Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China

Abstract

We aimed to clarify the epidemiologic and clinical importance of evolutionary events that occurred in carbapenem-resistant Klebsiella pneumoniae (CRKP). We collected 203 CRKP causing bloodstream infections in a tertiary hospital in China during 2013-2017. We detected a subclonal shift in the dominant clone sequence type (ST) 11 CRKP in which the previously prevalent capsular loci (KL) 47 had been replaced by KL64 since 2016. Patients infected with ST11-KL64 CRKP had a significantly higher 30-day mortality rate than other CRKP-infected patients. Enhanced virulence was further evidenced by phenotypic tests. Phylogenetic reconstruction demonstrated that ST11-KL64 is derived from an ST11-KL47-like ancestor through recombination. We identified a pLVPK-like virulence plasmid carrying rmpA and peg-344 in ST11-KL64 exclusively from 2016 onward. The pLVPK-like-positive ST11-KL64 isolates exhibited enhanced environmental survival. Retrospective screening of a national collection identified ST11-KL64 in multiple regions. Targeted surveillance of this high-risk CRKP clone is urgently needed.

Keywords: China; Klebsiella pneumoniae; ST11; antimicrobial resistance; bacteria; bacterial infections; carbapenem resistance; recombination; subclonal shift; virulence.

Figure 1

Kaplan–Meier survival estimates for patients with bloodstream infections caused by ST11-KL47, ST11-KL64, and non-ST11 CRKP, China, 2013–2017. A significant difference was found in the 30-day mortality among the 3 groups (p = 0.039). ST11-KL64–infected patients showed significantly higher overall 30-day mortality than ST11-KL47–infected patients (62.2% vs. 52.8%; p = 0.039) and non-ST11 CRKP–infected patients (62.2% vs. 44.8%; p = 0.05). No significant difference in 30-day mortality was found between patients infected with ST11-KL47 and non-ST11 CRKP (52.8% vs. 44.8%, p = 0.529). CRKP, carbapenem-resistant Klebsiella pneumoniae; KL, capsular loci; ST, sequence type.

Figure 2

Phylogenetic analysis of 216 CRKP ST11 isolates, China, 2013–2017, including 154 CRKP isolates collected during 2012–2017 in study of bloodstream infections in a tertiary hospital and 62 isolates that were sequenced in previous studies (Appendix 2 Table 1). The phylogenetic tree was obtained by mapping all sequence reads to the hybrid assembly of KP47434 and removing the recombined regions from the alignment. The tree was rooted using ST1731 isolate EuSCAPE_ES29 (ERR1541319), which was included in this analysis but later removed from the tree (a tree including this outgroup is shown in Appendix 1 Figure 1). Five capsular types (KL31, KL47, KL64, KL103, and KL105) were detected in our ST11 collection, which are indicated in different colors as shown in the legend. Some of virulence genes detected are shown here. The rmpA2 gene carried by KL64 isolates was frameshifted, namely rmpA2*. Aerobactin and salmochelin represent the iucABCD-iutA and iroBCDN gene clusters, respectively. The fatal outbreak clone reported in China recently (12) is highlighted on the tree. Lanes: 1, year; 2, country; 3, K-type; 4, rmpA; 5, rmpA2; 6, aerobactin; 7, peg-344; 8, salmochelin; 9, bla_KPC. Scale bar indicates single-nucleotide polymorphisms. CRKP, carbapenem-resistant Klebsiella pneumoniae; KL, capsular loci; ST, sequence type.