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. New Delhi metallo-ß-lactamase-1 (NDM-1) is a metallo-ß-lactamase that has spread rapidly in the last decade, causing worldwide alarm. This study aimed to describe the first isolate of NDM-1-producing and extensively drug resistant Klebsiella pneumoniae in Albania, its clinical context and genetic characterization.

Methods: Strain was isolated from both oral and rectal intensive care unit admission screening swabs of a 70-year-old male patient with no history of international travel in the previous 6 months. Sequencing was performed by Illumina NextSeq500 platform, with a paired-end run of 2 by 150bp, 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-15and 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 an 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 extensively drug resistant K. 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.

Keywords: Colistin resistance; Digestive carrier; Extensively drug resistant; Klebsiella pneumoniae; MBL (metallo-ß-lactamase); NDM-1 (New Delhi metallo-ß-lactamase-1).