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

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 (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.

Salmonella Typhimurium with Eight Tandem Copies of blaNDM-1 on a HI2 Plasmid

“…Our study also identified the existence of tandem copies of the bla NDM-1 gene in the pST_HI2_NDM-1. To our knowledge, the structure of the IS CR1 unit (IS CR1 - dsbD - trpF - ble - bla NDM-1 -IS Aba125 Δ1) with the tandem copies in this study is different from that previously reported [ 38 , 39 ]. Two tandem copies of the IS CR1 unit ( sul1 - arr - 3 - cat - bla NDM-1 - ble -IS CR1 ) were reported in the E. coli Y5 chromosome (CP013483) in 2016 [ 18 ].…”

Phylogeographical Analyses and Antibiotic Resistance Genes of Acinetobacter johnsonii Highlight Its Clinical Relevance

“…In addition to some clinical isolates, two sewage strains (Acsw19 and WCHAJo010049) and a strain collected from pig feces (18QD2AZ57W) had the largest amount of ARGs. In this regard, Tang et al determined that strain Acsw19 has 12 ARGs in plasmids and in the chromosome (10). Considering the OXA ␤-lactamases, we found several families: OXA-211-like, OXA-58-like, and OXA-23-like.…”

Genomic insights into the adaptation of Acinetobacter johnsonii RB2-047 to the heavy metal-contaminated subsurface mine environment

“…The members of the Acinetobacter genus frequently possess multiple plasmids which are the key players in the adaptability of Acinetobacter spp. to various living conditions in the environment and in the clinical setting (Zong and Zhang 2013 ; Tang et al 2020 ; Maslova et al 2022 ). In our study, plasmid-related contigs represented just a minor fraction of the RB2-047 genome (less than 2.5%) as identified by mlplasmid server v2.1.0.…”