Clinical and Molecular Characterizations of Carbapenem-Resistant Klebsiella pneumoniae Causing Bloodstream Infection in a Chinese Hospital

Abstract

Bloodstream infection (BSI) caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious and urgent threat for hospitalized patients. This study aims to describe the clinical and molecular characteristics of CRKP causing BSI in a tertiary-care hospital in Beijing, China. A total of 146 CRKP strains and 39 carbapenem-susceptible K. pneumoniae (CSKP) strains collected in the hospital from 2017 to 2020 were sent for whole-genome sequencing. Univariate and multivariate analyses were used to evaluate risk factors for in-hospital mortality of CRKP-BSI cases. Thirty (20.5%) of 146 CRKP-BSI patients and three (7.7%) of 39 CSKP-BSI patients died at discharge (χ² = 3.471, P = 0.062). Multivariate logistic regression analysis indicated that age and use of urinary catheters were independent risk factors for the death of CRKP-BSI. The 146 CRKP isolates belonged to 9 sequence types (STs) and 11 serotypes, while the 39 CSKP isolates belonged to 23 STs and 27 serotypes. The mechanism of carbapenem resistance for all the CRKP strains was the acquisition of carbapenemase, mainly KPC-2 (n = 127). There were 2 predominant serotypes for ST11 CRKP, namely, KL47 (n = 82) and KL64 (n = 42). Some virulent genes, including rmpA2, iucABCD and iutA, and repB gene, which was involved in plasmid replication, were detected in all ST11-KL64 strains. Evolutionary transmission analysis suggested that ST11 CRKP strains might have evolved from KL47 into KL64 and were accompanied by multiple outbreak events. This study poses an urgent need for enhancing infection control measures in the hospital, especially in the intensive care unit where the patients are at high-risk for acquiring CRKP-BSI. IMPORTANCE CRKP-BSI is demonstrated to cause high mortality. In this study, we demonstrated that ST11 CRKP strains might carry many virulent genes. Meanwhile, outbreak events occurred several times in the strains collected. Carbapenemase acquisition (mainly KPC-2 carbapenemase) was responsible for carbapenem resistance of all the 146 CRKP strains. As 2 predominant strains, all ST11-KL64 strains, but not ST11-KL47 strains, carried rmpA2, iucABCD, iutA, as well as a plasmid replication initiator (repB). Our study suggested that the occurrence of region-specific recombination events manifested by the acquisition of some virulence genes might contribute to serotype switching from ST11-KL47 to ST11-KL64. The accumulation of virulent genes in epidemic resistant strains poses a great challenge for the prevention and treatment of BSI caused by K. pneumoniae in high-risk patients.

Keywords: bloodstream infection; carbapenem resistance; genomic analysis; genomic evolution; transmission.

FIG 1

Pan-genome and phylogenetic analyses of 185 Klebsiella pneumoniae. The phylogenetic tree was structured by kSNP3, beautified, and visualized with iTOL. Isolates with light green branches are carbapenem-susceptible K. pneumoniae, and isolates with lavender branches are carbapenem-resistant K. pneumoniae. Virulence genes include rmpA, rmpA2, iroB, iucA and peg-344. Reference genome about KPN166 (Genome Accession: JAJQMM000000000) was a Klebsiella michiganensis, which was isolated from a tertiary hospital in 2018/7/31, Beijing, China. Empty positions of serotypes represent unknown serotypes and “-” means unknown wzi capsular types.

FIG 2

The distribution of department sources, ST types, and presence of virulence and resistance genes in 185 Klebsiella pneumoniae isolates. The solid dots of different colors represent strains that carry different hypervirulent and resistance genes. The cumulative histograms outside the scatterplot indicate the number of genes which belong to different ST types or department sources. ICU, Intensive Care Unit.

FIG 3

Temporal distribution of 146 Carbapenem-resistant Klebsiella pneumoniae isolates. A spot represents an isolate, blue spots, orange spots, green spots, and yellow spots indicate isolates carrying bla_KPC-2, bla_KPC-2 and bla_NDM-5, bla_NDM-1, bla_NDM-5, respectively. bla_KPC-2 was the mainly collected carbapenem drug resistance gene during 2017–2020. Other carbapenemase genes appeared occasionally.

FIG 4

A phylogenetic tree simulating the evolutionary relationships of strains. A transmission event is represented by a change from one color to another, which is highlighted with red stars. The shift in color from left to right indicates that a transmission event occurred between them, which is marked with a red star. The date of the star corresponds to the date of the transmission event, x axis represents the isolation time, and the colored tree includes all the information shown in the phylogenetic and transmission trees.