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

Authors Wang Y, Luo C, Du P, Hu J, Zhao X, Mo D, Du X, Xu X, Li M, Lu H, Zhou Z, Cui Z, Zhou H

Received 26 October 2019

Accepted for publication 11 January 2020

Published 15 April 2020 Volume 2020:13 Pages 1081—1090


Checked for plagiarism Yes

Review by Single anonymous peer review

Peer reviewer comments 2

Editor who approved publication: Professor Suresh Antony

Yuan Wang,1 Chunyu Luo,1 Pengcheng Du,2 Jinrui Hu,3 Xiaowei Zhao,1 Dianjun Mo,1 Xiaoli Du,3 Xin Xu,1 Man Li,1 Hong Lu,1 Zhiqiang Zhou,1 Zhigang Cui,3 Haijian Zhou3

1Affiliated Hospital of Chifeng University, Chifeng 024005, People’s Republic of China; 2Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, People’s Republic of China; 3State 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

Correspondence: Haijian Zhou
State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155, Changbai Road, Changping, Beijing 102206, People’s Republic of China
Tel +86-10-58900784
Fax +86-10-58900700

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 blaCTX-M-15, blaTEM-1, blaSHV-108, and blaOXA-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

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