Purpose: Klebsiella pneumoniae  producing extended-spectrum β-lactamases (ESBLs) causes nosocomial infections worldwide. The present study aimed to determine the molecular subtyping characteristics and antibiotic resistance mechanisms of ESBL-producing K. pneumoniae  strains collected during an outbreak. Moreover, we attempted to reveal the fine transmission route of the strains within this outbreak using whole-genome sequencing (WGS).
Methods: Collecting cases and strain information were carried out. Outbreak-related strains were identified using pulsed-field gel electrophoresis (PFGE). The antibiotic susceptibility, drug-resistant genes, and molecular subtype characteristics of ESBL-producing K. pneumoniae  were analyzed. The fine transmission route of the strains within this outbreak was revealed using WGS and minimum core genome (MCG) sequence typing.
Results: In mid-January, 2015, five cases of neonatal pneumonia caused by ESBL-producing K. pneumoniae  were observed in the neonatal intensive care unit (NICU) of the Affiliated Hospital of Chifeng University, China. Eight ESBL-producing K. pneumoniae  were isolated from these five cases, and two additional strains from another two cases were identified using PFGE. All ten isolates harbored bla _CTX-M-15, bla _TEM-1, bla _SHV-108, and bla _OXA-1 genes, and belonged to the sequence type 471 (ST471) clone. A putative transmission map was constructed via comprehensive consideration of genomic and epidemiological information. WGS identified the initial case and the “superspreader”. The genomic epidemiological investigation revealed that the outbreak was caused by the introduction of the bacteria one month before the first case appeared.
Conclusion: As far as we know, this is the first report to describe the characteristics of an ST471 ESBL-producing K. pneumoniae  outbreak. The data showed that epidemiological inferences could be greatly improved by interpretation in the context of WGS and that K. pneumoniae  strains isolated from the same outbreak contain sufficient genomic differences to refine epidemiological linkages on the basis of genetic lineage. These findings suggested that integration of genomic and epidemiological data can help us to have a clearer understanding of when and how outbreaks occur, so as to better control nosocomial transmission.
Keywords: whole-genome sequencing, minimum core genome, superspreader, transmission map