Emergence of Klebsiella variicola positive for NDM-9, a variant of New Delhi metallo-β-lactamase, in an urban river in South Korea

Objectives: To examine the presence of pathogenic bacteria carrying New Delhi metallo-β-lactamase in the environment and to characterize the genome structures of these strains. Methods: Phenotypic screening of antimicrobial susceptibility and WGS were conducted on three Klebsiella variicola strains possessing NDM-9 isolated froman urban river. Results: Three carbapenem-resistant K. variicola isolated from Gwangju tributary were found to possess bla_NDM-9 genes. Antimicrobial susceptibility testing indicated resistance of these strains to aminoglycosides, carbapenems, cephems, folate pathway inhibitors, fosfomycin and penicillins, but susceptibility to fluoroquinolones, phenicols, tetracyclines and miscellaneous agents. WGS revealed that the 108 kb IncFII(Y)-like plasmids carry bla_NDM-9 sandwiched between IS15 for the GJ1 strain, IS26 for the GJ2 strain, IS15D1 for the GJ3 strain and ISVsa3, and further bracketed by IS26 and TnAS3 along with the mercury resistance operon upstream and the class 1 integron composed of gene cassettes of aadA2, dfrA12 and sul1 downstream. An aph(30)-Ia gene conferring resistance to aminoglycosides is located after the integrons. Chromosomally encoded bla_LEN-13, fosA, aqxA and oqxB genes, as well as plasmid-mediated bla_TEM-1B and bla_CTX-M-65 encoding ESBL, ant(30)-Ia and mph(A) genes, were also identified. Conclusions: The findings of the present study provide us with the information that NDM-9 has been spreading into the environment. Dissemination of NDM-9 in the environment has raised a health risk alarm as this variant of NDM carries MDR genes with highly transferable mobile genetic elements, increasing the possibility of resistance gene transfer among microorganisms in the environment.