Genomic surveillance of ESBL-producing Escherichia coli from community wastewater in São Tomé and Príncipe

The emergence and increasing spread of Escherichia coli producing extended-spectrum β -lactamase (ESBL) in water reservoirs poses a significant public health threat, particularly in low-resource settings. In this study 115 ESBL-producing E. coli (ESBL-Ec) were isolated from six community wastewater sites in São Tomé city and analysed by long-read whole genome sequencing and bioinformatic tools. With a median read length of 2 kb and a median coverage of 76x, this approach yielded high-quality genome assemblies and associated plasmids, allowing in-depth analyses of antibiotic resistance genes (ARGs), virulence-associated genes, pathotypes, mobile genetic elements and the phylogenetic relationship of the isolates. 34% (39/115) of the bacterial isolates were known E. coli pathotypes and 22% (25/115) were found to be multidrug-resistant, including the emerging global high-risk clones ST131 and ST1193. The most frequent ARGs identified were bla CTX-M-15 in 80%, gyrA p.S83L in 57%, and sul2 in 54% of the ESBL-Ec isolates. Notably, ten of the 12 ESBL-encoding genes present in our data set were only plasmid-coded, highlighting the presence of highly mobile resistance genes in the aquatic environment. The phylogenetic analysis revealed a high genetic diversity, indicating a vast prevalence of ESBL-Ec from different sources in community wastewater in São Tomé. Our research highlights the importance of a comprehensive monitoring and management approach involving all sectors, the clinical, animal, and environmental sector to limit the spread of antibiotic resistance in areas lacking a formal sewage infrastructure.