Isolation of the first New Delhi metallo-ß-lactamase-1 (NDM-1)-producing and colistin-resistant Klebsiella pneumoniae sequence type ST15 from a digestive carrier in Albania, May 2018

Abstract Objectives Carbapenemases represent a public health threat as they can spread through horizontal gene transfer and cause outbreaks. NDM-1 is a metallo-s-lactamase that has spread rapidly in the last decade causing worldwide alarm. We aimed to describe the first isolate of NDM-1 producing and XDR Klebsiella pneumoniae in Albania, its clinical context and genetic characterization. Methods Strain was isolated from both oral and rectal ICU admission screening swabs of a 70 years old male patient with no history of international travel in the previous six months. Sequencing was performed by Illumina NextSeq500 platform, with a paired-end run of 2 by 150 bp, after Nextera XT paired-end library preparation. Sequencing reads were assembled using SPAdes Genome (version 3.6.1) with accurate de novo settings. The assembled contigs were uploaded into the online tools: BIGSdb-Kp, ResFinder and PlasmidFinder. Results Isolate was resistant to all tested antibiotics but tigecycline and trimethoprim-sulfamethoxazole. Sequencing revealed the presence of acquired resistance genes conferring resistance to β-lactams ( bla NDM-1 , bla CMY-6 , bla CTX-M-15 and bla SHV-28 ), aminoglycosides ( rmtC, aac(6')-Ib3 ), fluoroquinolones ( oqxA, oqxB, aac(6')-Ib-cr ), fosfomycin ( fosA ) and sulfonamides ( sul1 ). The bla NDM-1 gene was located on a IncA/C2 plasmid. Plasmid mediated mcr-1 to mcr-8 genes were absent in both isolates. Resistance to colistin was due to an amino acid substitution (Thr157Pro) in PmrB protein. Conclusions NDM-1-producing Enterobacteriaceae are spreading in the Balkans. Identification of NDM-1 producing and XDR Klebsiella pneumoniae ST15 in Albania is a cause for serious concern. There should be a continuous national and Balkan multinational surveillance of bla NDM-1 -carrying isolates.