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

Figure 1

Molecular phylogenetic analysis by maximum likelihood method with 1000 bootstraps of OXA-211 like (a novel variant of OXA-211 family) with the six Class D β-lactamases (CHDLs) OXA family (OXA-23, OXA-24/40, OXA-235/134, OXA-58, OXA-48, OXA-211) representative sequences retrieved from GenBank database. The black triangle was indicated the gene which was found in this study.

Figure 2

Molecular phylogenetic analysis by maximum likelihood method with 1000 bootstraps of CmlA/FloR family chloramphenicol efflux MFS (cmlB1-like) with the eight CmlA/FloR family chloramphenicol efflux MFS representative sequences retrieved from GenBank database. The black triangle was indicated the gene which was found in this study.

Figure 3

Schematic map of the genetic context of resistance gene regions in pAcSW19-2. The resistance genes are indicated by red arrows, the mobile genes are indicated by the green arrows and other function genes are indicated by the purple arrows. Gray areas between open reading frames (ORFs) denote nucleotide identities with the similarity context.

Figure 4

Schematic map of the genetic context of the GI_Acsw19-11. The resistance genes are indicated by red arrows, the mobile genes are indicated by the green arrows and other function genes are indicated by the purple arrows. Gray areas between open reading frames (ORFs) denote nucleotide identities with the similarity context.

Figure 5

Schematic map of the genetic context of the GI_Acsw19-2. The resistance genes are indicated by red arrows, the mobile genes are indicated by the green arrows and other function genes are indicated by the purple arrows. Gray areas between open reading frames (ORFs) denote nucleotide identities with the similarity context.