Genomic and microbiology surveillance of pathogens of importance to public and animal health: Escherichia coli and Staphylococcus aureus

Abstract

Genomic surveillance of clinically and zoonotically relevant bacterial pathogens is essential for elucidating the dynamics of antimicrobial resistance dissemination, the variability of virulence factors, and the evolutionary patterns that occur across different production systems and host populations. Escherichia coli and Staphylococcus aureus are among the most important agents in this context, both for their direct impact on animal health and the economic losses associated with diseases such as bovine mastitis, and for their potential for transmission to humans, reinforcing the One Health perspective. Although phenotypic methods remain essential in routine diagnostics, genomic approaches enable a more precise characterization of the repertoire of resistance genes, clonal structure, and phylogenetic relationships, enhancing the capacity for monitoring and responding to emerging threats. This work integrates phenotypic and genomic data from E. coli and S. aureus isolated from different hosts to evaluate antimicrobial resistance profiles, virulence diversity, and the phylogenetic structure of bacterial populations relevant to public and animal health. Standardized methodologies for antimicrobial susceptibility testing, including MIC determination and disk diffusion, were applied alongside next-generation sequencing for genome assembly and annotation. Analyses included identification of resistance and virulence genes, detection of mobile genetic elements, multilocus sequence typing (MLST), and ParSNP-based phylogenomics, enabling an integrated assessment of genetic diversity. The results revealed broad phenotypic and genotypic heterogeneity among isolates, with multiple antimicrobial resistance patterns and an extensive repertoire of resistance and virulence genes. Mobile elements and distinct clonal complexes were identified, highlighting the genomic plasticity of these pathogens. Comparison among hosts demonstrated circulation of lineages with zoonotic potential and marked structural diversity within bacterial populations. Together, these findings reinforce the importance of continuous and integrated genomic surveillance strategies to monitor the emergence and dissemination of resistance and clonal variants in contexts critical to public and animal health.