Background: The exposure of environmental bacteria to contaminants in aquatic ecosystems accelerates the dissemination of antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Methods: In this study, we sampled three locations along a contamination gradient of a polluted river, focusing on isolating Enterobacteria from the surface waters to investigate the relationship between urban pollution and antibiotic resistance. The genomes of 15 isolates (5 per site) were sequenced to identify plasmid-borne ARGs and their association with resistance phenotypes. Results: Isolates from the site with the highest contamination (Site 3) showeda larger number of ARGs, plasmids, and resistance phenotypes. Notably, one of the isolates analyzed, E. coli A231-12, exhibited phenotypic resistance to seven antibiotics, presumably conferred by a single plasmid carrying 12 ARGs. Comparative analysis of this plasmid revealed its close evolutionary relationship with another IncH plasmid hosted by Salmonella enterica, underscoring its high ARG burden in the aquatic environment. Other plasmids identified in our isolates carried sul and dfrA genes, conferring resistance to trimethoprim/sulfamethoxazole, a commonly prescribed antibiotic combination in clinical settings. Conclusions: These results highlight the critical need to expand research on the link between pollution and plasmid-mediated antimicrobial resistance in aquatic ecosystems, which can act as reservoirs of ARGs.

Toxin-antitoxin (TA) systems were initially described as “addiction” modules that promote plasmid maintenance through a post-segregational killing (PSK) mechanism. In this process, the cells are forced to retain plasmids to avoid death caused by the longer half-life of the toxin compared to the antitoxin. However, TA systems have since been widely identified across a broad range of mobile genetic elements (MGEs), suggesting that TA systems support the maintenance of these MGEs within bacterial hosts and contribute to the exclusion of competing MGEs such as plasmids and phages. This perspective highlights their broader role beyond plasmid addiction, functioning as key components in safeguarding MGE persistence and enhancing MGE fitness. Therefore, the concept of “plasmid addiction” should be reconsidered as a subset of a more comprehensive phenomenon referred to as “MGE selfishness,” which more accurately captures the widespread distribution and conserved, self-serving functions of TA systems across diverse MGEs. Additionally, TA systems facilitate the establishment of MGEs as “molecular symbionts” within bacterial cells. While initially considered parasitic, the relationships can evolve to provide mutual benefits for both the MGE and the host. From a gene-centered evolutionary perspective, the proposed molecular symbiosis may progress to a point where most of the MGE’s original content is lost, leaving only essential genes that are retained and functionally co-opted by the host. Further studies should investigate the role of TA systems in MGEs beyond plasmids, as well as their evolutionary trajectories toward specialized functions that may influence the adaptation and evolution of key bacterial groups, including pathogens.

Background/Objectives: This study examines how seasonality, pollution, and sample type (water and sediment) influence the presence and distribution of antibiotic resistance genes (ARGs), with a focus on antibiotic resistance genes (ARGs) located on plasmids (the complete set of plasmid-derived sequences, including ARGs) in a tropical urban river. Methods: Samples were collected from three sites along a pollution gradient in the Virilla River, Costa Rica, during three seasonal campaigns (wet 2021, dry 2022, and wet 2022). ARGs in water and sediment were quantified by qPCR, and metagenomic sequencing was applied to analyze chromosomal and plasmid-associated resistance profiles in sediments. Tobit and linear regression models, along with multivariate ordination, were used to assess spatial and seasonal trends. Results: During the wet season of 2021, the abundance of antibiotic resistance genes (ARGs) such as sul-1, intI-1, and tetA in water samples decreased significantly, likely due to dilution, while intI-1 and tetQ increased in sediments, suggesting particle-bound accumulation. In the wet season 2022, intI-1 remained low in water, qnrS increased, and sediments showed significant increases in tetQ, tetA, and qnrS, along with decreases in sul-1 and sul-2. Metagenomic analysis revealed spatial differences in plasmid-associated ARGs, with the highest abundance at the most polluted site (Site 3). Bacterial taxa also showed spatial differences, with greater plasmidome diversity and a higher representation of potential pathogens in the most contaminated site. Conclusions: Seasonality and pollution gradients jointly shape ARG dynamics in this tropical river. Plasmid-mediated resistance responds rapidly to environmental change and is enriched at polluted sites, while sediments serve as long-term reservoirs. These findings support the use of plasmid-based monitoring for antimicrobial resistance surveillance in aquatic systems.

Antimicrobial resistance (AMR) is one of the most critical threats to global public health, and in aquatic ecosystems, coastal environments act as reservoi

GenFlow is a streamlined bioinformatics pipeline that integrates multiple tools, including NCBI Datasets command-line, EDirect, Anvi’o, Prodigal, MAFFT, FastTree, and pyANI, to offer users an easy, one-command solution for performing phylogenomic and ANI analysis. Simply provide your genomes in FASTA format along with a text file listing the accession codes of the reference genomes for the analysis. The program will generate a phylogenomic tree in Newick format using all single-copy core genes shared among the genomes and a heatmap displaying the Average Nucleotide Identity values. All the necessary instructions and data to perform the analysis are available in theGenFlow GitHub repository.

The rapid dissemination of antibiotic resistance genes (ARGs) represents a significant global threat, with wastewater treatment plants (WWTPs) playing an important role as reservoirs and propagation hubs. In this study, we performed whole-genome sequencing and bioinformatic analyses on eight multidrug-resistant Escherichia coli isolates previously obtained from domestic WWTPs in Costa Rica. We identified 61 ARGs (23 unique), with 40 located on plasmids, and 21 on chromosomal sequences, seven of which were within integrons. Several ARGs were associated with resistance to clinically and veterinary important antibiotics, including sulfamethoxazole/trimethoprim, beta-lactams, and tetracyclines. One hundred twenty-one virulence-associated genes (29 unique) were detected, with 16 located on plasmids. Notably, the presence of virulence factors such as ompT and hlyF genes alongside ARGs on plasmids underscores the transmissible pathogenic potential of WWTP-associated E. coli strains. These findings highlight the role of small domestic WWTPs in disseminating pathogenic and multidrug-resistant bacteria and their mobile genetic elements, emphasizing the need for further research to understand how these discharges impact aquatic environments.