Complete Genome Sequence of a <i>bla</i> _KPC-2 -Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan

Abstract

Antimicrobial resistance genes (ARGs) and the bacteria that harbor them are widely distributed in the environment, especially in surface water, sewage treatment plant effluent, soil, and animal waste. In this study, we isolated a KPC-2-producing <i>Klebsiella pneumoniae</i> strain (GSU10-3) from a sampling site in Tokyo Bay, Japan, near a wastewater treatment plant (WWTP) and determined its complete genome sequence. Strain GSU10-3 is resistant to most β-lactam antibiotics and other antimicrobial agents (quinolones and aminoglycosides). This strain is classified as sequence type 11 (ST11), and a core genome phylogenetic analysis indicated that strain GSU10-3 is closely related to KPC-2-positive Chinese clinical isolates from 2011 to 2017 and is clearly distinct from strains isolated from the European Union (EU), United States, and other Asian countries. Strain GSU10-3 harbors four plasmids, including a <i>bla</i>_KPC-2-positive plasmid, pGSU10-3-3 (66.2 kb), which is smaller than other <i>bla</i>_KPC-2-positive plasmids and notably carries dual replicons (IncFII [pHN7A8] and IncN). Such downsizing and the presence of dual replicons may promote its maintenance and stable replication, contributing to its broad host range with low fitness costs. A second plasmid, pGSU10-3-1 (159.0 kb), an IncA/C2 replicon, carries a class 1 integron (containing <i>intI1</i>, <i>dfrA12</i>, <i>aadA2</i>, <i>qacEΔ1</i>, and <i>sul1</i>) with a high degree of similarity to a broad-host-range plasmid present in the family <i>Enterobacteriaceae</i> The plasmid pGSU10-3-2 (134.8 kb), an IncFII(K) replicon, carries the IS<i>26</i>-mediated ARGs [<i>aac</i>(<i>6'</i>)<i>Ib-cr</i><u>,</u><i>bla</i>_OXA-1, <i>catB4</i> (truncated), and <i>aac</i>(3)<i>-IId</i>], <i>tet</i>(A), and a copper/arsenate resistance locus. GSU10-3 is the first nonclinical KPC-2-producing environmental <i>Enterobacteriaceae</i> isolate from Japan for which the whole genome has been sequenced.<b>IMPORTANCE</b> We isolated and determined the complete genome sequence of a KPC-2-producing <i>K. pneumoniae</i> strain from a sampling site in Tokyo Bay, Japan, near a wastewater treatment plant (WWTP). In Japan, the KPC type has been very rarely detected, while IMP is the most predominant type of carbapenemase in clinical carbapenemase-producing <i>Enterobacteriaceae</i> (CPE) isolates. Although laboratory testing thus far suggested that Japan may be virtually free of KPC-producing <i>Enterobacteriaceae</i>, we have detected it from effluent from a WWTP. Antimicrobial resistance (AMR) monitoring of WWTP effluent may contribute to the early detection of future AMR bacterial dissemination in clinical settings and communities; indeed, it will help illuminate the whole picture in which environmental contamination through WWTP effluent plays a part.