{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T21:38:02Z","timestamp":1773265082825,"version":"3.50.1"},"reference-count":55,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T00:00:00Z","timestamp":1773014400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"RumiRes project\u2014\u201cVigil\u00e2ncia epidemiol\u00f3gica de resist\u00eancias antimicrobianas e res\u00edduos medicamentosos em Pequenos ruminantes da Regi\u00e3o Centro\u201d","award":["PRR-C05-i03-I-000190"],"award-info":[{"award-number":["PRR-C05-i03-I-000190"]}]},{"name":"Science and Technology Foundation","award":["GHTM-UID\/04413\/2020 e LA-REAL\u2014LA\/P\/0117\/2020"],"award-info":[{"award-number":["GHTM-UID\/04413\/2020 e LA-REAL\u2014LA\/P\/0117\/2020"]}]},{"name":"Science and Technology Foundation","award":["CERNAS UIDB\/00681\/2020"],"award-info":[{"award-number":["CERNAS UIDB\/00681\/2020"]}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ciencia e a Tecnologia","doi-asserted-by":"crossref","award":["2025.05151.BD"],"award-info":[{"award-number":["2025.05151.BD"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ciencia e a Tecnologia","doi-asserted-by":"crossref","award":["2025.04664.BD"],"award-info":[{"award-number":["2025.04664.BD"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored. Methods: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal. Results: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin. Conclusions: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies.<\/jats:p>","DOI":"10.3390\/antibiotics15030277","type":"journal-article","created":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T10:16:12Z","timestamp":1773051372000},"page":"277","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8374-3739","authenticated-orcid":false,"given":"Sara","family":"Gomes-Gon\u00e7alves","sequence":"first","affiliation":[{"name":"School of Medicine and Biomedical Sciences (ICBAS), Universidade do Porto (UP), 4050-313 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-1324-8902","authenticated-orcid":false,"given":"Jaqueline T.","family":"Bento","sequence":"additional","affiliation":[{"name":"School of Medicine and Biomedical Sciences (ICBAS), Universidade do Porto (UP), 4050-313 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2828-7202","authenticated-orcid":false,"given":"Guilherme","family":"Moreira","sequence":"additional","affiliation":[{"name":"School of Medicine and Biomedical Sciences (ICBAS), Universidade do Porto (UP), 4050-313 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1296-5964","authenticated-orcid":false,"given":"Joana","family":"Mour\u00e3o","sequence":"additional","affiliation":[{"name":"National Food Institute, Technical University of Denmark, Kongens Lyngby, 2800 Copenhagen, Denmark"}]},{"given":"Rita","family":"Cruz","sequence":"additional","affiliation":[{"name":"Instituto Polit\u00e9cnico de Viseu, Escola Superior Agr\u00e1ria de Viseu, Campus Polit\u00e9cnico, 3504-510 Viseu, Portugal"},{"name":"Epidemiology Research Unit (EPIUnit), Instituto de Sa\u00fade P\u00fablica da Universidade do Porto, 4050-091 Porto, Portugal"},{"name":"Laborat\u00f3rio para a Investiga\u00e7\u00e3o Integrativa e Translacional em Sa\u00fade Populacional (ITR), 4050-600 Porto, Portugal"}]},{"given":"Fernando","family":"Esteves","sequence":"additional","affiliation":[{"name":"Instituto Polit\u00e9cnico de Viseu, Escola Superior Agr\u00e1ria de Viseu, Campus Polit\u00e9cnico, 3504-510 Viseu, Portugal"},{"name":"CERNAS-IPV Research Centre, Instituto Polit\u00e9cnico de Viseu, Campus Polit\u00e9cnico, Repeses, 3504-510 Viseu, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-8137-1139","authenticated-orcid":false,"given":"Alexandra Lameira","family":"Baptista","sequence":"additional","affiliation":[{"name":"Instituto Polit\u00e9cnico de Viseu, Escola Superior Agr\u00e1ria de Viseu, Campus Polit\u00e9cnico, 3504-510 Viseu, Portugal"},{"name":"CERNAS-IPV Research Centre, Instituto Polit\u00e9cnico de Viseu, Campus Polit\u00e9cnico, Repeses, 3504-510 Viseu, Portugal"},{"name":"Universidade de Tr\u00e1s-os-Montes e Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4054-9124","authenticated-orcid":false,"given":"Maria Aires","family":"Pereira","sequence":"additional","affiliation":[{"name":"Instituto Polit\u00e9cnico de Viseu, Escola Superior Agr\u00e1ria de Viseu, Campus Polit\u00e9cnico, 3504-510 Viseu, Portugal"},{"name":"CERNAS-IPV Research Centre, Instituto Polit\u00e9cnico de Viseu, Campus Polit\u00e9cnico, Repeses, 3504-510 Viseu, Portugal"},{"name":"Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisboa, Portugal"}]},{"given":"Pedro","family":"Caseiro","sequence":"additional","affiliation":[{"name":"Diogo Themudo-Sociedade Unipessoal Lda, Lugar Fontanheiras, 3520-112 Nelas, Portugal"}]},{"given":"Pedro","family":"Carreira","sequence":"additional","affiliation":[{"name":"Arricom, Cl\u00ednica Veterin\u00e1ria, Lda. Avenida General Humberto Delgado, Lote 4, P\u00e1 Ribeira, R\/Ch\u00e3o, 2040-328 Rio Maior, Portugal"}]},{"given":"Lu\u00eds","family":"Figueira","sequence":"additional","affiliation":[{"name":"Instituto Polit\u00e9cnico de Castelo Branco (IPCB), Av. Pedro \u00c1lvares Cabral 12, 6000-084 Castelo Branco, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8769-8103","authenticated-orcid":false,"given":"Jo\u00e3o R.","family":"Mesquita","sequence":"additional","affiliation":[{"name":"School of Medicine and Biomedical Sciences (ICBAS), Universidade do Porto (UP), 4050-313 Porto, Portugal"},{"name":"LAQV, REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences and Technology, University NOVA de Lisboa, 2829-516 Caparica, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,9]]},"reference":[{"key":"ref_1","unstructured":"WHO Regional Office for Europe and European Centre for Disease Prevention and Control (2025, July 11). Surveillance of Antimicrobial Resistance in Europe, 2022 Data: Executive Summary. Available online: https:\/\/www.who.int\/europe\/publications\/i\/item\/9789289060387."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Silva, V., Monteiro, A., Pereira, J.E., Maltez, L., Igrejas, G., and Poeta, P. (2022). MRSA in Humans, Pets and Livestock in Portugal: Where We Came from and Where We Are Going. Pathogens, 11.","DOI":"10.3390\/pathogens11101110"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"100249","DOI":"10.1016\/j.modpat.2023.100249","article-title":"Emerging Antimicrobial Resistance","volume":"36","author":"Flynn","year":"2023","journal-title":"Mod. Pathol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"EClinicalMedicine (2021). Antimicrobial Resistance: A Top Ten Global Public Health Threat. eClinicalMedicine, 41, 101221.","DOI":"10.1016\/j.eclinm.2021.101221"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2857","DOI":"10.1080\/10408398.2015.1077192","article-title":"Antimicrobial Resistance: A Global Emerging Threat to Public Health Systems","volume":"57","author":"Ferri","year":"2017","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"121584","DOI":"10.1016\/j.watres.2024.121584","article-title":"Dissemination of Antibiotic Resistance Genes from Aboveground Sources to Groundwater in Livestock Farms","volume":"256","author":"Lei","year":"2024","journal-title":"Water Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"100324","DOI":"10.1016\/j.onehlt.2021.100324","article-title":"Mapping the Scientific Knowledge of Antimicrobial Resistance in Food-Producing Animals","volume":"13","author":"Torres","year":"2021","journal-title":"One Health"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Redman-White, C.J., Moran, D., Peters, A.R., and Muwonge, A. (2023). A Review of the Predictors of Antimicrobial Use and Resistance in European Food Animal Production. Front. Antibiot., 2.","DOI":"10.3389\/frabi.2023.1209552"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.envint.2016.03.023","article-title":"Discharge of Swine Wastes Risks Water Quality and Food Safety: Antibiotics and Antibiotic Resistance Genes from Swine Sources to the Receiving Environments","volume":"92","author":"He","year":"2016","journal-title":"Environ. Int."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"977","DOI":"10.14202\/vetworld.2023.977-986","article-title":"The Global Profile of Antibiotic Resistance in Bacteria Isolated from Goats and Sheep: A Systematic Review","volume":"16","author":"Herawati","year":"2023","journal-title":"Vet. World"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Elbehiry, A., Marzouk, E., Elbehiry, A., and Marzouk, E. (2025). From Farm to Fork: Antimicrobial-Resistant Bacterial Pathogens in Livestock Production and the Food Chain. Vet. Sci., 12.","DOI":"10.3390\/vetsci12090862"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"126541","DOI":"10.1016\/j.jenvman.2025.126541","article-title":"Rethinking Extensive Livestock Grazing to Revive Mediterranean Mountain Landscapes","volume":"391","author":"Errea","year":"2025","journal-title":"J. Environ. Manag."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Carreira, E., Serrano, J., Gomes, C.J.P., Shahidian, S., Paniagua, L.L., Pilirito, A., Lopes Castro, J., Carvalho, M., and Pereira, A.F. (2022). Effect of Sheep Grazing, Stocking Rates and Dolomitic Limestone Application on the Floristic Composition of a Permanent Dryland Pasture, in the Montado Agroforestry System of Southern Portugal. Animals, 12.","DOI":"10.3390\/ani12192506"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1007\/s13593-022-00842-z","article-title":"Organic Management of Cattle and Pigs in Mediterranean Systems: Energy Efficiency and Ecosystem Services","volume":"42","year":"2022","journal-title":"Agron. Sustain. Dev."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Alavedra, M., Moura, D., Cenci-Goga, B., Saraiva, S., Silva, F., Pires, I., Saraiva, C., Coelho, A.C., and Garc\u00eda-D\u00edez, J. (2025). Biosecurity Practices in Portuguese Small Ruminant Farms: Current Status and Future Directions. Vet. Sci., 12.","DOI":"10.3390\/vetsci12040334"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1111\/joac.12480","article-title":"Pastoralism, Multifunctionality, and Environmental Agency: Insights from Mountain Sheep Pastoralists in Northern Portugal","volume":"22","author":"Cabo","year":"2022","journal-title":"J. Agrar. Change"},{"key":"ref_17","unstructured":"(2026, January 14). Portal INE\u2014\u00c1rvore Indicadores. Available online: https:\/\/www.ine.pt\/xportal\/xmain?xpid=INE&xpgid=ine_bdc_tree&contexto=bd&selTab=tab2."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Pereira, M.A., Vila-Vi\u00e7osa, M.J., Coelho, C., Santos, C., Esteves, F., Cruz, R., Gomes, L., Henriques, D., Vala, H., and N\u00f3brega, C. (2024). Pulmonary and Gastrointestinal Parasitic Infections in Small Ruminant Autochthonous Breeds from Centre Region of Portugal\u2014A Cross Sectional Study. Animals, 14.","DOI":"10.3390\/ani14081241"},{"key":"ref_19","unstructured":"European Medicines Agency (2025). European Sales and Use of Antimicrobials for Veterinary Medicine: Annual Surveillance Report for 2023, Publications Office of the European Union."},{"key":"ref_20","unstructured":"European Medicines Agency (2023). Sales of Veterinary Antimicrobial Agents in 31 European Countries in 2022: Trends from 2010 to 2022: Thirteenth ESVAC Report, Publications Office."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1111\/1746-692X.12451","article-title":"Identifying Specific Targets for the Member States to Achieve the European Union\u2019s Goal of 50 per Cent Reduction in Sales of Veterinary Antimicrobials by 2030","volume":"23","author":"Beber","year":"2024","journal-title":"EuroChoices"},{"key":"ref_22","unstructured":"World Health Organization (2024). WHO\u2019s List of Medically Important Antimicrobials: A Risk Management Tool for Mitigating Antimicrobial Resistance Due to Non-Human Use."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Bento, J.T., Gomes-Gon\u00e7alves, S., Cruz, R., Esteves, F., Baptista, A.L., Aires Pereira, M., Caseiro, P., Carreira, P., Figueira, L., and Mesquita, J.R. (2025). The Prevalence of Antimicrobial Resistance Genes in the Environments of Small Ruminant Farms from Central Portugal. Antibiotics, 14.","DOI":"10.3390\/antibiotics14060576"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s40793-022-00437-x","article-title":"Metagenomic Assembly Reveals Hosts and Mobility of Common Antibiotic Resistome in Animal Manure and Commercial Compost","volume":"17","author":"Qiu","year":"2022","journal-title":"Environ. Microbiome"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1007\/s00253-023-12842-4","article-title":"Distribution of Antibiotic Resistance Genes and Their Pathogen Hosts in Duck Farm Environments in South-East Coastal China","volume":"108","author":"Liu","year":"2024","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.ibiod.2019.01.009","article-title":"Dissemination of Antibiotic Resistance Genes (ARGs) by Rainfall on a Cyclic Economic Breeding Livestock Farm","volume":"138","author":"Huang","year":"2019","journal-title":"Int. Biodeterior. Biodegrad."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e00518","DOI":"10.1002\/mbo3.518","article-title":"Bacterial and Fungal Communities and Contribution of Physicochemical Factors during Cattle Farm Waste Composting","volume":"6","author":"Huhe","year":"2017","journal-title":"MicrobiologyOpen"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s40793-020-00368-5","article-title":"The Distribution of Microbiomes and Resistomes across Farm Environments in Conventional and Organic Dairy Herds in Pennsylvania","volume":"15","author":"Pitta","year":"2020","journal-title":"Environ. Microbiome"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e01390-24","DOI":"10.1128\/aem.01390-24","article-title":"Assessing Antimicrobial Resistance in Pasture-Based Dairy Farms: A 15-Month Surveillance Study in New Zealand","volume":"90","author":"Collis","year":"2024","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Lawther, K., Santos, F.G., Oyama, L.B., Rubino, F., Morrison, S., Creevey, C.J., McGrath, J.W., and Huws, S.A. (2022). Resistome Analysis of Global Livestock and Soil Microbiomes. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.897905"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Rovira, P., McAllister, T., Lakin, S.M., Cook, S.R., Doster, E., Noyes, N.R., Weinroth, M.D., Yang, X., Parker, J.K., and Boucher, C. (2019). Characterization of the Microbial Resistome in Conventional and \u201cRaised Without Antibiotics\u201d Beef and Dairy Production Systems. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01980"},{"key":"ref_32","first-page":"7","article-title":"Orlando Ribeiro\u2019s Work on Transhumant Pastoralism in North-Central Portugal: Guidelines for a Research Project on Ethno-History and Archaeology","volume":"89","author":"Carvalho","year":"2023","journal-title":"HIST AGRAR"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1093\/jac\/dkt443","article-title":"Correlation between Veterinary Antimicrobial Use and Antimicrobial Resistance in Food-Producing Animals: A Report on Seven Countries","volume":"69","author":"Chantziaras","year":"2014","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"107986","DOI":"10.1016\/j.envint.2023.107986","article-title":"The Dynamics and Transmission of Antibiotic Resistance Associated with Plant Microbiomes","volume":"176","author":"Chen","year":"2023","journal-title":"Environ. Int."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1038\/s41579-021-00649-x","article-title":"Antibiotic Resistance in the Environment","volume":"20","author":"Larsson","year":"2022","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1002\/jobm.202100201","article-title":"Antibiotic Resistance Genes in Bacteria: Occurrence, Spread, and Control","volume":"61","author":"Jian","year":"2021","journal-title":"J. Basic Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1007\/s13213-019-01450-1","article-title":"Diversity of \u03b2-Lactam Resistance Genes in Gram-Negative Rods Isolated from a Municipal Wastewater Treatment Plant","volume":"69","author":"Piotrowska","year":"2019","journal-title":"Ann. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"172813","DOI":"10.1016\/j.ejphar.2019.172813","article-title":"Antimicrobial Pharmaceuticals in the Aquatic Environment\u2014Occurrence and Environmental Implications","volume":"866","author":"Felis","year":"2020","journal-title":"Eur. J. Pharmacol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1016\/j.envint.2018.12.065","article-title":"Antibiotics Bioremediation: Perspectives on Its Ecotoxicity and Resistance","volume":"124","author":"Kumar","year":"2019","journal-title":"Environ. Int."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"162194","DOI":"10.1016\/j.scitotenv.2023.162194","article-title":"Potential Reservoirs of Antimicrobial Resistance in Livestock Waste and Treated Wastewater That Can Be Disseminated to Agricultural Land","volume":"872","author":"Ibekwe","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"125018","DOI":"10.1016\/j.envpol.2024.125018","article-title":"Microbial Communities and Mobile Genetic Elements Determine the Variations of Antibiotic Resistance Genes for a Continuous Year in the Urban River Deciphered by Metagenome Assembly","volume":"362","author":"Liu","year":"2024","journal-title":"Environ. Pollut."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Horvat, O., and Kova\u010devi\u0107, Z. (2025). Human and Veterinary Medicine Collaboration: Synergistic Approach to Address Antimicrobial Resistance Through the Lens of Planetary Health. Antibiotics, 14.","DOI":"10.3390\/antibiotics14010038"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Daw Elbait, G., Daou, M., Abuoudah, M., Elmekawy, A., Hasan, S.W., Everett, D.B., Alsafar, H., Henschel, A., and Yousef, A.F. (2024). Comparison of qPCR and Metagenomic Sequencing Methods for Quantifying Antibiotic Resistance Genes in Wastewater. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0298325"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"xtad008","DOI":"10.1093\/femsmc\/xtad008","article-title":"Quantitative PCR versus Metagenomics for Monitoring Antibiotic Resistance Genes: Balancing High Sensitivity and Broad Coverage","volume":"4","author":"Ferreira","year":"2023","journal-title":"FEMS Microbes"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Taylor, W., Bohm, K., Dyet, K., Weaver, L., and Pattis, I. (2025). Comparative Analysis of qPCR and Metagenomics for Detecting Antimicrobial Resistance in Wastewater: A Case Study. BMC Res. Notes, 18.","DOI":"10.1186\/s13104-024-07027-9"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"116638","DOI":"10.1016\/j.jenvman.2022.116638","article-title":"Seasonal Dissemination of Antibiotic Resistome from Livestock Farms to Surrounding Soil and Air: Bacterial Hosts and Risks for Human Exposure","volume":"325","author":"Wang","year":"2023","journal-title":"J. Environ. Manag."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_48","unstructured":"Li, H. (2013). Aligning Sequence Reads, Clone Sequences and Assembly Contigs with BWA-MEM 2013. arXiv."},{"key":"ref_49","unstructured":"Langmead, B. (2025, December 04). K2 AWS Indexes: Kraken 2 and Bracken Database Index Files on AWS. Available online: https:\/\/benlangmead.github.io\/aws-indexes\/k2."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Lu, J., and Salzberg, S.L. (2018). Removing Contaminants from Databases of Draft Genomes. PLoS Comput. Biol., 14.","DOI":"10.1371\/journal.pcbi.1006277"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"119298","DOI":"10.1016\/j.envres.2024.119298","article-title":"Seasonal Dynamics of Antibiotic Resistance Genes and Mobile Genetic Elements in a Subtropical Coastal Ecosystem: Implications for Environmental Health Risks","volume":"257","author":"Peng","year":"2024","journal-title":"Environ. Res."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"121137","DOI":"10.1016\/j.watres.2024.121137","article-title":"CPR Bacteria and DPANN Archaea Play Pivotal Roles in Response of Microbial Community to Antibiotic Stress in Groundwater","volume":"251","author":"Tang","year":"2024","journal-title":"Water Res."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/s40793-024-00652-8","article-title":"Millennial-Scale Microbiome Analysis Reveals Ancient Antimicrobial Resistance Conserved despite Modern Selection Pressures","volume":"19","author":"Gomathinayagam","year":"2024","journal-title":"Environ. Microbiome"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2815","DOI":"10.1038\/s41596-022-00738-y","article-title":"Metagenome Analysis Using the Kraken Software Suite","volume":"17","author":"Lu","year":"2022","journal-title":"Nat. Protoc."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"btae086","DOI":"10.1093\/bioinformatics\/btae086","article-title":"ARGprofiler\u2014A Pipeline for Large-Scale Analysis of Antimicrobial Resistance Genes and Their Flanking Regions in Metagenomic Datasets","volume":"40","author":"Martiny","year":"2024","journal-title":"Bioinformatics"}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/15\/3\/277\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T05:34:29Z","timestamp":1773207269000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/15\/3\/277"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,9]]},"references-count":55,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,3]]}},"alternative-id":["antibiotics15030277"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics15030277","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,9]]}}}