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

During 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 summary Genome 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 . ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by research grants from the National Natural Science Foundation of China (no. 81171614), the Health Department of Zhejiang Province of the People's Republic of China (no. 2011KYA106), the Zhejiang Provincial Program for the Cultivation of High-level Innovative Health Talents (no. 2012, 241) and Program Grant 1092262 from the National Health and Medical Research Council, Australia. ### Author Declarations All relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript. Yes All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All newly generated sequence data has been submitted to GenBank, and the accession numbers are included.