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Long-Term Genomic Surveillance Unveils Key Drivers of Salmonella Contamination and Antimicrobial Resistance Dynamics in Surface Waters from Central Mexico

Year: 2026

Type: article

Abstract: We assessed the prevalence, persistence, genetic diversity, and AMR dynamics of Salmonella spp. (SAL) in surface waters (SuWa) of Central Mexico. On-site, 953 samples (10 L each) from 49 watersheds were collected in 24 sampling rounds (2019-2023) using the modified Moore swab technique. SAL was isolated and identified using conventional microbiological procedures and sequenced on Illumina platforms. Overall, the prevalence of SAL was 54%, with higher values (χ2=23.9, P<0.0001) observed in Tlaxcala and the State of Mexico (64%) than in the other regions (42-50%). The top 10 serovars (Agona, Anatum, Newport, London, Adelaide, Derby, Senftenberg, Infantis, Typhimurium, and Muenchen) represented nearly half of the population and were systematically isolated across sampling rounds and years. The most frequent antimicrobial resistance (AMR) phenotypes involved older antibiotics (e.g., tetracycline, streptomycin, and chloramphenicol: 36%, 33%, and 24%, respectively). Approximately 12% of the isolates showed resistance to azithromycin, whereas resistance to cephalosporins, carbapenems, amikacin, and fluoroquinolones was rarely observed (~0-5%). One-third of the isolates exhibited multidrug-resistant (MDR) phenotypes and genotypes. The overall pool of AMR determinants (62 genes and four gene point mutations) encoded 15 different resistance mechanisms at the population level. The prevalence of AMR phenotypes to older antibiotics and the abundance of AMR genes against all antimicrobial classes increased in the post-COVID-19 pandemic period (0.1-0.4 and 0.1-0.6 Log10-fold change, respectively). These results underscore the public health risks associated with agricultural SuWa and the need for further research to identify the sources of SAL contamination.

Source: Water Air & Soil Pollution

DOI: 10.1007/s11270-026-09832-3