Whole-Genome Analysis of Two Copies of bla NDM-1 Gene Carrying Acinetobacter johnsonii Strain Acsw19 Isolated from Sichuan, 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 (3')-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.