Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307

Abstract

Klebsiella pneumoniae is a major human pathogen responsible for high morbidity and mortality rates. The emergence and spread of strains resistant to multiple antimicrobial agents and documented large nosocomial outbreaks are especially concerning. To develop new therapeutic strategies for K. pneumoniae, it is imperative to understand the population genomic structure of strains causing human infections. To address this knowledge gap, we sequenced the genomes of 1,777 extended-spectrum beta-lactamase-producing K. pneumoniae strains cultured from patients in the 2,000-bed Houston Methodist Hospital system between September 2011 and May 2015, representing a comprehensive, population-based strain sample. Strains of largely uncharacterized clonal group 307 (CG307) caused more infections than those of well-studied epidemic CG258. Strains varied markedly in gene content and had an extensive array of small and very large plasmids, often containing antimicrobial resistance genes. Some patients with multiple strains cultured over time were infected with genetically distinct clones. We identified 15 strains expressing the New Delhi metallo-beta-lactamase 1 (NDM-1) enzyme that confers broad resistance to nearly all beta-lactam antibiotics. Transcriptome sequencing analysis of 10 phylogenetically diverse strains showed that the global transcriptome of each strain was unique and highly variable. Experimental mouse infection provided new information about immunological parameters of host-pathogen interaction. We exploited the large data set to develop whole-genome sequence-based classifiers that accurately predict clinical antimicrobial resistance for 12 of the 16 antibiotics tested. We conclude that analysis of large, comprehensive, population-based strain samples can assist understanding of the molecular diversity of these organisms and contribute to enhanced translational research.IMPORTANCE Klebsiella pneumoniae causes human infections that are increasingly difficult to treat because many strains are resistant to multiple antibiotics. Clonal group 258 (CG258) organisms have caused outbreaks in health care settings worldwide. Using a comprehensive population-based sample of extended-spectrum betalactamase (ESBL)-producing K. pneumoniae strains, we show that a relatively uncommon clonal type, CG307, caused the plurality of ESBL-producing K. pneumoniae infections in our patients. We discovered that CG307 strains have been abundant in Houston for many years. As assessed by experimental mouse infection, CG307 strains

Convergence of virulence and multidrug resistance in a single plasmid vector in multidrug-resistant Klebsiella pneumoniae ST15

“…Both of the Norwegian hv-MDR isolates belonged to ST15 and carried the siderophore yersiniabactin (in genomic island ICEKp2) and the KL24 locus encoding capsular serotype K24. ST15 is a well-documented international ESBL-producing clone associated with nosocomial outbreaks worldwide, which frequently carries bla CTX-M-15 -encoding IncFII plasmids [16][17][18][19] . To explore the relatedness of the Norwegian isolates to one another and to the wider ST15 Kp population, we constructed a recombination-filtered, core-genome maximum likelihood phylogeny including KP_104014, KP_112126, ten additional ST15 isolates from Norway and 306 publicly available ST15 genomes from 29 other countries (Figure 2, Supplementary data 1).…”

Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov

“…In a recent study of 1,777 K. pneumoniae isolates producing extended-spectrum β-lactamase (ESBL), which were recovered from patients in our health care system, we identified strain KPN1705 as a distinct outlier in the phylogenetic analysis (3, 4). It shared a common branch with K. variicola , yet was as distant from the K. pneumoniae , K. quasipneumoniae , and K. variicola reference genomes as they were from each other.…”

“…The genome of strain KPN1705 was previously described using Illumina short-read data (3). We sequenced the genome of strain KPN1705 to closure using a one-dimensional ligation sequencing kit, an R9.4 flow cell, and an Oxford Nanopore Technologies MinION Mk-Ib sequencer.…”

Developing anin silicominimum inhibitory concentration panel test forKlebsiella pneumoniae

“…Over the past several years, the emergence of antimicrobial resistant (AMR) K. pneumoniae strains has been increasing at an alarming rate, with reports of pan-resistant strains appearing in the literature and lay press 1-3 . Reports of hospital-based outbreaks are particularly concerning, and recent evidence suggests that AMR K. pneumoniae clones are circulating in the community [3][4][5] . As antimicrobial resistance increases, fewer effective antibiotics are available for physicians to treat these life-threatening infections.…”

“…Other studies have successfully used AMR genes, SNPs, and whole genome sequence data (or a combination thereof) to build ML classifiers with good accuracies [22][23][24][25][26][27] . Recent examples of gene-based and whole genome-based classification approaches for Klebsiella were reported by Stoesser et al 27 , Long et al 3 , and Pesesky et al 24 .…”