To characterize environmental antimicrobial resistance (AMR) in urban areas, extended-spectrum β-lactamase- (ESBL)/carbapenemase-producing bacteria (EPB/CPB, respectively) from urban wastewater treatment plant effluents in Tokyo were isolated on CHROMagar ESBL plate. Complete genome sequence analysis, including plasmids, indicated that 126 CTX-M-positive isolates (31%) were identified among the 404 obtained isolates. The CTX-M-9 group was predominant (n = 65, 52%), followed by the CTX-M-1 group (n = 44, 35%). Comparative genome analysis revealed that CTX-M-27-positive E. coli O16:H5-ST131-fimH41 exhibited a stable genome structure and clonal-global dissemination. Plasmidome network analysis revealed that 304 complete plasmid sequences among 85 isolates were grouped into 14 incompatibility (Inc) network communities (Co1 to Co14). Co10 consisted of primarily IncFIA/IncFIB plasmids harboring bla_CTX-M in E. coli, whereas Co12 consisted primarily of IncFIA(HI1)/Inc FIB(K) plasmids harboring bla_CTX-M, bla_KPC, and bla_GES in Klebsiella spp. Co11 was markedly located around Co10 and Co12. Co11 exhibited bla_CTX-M, bla_KPC, and bla_NDM, and was mainly detected in E. coli and Klebsiella spp. from human and animal sources, suggesting a mutual role of Co11 in horizontal gene transfer between E. coli and Klebsiella spp. This comprehensive resistome analysis uncovers the mode of relational transfer among bacterial species, highlighting the potential source of AMR burden on public health in urban communities.

中文翻译：

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东京污水处理厂出水中抗菌素耐药菌的基因组和质粒组综合分析

为了表征城市地区的环境抗菌素耐药性 (AMR)，在科玛嘉 ESBL 板上分离了东京城市污水处理厂流出物中的超广谱 β-内酰胺酶 (ESBL)/产碳青霉烯酶细菌 (EPB/CPB)。包括质粒在内的完整基因组序列分析表明，在获得的 404 个分离物中鉴定出 126 个 CTX-M 阳性分离物（31%）。CTX-M-9 组占主导地位（n = 65, 52%），其次是 CTX-M-1 组（n = 44, 35%）。比较基因组分析显示 CTX-M-27 阳性大肠杆菌O16:H5-ST131- fimH41表现出稳定的基因组结构和克隆全球传播。质粒组网络分析显示，85 个分离株中的 304 个完整质粒序列被分为 14 个不相容 (Inc) 网络群落（Co1 到 Co14）。Co10 主要由在大肠杆菌中含有bla _CTX-M的IncFIA/IncFIB 质粒组成，而 Co12 主要由在克雷伯氏菌属中含有 bla CTX-M、bla KPC 和 bla GES 的 IncFIA( HI1 ) / _Inc FIB ( _K )质粒_组成。Co11 明显位于 Co10 和 Co12 周围。Co11 展出了bla _CTX-M、bla _KPC和bla_NDM，主要在大肠杆菌和克雷伯氏菌中检测到。来自人类和动物来源，表明 Co11 在大肠杆菌和克雷伯氏菌之间的水平基因转移中的相互作用。这种全面的耐药组分析揭示了细菌物种之间相关转移的模式，突出了 AMR 对城市社区公共卫生造成负担的潜在来源。