Genomic Epidemiology of an Outbreak of Klebsiella pneumoniae ST471 Producing Extended-Spectrum β-Lactamases in a Neonatal Intensive Care Unit

Yuan Wang; Chunyu Luo; Pengcheng Du; Jinrui Hu; Xiaowei Zhao; Dianjun Mo; Xiaoli Du; Xin Xu; Man Li; Hong Lu; Zhiqiang Zhou; Zhigang Cui; Haijian Zhou

doi:10.2147/IDR.S236212

Genomic Epidemiology of an Outbreak of Klebsiella pneumoniae ST471 Producing Extended-Spectrum β-Lactamases in a Neonatal Intensive Care Unit

Infect Drug Resist. 2020 Apr 15:13:1081-1090. doi: 10.2147/IDR.S236212. eCollection 2020.

Authors

Yuan Wang¹, Chunyu Luo¹, Pengcheng Du², Jinrui Hu³, Xiaowei Zhao¹, Dianjun Mo¹, Xiaoli Du³, Xin Xu¹, Man Li¹, Hong Lu¹, Zhiqiang Zhou¹, Zhigang Cui³, Haijian Zhou³

Affiliations

¹ Affiliated Hospital of Chifeng University, Chifeng 024005, People's Republic of China.
² Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, People's Republic of China.
³ State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China.

Abstract

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: minimum core genome; superspreader; transmission map; whole-genome sequencing.