Genomic Analysis of KPC-2-Producing ST11 Isolates at the Respiratory Department of a Tertiary Care Hospital in Beijing, China.

Background: Carbapenem-resistant (CRKP) is an important pathogen causing hospital-associated outbreaks worldwide. The spread of carbapenemase-2 (KPC-2)-producing CRKP is primarily associated with sequence type (ST) 11.

Methods: A total of 152 KPC-2-producing ST11 isolates were collected from the respiratory department of a tertiary care hospital in Beijing, China between 2009 and 2018. The genome sequencing of these isolates was performed on the HiSeq X Ten sequencer. Multilocus sequence typing (MLST), capsular type, plasmid replicon types and resistance genes were identified. Fifteen isolates were selected for the subsequent single-molecule real-time (SMRT) sequencing on the PacBio RS II. Alignment of the complete sequences of the plasmids carrying and/or virulence genes was performed by using BRIG and Easyfig.

Results: From 2012 to 2018, the detection rate of the -carrying CRKP rose rapidly from 3.3 to 28.1%. KPC-2-producing ST11 isolates were dominant in CRKP, which emerged in 2012 and caused several outbreaks. Most isolates exhibited multidrug-resistant to commonly used antibiotics, while all the isolates remained susceptible to tigecycline and polymyxin B. The single nucleotide polymorphism (SNP) analysis showed that all these 152 KPC-2-producing ST11 isolates could be divided into three genetically distinct clades (A, B, and C) and eleven subclades (A1-A9 and B1-B2). The majority belonged to clade A with KL47 serotype ( = 117, 77.0%), while KL64 and KL16 were identified in clades B and C, respectively. The -carrying plasmids exhibited diverse types, namely, IncFII (pHN7A8)/IncR(6/15), IncFII (pHN7A8)/Inc (5/15), IncFII (pHN7A8) (1/15), IncR (1/15), and Inc (1/15). The genetic environment of showed nine IS-based composite transposons, which had a basic core structure IS -ΔIS. About 27.6% (42/152) isolates co-carried 2 to 4 virulence marker genes (namely, , , , , and ) for hvKp strains. At least three isolates were identified to harbor virulence gene-carrying plasmids.

Conclusion: KPC-2-producing ST11 was highly heterogeneous in our hospital. Transmission of these strains was mainly mediated by twelve high-risk clones. The -carrying plasmids and genetic environment of genes exhibited active evolution in ST11. More attention should be paid to the tendency of KPC-2-ST11 to acquire hypervirulent plasmids.