A case study on pharmaceutical residues and antimicrobial resistance genes in Costa Rican rivers: A possible route of contamination for feline and other species

Antimicrobial-resistant genes in feces from otters (Lontra longicaudis) within the Peñas Blancas river basin, Costa Rica

Antimicrobial resistance poses a growing threat to human health, yet its implications for wildlife remain a subject of ongoing research. River otters inhabiting the Peñas Blancas River face exposure to various anthropogenic activities in their habitat, potentially leading to the accumulation of antibiotic-resistant genes (ARGs) with unknown consequences for their health. This study aimed to identify specific ARGs in otter feces from this river basin, employing quantitative polymerase chain reaction (qPCR), DNA sequencing of ARGs, and phylogenetic analysis techniques. Over the period from 2019 to 2022, we collected 102 fecal samples from otters through the Peñas Blancas River watershed, spanning its upper and middle basins. We assessed the bacterial presence via the 16S rRNA gene through qPCR analysis and screened for 12 ARGs. Sequences of 16 ARG-positive samples were subsequently analyzed using Maximum-likelihood-base taxonomic placement. In total, 56 samples tested positive for the 16S rRNA gene, with 24 exhibiting at least one ARG. Notably, three samples showcased a "multi-resistance microbiome". qPCR analyses identified seven distinct ARGs: tetB (in 26.8 % of the samples), sulI (21.4 %), sulII (21.4 %), qnrS (10.7 %), tetQ (8.9 %), tetW (7.1 %), and tetA (3.6 %). Phylogenetic analysis confirmed the taxonomic association of all detected ARGs, which were compared with The Comprehensive Antibiotic Resistance Database. Our findings underscore the importance of comprehending the spread of ARGs in wildlife populations, with river otters serving as potential sentinels for ARG dissemination. Moreover, they highlight the potential impact of anthropogenic activities on the health of aquatic ecosystems, emphasizing the need for proactive measures to mitigate antimicrobial resistance in natural environments.

The source and dissemination of ARGs in pristine environments: Elucidating the role of migratory birds in the Arctic

Antibiotic resistance genes (ARGs) are a class of emerging contaminants that significantly threaten public health. In this work, the profiles of ARGs and microbial communities in the soil, sediment, migratory bird, and local deer fecal samples collected from the Arctic were characterized using a metagenomic approach. The results retrieved the baseline profiles of ARGs and identified the role of migratory birds in disseminating ARGs in the Arctic. A total of 26 ARG types and 718 subtypes were determined, and 131 core ARGs were identified. All the samples were dominated by multidrug resistance genes, and some genes resistant to antibiotics commonly used in anthropogenic were also detected. Characterization of ARGs in bird fecal samples was significantly distinct from other media, with higher abundance, richness, and unique ARGs detected. Proteobacteria was the most predominant phylum in soil and fecal samples, while Thaumarchaeota was prevalent in sediment samples. Firmicutes harbored the majority of ARGs in all samples. The results of FEAST indicated that migratory birds were crucial allochthonous ARG sources in the Arctic. These significant findings shed light on the global spread of ARGs and should facilitate efforts to map baseline levels of ARGs before the era of antibiotics.

Occurrence and distribution of antibiotic resistance genes in urban rivers with black-odor water of Harbin, China

Antibiotic resistance gene contamination in polluted rivers remains a widely acknowledged environmental issue. This study focused on investigating the contamination conditions of antibiotic resistance genes (ARGs) in Harbin's urban black-odor rivers, specifically Dongfeng Ditch and Hejia Ditch. The research employed a SmartChip Real-Time PCR System to explore the types, abundance, and distribution of ARGs in diverse habitats, such as surface water and sediment. Additionally, the study examined the correlation of ARGs with mobile genetic elements (MGEs) and various environmental factors. It was found that antibiotic resistance genes were prevalent in both water and sediment within the black-odor ditches. The dominant types of ARGs identified included aminoglycoside, sulfonamide, multidrug-resistant, and β-lactam ARGs. Notably, the top four ARGs, in terms of relative abundance, were sul1, fox5, qacEdelta1-01 and aadA1. Most categories of ARGs have significant positive connections with MGEs, indicating that the enrichment and spreading of ARGs in rivers are closely related to MGEs. Based on the correlation analysis, it is found that environmental factors such as dissolved oxygen (DO), ammonia nitrogen (NH4-N), and phosphate (PO4-P) played a substantial role in influencing the variations observed in ARGs. By employing a risk assessment framework based on the human association, host pathogenicity, and mobility of ARGs, the identification of seven high-risk ARGs was achieved. In addition, it is important to assess the environmental risk of ARGs from multiple perspectives (abundance,detection rateand mobility). This study provides a significant reference regarding the presence of ARGs contamination in urban inland black-odor rivers, essential for assessing the health risks associated with ARGs and devising strategies to mitigate the threat of antibiotic resistance.

A multidisciplinary approach to analyze the antimicrobial resistance in natural ecosystems

Antimicrobial Resistance (AMR) poses a global threat to both human health and environmental well-being. Our study delved into Costa Rican wildlife reserves, uncovering a substantial human impact on these ecosystems and underscoring the imperative to pinpoint AMR hotspots. Embracing a One Health perspective, we advocated for a comprehensive landscape analysis that intricately intertwined geographic, climatic, forest, and human factors. This study illuminated the link between laboratory results and observed patterns of antimicrobial use, thereby paving the way for sustainable solutions. Our innovative methodology involved deploying open-ended questions to explore antimicrobial usage across livestock activities, contributing to establishing a comprehensive methodology. Non-invasive sampling in wildlife emerged as a critical aspect, shedding light on areas contaminated by AMR. Feline species, positioned at the apex of the food chain, acted as sentinels for environmental health due to heightened exposure to improperly disposed waste. Regarding laboratory findings, each sample revealed the presence of at least one antimicrobial resistance gene (ARG). Notably, genes encoding resistance to tetracyclines dominated (94.9%), followed by beta-lactams (75.6%), sulfonamides (53.8%), aminoglycosides (51.3%), quinolones (44.9%), phenicols (25.6%), and macrolides (20.5%). Genes encoding polymyxins were not detected. Moreover, 66% of samples carried a multi-resistant microbiome, with 15% exhibiting resistance to three antimicrobial families and 51% to four. The absence of a correlation between forest coverage and ARG presence underscored the profound human impact on wildlife reserves, surpassing previous estimations. This environmental pressure could potentially modify microbiomes and resistomes in unknown ways. As not all antimicrobial families encoding ARGs were utilized by farmers, our next step involved evaluating other human activities to identify the primary sources of contamination. This comprehensive study contributed crucial insights into the intricate dynamics of AMR in natural ecosystems, paving the way for targeted interventions and sustainable coexistence.