Escherichia coli is present in multiple hosts and environmental compartments as a normal inhabitant, temporary or persistent colonizer, and as a pathogen. Transmission of E. coli between hosts and with the environment is considered to occur more often in areas with poor sanitation. We performed whole-genome comparative analyses on 60 E. coli isolates from soils and fecal sources (cattle, chickens, and humans) in households in rural Bangladesh. Isolates from household soils were in multiple branches of the reconstructed phylogeny, intermixed with isolates from fecal sources. Pairwise differences between all strain pairs were large (minimum, 189 single nucleotide polymorphisms [SNPs]), suggesting high diversity and heterogeneous origins of the isolates. The presence of multiple virulence and antibiotic resistance genes is indicative of the risk that E. coli from soil and feces represent for the transmission of variants that pose potential harm to people. Analysis of the accessory genomes of the Bangladeshi E. coli relative to E. coli genomes available in NCBI identified a common pool of accessory genes shared among E. coli isolates in this geographic area. Together, these findings indicate that in rural Bangladesh, a high level of E. coli in soil is likely driven by contributions from multiple and diverse E. coli sources (human and animal) that share an accessory gene pool relatively unique to previously published E. coli genomes. Thus, interventions to reduce environmental pathogen or antimicrobial resistance transmission should adopt integrated One Health approaches that consider heterogeneous origins and high diversity to improve effectiveness and reduce prevalence and transmission.IMPORTANCE Escherichia coli is reported in high levels in household soil in low-income settings. When E. coli reaches a soil environment, different mechanisms, including survival, clonal expansion, and genetic exchange, have the potential to either maintain or generate E. coli variants with capabilities of causing harm to people. In this study, we used whole-genome sequencing to identify that E. coli isolates collected from rural Bangladeshi household soils, including pathogenic and antibiotic-resistant variants, are diverse and likely originated from multiple diverse sources. In addition, we observed specialization of the accessory genome of this Bangladeshi E. coli compared to E. coli genomes available in current sequence databases. Thus, to address the high level of pathogenic and antibiotic-resistant E. coli transmission in low-income settings, interventions should focus on addressing the heterogeneous origins and high diversity.

中文翻译：

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家庭环境中致病性和抗生素耐药性大肠杆菌的高基因组多样性和异质起源对减少低收入环境中的传播构成了挑战。


大肠杆菌作为正常居民、临时或持久定殖者以及病原体存在于多种宿主和环境隔室中。大肠杆菌在宿主之间以及与环境之间的传播被认为更常发生在卫生条件差的地区。我们对孟加拉国农村家庭土壤和粪便来源（牛、鸡和人类）中的 60 株大肠杆菌分离物进行了全基因组比较分析。来自家庭土壤的分离物位于重建系统发育的多个分支中，与来自粪便来源的分离物混合。所有菌株对之间的成对差异很大（最少 189 个单核苷酸多态性 [SNP]），表明分离株具有高度多样性和异质起源。多种毒力和抗生素抗性基因的存在表明来自土壤和粪便的大肠杆菌存在传播对人类造成潜在伤害的变体的风险。相对于 NCBI 中可用的大肠杆菌基因组，对孟加拉国大肠杆菌的辅助基因组进行分析，确定了该地理区域的大肠杆菌分离株共享的辅助基因的共同库。总之，这些发现表明，在孟加拉国农村地区，土壤中大肠杆菌的高水平可能是由多种不同的大肠杆菌来源（人类和动物）的贡献驱动的，这些大肠杆菌来源共享一个与之前发表的大肠杆菌相对独特的辅助基因库。大肠杆菌基因组。因此，减少环境病原体或抗菌药物耐药性传播的干预措施应采用综合“同一个健康”方法，考虑异质来源和高度多样性，以提高有效性并减少流行和传播。重要性 据报道，低收入环境中的家庭土壤中大肠杆菌含量很高。当大肠杆菌到达土壤环境时，不同的机制，包括生存、克隆扩增和基因交换，有可能维持或产生对人类造成伤害的大肠杆菌变体。在这项研究中，我们使用全基因组测序来鉴定从孟加拉国农村家庭土壤中收集的大肠杆菌分离株（包括致病性和抗生素抗性变种）是多种多样的，并且可能源自多个不同来源。此外，与当前序列数据库中可用的大肠杆菌基因组相比，我们观察到该孟加拉国大肠杆菌的辅助基因组的特化。因此，为了解决低收入环境中致病性和抗生素耐药性大肠杆菌的高水平传播，干预措施应侧重于解决异质性起源和高度多样性问题。