ArticleScientific reports2025
Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics.
Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Intra-amniotic infection: diagnosis, nomenclature, clinical significance, management, and microbiologic tools used for the diagnosis.Clinical microbiology reviews · 2026Review
- Soil to host environmental determinants fueling horizontal gene transfer and global AMR dissemination.Folia microbiologica · 2026Review
- Review
- Big data and artificial intelligence in animal nutrition: a new era of precision feeding.Tropical animal health and production · 2026Review
- Dietary supplementation with allicin enhances growth performance and antioxidant capacity, and reduces gut pathogens and antibiotic resistance genes in Trachidermus fasciatus.Fish physiology and biochemistry · 2026Article
- Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection.npj antimicrobials and resistance · 2026Review
- Antibiotic Resistance Profiles of Commensal and Pathogenic Bacteria Isolated from Wild Boar Carcasses in Campania Region, Southern Italy.Antibiotics (Basel, Switzerland) · 2026Article
- The role of the gut microbiome in antibiotic-driven antimicrobial resistance.Frontiers in microbiology · 2026Review
- Current advances and challenges in microbiome-based mitigation of volatile organic compounds from livestock waste systems.Frontiers in cellular and infection microbiology · 2026Review
- Editorial: Integrative microbial and chemical genomics to decipher antibiotic resistance mechanisms and developing innovative antimicrobial approaches.Frontiers in microbiology · 2026Article
- Development and application of a triplex ddPCR method for simultaneous detection of MLSB resistance genes in feces and environmental samples.Frontiers in microbiology · 2026Article
- Probiotic-based therapeutics for a One Health future: redefining antibiotic dependency to combat antimicrobial resistance.Frontiers in microbiology · 2026Article
- Diverse enteric bacterial, viral, and parasitic pathogen genes are shed in animal feces in Indiana.PloS one · 2026Article
- The resistome bridge between livestock and workers: novel frameworks for early detection and monitoring of antimicrobial resistance.Frontiers in public health · 2026Review
- Organosulfur compounds as dual-action agents: a critical review of antimicrobial and immunomodulatory potentials, and translational barriers.Frontiers in pharmacology · 2026Review
- One health analysis of antimicrobial resistance inBioinformatics advances · 2026Article
- Characterization and pathogenic mechanisms of aFrontiers in microbiology · 2026Article
- Prevalence of Methicillin-ResistantAntibiotics (Basel, Switzerland) · 2025Article
- Tetracyclines in the Modern Era: Global Consumption, Antimicrobial Resistance, Environmental Occurrence, and Degradation Techniques.Antibiotics (Basel, Switzerland) · 2025Review
- Use of Two PGPB Strains for the Valorization of Wastewater Sludge and Formulation of a Biofertilizer for the Recovery ofLife (Basel, Switzerland) · 2025Article
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.
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