Transmission Networks of Extended-spectrum beta-lactamase producing-Enterobacteriaceae in communities and hospitals in rural sub-Sahara Africa
Final Report Abstract
The project aims to perform WGS on a bacterial isolate collection of ESBL-producing E. coli and K. pneumoniae to holistically examine transmission networks between the human and animal reservoirs in the community and a hospital population, as well as within the hospital population. The short-read sequencing has been successfully completed. All sequence data have been obtained at the time of report writing. The still in progress but advanced bioinformatic analysis has yielded 123 clusters of clonal transmission of E. coli. Clusters were identified based on SNP differences between isolates from patients, community members and isolates obtained from animals (goats, sheep). Transmission in hospital, between hospitals and the community, and also between animal and human hosts were identified. Reconstruction of plasmid of bacterial isolates demonstrates carriage of as many as 11 plasmids per solate. Moreover ESBL resistance genes could be located on the genomes and plasmids with the majority found on the latter ones. Detailed ESBL analysis yield carriage of more than 1 ESBL gene per isolate up to 7 resistance genes found in 3 isolates. The ongoing analysis to identify the main transmission routes by comparing temporal and spatial similarities between patients carrying clonal strains will enable the public health authorities in rural Ghana to target specific transmission sources of ESBL-producing bacteria and to implement appropriate surveillance activities. The bioinformatic project has still been severely affected by the COVID-19 pandemic. Laboratory closures, prioritization of virology diagnostics and home office regulations prolonged all project activities.
