Genomic and biocomputational analysis of genomic resistance island 3 in Acinetobacter baumannii

• Main Author: Loo, Samuel Shi Hao
• Other Authors: Kevin Pethe
• Format: Final Year Project
• Language: English
• Published: Nanyang Technological University 2020
• Subjects: Science::Biological sciences::Microbiology
• Online Access: https://hdl.handle.net/10356/140966
• Institution: Nanyang Technological University

Acinetobacter baumannii is an opportunistic nosocomial pathogen rapidly developing resistance to most clinically used antibiotics, partly attributed to novel genetic elements such as genomic resistance islands (GRIs), which comprise a cluster of diverse antimicrobial resistance genes (ARGs). The recently characterised GRI3, which comprise an armA-carrying transposon, has not been extensively studied collectively in A. baumannii. Thus, this in silico study aims to investigate the prevalence, variants and transmission of GRI3 in all publicly available A. baumannii isolates. Database-wide analysis revealed increased armA prevalence in A. baumannii in recent years and its co-existence with the core GRI3 ARGs msr(E) and mph(E), suggesting dissemination of armA largely occurred concurrently with GRI3. In addition, armA was positively associated with 2 ARGs, blaTEM-1 and blaOXA-23, suggesting the presence of selective pressure. Also, 3 novel GRI3 variant types were identified with either loss of, or additional ARGs, highlighting GRI3 plasticity and continual evolution. Finally, we hypothesised the possibility of intraspecies transmission of GRI3 from international clone 2 (IC2) to non-IC2 isolates based on phylogeny and genomic localisation. Taken together, this study highlights the availability of rich data from publicly accessible databases and the potential of genomic epidemiology in facilitating genomic surveillance and analysing transmission dynamics.