{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T15:46:22Z","timestamp":1770392782991,"version":"3.49.0"},"reference-count":81,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T00:00:00Z","timestamp":1769558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Universidad de Panam\u00e1","award":["CUFI-2022-CNET-EP-005"],"award-info":[{"award-number":["CUFI-2022-CNET-EP-005"]}]},{"DOI":"10.13039\/501100007061","name":"Secretar\u00eda Nacional de Ciencia, Tecnolog\u00eda e Innovaci\u00f3n","doi-asserted-by":"publisher","award":["APY-NI-2022-14"],"award-info":[{"award-number":["APY-NI-2022-14"]}],"id":[{"id":"10.13039\/501100007061","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sistema Nacional de Investigaci\u00f3n, Panam\u00e1","award":["2038-2022"],"award-info":[{"award-number":["2038-2022"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background\/Objetives: The bacterial ribosome is a key target for several classes of antibiotics, including aminoglycosides, macrolides, tetracyclines, and amphenicols. Although resistance to these antibiotics is well documented in clinical settings, ribosome-targeting antibiotic resistance genes have received comparatively little attention in studies comprising aquatic environments, where research has primarily focused on \u03b2-lactams and fluoroquinolones. Moreover, while plasmid-mediated dissemination of resistance is well recognized, the chromosomal integration of resistance genes in Escherichia coli remains underexplored. Methods: In this study, E. coli isolates were recovered from two contaminated aquatic environments in Panama: surface water from the Juan D\u00edaz River and influent wastewater from the Panama City wastewater treatment plant. Results: Overall, 80.8% of the isolates exhibited resistance to aminoglycosides, 37.4% to tetracycline, and 18.2% to chloramphenicol. Resistance genes against these antibiotics were identified via PCR, and their genomic location (plasmid or chromosome) was determined by whole-genome sequencing. Our results revealed a higher prevalence of plasmid-associated resistance genes in river isolates, while chromosomal integration was more frequent among wastewater isolates. Notably, ribosome-targeting antibiotic resistance genes were more frequently detected than those conferring resistance to \u03b2-lactams, quinolones, and sulfonamides together. Conclusions: These findings highlight distinct mechanisms underlying the dissemination of ribosome-targeting antibiotic resistance genes in aquatic environments, where pollutant pressure in surface waters may favor plasmid maintenance, while chromosomal integration may represent a strategy to reduce the fitness cost associated with plasmid carriage and ensure stable resistance persistence.<\/jats:p>","DOI":"10.3390\/antibiotics15020132","type":"journal-article","created":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T15:04:46Z","timestamp":1769612686000},"page":"132","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Prevalence and Differential Plasmid Versus Chromosomal Distribution of Ribosome-Targeting Antibiotic Resistance Genes in Escherichia coli Isolates from River and Untreated Wastewater Environments"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8137-4017","authenticated-orcid":false,"given":"Juan R.","family":"Medina-S\u00e1nchez","sequence":"first","affiliation":[{"name":"Laboratory of Experimental and Applied Microbiology, Universidad de Panam\u00e1, Panama City 0830-00929, Panama"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-8363-4644","authenticated-orcid":false,"given":"Marialena","family":"Salvatierra","sequence":"additional","affiliation":[{"name":"Laboratory of Experimental and Applied Microbiology, Universidad de Panam\u00e1, Panama City 0830-00929, Panama"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9046-4081","authenticated-orcid":false,"given":"Carmen Indira","family":"Espino","sequence":"additional","affiliation":[{"name":"Department of Human Microbiology, Faculty of Medicine, Universidad de Panam\u00e1, Panama City 0830-00929, Panama"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5001-6217","authenticated-orcid":false,"given":"Alex O.","family":"Mart\u00ednez-Torres","sequence":"additional","affiliation":[{"name":"Laboratory of Experimental and Applied Microbiology, Universidad de Panam\u00e1, Panama City 0830-00929, Panama"},{"name":"Sistema Nacional de Investigaci\u00f3n (SNI), Secretar\u00eda Nacional de Ciencia Tecnolog\u00eda e Innovaci\u00f3n (SENACYT), Panama City 0816-02852, Panama"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6949-2782","authenticated-orcid":false,"given":"Alejandro","family":"Llanes","sequence":"additional","affiliation":[{"name":"Sistema Nacional de Investigaci\u00f3n (SNI), Secretar\u00eda Nacional de Ciencia Tecnolog\u00eda e Innovaci\u00f3n (SENACYT), Panama City 0816-02852, Panama"},{"name":"Divisi\u00f3n de Salud Humana y Enfermedades, Instituto de Investigaciones Cient\u00edficas y Servicios de Alta Tecnolog\u00eda AIP (INDICASAT-AIP), Panama City 0843-01103, Panama"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2892-7599","authenticated-orcid":false,"given":"Jordi","family":"Querol-Audi","sequence":"additional","affiliation":[{"name":"Laboratory of Experimental and Applied Microbiology, Universidad de Panam\u00e1, Panama City 0830-00929, Panama"},{"name":"Sistema Nacional de Investigaci\u00f3n (SNI), Secretar\u00eda Nacional de Ciencia Tecnolog\u00eda e Innovaci\u00f3n (SENACYT), Panama City 0816-02852, Panama"},{"name":"Department of Biochemistry and Nutrition, Faculty of Medicine, Universidad de Panam\u00e1, Panama City 0830-00929, Panama"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Muteeb, G., Rehman, M.T., Shahwan, M., and Aatif, M. (2023). Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review. Pharmaceuticals, 16.","DOI":"10.20944\/preprints202306.1921.v1"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Halawa, E.M., Fadel, M., Al-Rabia, M.W., Behairy, A., Nouh, N.A., Abdo, M., Olga, R., Fericean, L., Atwa, A.M., and El-Nablaway, M. (2024). Antibiotic Action and Resistance: Updated Review of Mechanisms, Spread, Influencing Factors, and Alternative Approaches for Combating Resistance. Front. Pharmacol., 14.","DOI":"10.3389\/fphar.2023.1305294"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1039\/D2MD00459C","article-title":"Ribosome-Targeting Antibiotics and Resistance via Ribosomal RNA Methylation","volume":"14","author":"Jeremia","year":"2023","journal-title":"RSC Med. Chem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"137015","DOI":"10.1016\/j.ijbiomac.2024.137015","article-title":"Ribosomal A Site Binding Pattern Differs between Arm Methyltransferases from Clinical Pathogens and a Natural Producer of Aminoglycosides","volume":"282","year":"2024","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1855","DOI":"10.1002\/med.21780","article-title":"Ribosome-Targeting Antibacterial Agents: Advances, Challenges, and Opportunities","volume":"41","author":"Zhang","year":"2021","journal-title":"Med. Res. Rev."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Xu, C., Kong, L., Gao, H., Cheng, X., and Wang, X. (2022). A Review of Current Bacterial Resistance to Antibiotics in Food Animals. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.822689"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Prescott, J.F. (2017). History and Current Use of Antimicrobial Drugs in Veterinary Medicine. Microbiol. Spectr., 5.","DOI":"10.1128\/microbiolspec.ARBA-0002-2017"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/s12302-021-00505-y","article-title":"Environmental Fate of Tetracycline Antibiotics: Degradation Pathway Mechanisms, Challenges, and Perspectives","volume":"33","author":"Ahmad","year":"2021","journal-title":"Environ. Sci. Eur."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"108729","DOI":"10.1016\/j.microc.2023.108729","article-title":"Determination of Amphenicol Antibiotic Residues in Aquaculture Products by Response Surface Methodology Modified QuEChERS Method Combined with UPLC-MS\/MS","volume":"190","author":"Zhou","year":"2023","journal-title":"Microchem. J."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Anti\u00f1olo Berm\u00fadez, L., Mart\u00ednez S\u00e1nchez, E.M., Leyva D\u00edaz, J.C., Mu\u00f1io Mart\u00ednez, M.D.M., Poyatos Capilla, J.M., and Mart\u00edn Pascual, J. (2023). Impacts of Organic Emerging Contaminants (Erythromycin, Ibuprofen, and Diclofenac) on the Performance of a Membrane Bioreactor Treating Urban Wastewater: A Heterotrophic Kinetic Investigation. Membranes, 13.","DOI":"10.3390\/membranes13080697"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Amangelsin, Y., Semenova, Y., Dadar, M., Aljofan, M., and Bj\u00f8rklund, G. (2023). The Impact of Tetracycline Pollution on the Aquatic Environment and Removal Strategies. Antibiotics, 12.","DOI":"10.3390\/antibiotics12030440"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1007\/s10311-022-01416-x","article-title":"Occurrence, Toxicity and Adsorptive Removal of the Chloramphenicol Antibiotic in Water: A Review","volume":"20","author":"Nguyen","year":"2022","journal-title":"Environ. Chem. Lett."},{"key":"ref_13","first-page":"1335","article-title":"RRNA Methylation and Antibiotic Resistance","volume":"85","author":"Osterman","year":"2020","journal-title":"Biochemistry"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"9192424","DOI":"10.1155\/2022\/9192424","article-title":"Tetracycline-Resistant Genes in Escherichia coli from Clinical and Nonclinical Sources in Rivers State, Nigeria","volume":"2022","author":"Perewari","year":"2022","journal-title":"Int. J. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Mayers, D.L. (2009). Tetracycline and Chloramphenicol Resistance Mechanisms. Antimicrobial Drug Resistance: Mechanisms of Drug Resistance, Humana Press.","DOI":"10.1007\/978-1-59745-180-2"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Li, P., Zhu, T., Zhou, D., Lu, W., Liu, H., Sun, Z., Ying, J., Lu, J., Lin, X., and Li, K. (2020). Analysis of Resistance to Florfenicol and the Related Mechanism of Dissemination in Different Animal-Derived Bacteria. Front. Cell. Infect. Microbiol., 10.","DOI":"10.3389\/fcimb.2020.00369"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1038\/s41589-023-01525-w","article-title":"Structural Basis of Cfr-Mediated Antimicrobial Resistance and Mechanisms to Evade It","volume":"20","author":"Aleksandrova","year":"2024","journal-title":"Nat. Chem. Biol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Miklasi\u0144ska-Majdanik, M. (2021). Mechanisms of Resistance to Macrolide Antibiotics among Staphylococcus aureus. Antibiotics, 10.","DOI":"10.3390\/antibiotics10111406"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.bsheal.2023.01.001","article-title":"The Prevalence and Distribution of Aminoglycoside Resistance Genes","volume":"5","author":"Zhang","year":"2023","journal-title":"Biosaf. Health"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"107382","DOI":"10.1016\/j.ijantimicag.2024.107382","article-title":"NpmC, a Novel A1408 16S RRNA Methyltransferase in the Gut of Humans and Animals","volume":"65","author":"Matamoros","year":"2024","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1038\/s42003-023-05174-6","article-title":"Extensive Screening Reveals Previously Undiscovered Aminoglycoside Resistance Genes in Human Pathogens","volume":"6","author":"Lund","year":"2023","journal-title":"Commun. Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"7445","DOI":"10.1021\/es060413l","article-title":"Antibiotic Resistance Genes as Emerging Contaminants: Studies in Northern Colorado","volume":"40","author":"Pruden","year":"2006","journal-title":"Environ. Sci. Technol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e0447822","DOI":"10.1128\/spectrum.04478-22","article-title":"Global Increase of Antibiotic Resistance Genes in Conjugative Plasmids","volume":"11","author":"Wang","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"msaf060","DOI":"10.1093\/molbev\/msaf060","article-title":"The Spread of Antibiotic Resistance Is Driven by Plasmids Among the Fastest Evolving and of Broadest Host Range","volume":"42","author":"Coluzzi","year":"2025","journal-title":"Mol. Biol. Evol."},{"key":"ref_25","first-page":"e000353","article-title":"Origin, Maintenance and Spread of Antibiotic Resistance Genes within Plasmids and Chromosomes of Bloodstream Isolates of Escherichia coli","volume":"6","author":"Goswami","year":"2020","journal-title":"Microb. Genom."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Singh, A.K., Kaur, R., Verma, S., and Singh, S. (2022). Antimicrobials and Antibiotic Resistance Genes in Water Bodies: Pollution, Risk, and Control. Front. Environ. Sci., 10.","DOI":"10.3389\/fenvs.2022.830861"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"15064","DOI":"10.1021\/acs.est.2c00218","article-title":"(Antibiotic-Resistant) E. coli in the Dutch\u2013German Vecht Catchment\u2500Monitoring and Modeling","volume":"56","author":"Niebaum","year":"2022","journal-title":"Environ. Sci. Technol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1093\/jac\/dkx488","article-title":"Plasmids Carrying Antimicrobial Resistance Genes in Enterobacteriaceae","volume":"73","author":"Rozwandowicz","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Skof, A., Koller, M., Baumert, R., Hautz, J., Treiber, F., Kittinger, C., and Zarfel, G. (2024). Comparison of the Antibiotic Resistance of Escherichia coli Populations from Water and Biofilm in River Environments. Pathogens, 13.","DOI":"10.3390\/pathogens13020171"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Ram\u00edrez-Bayard, I.E., Mej\u00eda, F., Medina-S\u00e1nchez, J.R., Cornejo-Reyes, H., Castillo, M., Querol-Audi, J., and Mart\u00ednez-Torres, A.O. (2023). Prevalence of Plasmid-Associated Tetracycline Resistance Genes in Multidrug-Resistant Escherichia coli Strains Isolated from Environmental, Animal and Human Samples in Panama. Antibiotics, 12.","DOI":"10.3390\/antibiotics12020280"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"11260","DOI":"10.1038\/s41598-024-62037-8","article-title":"Multidrug-Resistant Phenotypes of Genetically Diverse Escherichia coli Isolates from Healthy Domestic Cats","volume":"14","author":"Landires","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Dom\u00ednguez, D.C., Chac\u00f3n, L.M., and Wallace, D. (2021). Anthropogenic Activities and the Problem of Antibiotic Resistance in Latin America: A Water Issue. Water, 13.","DOI":"10.3390\/w13192693"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"289","DOI":"10.2174\/1874070701610010289","article-title":"Diversity of Tetracycline Resistant Genes in Escherichia coli from Human and Environmental Sources","volume":"10","author":"Yaish","year":"2016","journal-title":"Open Biotechnol. J."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Park, J.-H., Bae, K.-S., Kang, J., Yoon, J.-K., and Lee, S.-H. (2024). Comprehensive Assessment of Multidrug-Resistant and Extraintestinal Pathogenic Escherichia coli in Wastewater Treatment Plant Effluents. Microorganisms, 12.","DOI":"10.3390\/microorganisms12061119"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"741","DOI":"10.3201\/eid1805.111153","article-title":"Antimicrobial Drug Resistance in Escherichia coli from Humans and Food Animals, United States, 1950\u20132002","volume":"18","author":"Tadesse","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1089\/mdr.2022.0296","article-title":"Resistome Diversity in Escherichia coli Isolates of Global Wastewaters","volume":"30","author":"Sudhakari","year":"2023","journal-title":"Microb. Drug Resist."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"fnx129","DOI":"10.1093\/femsle\/fnx129","article-title":"Occurrence of Aminoglycoside-Modifying Enzymes among Isolates of Escherichia coli Exhibiting High Levels of Aminoglycoside Resistance Isolated from Korean Cattle Farms","volume":"364","author":"Belaynehe","year":"2017","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Garcias, B., Martin, M., and Darwich, L. (2024). Characterization of Antimicrobial Resistance in Escherichia coli Isolated from Diarrheic and Healthy Weaned Pigs in Catalonia. Animals, 14.","DOI":"10.3390\/ani14030487"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2425564","DOI":"10.1155\/2023\/2425564","article-title":"A Systematic Review on the Occurrence of Antimicrobial-Resistant Escherichia coli in Poultry and Poultry Environments in Bangladesh between 2010 and 2021","volume":"2023","author":"Islam","year":"2023","journal-title":"BioMed Res. Int."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Qing, Y., Zou, Z., Jiang, G., Qin, L., Liu, K., and Liu, Z. (2024). A Global Perspective on the Abundance, Diversity and Mobility of Antibiotic Resistance Genes in Escherichia coli. Front. Vet. Sci., 11.","DOI":"10.3389\/fvets.2024.1442159"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"116736","DOI":"10.1016\/j.envpol.2021.116736","article-title":"Metagenomic Analysis of Urban Wastewater Resistome and Mobilome: A Support for Antimicrobial Resistance Surveillance in an Endemic Country","volume":"276","author":"Ramirez","year":"2021","journal-title":"Environ. Pollut."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e00559-23","DOI":"10.1128\/aem.00559-23","article-title":"Genetic Background of Neomycin Resistance in Clinical Escherichia coli Isolated from Danish Pig Farms","volume":"89","author":"Prabha","year":"2023","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1093\/jac\/48.suppl_1.87","article-title":"Interpretative Reading: Recognizing the Unusual and Inferring Resistance Mechanisms from Resistance Phenotypes","volume":"48","author":"Livermore","year":"2001","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Ibacache-Quiroga, C., Oliveros, J.C., Couce, A., and Bl\u00e1zquez, J. (2018). Parallel Evolution of High-Level Aminoglycoside Resistance in Escherichia coli under Low and High Mutation Supply Rates. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.00427"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"100273","DOI":"10.1016\/j.bioflm.2025.100273","article-title":"Strain-Dependent Emergence of Aminoglycoside Resistance in Escherichia coli Biofilms","volume":"9","author":"Charron","year":"2025","journal-title":"Biofilm"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"4163","DOI":"10.1038\/s41598-024-54169-8","article-title":"Genome-Wide Identification of Fitness-Genes in Aminoglycoside-Resistant Escherichia coli during Antibiotic Stress","volume":"14","author":"Wellner","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e213883","DOI":"10.11606\/issn.1678-4456.bjvras.2023.213883","article-title":"A Systematic Review of Tetracycline Resistance Genes in Animals and Derived Products in Latin America and the Caribbean","volume":"60","year":"2023","journal-title":"Braz. J. Vet. Res. Anim. Sci."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.1093\/jac\/dkv186","article-title":"WGS Accurately Predicts Antimicrobial Resistance in Escherichia coli","volume":"70","author":"Tyson","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Jurado-Rabad\u00e1n, S., de la Fuente, R., Ruiz-Santa-Quiteria, J.A., Orden, J.A., de Vries, L.E., and Agers\u00f8, Y. (2014). Detection and Linkage to Mobile Genetic Elements of Tetracycline Resistance Gene Tet(M) in Escherichia coli Isolates from Pigs. BMC Vet. Res., 10.","DOI":"10.1186\/1746-6148-10-155"},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Belaynehe, K.M., Shin, S.W., and Yoo, H.S. (2018). Interrelationship between Tetracycline Resistance Determinants, Phylogenetic Group Affiliation and Carriage of Class 1 Integrons in Commensal Escherichia coli Isolates from Cattle Farms. BMC Vet. Res., 14.","DOI":"10.1186\/s12917-018-1661-3"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"102019","DOI":"10.1016\/j.cimid.2023.102019","article-title":"Genomic Analysis of Multidrug-Resistant Escherichia coli Strains Carrying the Mcr-1 Gene Recovered from Pigs in Lima-Peru","volume":"99","author":"Espinoza","year":"2023","journal-title":"Comp. Immunol. Microbiol. Infect. Dis."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Liao, C.Y., Balasubramanian, B., Peng, J.J., Tao, S.R., Liu, W.C., and Ma, Y. (2021). Antimicrobial Resistance of Escherichia coli From Aquaculture Farms and Their Environment in Zhanjiang, China. Front. Vet. Sci., 8.","DOI":"10.3389\/fvets.2021.806653"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Inuwa, A.B., Mahmood, Q., Iqbal, J., Widemann, E., Shafiq, S., Irshad, M., Irshad, U., Iqbal, A., Hafeez, F., and Nazir, R. (2022). Removal of Antibiotic Resistance Genes, Class 1 Integrase Gene and Escherichia coli Indicator Gene in a Microalgae-Based Wastewater Treatment System. Antibiotics, 11.","DOI":"10.3390\/antibiotics11111531"},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Obayiuwana, A., and Ibekwe, A.M. (2020). Antibiotic Resistance Genes Occurrence in Wastewaters from Selected Pharmaceutical Facilities in Nigeria. Water, 12.","DOI":"10.3390\/w12071897"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Voolaid, V., J\u00f5ers, A., Kisand, V., and Tenson, T. (2012). Co-Occurrence of Resistance to Different Antibiotics among Aquatic Bacteria. BMC Microbiol., 12.","DOI":"10.1186\/1471-2180-12-225"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"e0045224","DOI":"10.1128\/aac.00452-24","article-title":"The Intrinsic Macrolide Resistome of Escherichia coli","volume":"68","author":"Ma","year":"2024","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"e02703-16","DOI":"10.1128\/AEM.02703-16","article-title":"Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water","volume":"83","author":"Gomi","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1093\/jac\/dkae161","article-title":"Azithromycin Resistance in Escherichia coli and Salmonella from Food-Producing Animals and Meat in Europe","volume":"79","author":"Ivanova","year":"2024","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Wang, M., Wu, S., Wang, Y., Chen, F., Shen, Z., and Lan, Z. (2025). Antimicrobial Resistance Genes in Clinical Escherichia coli Strains from Livestock and Poultry in Shandong Province, China During 2015\u20132020. Antibiotics, 14.","DOI":"10.3390\/antibiotics14010095"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Zhou, W., Lin, R., Zhou, Z., Ma, J., Lin, H., Zheng, X., Wang, J., Wu, J., Dong, Y., and Jiang, H. (2022). Antimicrobial Resistance and Genomic Characterization of Escherichia coli from Pigs and Chickens in Zhejiang, China. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.1018682"},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Savin, M., Bierbaum, G., Kreyenschmidt, J., Schmithausen, R.M., Sib, E., Schmoger, S., K\u00e4sbohrer, A., and Hammerl, J.A. (2021). Clinically Relevant Escherichia coli Isolates from Process Waters and Wastewater of Poultry and Pig Slaughterhouses in Germany. Microorganisms, 9.","DOI":"10.3390\/microorganisms9040698"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Craig, S., Tyler, A., Megan, W., Austin, H., Andres, G., Matthew, G., Mark, P., and David, H. (2020). F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli. mSphere, 5.","DOI":"10.1128\/msphere.00709-20"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e0355221","DOI":"10.1128\/mbio.03552-21","article-title":"The Role of Antibiotic Resistance Genes in the Fitness Cost of Multiresistance Plasmids","volume":"13","author":"Rajer","year":"2022","journal-title":"MBio"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"364","DOI":"10.3390\/applmicrobiol4010025","article-title":"Antibiotic-Resistant Bacteria across a Wastewater Treatment Plant","volume":"4","author":"Godinho","year":"2024","journal-title":"Appl. Microbiol."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Adefisoye, M.A., and Olaniran, A.O. (2022). Does Chlorination Promote Antimicrobial Resistance in Waterborne Pathogens? Mechanistic Insight into Co-Resistance and Its Implication for Public Health. Antibiotics, 11.","DOI":"10.3390\/antibiotics11050564"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1016\/j.scitotenv.2019.07.050","article-title":"Growth and Antibiotic Resistance Acquisition of Escherichia coli in a River That Receives Treated Sewage Effluent","volume":"690","author":"Suzuki","year":"2019","journal-title":"Sci. Total Environ."},{"key":"ref_67","unstructured":"Csuros, M., and Csuros, C. (1999). Microbiological Examination of Water and Wastewater, CRC Press."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1111\/j.1365-2672.2008.03838.x","article-title":"Specific Detection of Escherichia coli Isolated from Water Samples Using Polymerase Chain Reaction Targeting Four Genes: Cytochrome Bd Complex, Lactose Permease, \u03b2-d-Glucuronidase, and \u03b2-d-Galactosidase","volume":"105","author":"Horakova","year":"2008","journal-title":"J. Appl. Microbiol."},{"key":"ref_69","unstructured":"European Committee on Antimicrobial Susceptibility Testing (2025, July 14). EUCAST Reading Guide for Broth Microdilution. Available online: https:\/\/www.eucast.org\/fileadmin\/src\/media\/PDFs\/EUCAST_files\/MIC_testing\/Reading_guide_BMD_v_5.0_2024.pdf."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: Scalable and Accurate Long-Read Assembly via Adaptive k-Mer Weighting and Repeat Separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI Prokaryotic Genome Annotation Pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1093\/molbev\/msx319","article-title":"BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics","volume":"35","author":"Waterhouse","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for Predictions of Phenotypes from Genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: Expanded Curation, Support for Machine Learning, and Resistome Prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: The Reference Centre for Bacterial Insertion Sequences","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_76","unstructured":"R Core Team (2023). R: A Language and Environment for Statistical Computing, Foundation for Statistical Computing."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.ijantimicag.2015.03.008","article-title":"Molecular Identification of Aminoglycoside-Modifying Enzymes in Clinical Isolates of Escherichia coli Resistant to Amoxicillin\/Clavulanic Acid Isolated in Spain","volume":"46","author":"Ortega","year":"2015","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1006\/mcpr.2001.0363","article-title":"Multiplex PCR for the Detection of Tetracycline Resistant Genes","volume":"15","author":"Ng","year":"2001","journal-title":"Mol. Cell. Probes"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1648","DOI":"10.3201\/eid1510.090696","article-title":"Escherichia coli as Reservoir for Macrolide Resistance Genes","volume":"15","author":"Woerther","year":"2009","journal-title":"Emerg. Infect. Dis."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1093\/jac\/dky563","article-title":"ChloS-HRM, a Novel Assay to Identify Chloramphenicol-Susceptible Escherichia coli and Klebsiella pneumoniae in Malawi","volume":"74","author":"Williams","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1093\/jac\/dki412","article-title":"Multiplex PCR for Rapid Detection of Genes Encoding CTX-M Extended-Spectrum \u03b2-Lactamases","volume":"57","author":"Woodford","year":"2006","journal-title":"J. Antimicrob. Chemother."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/15\/2\/132\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T05:10:26Z","timestamp":1770354626000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/15\/2\/132"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,28]]},"references-count":81,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2]]}},"alternative-id":["antibiotics15020132"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics15020132","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,28]]}}}