Whole-Genome Analysis of Two Copies of blaNDM-1 Gene Carrying Acinetobacter johnsonii Strain Acsw19 Isolated from Sichuan, China
Received 26 October 2019
Accepted for publication 3 March 2020
Published 23 March 2020 Volume 2020:13 Pages 855—865
Checked for plagiarism Yes
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Peer reviewer comments 2
Editor who approved publication: Dr Joachim Wink
Lingtong Tang, 1, 2 Wei Shen, 2, 3 Zhikun Zhang, 2 Jingping Zhang, 2 Guangxi Wang, 2 Li Xiang, 2 Junping She, 2 Xiaoyan Hu, 2 Guoyuan Zou, 4 Baoli Zhu, 5 Yingshun Zhou 2
1Department of Clinical Laboratory, The People’s Hospital of Gao County, Sichuan 644000, People’s Republic of China; 2Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People’s Republic of China; 3Department of Clinical Laboratory, The First People’s Hospital of Yibin, Yibin 644000, Sichuan, People’s Republic of China; 4Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Science, Beijing, People’s Republic of China; 5Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
Correspondence: Yingshun Zhou
Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, No. 319, Zhongshan Road, Luzhou 646000, Sichuan, People’s Republic of China
Tel +86– 0830– 3160073
Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Science, Beijing, People’s Republic of China
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 blaNDM-1, cmlB1-like gene, and blaOXA-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, blaNDM-1, blaOXA-58, aph ( 3ʹ)-VIa, msr(E) and mph(E)] in the plasmid pAcsw19-2 and 6 (blaOXA-211-like, blaNDM-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 blaOXA-211-like gene shared 94.4%, 95.39% and 96.36% similarities with blaOXA-211, blaOXA-643 and blaOXA-652, at the nucleotide level, respectively. Phylogenetic analysis showed that the blaOXA-211-like gene and cmlB1-like gene had the closest evolutionary relationship with blaOXA-643 and cmlB1, respectively. These results indicated that the blaOXA-211-like and cmlB1-like genes identified in the current study should be the novel variant resistance genes.
Conclusion: Carrying of two copies of blaNDM-1, cmlB1-like, blaOXA-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
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