Clonality and Resistome Analysis of KPC-ProducingKlebsiella pneumoniaeStrain Isolated in Korea Using Whole Genome Sequencing

Abstract

We analyzed the whole genome sequence and resistome of the outbreakKlebsiella pneumoniaestrain MP14 and compared it with those ofK. pneumoniaecarbapenemase- (KPC-) producing isolates that showed high similarity in the NCBI genome database. A KPC-2-producing multidrug-resistant (MDR)K. pneumoniaeclinical isolate was obtained from a patient admitted to a Korean hospital in 2011. The strain MP14 was resistant to all testedβ-lactams including monobactam, amikacin, levofloxacin, and cotrimoxazole, but susceptible to tigecycline and colistin. Resistome analysis showed the presence ofβ-lactamase genes includingblaKPC-2,blaSHV-11,blaTEM-169, andblaOXA-9. MP14 also possessedaac(6′-)Ib,aadA2,andaph(3′-)Iaas aminoglycoside resistance-encoding genes,mph(A)for macrolides,oqxAandoqxBfor quinolone,catA1for phenicol,sul1for sulfonamide, anddfrA12for trimethoprim. Both SNP tree and cgMLST analysis showed the close relatedness with the KPC producers (KPNIH strains) isolated from an outbreak in the USA and colistin-resistant strains isolated in Italy. The plasmid-scaffold genes in plasmids pKpQil, pKpQil-IT, pKPN3, or pKPN-IT were identified in MP14, KPNIH, and Italian strains. The KPC-2-producing MDRK. pneumoniaeST258 stain isolated in Korea was highly clonally related with MDRK. pneumoniaestrains from the USA and Italy. Global spread of KPC-producingK. pneumoniaeis a worrying phenomenon.