Drug Resistance and Whole Genome Sequencing Analysis of A Colonized ST23-K1 Strain of Carbapenem-resistant Highly Virulent Klebsiella Pneumoniae
Objective To investigate the drug resistance of clinical isolates of klebsiella pneumoniae K63(klebsiella pneumoniae clinical isolate No.63)and features of genome.Methods The klebsiella pneumoniae K63 strain was collected from sputum specimens of male children in the neonatal intensive care unit of a hospi-tal in Ningxia.The VITEK 2 compact system was used for identification and drug susceptibility testing.PCR was performed to detect the virulence genes(ybtS、iutA、iucA、iroB、rmpA2、fimH、mrkD、peg344)and drug re-sistance genes(blaTEM、blaSHV、blaNDM、blaIMP、blaOXA-48、blaVIM).Whole genome sequencing and bioinformatics anal-ysis were performed on PacBio RS Ⅲ and illuminate high-throughput sequencing platforms to clarify the genomic characteristics of the strain.Results A carbapenem-resistant klebsiella pneumoniae(CRKP)strain named K63 was successfully isolated from a sputum specimen on the hospitalisation for respira-tory distress and neonatal lung infection.The drug sensitivity results showed that it was resistant to antibiotics such as carbapenems,sulfonamides,cephalosporins,β-lactams,and β-lactamase inhibitor complexes.PCR results showed that the virulence genes ybtS、iutA、iucA、iroB、rmpA2、fimH、mrkD、peg344 were positive,and it also carried blaTEM、blaSHV、blaNDM、blaVIM resistance genes.Whole genome sequencing and assembly yielded one complete genome sequence and one plasmid sequence.Sequence alignment showed that strain K63 was ST23-K1 type.The result showed that its genome was 5 880 871 bp and one complete plasmid sequence was assembled.Eight virulence genes were found in the chromosomal genome.There were seven resistance-associ-ated genes.The plasmid carried resistance genes such as blaSHV-66,blaNDM-5,sul1,mphA and aph(3')-Ia,tetC,vanA,and mexe.clb(ABCDFGHIJKLMNOPQS),glf,pilW,ibeB and other virulence genes were also annotated.Meanwhile horizontal transfer region prediction results showed a potential for transfer.Gene enrichment and functional analyses showed that it had the most genes and pathways related to metabolism.Conclusion The isolated and colonized K63 strain may be a highly virulent carbapenem-resistant and hypervirulent K.pneumo-niae,with potential risk of transmission,and requires high clinical attention.
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