Comparing core-genome MLST with PFGE and MLST for cluster analysis of carbapenem-resistant Acinetobacter baumannii

Tingting Li; Yunxing Yang; Rushuang Yan; Peng Lan; Haiyang Liu; Ying Fu; Xiaoting Hua; Yan Jiang; Zhihui Zhou; Yunsong Yu

doi:10.1016/j.jgar.2022.06.014

Comparing core-genome MLST with PFGE and MLST for cluster analysis of carbapenem-resistant Acinetobacter baumannii

J Glob Antimicrob Resist. 2022 Sep:30:148-151. doi: 10.1016/j.jgar.2022.06.014. Epub 2022 Jun 19.

Authors

Tingting Li¹, Yunxing Yang², Rushuang Yan³, Peng Lan³, Haiyang Liu³, Ying Fu⁴, Xiaoting Hua³, Yan Jiang³, Zhihui Zhou³, Yunsong Yu⁵

Affiliations

¹ Department of Clinical Laboratory, The First People's Hospital of Linhai, Taizhou, Zhejiang, China.
² Department of Clinical Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
³ Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
⁴ Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
⁵ Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China. Electronic address: yvys119@zju.edu.cn.

PMID: 35732264
DOI: 10.1016/j.jgar.2022.06.014

Abstract

Objectives: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a prevalent pathogen contributing to hospital infections. Pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and core-genome MLST (cgMLST) are frequently used methods to illuminate the nosocomial transmission of CRAB. In this study, we compared the discriminatory power of the three typing methods.

Methods: Antimicrobial susceptibility tests were performed by the broth microdilution and Vitek2 methods. PFGE, MLST and cgMLST were conducted to determine the clonality and phylogenetic relationship of the strains. Whole-genome sequence data were acquired by an Illumina HiSeq 2000, and cgMLST was analysed by the Ridom SeqSphere+ v.7.2.3 software.

Results: A total of 149 carbapenem-resistant A. baumannii isolates had 15 different PFGE profiles (A-O type), and 73 of the isolates had related subtypes (A1 and A2), accounting for the majority of type A isolates. The maximum-likelihood phylogenetic analysis based on the cgMLST genes grouped the same PFGE clonal pattern A into nine different clusters. ST_Pasteur grouped all the strains into ST2, whereas ST_Oxford grouped the PFGE clonal pattern A isolates into six STs. In addition, the gdhB allele in the ST_Oxford scheme had two copies in five strains, which complicated the ST_Oxford typing.

Conclusions: cgMLST was more discriminant than PFGE and MLST. CgMLST is the most suitable and comprehensive method for genotyping A. baumannii in surveillance and epidemiological research.

Keywords: Carbapenem-resistant Acinetobacter baumannii; MLST; PFGE; cgMLST.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Acinetobacter Infections* / epidemiology
Acinetobacter baumannii*
Carbapenems / pharmacology
Cluster Analysis
Electrophoresis, Gel, Pulsed-Field
Humans
Molecular Epidemiology
Multilocus Sequence Typing / methods
Phylogeny

Substances

Carbapenems