The role of the accessory genome in nosocomial and extranocosomial isolates of Acinetobacter baumannii
thesisposted on 2022-03-28, 10:46 authored by Daniel J. Farrugia
Acinetobacter baumannii is an opportunistic nosocomial pathogen that is frequently able to resist antimicrobial treatment and persist in the clinical milieu. This organism is also able to cause infection outside the hospital environment as the clinically and epidemiologically distinct community-acquired A. baumannii (CA-AB). CA-AB forms part of a larger collective of extranosocomial A. baumannii (XN-AB) originating outside the clinical milieu, including A. baumannii isolated from industrial and environmental sites. Whole genome sequencing has provided useful insight into the clonal population structure, the influence of lateral gene transfer, and the virulence and drug resistance capabilities of nosocomial A. baumannii. Prior to the commencement of this project, complete genomes of several nosocomial isolates were available, whilst genomic data regarding XN-AB isolates was limited to only that of a louse isolate, A. baumannii SDF. In this work, the first complete genome sequence of a community-acquired A. baumannii (CA-AB) isolate, A. Baumannii D1279779, was determined. In addition to the genomic sequence, the phenotypic profile of this organism, and several nosocomial isolates, were assayed, using phenotype microarrays. Comparative genomics and phenomics confirmed the distinctive nature of CA-AB, revealing D1279779 to be both metabolically diverse and antimicrobial susceptible compared to nosocomial A. baumannii. Additionally, the genome of A. baumannii D1279779 encoded several novel gene clusters, presumably acquired through lateral gene transfer. One putative laterally acquired gene cluster, identified during the D1279779 studyabove, became the focus for a second project. This genomic region encoded a putative integrase gene that was adjacent to the 5' end of the tRNA-dihydrouridine synthase (dusA) gene in several A. baumannii and Pseudomonas spp. genomes sequenced by our research group. Homologues of the gene encoding this integrase were discovered in the genomes of over two hundred Proteobacterial organisms, and was established to be a component of a novel family of genomic islands in these organisms. These genomic islands were found to be highly variable in both size and gene composition, and capable of chromosomal excision as a circularised intermediate. On that basis, this family of genomic islands was dubbed the dusA specific Mobile Genetic Elements (DAMGEs). The genomes of various other A. baumannii isolates were sequenced, amongst these an Australian multidrug resistant outbreak isolate, A. baumannii WM99c. The genome of this isolate was found to encode several putatively laterally transferred regions, including the AbaR and AbGRI2 genomic islands, which encoded resistance to various antimicrobials such as tetracyclines and aminoglycosides. Another putative genomic island, known as G41, encoded a single aminoglycoside resistance gene and several other genes putatively involved in fatty acid metabolism. This island was discovered to be exclusive to complete genomes of international clone II lineage A. baumannii, a phylogenetic grouping of A. baumannii often associated with multidrug resistant nosocomial infection. The genome sequences of several other nosocomial and community-acquired A. baumannii isolates, originating from the Asia-Pacific region, were bioinformatically analysed as part of a collaborative project. Previously conducted phenotypic testing of these isolates had revealed that the CA-AB generally outperformed the nosocomial A. baumannii isolates with respect to virulence, including biofilm formation, phospholipase D production, murine mortality, and in vitro growth in LB, sera and 1% ethanol. Bioinformatic analysis of the CA-AB genomes revealed that many genes known to be involved in virulence in nosocomial A. baumannii were present, but there were few (if any) novel virulence traits that could conclusively account for the observed differences in virulence for nosocomial and CA-AB isolates. The comparative genomic analyses of nosocomial and CA-AB had somewhat demarcated the clinical idiosyncrasies of the latter, including its antimicrobial susceptibility. Data resultant from the analysis of the various CA-AB genomes sequences, including that of D1279779, had suggested that the current focus on nosocomial A. baumannii genomics did not reflect the true diversity of this species. To that end, the genomes of several XN-AB isolates originating from industrial and environmental sites were sequenced for the purpose of comparison to previously sequenced nosocomial A. baumannii strains. It was discovered that the genomes of XN-AB isolates were generally smaller than those of nosocomial isolates, presumably owing to the lack of laterally acquired regions, such as prophages and the AbaR antimicrobial resistance island, and extensive insertion sequence-mediated genome decay in the case of one isolate. While accessory elements present in the genomes of nosocomial A. baumannii tended to confer resistance to antimicrobials, those present in the genomes of XN-AB isolates were devoted to the metabolism of varying compounds, including sarcosine and monocyclic aromatic compounds. Overall, the genomic analyses conducted during this PhD project indicate that A. baumannii isolates share a common gene pool quintessential to this organism, regardless of their nosocomial, community or environmental origin. This core gene set includes various genes that were hitherto associated with virulence and intrinsic antimicrobial resistance in nosocomial A. baumannii. These analyses have also identified an expanding pool of accessory genetic material, and lateral gene transfer has likely been a significant factor in the acquisition of these accessory genes. The differences in the accessory genome is likely a key factor in the differentiation between nosocomial and extranosocomial isolates of A. baumannii. The accessory genome of nosocomial A. baumannii is biased towards antimicrobial resistance, which would presumably facilitate its survival in both the human host and within the clinical milieu. Conversely, the accessory genome of XN-AB is geared towards utilisation of novel carbonaceous and nitrogenous compounds, which would presumably allow these isolates to thrive in their respective natural and industrial environments.