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

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:

• whole-genome sequencing
• minimum core genome
• superspreader
• transmission map

Acknowledgments

We thank the team of curators of the Institute Pasteur MLST and whole genome MLST databases for curating the data and making them publicly available at http://bigsdb.pasteur.fr/. This work was supported by a grants from the Priority Project on Infectious Disease Control and Prevention (grant number 2017ZX10303405-002) from the Ministry of Science and Technology of the People’s Republic of China. The funding body played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Ethics and Consent Statement

This study was approved by the scientific and ethics committees of the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention. All clinical specimens from patients were collected for diagnostic testing in hospitals at the request of the attending doctors. All experiments on K. pneumoniae strains were reviewed and approved by the scientific and ethics committees. All experiments were performed in accordance with relevant guidelines and regulations. Furthermore, to protect patient privacy, the hospital set up a patient privacy and medical record management system according to the criminal procedure law, civil procedure law, tort liability law, and medical malpractice law in China. Excepting for the patient’s doctor, no one can enter the management system. Although no written informed consent was provided by patients or their guardians, the above measures were considered sufficient to protect the patients’ privacy.

Disclosure

The authors report no conflicts of interest in this work.