Epidemiologia baseada em esgoto como ferramenta de uma só saúde: vigilância do SARS-CoV-2 e da resistência antimicrobiana em Escherichia coli e Klebsiella pneumoniae.

Abstract

Wastewater-Based Epidemiology (WBE) has established itself as a strategic tool for health surveillance, enabling non-invasive pathogen monitoring and community health assessment from a One Health perspective. This thesis aimed to investigate the circulation dynamics of SARS-CoV-2 and characterize the antimicrobial resistance profile of Escherichia coli and Klebsiella pneumoniae in raw sewage in the municipality of Uberlândia-MG, Brazil. The study was divided into two surveillance axes: virological and bacterial. In the first axis, SARS-CoV-2 viral load was quantified by RT-qPCR and variants were genomically identified by sequencing at the four wastewater treatment plants of Uberlândia-MG throughout the pandemic and post-pandemic periods, correlating environmental data with clinical indicators of reported cases and deaths. The results evidenced the effectiveness of WBE as an early warning system, demonstrating concordance between viral load in effluents and the epidemiological waves of COVID- 19. In the second axis, six E. coli and three K. pneumoniae isolates recovered from the Uberabinha wastewater treatment plant were characterized for antimicrobial susceptibility and whole-genome sequence data, including sequence types, resistance genes and mutations, virulence factors and plasmid replicons; the same sewage samples were subjected to targeted enrichment metagenomics, expanding the detection of ESKAPEE taxa (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli) and resistance determinants not recovered by culture. The analyses revealed a high prevalence of multidrug-resistant (MDR) strains, including the detection of critical resistance mechanisms (blaCTX-M, blaKPC-2, blaNDM, blaVIM), evidencing complementarity between culture, genomic sequencing and targeted metagenomics. It is concluded that integrated raw sewage surveillance is essential for public health, providing robust data for managing viral outbreaks and controlling the spread of bacterial resistance from a One Health perspective.