Molecular epidemiology and clinical characteristics of carbapenem-resistant Klebsiella pneumoniae bloodstream and pneumonia isolates

Abstract

Appropriate antibiotic therapy in patients with carbapenem-resistant Klebsiella pneumoniae (CRKp) infections often requires knowledge of resistance mechanisms. Therefore, we aimed to define the clonal diversity, mechanisms of carbapenem resistance, potential for carbapenem resistance transmissibility, virulence gene repertoire, and potential clinical impact of these genetic elements in patients with CRKp bloodstream infection and/or pneumonia, which are associated with high mortality. Clinical data and CRKp isolates at a site in Singapore and in the United States were examined. Whole-genome sequencing and bioinformatic analysis of CRKp isolates were performed. In total, 125 patients (n = 118 from Singapore; n = 7 from the United States) were included. Clonal diversity was high as 58 sequence types were identified. Carbapenemases were present in 109 (87%) of the CRKp isolates; KPC-, OXA-, and NDM-type enzymes were identified in significant quantity. The majority (87%) of carbapenemases were encoded on conjugative or mobilizable plasmids and thus potentially transmissible to other strains. Of the 16 CRKp isolates without a carbapenemase, the predominant predicted mechanism of carbapenem resistance was extended-spectrum β-lactamases along with truncation of porins ompK35 and/or ompK36. Patients with carbapenemase-producing CRKp strains had increased in-hospital mortality. Recurrent CRKp infections were primarily due to either the same CRKp genomic group or similar carbapenemase-encoding conjugative plasmids within a different K. pneumoniae strain. Our findings suggest that in CRKp isolates causing serious infections, carbapenem resistance arises through diverse mechanisms, is easily transmissible between isolates, and impacts patient outcomes. These findings highlight the importance of diagnostic tools to identify mechanisms of carbapenem resistance in the clinical setting.IMPORTANCETo design more effective therapies and better understand treatment failure in patients with carbapenem-resistant Klebsiella pneumoniae (CRKp) infections, we must identify the mechanisms of carbapenem resistance and their impact on patient outcomes. However, prior studies are often limited by the inclusion of CRKp that are colonizers or from non-severe infections, a focus on a single general mechanism (i.e., presence of carbapenemases), lack of whole-genome sequencing to fully characterize the underlying genetic architecture of CRKp strains, and no analyses of associations between resistance mechanisms and clinical outcomes. Here, we attempt to address some of these gaps by sequencing a large set of invasive CRKp isolates to characterize the underlying clonal diversity, mechanisms of carbapenem resistance, potential carbapenemase transmissibility, virulence gene repertoire, and the possible impact of these genetic elements on patient mortality.

Keywords: Klebsiella pneumoniae; antibiotic resistance; carbapenem.

Fig 1

ST distribution of CRKp in this study. The x-axis is the number of CRKp isolates within each ST (i.e., ST count 1 corresponds to STs with only one CRKp isolate in this study), while the y-axis is the number of such occurrences. The majority of STs were unique and only identified through one CRKp isolate in this study.

Fig 2

Phylogenetic relationships and distribution of carbapenemases in CRKp isolates in this study. STs with five or more CRKp isolates are indicated as internal colored ranges. The presence of IMP (filled green star), KPC (filled red square), NDM (filled blue circle), and OXA (filled black triangle) carbapenemases is indicated through filled symbols. The lack of these enzymes is indicated through open symbols. CRKp isolates without a carbapenemase are highlighted with a purple circle in the outer ring.

Fig 3

Genetic analysis of recurrent CRKp infections. Eighteen patients (A through R) in this study had multiple instances of CRKp isolation from the blood (circles) or respiratory tract (squares). The time (months) from the initial CRKp isolation to the subsequent CRKp-positive cultures is indicated by the x-axis. CRKp isolates that are the same genomic group as the initial infection are shown in white, and CRKp strains that differ from the initial are shown in black.