Whole-Genome Analysis of Two Copies of bla NDM-1 Gene Carrying Acinetobacter johnsonii Strain Acsw19 Isolated from Sichuan, China

Lingtong Tang; Wei Shen; Zhikun Zhang; Jingping Zhang; Guangxi Wang; Li Xiang; Junping She; Xiaoyan Hu; Guoyuan Zou; Baoli Zhu; Yingshun Zhou

doi:10.2147/IDR.S236200

Whole-Genome Analysis of Two Copies of bla _NDM-1 Gene Carrying Acinetobacter johnsonii Strain Acsw19 Isolated from Sichuan, China

Infect Drug Resist. 2020 Mar 23:13:855-865. doi: 10.2147/IDR.S236200. eCollection 2020.

Authors

Lingtong Tang^{1

2}, Wei Shen^{2

3}, Zhikun Zhang², Jingping Zhang², Guangxi Wang², Li Xiang², Junping She², Xiaoyan Hu², Guoyuan Zou⁴, Baoli Zhu⁵, Yingshun Zhou²

Affiliations

¹ Department of Clinical Laboratory, The People's Hospital of Gao County, Sichuan 644000, People's Republic of China.
² Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.
³ Department of Clinical Laboratory, The First People's Hospital of Yibin, Yibin 644000, Sichuan, People's Republic of China.
⁴ Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Science, Beijing, People's Republic of China.
⁵ Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.

Abstract

Purpose: To characterize the genetic feature of the carbapenems resistant Acinetobacter johnsonii strain Acsw19 isolated from municipal sludge. This strain was found to carry two copies of bla _NDM-1, cmlB1-like gene, and bla _OXA-211-like gene along with other 8 antimicrobial resistance genes, 3 plasmids, 15 genomic islands and 8 prophages.

Methods: A carbapenem-resistant Acinetobacter johnsonii strain Acsw19 isolated from municipal sludge was subjected to whole-genome sequencing (WGS) via the PacBio and Illumina MiSeq platforms. Thereafter, the characteristic was analyzed by a series of bioinformatics software.

Results: The results showed that the genome of Acsw19 was consisted of a 3,433,749 bp circular chromosome and 3 circular plasmids, pAcsw19-1 (11,161 bp), pAcsw19-2 (351,885 bp) and pAcsw19-3 (38,391bp), respectively. Resistome analysis showed that Acsw19 carried 12 antimicrobial resistance genes, including 6 [cmlB1-like, bla _NDM-1, bla _OXA-58, aph (3')-VIa, msr(E) and mph(E)] in the plasmid pAcsw19-2 and 6 (bla _OXA-211-like, bla _NDM-1, aph(3")-Ib, aph(6)-Id, sul2, and floR) in the chromosome genome. Specifically, the cmlB1-like gene shared 86.33%, 71.7% and 71.9% similarities with the cmlB1, cmlA4 and cmlA8 gene, and the bla _OXA-211-like gene shared 94.4%, 95.39% and 96.36% similarities with bla _OXA-211, bla _OXA-643 and bla _OXA-652, at the nucleotide level, respectively. Phylogenetic analysis showed that the bla _OXA-211-like gene and cmlB1-like gene had the closest evolutionary relationship with bla _OXA-643 and cmlB1, respectively. These results indicated that the bla _OXA-211-like and cmlB1-like genes identified in the current study should be the novel variant resistance genes.

Conclusion: Carrying of two copies of bla _NDM-1, cmlB1-like, bla _OXA-211-like and along with other 8 antimicrobial resistance genes, 3 plasmids, 15 genomic islands and 8 prophages Acinetobacter johnsonii strain might increase the possibility of spreading of resistance genes.

Keywords: Acinetobacter johnsonii; blaNDM-1; blaOXA; genomic island.

Grants and funding

This work was supported by the National Natural Science Foundation of China (31500114), and United Funds of Luzhou and Southwest Medical University [2018LZXNYD-ZK51].