Transmission Dynamics of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 Strains Carrying Capsular Loci KL64 and rmpA/rmpA2 Genes

Abstract

The presence and dissemination of carbapenem-resistant Klebsiella pneumoniae (CRKP) often cause life-threatening infections worldwide, but the therapeutic option is limited. In this study, whole-genome sequencing (WGS) was applied to assess the epidemiological characteristics and transmission dynamics of CRKP isolates recovered from two fetal outbreaks of nosocomial infections. Between April 2016 and March 2018, a total of 70 isolates of K. pneumoniae were collected from sterile samples in a tertiary hospital in Hangzhou, China. The minimal inhibitory concentrations (MICs) of 21 antimicrobial agents were determined using the broth microdilution methods. Pulsed-field gel electrophoresis (PFGE) was performed on 47 CRKP isolates, and 16 clonally related isolates were further characterized by Illumina sequencing. In addition, the complete genome sequences of three representative isolates (KP12, KP36, and KP37) were determined by Oxford Nanopore sequencing. The K. pneumoniae isolates were recovered from patients diagnosed with pulmonary infection, cancer, or encephalopathy. For all CRKP isolates, PFGE separated three clusters among all strains. The most predominant PFGE cluster contained 16 isolates collected from patients who shared close hospital units and represented a potential outbreak. All 16 isolates showed an extremely high resistance level (≥87.5%) to 18 antimicrobials tested but remain susceptible to colistin (CST). Multiple antimicrobial resistance and virulence determinants, such as the carbapenem resistance gene blaKPC-2, and genes encoding the virulence factor aerobactin and the regulator of the mucoid phenotype (rmpA and rmpA2), were observed in the 16 CRKP isolates. These isolates belonged to sequence type 11 (ST11) and capsular serotype KL64. A core genome single nucleotide polymorphism (cgSNP)-based phylogenetic analysis indicated that the 16 CRKP isolates could be partitioned into two separate clades (≤15 SNPs), suggesting the two independent transmission scenarios co-occurred. Moreover, a high prevalence of IncFIB/IncHI1B type virulence plasmid with the iroBCDN locus deleted, and an IncFII/IncR type blaKPC-2-bearing plasmid was co-harbored in ST11-KL64 CRKP isolates. In conclusion, our data indicated that the nosocomial dissemination of ST11-KL64 CRKP clone is a potential threat to anti-infective therapy. The development of novel strategies for surveillance, diagnosis, and treatment of this high-risk CRKP clone is urgently needed.

An outbreak of extensively drug-resistant and hypervirulent Klebsiella pneumoniae in an intensive care unit of a teaching hospital in Southwest China

“…Therefore, based on the LD 50 , which was not statistically different from NTUH-K2044, and the virulence factors described above, it can be judged that all strains in this study were hvKp ( Choby et al., 2020 ). In addition, the loss of iroBCD might be due to the insertion of IS Kpn26 , which has been similarly reported previously ( Kong et al., 2021 ). The amino acid substitution in rcsA (ser35Asn) of all strains was identical to the mutation reported in a Chilean’s study, such a condition could affect the synthesis of CPS, thereby enhancing the virulence of the strains ( Morales-León et al., 2021 ).…”

Recombination Drives Evolution of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 KL47 to KL64 in China

“…Currently, more concerning is the emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP), which may lead to even higher mortality and morbidity ( 11 ). Of note, several interhospital outbreaks of ST11 CR-hvKP with capsular locus 64 (KL64) and plasmid-encoded virulence genes were reported recently ( 12 , 13 ). Among ST11 CR-hvKP in China, the group of KL64 strains is the most widespread, as it has been observed to harbor more plasmid-encoded virulence genes than ST11 non-KL64 strains ( 14 – 16 ).…”

Emergence of a Fatal ST11-KL64 Tigecycline-Resistant Hypervirulent Klebsiella pneumoniae Clone Cocarrying bla NDM and bla KPC in Plasmids

“…The coproduction of KPC and NDM carbapenems in a single strain should be taken seriously because it is capable of conferring higher-level carbapenem resistance and mediating the spread of carbapenems genes ( 7 ). Sequence type 11 (ST11) is one of the most common clones of CRKP observed in China, and it has received much attention recently since an increasing proportion of clinical strains are hypervirulent and antibiotic resistant ( 8 ). To date, most reported hvKP strains have belonged to the K1 and K2 capsular serotypes of K. pneumoniae ( 9 ).…”