Acinetobacter baumannii is an important contributor to the global dissemination of antimicrobial resistance and has been the primary species of focus regarding research conducted on the Acinetobacter genus. It has been identified as a clinically significant pathogen that has played a major role in nosocomial infections and hospital-related deaths. Consequently, the number of studies conducted on clinical A. baumannii greatly overshadows the research conducted on environmental A. baumannii and other Acinetobacter species. Furthermore, elucidating the pathogenic potential of Acinetobacter sourced from natural environments has been neglected. This study aimed to use whole genome sequencing to find genetic links between clinically significant A. baumannii clones and environmental Acinetobacter and determine the role of the environment as a potential reservoir for clinically important antibiotic resistance genes.
Ten Acinetobacter genomes were examined, sourced from influent wastewater and a pond from South Australia. The genomes of all ten isolates were sequenced using Illumina MiSeq, while Oxford Nanopore MinION sequencing data was additionally available for five isolates. The genomes of isolates with short-read data only were assembled using Shovill, while the genomes of isolates with both short and long-read data were assembled using Trycycler to produce hybrid assemblies. Phylogenetic analysis using Panaroo and IQ-TREE was performed to determine the species of isolates. Resistance and virulence genes were located on genomes using the Abricate, Kaptive and BLAST software in conjunction with well curated public databases. Comparative sequence analysis of environmental Acinetobacter and clinical A. baumannii were established using several bioinformatics tools including BLAST. Further, plasmid transfer assays were performed to observe the uptake of clinically relevant plasmids within an environmental isolate.
The five hybrid assemblies in this study represented completed genomes. All but one of the complete assemblies were carriers of resolved plasmid sequences. All isolates were successfully categorised into Acinetobacter species. These species were: A. johnsonii (n = 1), A. towneri (n = 3), A. chinensis (n = 2), A. gerneri (n = 1), A. baumannii (n = 1) and a potentially novel Acinetobacter spp. (n = 2). Notably, isolates were phylogenetically distinct compared to clinical and non-clinical strains from their respective species. Despite genetic diversity, the isolates were observed to harbour plasmids with pdif modules encoding clinically relevant antimicrobial resistance genes; including carbapenamase oxa58, tetracycline resistance gene tet(39), and macrolide resistance genes msr(E)-mph(E). Further, these plasmids shared high sequence identity with plasmids circulating in globally distributed A. baumannii ST1 and ST2 clones. Despite not carrying any of its own native plasmids, the environmental A. baumannii isolate (named here as SAAb472) displayed a capacity to uptake clinically relevant plasmids (pRAY and pACICU2), encoding aminoglycoside resistance genes, with high transfer frequencies. Further, isolate SAAb472 was shown to possess a virulence and capsular polysaccharide profile analogous to that of clinical A. baumannii strains.