Comparative genomic analysis and multi-drug resistance differences of Acinetobacter baumannii in Chongqing, China

Abstract

Ling Pu,1 Zuoyi Jian,2 Fen Pan,3 Yang Geng,4 Miao He,5 Pu Liao1,6 1Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education of China), College of Laboratory Medicine, Chongqing Medical University, Chongqing, People’s Republic of China; 2Department of Bioinformatics, Novogene Biotechnology Co., Ltd, Sichuan, People’s Republic of China; 3Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai, People’s Republic of China; 4College of Life Sciences, Sichuan University, Sichuan, People’s Republic of China; 5Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan, People’s Republic of China; 6Department of Clinical Laboratory, Chongqing People’s Hospital, Chongqing, People’s Republic of ChinaCorrespondence: Pu LiaoCollege of Laboratory Medicine, Chongqing Medical University, No.1, Yixueyuan Road, Chongqing 400016, People’s Republic of ChinaTel [phone]Fax [phone]Email [email protected] Miao HeInstitute of Blood Transfusion, Chinese Academy of Medical Sciences, No. 26, Huacai Road, Chengdu 610052, Sichuan, People’s Republic of ChinaTel [phone]Fax [phone]Email [email protected]: Multidrug-resistance in Acinetobacter baumannii has emerged as a serious problem to public health. There is still a significant gap in the understanding of the multidrug-resistance and the genome diversity evolutionary process of A. baumannii in China, especially in the central and western regions.Methods: Ten A. baumannii strains were collected from three hospitals in Chongqing, China. Whole-genome re-sequencing was used to obtain differences in genomic levels among strains. The diversity were determined by multi-locus sequence typing method, and investigate the genetic relationship between the ten strains and others by phylogenetic analysis. Comparative analysis focused on resistance genes related to insertions and deletions (InDels) and single-nucleotide polymorphisms (SNPs) was performed.Results: The overall G+C% content was 39.05%∼39.43%, the average sequencing depth was 273.95∼428.99, and the alignment ratio of the sequencing data was 92.93%∼99.27%. A total of 42 InDels and 11,387 SNPs were detected in the coding sequence region of the isolates. Phylogenetic tree shows that the 10 A. baumannii isolates were divided into four relative groups, and there exist the possibility of cross-regional spread pattern. A total number of 19 drug resistance genes had been found in each strain, and efflux pump-related genes accounted for the most. Only AacA4 underwent a change in InDel. Six types of drug resistance genes were found in the SNPs resistance gene-related loci, among which gene ANT(3’’)-II and QacE mutations were found in each strain.Conclusion: In this study, the main mechanism of A. baumannii multi-drug resistance is due to the multi-drug efflux pump related genes. The point mutations at the SNPs sites of the six types of resistance genes are the main differences in A. baumannii between Chongqing and the eastern coastal areas of China.Keywords: Acinetobacter baumannii, antimicrobial resistance, genome-wide re-sequencing, MLST, phylogenetic analysis, SNP

Keywords

• Acinetobacter baumannii
• antimicrobial resistance
• genome-wide re-sequencing
• MLST
• phylogenetic analysis
• SNP