Title : Genomic characterisation of acinetobacter baumannii associated with neonatal sepsis and stillbirths in a south african population
BACKGROUND: The proposed study will characterise the genomes of multi-drug resistant hospital-acquired invasive Acinetobacter baumannii (A. baumannii) which overwhelmingly contributes to neonatal deaths, particularly in low-middle income countries (LMICs) where the burden of sepsis in neonates is higher. The study will contribute genomic data and analysis of A. baumannii using whole-genome sequencing (WGS) to allocate the isolates into different clonal lineages and investigate the evolutionary pathways resulting in neonatal sepsis.
METHODS: The study will use whole-genome sequencing to genetically characterize A. baumannii neonatal sepsis isolates that have been collected as part of the CHAMPS platform, MITS-lite study, and the GBS/Kpn Cohort studies at Baragwanath and related hospitals that are underway at the Wits-VIDA unit. All isolates have been sub-cultured on selective CHROMagar plates and their identifies confirmed using Analytica profile index kit. Genomic DNA extraction was done using NucliSENS easyMAG platform following manufacturers guidelines and integrity of DNA was assessed using TapeStation. Sequencing will be undertaken by our long-standing collaborators at the National Institute For Communicable Diseases Of South Africa (CHAMPS and MITS-lite) and Pfizer (GBS-Cohort).
RESULTS: Antimicrobial resistance phenotypes show that most isolates are sensitive to ceftazidime and colistin. Through WGS will enable us to understand the link between A. baumannii phylogenic and extra-intestinal virulence. Also, provide an improved understanding of the causative invasive strains which is imperative in developing and implementing effective prevention strategies.
CONCLUSION: Genome characterisation studies of A. baumannii isolates could help define the pathogen's global population structure, its antibiotic resistance gene repertoire, the size and content of its pan-genome, and phylogenetic relationships among outbreak strains.
Audience Take Away:
The aim is to address the issue of antimicrobial resistance by showing the epidemiological data to investigate the pathogenicity of A. baumannii associated with neonatal invasive disease and stillbirths in the South African population. o The study addresses what most studies in LMICs do not incorporate by combining phenotypic and genotypic typing of A. baumannii isolates, thus, making it easy to determine the extent of genomic diversity (which would usually be done by comparing the lineages across geographical areas) and resistance of the pathogen. o The presentation will also aim to present the problems of different study designs in addressing the clinical problem of genetic diversity, resistome, virulomes, and circulating mobile genetic element to analyse the diversity of sequencing types (and their antimicrobial resistance patterns) in neonates with invasive A. baumannii.