title: Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae.
abstract: Infections caused by drug-resistant bacteria are a major problem worldwide. Carbapenem-resistant Klebsiella pneumoniae, most notably isolates classified as multilocus sequence type (ST) 258, have emerged as an important cause of hospital deaths. ST258 isolates are predominantly multidrug resistant, and therefore infections caused by them are difficult to treat. It is not known why the ST258 lineage is the most prevalent cause of multidrug-resistant K. pneumoniae infections in the United States and other countries. Here we tested the hypothesis that carbapenem-resistant ST258 K. pneumoniae is a single genetic clone that has disseminated worldwide. We sequenced to closure the genomes of two ST258 clinical isolates and used these genomes as references for comparative genome sequencing of 83 additional clinical isolates recovered from patients at diverse geographic locations worldwide. Phylogenetic analysis of the SNPs in the core genome of these isolates revealed that ST258 K. pneumoniae organisms are two distinct genetic clades. This unexpected finding disproves the single-clone hypothesis. Notably, genetic differentiation between the two clades results from an ∼ 215-kb region of divergence that includes genes involved in capsule polysaccharide biosynthesis. The region of divergence appears to be a hotspot for DNA recombination events, and we suggest that this region has contributed to the success of ST258 K. pneumoniae. Our findings will accelerate research on novel diagnostic, therapeutic, and vaccine strategies designed to prevent and/or treat infections caused by multidrug resistant K. pneumoniae.
authors.affiliation: Laboratory of Human Bacterial Pathogenesis and Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840.
authors.forename: Frank R
authors.initials: FR
authors.lastname: Deleo
authors.forename: Liang
authors.initials: L
authors.lastname: Chen
authors.forename: Stephen F
authors.initials: SF
authors.lastname: Porcella
authors.forename: Craig A
authors.initials: CA
authors.lastname: Martens
authors.forename: Scott D
authors.initials: SD
authors.lastname: Kobayashi
authors.forename: Adeline R
authors.initials: AR
authors.lastname: Porter
authors.forename: Kalyan D
authors.initials: KD
authors.lastname: Chavda
authors.forename: Michael R
authors.initials: MR
authors.lastname: Jacobs
authors.forename: Barun
authors.initials: B
authors.lastname: Mathema
authors.forename: Randall J
authors.initials: RJ
authors.lastname: Olsen
authors.forename: Robert A
authors.initials: RA
authors.lastname: Bonomo
authors.forename: James M
authors.initials: JM
authors.lastname: Musser
authors.forename: Barry N
authors.initials: BN
authors.lastname: Kreiswirth
mesh_terms: D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D015780:Carbapenems / Q000494:pharmacology*; D024901:Drug Resistance, Multiple, Bacterial / Q000187:drug effects* / Q000235:genetics*; D019143:Evolution, Molecular; D016680:Genome, Bacterial / Q000235:genetics; D005843:Geography; D006801:Humans; D007711:Klebsiella pneumoniae / Q000145:classification* / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D015780:Carbapenems
keywords: Enterobacteriaceae; antibiotic resistance; carbapenemase; plasmid