AUTHOR=Guo Ling , Wang Lifeng , Zhao Qiang , Ye Liyan , Ye Kun , Ma Yanning , Shen Dingxia , Yang Jiyong 

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

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.929826

DOI=10.3389/fmicb.2022.929826

ISSN=1664-302X

ABSTRACT=<sec><title>Background</title><p>Carbapenem-resistant <italic>Klebsiella pneumoniae</italic> (CRKP) is an important pathogen causing hospital-associated outbreaks worldwide. The spread of <italic>K. pneumoniae</italic> carbapenemase-2 (KPC-2)-producing CRKP is primarily associated with sequence type (ST) 11.</p></sec><sec><title>Methods</title><p>A total of 152 KPC-2-producing <italic>K. pneumoniae</italic> 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 <italic>bla</italic><sub>KPC–2</sub> and/or virulence genes was performed by using BRIG and Easyfig.</p></sec><sec><title>Results</title><p>From 2012 to 2018, the detection rate of the <italic>bla</italic><sub>KPC–2</sub>-carrying CRKP rose rapidly from 3.3 to 28.1%. KPC-2-producing <italic>K. pneumoniae</italic> 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 <italic>K. pneumoniae</italic> 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 (<italic>n</italic> = 117, 77.0%), while KL64 and KL16 were identified in clades B and C, respectively. The <italic>bla</italic><sub>KPC–2</sub>-carrying plasmids exhibited diverse types, namely, IncFII (pHN7A8)/IncR(6/15), IncFII (pHN7A8)/Inc<sub>pA1763–KPC</sub> (5/15), IncFII (pHN7A8) (1/15), IncR (1/15), and Inc<sub>pA1763–KPC</sub> (1/15). The genetic environment of <italic>bla</italic><sub>KPC–2</sub> showed nine IS<italic>26</italic>-based composite transposons, which had a basic core structure IS<italic>Kpn27-bla</italic><sub>KPC–2</sub>-ΔIS<italic>Kpn6</italic>. About 27.6% (42/152) isolates co-carried 2 to 4 virulence marker genes (namely, <italic>peg344</italic>, <italic>iucA</italic>, <italic>iroB</italic>, <italic>rmpA</italic>, and <italic>rmpA2</italic>) for hvKp strains. At least three isolates were identified to harbor virulence gene-carrying plasmids.</p></sec><sec><title>Conclusion</title><p>KPC-2-producing <italic>K. pneumoniae</italic> ST11 was highly heterogeneous in our hospital. Transmission of these strains was mainly mediated by twelve high-risk clones. The <italic>bla</italic><sub>KPC–2</sub>-carrying plasmids and genetic environment of <italic>bla</italic><sub>KPC–2</sub> genes exhibited active evolution in <italic>K. pneumoniae</italic> ST11. More attention should be paid to the tendency of KPC-2-ST11 to acquire hypervirulent plasmids.</p></sec>