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 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 (3ʹ)-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.