in >71% of the strains within each ST. Overall, the sizes of plasmids analyzed in this study ranged from 4 to 170 kbp with a median plasmid size of 61 kbp. We also identified two novel groups of putative plasmids based on the amino acid sequences of the plasmid replication protein, RepA. We show that highly conserved plasmids are shared among strains which have been isolated from around the world over the last few decades. To investigate the potential roles of plasmids, nine genes related to stress-response were selected for an assessment of their abundance and conservation among plasmids. The results demonstrated that these plasmid genes exhibited high sequence conservation but that their presence in plasmids was highly variable. Additionally, we identified a novel transposon, Tn, predicted to be involved in mercury-resistance. Here, we provide the largest plasmid survey of to date with a comprehensive examination of the distribution of plasmids among strains. Our results significantly increase our knowledge about the distribution, composition, and conservation of plasmids and suggest that plasmids are likely important for the survival of in food and FPEs.
食源性病原体以其应对食品及食品生产环境（FPEs）中多种应激条件的能力而闻名。质粒可为其宿主菌株带来益处，且已知多种菌株含有质粒。然而，目前对于菌株中质粒频率和功能的了解仍然相当有限。为了确定菌株中质粒的存在情况及其对压力生存的潜在贡献，基于代表14种序列类型（STs）的菌株的1921个已发表基因组建立了一个综合数据集。我们的结果表明，数据集中所有菌株平均有54%含有推定质粒。质粒的存在在不同STs之间差异很大。虽然一些STs，如ST1、ST2和ST4，含质粒菌株很少（每个ST的菌株中<15%），但其他STs，如ST121、ST5、ST8、ST3和ST204，含有较高比例的含质粒菌株，每个ST内>71%的菌株中发现有质粒。总体而言，本研究中分析的质粒大小范围为4至170 kbp，质粒大小中位数为61 kbp。我们还基于质粒复制蛋白RepA的氨基酸序列鉴定出两组新的推定质粒。我们表明，高度保守的质粒在过去几十年从世界各地分离出的菌株中共享。为了研究质粒的潜在作用，选择了9个与应激反应相关的基因来评估它们在质粒中的丰度和保守性。结果表明，这些质粒基因表现出高度的序列保守性，但其在质粒中的存在差异很大。此外，我们鉴定出一个新的转座子Tn，预计与汞抗性有关。在此，我们提供了迄今为止最大规模的质粒调查，全面检查了质粒在菌株中的分布。我们的结果显著增加了我们对质粒分布、组成和保守性的了解，并表明质粒可能对菌株在食品和FPEs中的生存很重要。
