Acinetobacter baumannii is known as a clinically significant pathogen that has played a major role in hospital-related deaths. However, due to the clinical relevance of A. baumannii, little emphasis has been placed on 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 to 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. Their genomes were sequenced using Illumina MiSeq, while Oxford Nanopore MinION reads were additionally available for five isolates. The genomes of isolates were assembled using either Shovill or Trycycler based on short and/or long-read data availability. Phylogenetic analysis using Panaroo and IQ-TREE was performed to determine the species of isolates. Comparative sequence analysis of environmental Acinetobacter and clinical A. baumannii were established using bioinformatics tools including BLAST.
The five hybrid assemblies in this study represented completed genomes. All isolates were successfully categorised into Acinetobacter species. Clinically important antimicrobial resistance genes were present, such as those conferring resistance to carbapenem, aminoglycoside and tetracycline were observed in isolates sourced from influent wastewater and pond water. The presence of resistance genes in the secluded pond environment suggested that the natural environment is likely to act as a potential reservoir for naturally occurring, clinically significant genes. The genetic context of antimicrobial resistance genes was investigated, and it was observed that several were located on plasmids within pdif modules. pdif modules were observed to share identity between clinical and environmental Acinetobacter, suggesting genetic exchange events occurred between strains. These findings emphasised the necessity to analyse the occurrence of antimicrobial resistance using a One Health approach, to establish the connections between environmental and the impact it has on humans.