Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae

• Published in: Microbial genomics Vol. 4; no. 3
• Main Authors: Pitt, Miranda E, Elliott, Alysha G, Cao, Minh Duc, Ganesamoorthy, Devika, Karaiskos, Ilias, Giamarellou, Helen, Abboud, Cely S, Blaskovich, Mark A T, Cooper, Matthew A, Coin, Lachlan J M
• Format: Journal Article
• Language: English
• Published: England Microbiology Society 01.03.2018
• Subjects: Anti-Bacterial Agents - pharmacology; Brazil; Chromosomes, Bacterial - genetics; Colistin - pharmacology; DNA, Bacterial - genetics; DNA, Bacterial - isolation & purification; Drug Resistance, Bacterial - genetics; Escherichia coli - drug effects; Escherichia coli - genetics; Gene Expression Regulation, Bacterial; Gene Library; Genes, Bacterial; Genetic Variation; Greece; Klebsiella pneumoniae - drug effects; Klebsiella pneumoniae - genetics; Klebsiella pneumoniae - isolation & purification; Microbial Sensitivity Tests; Mutation; Polymyxins - pharmacology; Sequence Analysis, DNA; Greece; Brazil; polymyxin; chromosomal variants; antibiotic resistance; Klebsiella pneumoniae
• ISSN: 2057-5858; 2057-5858
• DOI: 10.1099/mgen.0.000158

Extensively drug-resistant Klebsiella pneumoniae (XDR-KP) infections cause high mortality and are disseminating globally. Identifying the genetic basis underpinning resistance allows for rapid diagnosis and treatment. XDR isolates sourced from Greece and Brazil, including 19 polymyxin-resistant and five polymyxin-susceptible strains, were subjected to whole genome sequencing. Seventeen of the 19 polymyxin-resistant isolates harboured variations upstream or within mgrB. The most common mutation identified was an insertion at nucleotide position 75 in mgrB via an ISKpn26-like element in the ST258 lineage and ISKpn13 in one ST11 isolate. Three strains acquired an IS1 element upstream of mgrB and another strain had an ISKpn25 insertion at 133 bp. Other isolates had truncations (C28STOP, Q30STOP) or a missense mutation (D29E) affecting mgrB. Complementation assays revealed all mgrB perturbations contributed to resistance. Missense mutations in phoQ (T281M, G385C) were also found to facilitate resistance. Several variants in phoPQ co-segregating with the ISKpn26-like insertion were identified as potential partial suppressor mutations. Three ST258 samples were found to contain subpopulations with different resistance-conferring mutations, including the ISKpn26-like insertion colonizing with a novel mutation in pmrB (P158R), both confirmed via complementation assays. These findings highlight the broad spectrum of chromosomal modifications which can facilitate and regulate resistance against polymyxins in K. pneumoniae.