Escherichia coli Genome sequencing

This multicentre study, conducted in Brazil, Cameroon and Madagascar, aims to assess the impact of the COVID-19 pandemic on the spread of antimicrobial and biocide resistance in the environment, particularly in wastewater from health facilities receiving COVID-19 patients, municipal wastewater and slums. Whole genome culture and sequencing will allow the assessment of bacteria (diversity and relative abundance) and antimicrobial/biocide resistance genes respectively. Phylogenetic relationships between the isolated strains will be investigated using MLST and single nucleotide polymorphisms. This study will provide timely information on the potential risk of AMR spread in the downstream ecology during the Covid-19 pandemic and its consequences on public health.