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. 2018 Jun 1:7:70.
doi: 10.1186/s13756-018-0363-8. eCollection 2018.

Whole genome sequence revealed the fine transmission map of carbapenem-resistant Klebsiella pneumonia isolates within a nosocomial outbreak

Wenjun Sui #  1 , Haijian Zhou #  2   3 , Pengcheng Du #  4 , Lijun Wang  1 , Tian Qin  2   3 , Mei Wang  1 , Hongyu Ren  2   3 , Yanfei Huang  1 , Jing Hou  5 , Chen Chen  4 , Xinxin Lu  1
Affiliations

Whole genome sequence revealed the fine transmission map of carbapenem-resistant Klebsiella pneumonia isolates within a nosocomial outbreak

Wenjun Sui et al. Antimicrob Resist Infect Control. .

Abstract

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major cause of nosocomial infections worldwide. The transmission route of CRKP isolates within an outbreak is rarely described. This study aimed to reveal the molecular characteristics and transmission route of CRKP isolates within an outbreak of nosocomial infection.

Methods: Collecting case information, active screening and targeted environmental monitoring were carried out. The antibiotic susceptibility, drug-resistant genes, molecular subtype and whole genome sequence of CRKP strains were analyzed.

Results: Between October and December 2011, 26 CRKP isolates were collected from eight patients in a surgical intensive care unit and subsequent transfer wards of Beijing Tongren hospital, China. All 26 isolates harbored blaKPC-2, blaSHV-1, and blaCTX-M-15 genes, had the same or similar pulsed-field gel electrophoresis patterns, and belonged to the sequence type 11 (ST11) clone. By comprehensive consideration of genomic and epidemiological information, a putative transmission map was constructed, including identifying one case as an independent event distinct from the other seven cases, and revealing two transmissions starting from the same case.

Conclusions: This study provided the first report confirming an outbreak caused by K. pneumoniae ST11 clone co-harboring the blaKPC-2, blaCTX-M-15, and blaSHV-1 genes, and suggested that comprehensive consideration of genomic and epidemiological data can yield a fine transmission map of an outbreak and facilitate the control of nosocomial transmission.

Keywords: Carbapenemases; K. pneumoniae; KPC-2; Outbreak; Whole genome sequencing.

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Conflict of interest statement

This study was approved by the scientific and ethics committees of Beijing Tongren Hospital. All clinical specimens from patients were collected for diagnostic testing in hospitals at the request of the attending doctors. The active screening and targeted environmental monitoring was carried out in the case of an emergency investigation and in accordance with the recommendations of “Emergency treatment plan for hospital infection outbreak in Tongren Hospital” and “2007 Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Healthcare Settings (https://www.cdc.gov/infectioncontrol/pdf/guidelines/isolation-guidelines.pdf)”. All experiments were performed in accordance with relevant guidelines and regulations. The consent of the patients for the active screening of specimens, including K. pneumoniae detection, was obtained verbally by medical staff in the hospital. The medical records were considered as legal documents. 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, the above measures are sufficient to protect the patients’ privacy.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
The timeline of patient admission and CRKP isolation. Shadows on the timeline represent the admitting’s duration of the case. Different wards are indicated in different colors. The red arrow indicates the isolation of the strains
Fig. 2
Fig. 2
Clustering of the 26 K. pneumoniae isolates based on PFGE patterns. The first positive cultures of each case are marked by an asterisk. The information of strain ID, PFGE type, patient ID, isolation date, ward, type of specimen, and MLST type is listed to the left of the patterns. ADF, abdominal drainage fluid; BAL, bronchoalveolar lavage
Fig. 3
Fig. 3
Clustering of the 26 K. pneumoniae isolates based on MCG typing. The first positive cultures of each case are marked by an asterisk. The information of strain ID, patient ID, type of specimen, isolation date, and ward are listed to the left of the patterns. ADF, abdominal drainage fluid; BAL, bronchoalveolar lavage
Fig. 4
Fig. 4
Evolutionary relationships based on MCG typing of 26 CRKP isolates. Isolates from different patients are indicated in different colors. The first positive cultures of each case are marked by an asterisk
Fig. 5
Fig. 5
Clustering of the eight first positive CRKP cultures of each case based on MCG typing. The matrix of the SNP differences is presented on the left of the cluster tree
Fig. 6
Fig. 6
Putative map of CRKP transmission during the outbreak. The transmission map was constructed with genetic and patient trace data. Nodes represent patients, and arrows indicate a transmission event directly from one patient to another
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