Genetic identity card of drug-resistant bacteria (WP3)
Leaders: Dr. Sokleaph Cheng, IPC and Dr. Mallorie Hidé, IRD-IPC, Phnom Penh, Cambodia
Resistance transmission pathways between humans, environment and animals are complex and the results of studies comparing antibiotic resistant bacteria within humans, environment and animals are contradictory. The introduction of New Generation Sequencing (NGS) methods, i.e. Whole Genome Sequencing (WGS) and metagenomics, has provided a more accurate analysis of the circulation of ABR. Several studies using NGS carried out in LMICs supported epidemiological links between humans, animals and their environment, such as between poultry and humans in India (Hussain et al., 2017) or between humans and caecal contents, carcass swabs and water taken in abattoirs in Ethiopia (Dulo et al., 2015).
Nevertheless, despite numerous studies on molecular characteristics, the epidemiology of drug resistant bacteria and particularly the circulation of antibiotic resistant genes (ARGs) between humans and animals and their environment is not fully understood especially in LMICs. The use of these tools will allow us to explore the epidemiological link between the drug resistant bacteria isolated from the patients and the resistant bacteria population circulating in their own environment in Battambang province.
Overarching objective: To get the genetic identity card of the antibiotic resistant strains isolated from patients of the two hospitals in the WP1 and from patients’ environment (animals, water, soil and food) in the WP2 and to get genetic information on the bacterial population diversity and ARGs circulating in the patient’s environment.
Specific objectives: To compare by comparative genomic analysis the WGS data acquired from drug resistant bacteria isolated in the two hospitals on one hand and the WGS data of drug resistant bacteria from patients of Battambang central hospital with the data obtained from the drug resistant bacteria isolated from their own environment on the other hand. To use metagenomics to acquire information on the diversity of bacterial population and ARGs circulating in the patients’ environment.