Emergence of mgrB locus deletion mediating polymyxin resistance in pandemic KPC-producing Klebsiella pneumoniae ST15 lineage

Abstract

<i>Klebsiella pneumoniae</i> causes a diversity of infections in both healthcare and community settings. This pathogen is showing an increased ability to accumulate antimicrobial resistance and virulence genes, making it a public health concern. Here we describe the whole-genome sequence characteristics of an ST15 colistin-resistant <i>K. pneumoniae</i> isolate obtained from a blood culture of a 79-year-old female patient admitted to a university hospital in Brazil. Kp14U04 was resistant to most clinically useful antimicrobial agents, remaining susceptible only to aminoglycosides and fosfomycin. The colistin resistance in this isolate was due to a ~1.3 kb deletion containing four genes, namely <i>mgrB</i>, <i>yebO</i>, <i>yobH</i> and the transcriptional regulator <i>kdgR</i>. The study isolate presented a variety of antimicrobial resistance genes, including the carbapenemase-encoding gene <i>bla</i> _KPC-2, the extended-spectrum beta-lactamase (ESBL)-encoding gene <i>bla</i> _SHV-28 and the beta-lactamase-encoding gene <i>bla</i> _OXA-1. Additionally, Kp14U04 harboured a multiple stress resistance protein, efflux systems and regulators, heavy metal resistance and virulence genes, plasmids, prophage-related sequences and genomic islands. These features revealed the high potential of this isolate to resist antimicrobial therapy, survive in adverse environments, cause infections and overcome host defence mechanisms.