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

Abstract

Acinetobacter baumannii is an important opportunistic pathogen known for its high levels of resistance to many antibiotics, particularly those considered last resorts such as colistin and carbapenems. Plasmids of this organism are increasingly associated with the spread of clinically important antibiotic resistance genes. Although A. baumannii is a ubiquitous organism, to date, most of the focus has been on studying strains recovered from clinical samples ignoring those isolated in the environment (soil, water, food, etc.). Here, we analysed the genetic structures of eight novel plasmids carried by an environmental colistin-resistant A. baumannii (strain E-072658) recovered in a recycled fibre pulp in a paper mill in Finland. It was shown that E-072658 carries a new variant of the mcr-4 colistin resistance gene (mcr-4.7) in a novel Tn3-family transposon (called Tn6926) carried by a novel plasmid p8E072658. E-072658 is also resistant to sulphonamide compounds; consistent with this, the sul2 sulphonamide resistance gene was found in a pdif module. E-072658 also carries six additional plasmids with no antibiotic resistance genes, but they contained several pdif modules shared with plasmids carried by clinical strains. Detailed analysis of the genetic structure of all eight plasmids carried by E-072658 showed a complex evolutionary history revealing genetic exchange events within the genus Acinetobacter beyond the clinical or environmental origin of the strains. This work provides evidence that environmental strains might act as a source for some of the clinically significant antibiotic resistance genes.

Examining the role ofAcinetobacter baumanniiPlasmid Types in Disseminating Antimicrobial Resistance

“…These included 4 plasmids with the mcr-4.3 gene carried by strains recovered in clinical samples (two strains isolated in each of China and the Czech Republic) on an R3-T22 plasmid (Table S2). The remaining plasmid, p8E072658, was recently described in an environmental isolate from recycled fibre pulp in a paper mill in Finland 14 . This plasmid carries the novel mcr-4.7 colistin resistance gene in a Tn 3 -family transposon and encodes two novel R3-type Reps (R3-T73 and R3-T74).…”

“…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).…”

“…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 .…”

Mixed Waste Contamination Selects for a Mobile Genetic Element Population Enriched in Multiple Heavy Metal Resistance Genes

“…This is similar to the results of Kirstahler, et al 19 who found that 53% of the circular DNA elements in their global sewage mobilome did not carry any identifiable MGE-related Pfam domains. However, several studies have identified small cryptic plasmids in bacterial isolates that contain no recognizable replication machinery [89][90][91][92] . It has been speculated that cryptic plasmids may play roles in viral defense 93 or functionally serving as empty backbones acquisition of novel genes 94 Additionally, some of these cryptic elements may represent currently undescribed classes of MGEs.…”