Forensic genomics of a novel Klebsiella quasipneumoniae type from an NICU in China reveals patterns of genetic diversity, evolution and epidemiology

Abstract

ABSTRACTDuring March of 2017 a neonate patient suffered severe diarrhea and subsequently developed septicemia and died, with Klebsiella isolated as the causative microorganism. Coincident illness of an attending staff member and three other neonates with Klebsiella triggered a response, leading to a detailed microbiological and genomics investigation of isolates collected from the staff member and all 21 co-housed neonates. Multilocus sequence typing and genomic sequencing identified that the Klebsiella from all 21 neonates was a new MLST ST2727, and belonged to a less frequently detected subspecies K. quasipneumoniae subsp. similipneumoniae (KpIIB). Genomic characterization showed that the isolated ST2727 strains had diverged from other KpIIB strains at least >90 years ago, whereas the neonate samples were highly similar with a genomic divergence of 3.6 months and not related to the staff member, indicating that transmission did not occur from staff to patient or between patient to patient, but were acquired from a common hospital source. The genomes revealed that the isolates contained the ubiquitous ampH gene responsible for resistance to penicillin G, cefoxitin and cephalosporin C, and all Kp-IIB strains were competent for host cell adhesion. Our results highlight the clinical significance and genomic properties of relatively mild, but persistent MLST types such as ST2727, and urges for genomic surveillance and eradication within hospital environments.Data summaryGenome sequences generated in this study are available in NCBI under BioProject ID PRJNA610124. All bioinformatic protocols used to process the genomic data are available at https://github.com/vjlab/KpIIB_ST2727.