Vegetable-Derived Carbapenemase-Producing High-Risk Klebsiella pneumoniae ST15 and Acinetobacter baumannii ST2 Clones in Japan: Coexistence of <i>bla</i> _NDM-1 , <i>bla</i> _OXA-66 , <i>bla</i> _OXA-72 , and an AbaR4-Like Resistance Island in the Same Sample

Abstract

This study was conducted to characterize carbapenemase-producing <i>Klebsiella pneumoniae</i> and <i>Acinetobacter baumannii</i> isolated from fresh vegetables in Japan. Two <i>K. pneumoniae</i> isolates (AO15 and AO22) and one <i>A. baumannii</i> isolate (AO22) were collected from vegetables in the city of Higashihiroshima, Japan, and subjected to antimicrobial susceptibility testing, conjugation experiments, and complete genome sequencing using Illumina MiniSeq and Oxford Nanopore MinION sequencing platforms. The two <i>K. pneumoniae</i> isolates were clonal, belonging to sequence type 15 (ST15), and were determined to carry 19 different antimicrobial resistance genes, including <i>bla</i>_NDM-1 Both the isolates carried <i>bla</i>_NDM-1 on a self-transmissible IncFII(K):IncR plasmid of 122,804 bp with other genes conferring resistance to aminoglycosides [<i>aac(6')-Ib</i>, <i>aadA1</i>, and <i>aph(3')-VI</i>], β-lactams (<i>bla</i>_CTX-M-15, <i>bla</i>_OXA-9, and <i>bla</i>_TEM-1A), fluoroquinolones [<i>aac(6')-Ib-cr</i>], and quinolones (<i>qnrS1</i>). <i>A. baumannii</i> AO22 carried <i>bla</i>_OXA-66 on the chromosome, while <i>bla</i>_OXA-72 was found as two copies on a GR2-type plasmid of 10,880 bp. Interestingly, <i>A. baumannii</i> AO22 harbored an AbaR4-like genomic resistance island (GI) of 41,665 bp carrying genes conferring resistance to tetracycline [<i>tet</i>(B)], sulfonamides (<i>sul2</i>), and streptomycin (<i>strAB</i>). Here, we identified Japanese carbapenemase-producing Gram-negative bacteria isolated from vegetables, posing a food safety issue and a public health concern. Additionally, we reported a GR2-type plasmid carrying two copies of <i>bla</i>_OXA-72 and an AbaR4-like resistance island from a foodborne <i>A. baumannii</i> isolate.<b>IMPORTANCE</b> Carbapenemase-producing Gram-negative bacteria (CPGNB) cause severe health care-associated infections and constitute a major public health threat. Here, we investigated the genetic features of CPGNB isolated from fresh vegetable samples in Japan and found CPGNB, including <i>Klebsiella pneumoniae</i> and <i>Acinetobacter baumannii</i>, with dissimilar carbapenemases. The NDM carbapenemase, rarely described in Japan, was detected in two <i>K. pneumoniae</i> isolates. The <i>A. baumannii</i> isolate identified in this study carried <i>bla</i>_OXA-66 on the chromosome, while <i>bla</i>_OXA-72 was found as two copies on a GR2-type plasmid. This study indicates that even one fresh ready-to-eat vegetable sample might serve as a significant source of genes (<i>bla</i>_NDM-1, <i>bla</i>_OXA-72, <i>bla</i>_CTX-M-14b, and <i>bla</i>_CTX-M-15) encoding resistance to frontline and clinically important antibiotics (carbapenems and cephalosporins). Furthermore, the detection of these organisms in fresh vegetables in Japan is alarming and poses a food safety issue and a public health concern.