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Co-outbreak of ST37 and a novel ST3006 Klebsiella pneumoniae from multi-site infection in a neonatal intensive care unit: a retrospective study

Background The outbreak of carbapenems resistant Klebsiella pneumoniae (K. pneumoniae) is a serious public health problem, especially in the neonatal intensive care unit (NICU). Methods Fifteen strains of K. pneumoniae were isolated from seven neonates during June 3–28, 2017 in a NICU. Antimicrobial susceptibility was determined by the Vitek 2 system and micro-broth dilution method. Multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used to analyse the genetic relatedness of isolates. Genome sequencing and gene function analyses were performed for investigating pathogenicity and drug resistance and screening genomic islands. Findings Two K. pneumoniae clones were identified from seven neonates, one ST37 strain and another new sequence type ST3006. The ST37 strain exhibited multi-drug resistance genes and resistance to carbapenem. MLST and PFGE showed that 15 strains were divided into three groups, with a high level of homology. Gene sequencing and analysis indicated that KPN1343 harboured 12 resistance genes, 15 genomic islands and 205 reduced virulence genes. KPN1344 harboured four resistance genes, 19 genomic islands and 209 reduced virulence genes. Conclusion Co-outbreak of K. pneumoniae involved two clones, ST36 and ST3006, causing multi-site infection. Genome sequencing and analysis is an effective method for studying bacterial resistance genes and their functions.