{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T22:40:11Z","timestamp":1793054411610,"version":"4.5.0"},"reference-count":41,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2024,8,26]],"date-time":"2024-08-26T00:00:00Z","timestamp":1724630400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Department of Comparative Biomedicine and Food Science","award":["2024BCA1SIDPROGETTI-00139"],"award-info":[{"award-number":["2024BCA1SIDPROGETTI-00139"]}]},{"name":"Department of Comparative Biomedicine and Food Science","award":["PHD@UNIPD"],"award-info":[{"award-number":["PHD@UNIPD"]}]},{"name":"Fondazione Cassa di Risparmio di Padova e Rovigo","award":["2024BCA1SIDPROGETTI-00139"],"award-info":[{"award-number":["2024BCA1SIDPROGETTI-00139"]}]},{"name":"Fondazione Cassa di Risparmio di Padova e Rovigo","award":["PHD@UNIPD"],"award-info":[{"award-number":["PHD@UNIPD"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Drinking water distribution systems (DWDSs) represent an ideal environment for biofilm formation, which can harbor pathogenic and antimicrobial-resistant bacteria. This study aimed to assess longitudinally the microbial community composition and antimicrobial resistance (AMR), as determined by 16S rRNA NGS and qPCR, respectively, in drinking water (DW) and biofilm from DWDSs, as well as faeces, of free-range organic broiler farms. The role of DWDSs in AMR gene (ARG) dissemination within the farm environment and transmission to animals, was also assessed. DW and biofilm microbial communities differed from those of faecal samples. Moreover, potentially pathogenic and opportunistic bacteria (e.g., Staphylococcaceae) were identified in water and biofilms. High prevalence and abundance of ARGs conferring resistance to carbapenems (i.e., blaNDM), 3rd and 4th generation cephalosporins (i.e., blaCMY-2), (fluoro)quinolones (i.e., qnrS), and polymyxins (i.e., mcr-3 and mcr-5) were detected in DW, biofilm, and faecal samples, which is of concern for both animal and human health. Although other factors (e.g., feed, pests, and wildlife) may contribute to the dissemination of AMR in free-range organic poultry farms, this study indicates that DWDSs can also play a role.<\/jats:p>","DOI":"10.3390\/antibiotics13090808","type":"journal-article","created":{"date-parts":[[2024,8,26]],"date-time":"2024-08-26T07:53:37Z","timestamp":1724658817000},"page":"808","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Drinking Water and Biofilm as Sources of Antimicrobial Resistance in Free-Range Organic Broiler Farms"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6207-4721","authenticated-orcid":false,"given":"Alessandra","family":"Piccirillo","sequence":"first","affiliation":[{"name":"Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell\u2019Universit\u00e0 16, 35020 Legnaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberta","family":"Tolosi","sequence":"additional","affiliation":[{"name":"Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell\u2019Universit\u00e0 16, 35020 Legnaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lapo","family":"Mughini-Gras","sequence":"additional","affiliation":[{"name":"Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 BA Bilthoven, The Netherlands"},{"name":"Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, De Uithof, 3584 CL Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9951-7549","authenticated-orcid":false,"given":"Jannigje G.","family":"Kers","sequence":"additional","affiliation":[{"name":"Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, De Uithof, 3584 CL Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0102-7021","authenticated-orcid":false,"given":"Andrea","family":"Laconi","sequence":"additional","affiliation":[{"name":"Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell\u2019Universit\u00e0 16, 35020 Legnaro, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,8,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1017\/S0043933909000324","article-title":"The Role of the Water Supply System in the Infection and Control of Campylobacter in Chicken","volume":"65","author":"Sparks","year":"2009","journal-title":"Worlds Poult. Sci. J."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1128\/JCM.37.6.1771-1776.1999","article-title":"The Calgary Biofilm Device: New Technology for Rapid Determination of Antibiotic Susceptibilities of Bacterial Biofilms","volume":"37","author":"Ceri","year":"1999","journal-title":"J. Clin. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/S0140-6736(01)05321-1","article-title":"Antibiotic Resistance of Bacteria in Biofilms","volume":"358","author":"Stewart","year":"2001","journal-title":"Lancet"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/nrmicro3439","article-title":"Tackling Antibiotic Resistance: The Environmental Framework","volume":"13","author":"Berendonk","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.jenvman.2016.01.040","article-title":"Effects of Tillage and Poultry Manure Application Rates on Salmonella and Fecal Indicator Bacteria Concentrations in Tiles Draining Des Moines Lobe Soils","volume":"171","author":"Hruby","year":"2016","journal-title":"J. Environ. Manag."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"5701","DOI":"10.1128\/AEM.01682-13","article-title":"Impact of Manure Fertilization on the Abundance of Antibiotic-Resistant Bacteria and Frequency of Detection of Antibiotic Resistance Genes in Soil and on Vegetables at Harvest","volume":"79","author":"Marti","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"11541","DOI":"10.1021\/es302657r","article-title":"Correlation Between Upstream Human Activities and Riverine Antibiotic Resistance Genes","volume":"46","author":"Pruden","year":"2012","journal-title":"Environ. Sci. Technol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.envpol.2016.02.013","article-title":"High-Throughput Profiling of Antibiotic Resistance Genes in Drinking Water Treatment Plants and Distribution Systems","volume":"213","author":"Xu","year":"2016","journal-title":"Environ. Pollut."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.envpol.2018.11.077","article-title":"Impact of Disinfectant on Bacterial Antibiotic Resistance Transfer between Biofilm and Tap Water in a Simulated Distribution Network","volume":"246","author":"Zhang","year":"2019","journal-title":"Environ. Pollut."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.watres.2018.12.069","article-title":"New Insights into Antibiotic Resistome in Drinking Water and Management Perspectives: A Metagenomic Based Study of Small-Sized Microbes","volume":"152","author":"Ma","year":"2019","journal-title":"Water Res."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Maes, S., Vackier, T., Nguyen Huu, S., Heyndrickx, M., Steenackers, H., Sampers, I., Raes, K., Verplaetse, A., and De Reu, K. (2019). Occurrence and Characterisation of Biofilms in Drinking Water Systems of Broiler Houses. BMC Microbiol., 19.","DOI":"10.1186\/s12866-019-1451-5"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"17","DOI":"10.2527\/af.2012-0039","article-title":"Role of Livestock in Microbiological Contamination of Water: Commonly the Blame, but Not Always the Source","volume":"2","author":"McAllister","year":"2012","journal-title":"Anim. Front."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Kelly, J.J., Minalt, N., Culotti, A., Pryor, M., and Packman, A. (2014). Temporal Variations in the Abundance and Composition of Biofilm Communities Colonizing Drinking Water Distribution Pipes. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0098542"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Van Assche, A., Crauwels, S., De Brabanter, J., Willems, K.A., and Lievens, B. (2019). Characterization of the Bacterial Community Composition in Water of Drinking Water Production and Distribution Systems in Flanders, Belgium. Microbiologyopen, 8.","DOI":"10.1002\/mbo3.726"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"128410","DOI":"10.1016\/j.chemosphere.2020.128410","article-title":"Effects of Bacterial Community Composition and Structure in Drinking Water Distribution Systems on Biofilm Formation and Chlorine Resistance","volume":"264","author":"Zhu","year":"2021","journal-title":"Chemosphere"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"5697","DOI":"10.1128\/AEM.00579-11","article-title":"Diversity and Antibiotic Resistance Patterns of Sphingomonadaceae Isolates from Drinking Water","volume":"77","author":"Nunes","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E., and Thompson, F. (2014). The Family Comamonadaceae BT\u2014The Prokaryotes: Alphaproteobacteria and Betaproteobacteria, Springer.","DOI":"10.1007\/978-3-642-30197-1"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1080\/01652176.2022.2033880","article-title":"Review on Skeletal Disorders Caused by Staphylococcus Spp. in Poultry","volume":"42","author":"Szafraniec","year":"2022","journal-title":"Vet. Q."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1128\/CMR.00019-11","article-title":"Stenotrophomonas Maltophilia: An Emerging Global Opportunistic Pathogen","volume":"25","author":"Brooke","year":"2012","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"103140","DOI":"10.1016\/j.psj.2023.103140","article-title":"Regulating Effects of Chlorinated Drinking Water on Cecal Microbiota of Broiler Chicks","volume":"102","author":"Meng","year":"2023","journal-title":"Poult. Sci."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Rychlik, I. (2020). Composition and Function of Chicken Gut Microbiota. Animals, 10.","DOI":"10.3390\/ani10010103"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Schokker, D., Jansman, A.J.M., Veninga, G., de Bruin, N., Vastenhouw, S.A., de Bree, F.M., Bossers, A., Rebel, J.M.J., and Smits, M.A. (2017). Perturbation of Microbiota in One-Day Old Broiler Chickens with Antibiotic for 24 Hours Negatively Affects Intestinal Immune Development. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3625-6"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Laconi, A., Tilli, G., Galuppo, F., Grilli, G., Souillard, R., and Piccirillo, A. (2023). Stakeholders\u2019 Perceptions of Biosecurity Implementation in Italian Poultry Farms. Animals, 13.","DOI":"10.3390\/ani13203246"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/S0140-6736(15)00473-0","article-title":"V Understanding the Mechanisms and Drivers of Antimicrobial Resistance","volume":"387","author":"Holmes","year":"2016","journal-title":"Lancet"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Laconi, A., Tolosi, R., Mughini-Gras, L., Cuccato, M., Cannizzo, F.T., and Piccirillo, A. (2022). Amoxicillin and Thiamphenicol Treatments May Influence the Co-Selection of Resistance Genes in the Chicken Gut Microbiota. Sci. Rep., 12.","DOI":"10.1038\/s41598-022-24927-7"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1447","DOI":"10.3382\/ps\/pey486","article-title":"Prevalence and Antimicrobial Resistance of Campylobacter from Antibiotic-Free Broilers during Organic and Conventional Processing","volume":"98","author":"Bailey","year":"2019","journal-title":"Poult. Sci."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"101675","DOI":"10.1016\/j.psj.2021.101675","article-title":"Antibiotic Resistance Genes Load in an Antibiotic Free Organic Broiler Farm","volume":"101","author":"Salerno","year":"2022","journal-title":"Poult. Sci."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Smoglica, C., Farooq, M., Ruffini, F., Marsilio, F., and Di Francesco, C.E. (2023). Microbial Community and Abundance of Selected Antimicrobial Resistance Genes in Poultry Litter from Conventional and Antibiotic-Free Farms. Antibiotics, 12.","DOI":"10.3390\/antibiotics12091461"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Farooq, M., Smoglica, C., Ruffini, F., Soldati, L., Marsilio, F., and Di Francesco, C.E. (2022). Antibiotic Resistance Genes Occurrence in Conventional and Antibiotic-Free Poultry Farming, Italy. Animals, 12.","DOI":"10.3390\/ani12182310"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"143404","DOI":"10.1016\/j.scitotenv.2020.143404","article-title":"Microbial Community Composition and Antimicrobial Resistance in Agricultural Soils Fertilized with Livestock Manure from Conventional Farming in Northern Italy","volume":"760","author":"Laconi","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref_31","first-page":"453","article-title":"Persistence of antibiotic resistance genes and bacterial community changes in drinking water treatment system: From drinking water source to tap water","volume":"616\u2013617","author":"Su","year":"2015","journal-title":"Sci. Total Environ."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"151131","DOI":"10.1016\/j.scitotenv.2021.151131","article-title":"Beehive Products as Bioindicators of Antimicrobial Resistance Contamination in the Environment","volume":"823","author":"Laconi","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Lopatto, E., Choi, J., Colina, A., Ma, L., Howe, A., and Hinsa-Leasure, S. (2019). Characterizing the Soil Microbiome and Quantifying Antibiotic Resistance Gene Dynamics in Agricultural Soil Following Swine CAFO Manure Application. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0220770"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.jgar.2021.07.021","article-title":"Epidemiology of Mobile Colistin Resistance (Mcr) Genes in Aquatic Environments","volume":"27","author":"Cherak","year":"2021","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"113818","DOI":"10.1016\/j.envpol.2019.113818","article-title":"Behavior of Last Resort Antibiotic Resistance Genes (Mcr-1 and BlaNDM-1) in a Drinking Water Supply System and Their Possible Acquisition by the Mouse Gut Flora","volume":"259","author":"Khan","year":"2020","journal-title":"Environ. Pollut."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Apostolakos, I., Mughini-Gras, L., Fasolato, L., and Piccirillo, A. (2019). Assessing the Occurrence and Transfer Dynamics of ESBL\/PAmpC-Producing Escherichia Coli across the Broiler Production Pyramid. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0217174"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1089\/mdr.2017.0150","article-title":"Extended-Spectrum Beta-Lactamase-\/AmpC Beta-Lactamase-Producing Enterobacteriaceae in Broiler Farms: Transmission Dynamics at Farm Level","volume":"24","author":"Daehre","year":"2017","journal-title":"Microb. Drug Resist."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-Resolution Sample Inference from Illumina Amplicon Data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1093\/nar\/gkt1209","article-title":"The SILVA and \u201cAll-Species Living Tree Project (LTP)\u201d Taxonomic Frameworks","volume":"42","author":"Yilmaz","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1080\/0266476042000214501","article-title":"Beta Regression for Modelling Rates and Proportions","volume":"31","author":"Ferrari","year":"2004","journal-title":"J. Appl. Stat."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/13\/9\/808\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:42:51Z","timestamp":1760110971000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/13\/9\/808"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,26]]},"references-count":41,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2024,9]]}},"alternative-id":["antibiotics13090808"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics13090808","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,26]]}}}