Comprehensive Genome and Plasmidome Analysis of Antimicrobial Resistant Bacteria in Wastewater Treatment Plant Effluent of Tokyo

Abstract

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 (<i>n</i> = 65, 52%), followed by the CTX-M-1 group (<i>n</i> = 44, 35%). Comparative genome analysis revealed that CTX-M-27-positive <i>E. coli</i> O16:H5-ST131-<i>fimH41</i> 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 <i>bla</i>_CTX-M in <i>E. coli</i>, whereas Co12 consisted primarily of IncFIA(HI1)/Inc FIB(K) plasmids harboring <i>bla</i>_CTX-M, <i>bla</i>_KPC, and <i>bla</i>_GES in <i>Klebsiella</i> spp. Co11 was markedly located around Co10 and Co12. Co11 exhibited <i>bla</i>_CTX-M, <i>bla</i>_KPC, and <i>bla</i>_NDM, and was mainly detected in <i>E. coli</i> and <i>Klebsiella</i> spp. from human and animal sources, suggesting a mutual role of Co11 in horizontal gene transfer between <i>E. coli</i> and <i>Klebsiella</i> 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.