Analysis of pCl107 a large plasmid carried by an ST25Acinetobacter baumanniistrain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways

Abstract

Acinetobacter baumannii has successfully spread during the last decades as one of the main critically important pathogens. However, many aspects including plasmids, are still under-investigated. Here, we report the complete sequence of an Acinetobacter baumannii strain, belonging to the ST25IP (Institut Pasteur) sequence type and recovered in 2012 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. This strain (Cl107) carries a 198 kb plasmid called pCl107 that encodes the MPFI conjugative transfer system. The plasmid carries the aacA1, aacC2, sul2, strAB, and tetA(B) antibiotic resistance genes. pCl107 region encompassing the sul2, strAB, tetA(B) is closely related to AbGRI1 chromosomal resistance islands, which are widespread in A. baumannii strains belonging to Global Clone 2. The resistance region found in pCl107 is one of the missing links in the evolutionary history of the AbGRI1 islands. pCl107 also contains a BREX Type 1 region and represents one of the two main evolution patterns observed in BREX clusters found in plasmids related to pCl107. pCl107 also harbours a ptx phosphonate metabolism module, which plays an ancestral structure compared to other large plasmids in ST25 strains. While the uric acid metabolic module found in pCl107 is incomplete, we identified possible ancestors from plasmids and chromosomes of Acinetobacter spp. Our analyses indicate a complex evolutionary history of plasmids related to pCl107 with many links to multiple antibiotic resistance and metabolic pathways.

The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate

“…(GenBank accession number AP024709.1) that belongs to the diverse plasmid family of A. baumannii conjugative plasmids represented by pA297-3 (GenBank accession number KU744946) [23, 40]. BREX determinants were found in another Acinetobacter plasmid type, as recently described [41].…”

Genomic characterization of an NDM-9-producing Acinetobacter baumannii clinical isolate and role of Glu152Lys substitution in the enhanced cefiderocol hydrolysis of NDM-9

“…MLST assigned A. baumannii 13A297 strain to ST Pas 25, and ST Ox 2280, according to the MLST Pasteur and Oxford schemes, respectively. In addition to the globally disseminated multidrug-resistant ST Pas 1 and ST Pas 2, ST Pas 25, which belongs to international clone 7 (IC7), has emerged worldwide as epidemic, endemic or sporadic cases in the last two decades ( Sahl et al, 2015 ; Rodríguez et al, 2018 ; Rafei et al, 2022 ). A hallmark of this clone is its evolution toward multidrug resistance and a high capacity for biofilm formation ( Rafei et al, 2022 ).…”

Examining the role ofAcinetobacter baumanniiPlasmid Types in Disseminating Antimicrobial Resistance

“…These plasmids were carried by strains recovered in clinical, environmental (wastewater) and animal samples in different countries including China, Japan, US, Colombia, and Brazil showing their wide geographical distribution. They were found in various sequence types, of which only one (p1AR_0088; GenBank accession number CP027532.1; Table S2 and Table S5) was in a ST25 strain, which is an important globally distributed ST 3,15,[33][34][35] . Given the potential for accelerated resistance dissemination of resistance to a last-line antimicrobial and hence heightened therapeutic challenges, targeted surveillance of MPFT type plasmids with blaNDM may be warranted.…”

“…A. baumannii has a unique repertoire of plasmids that capture and mobilise a wide range of genetic material involved in pathogenesis and AMR (6,(15)(16)(17)(18). Recently, we developed a plasmid typing scheme based on the sequence of replication initiation genes from 621 complete A. baumannii plasmids called Acinetobacter Plasmid Typing (APT) scheme 13 .…”

“…However, the role of each plasmid type in dissemination of AMR genes remains to be established. To date, several studies have examined the role of A. baumannii plasmids in the spread of AMR genes 9,10,[14][15][16][17] but most of these studies have only reported on individual or a limited number of plasmids and thus, a comprehensive overview of how various plasmid types are involved in the dissemination of AMR genes remains elusive. In this study, we address this gap by examining the distribution of chromosomal sequence types, sampling, geographies, and AMR genes carried on plasmids originally included in the APT database alongside an additional 193 complete plasmids that have since been deposited in GenBank (as of August 18, 2022).…”