{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T14:59:44Z","timestamp":1767970784870,"version":"3.49.0"},"reference-count":42,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2021,9,16]],"date-time":"2021-09-16T00:00:00Z","timestamp":1631750400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["PD\/BD\/128203\/2016"],"award-info":[{"award-number":["PD\/BD\/128203\/2016"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"name":"AgriWWater Project","award":["PTDC\/CTA-AMB\/29586\/2017"],"award-info":[{"award-number":["PTDC\/CTA-AMB\/29586\/2017"]}]},{"name":"INTERFACE Programme, through the Innovation, Technology and Circular Economy Fund (FITEC)","award":["CIT\/2018\/15"],"award-info":[{"award-number":["CIT\/2018\/15"]}]},{"name":"iNOVA4Health","award":["UID\/Multi\/04462\/2019"],"award-info":[{"award-number":["UID\/Multi\/04462\/2019"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Wastewater treatment plants are important reservoirs and sources for the dissemination of antibiotic resistance into the environment. Here, two different groups of carbapenem resistant bacteria\u2014the potentially environmental and the potentially pathogenic\u2014were isolated from both the wastewater influent and discharged effluent of a full-scale wastewater treatment plant and characterized by whole genome sequencing and antibiotic susceptibility testing. Among the potentially environmental isolates, there was no detection of any acquired antibiotic resistance genes, which supports the idea that their resistance mechanisms are mainly intrinsic. On the contrary, the potentially pathogenic isolates presented a broad diversity of acquired antibiotic resistance genes towards different antibiotic classes, especially \u03b2-lactams, aminoglycosides, and fluoroquinolones. All these bacteria showed multiple \u03b2-lactamase-encoding genes, some with carbapenemase activity, such as the blaKPC-type genes found in the Enterobacteriaceae isolates. The antibiotic susceptibility testing assays performed on these isolates also revealed that all had a multi-resistance phenotype, which indicates that the acquired resistance is their major antibiotic resistance mechanism. In conclusion, the two bacterial groups have distinct resistance mechanisms, which suggest that the antibiotic resistance in the environment can be a more complex problematic than that generally assumed.<\/jats:p>","DOI":"10.3390\/antibiotics10091118","type":"journal-article","created":{"date-parts":[[2021,9,16]],"date-time":"2021-09-16T21:38:12Z","timestamp":1631828292000},"page":"1118","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Environmental and Pathogenic Carbapenem Resistant Bacteria Isolated from a Wastewater Treatment Plant Harbour Distinct Antibiotic Resistance Mechanisms"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0540-674X","authenticated-orcid":false,"given":"Micaela","family":"Oliveira","sequence":"first","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, Avenida da Rep\u00fablica, 2780-157 Oeiras, Portugal"},{"name":"iBET, Instituto de Biologia Experimental e Tecnol\u00f3gica, Apartado 12, 2781-901 Oeiras, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8516-2487","authenticated-orcid":false,"given":"In\u00eas","family":"Leonardo","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, Avenida da Rep\u00fablica, 2780-157 Oeiras, Portugal"},{"name":"iBET, Instituto de Biologia Experimental e Tecnol\u00f3gica, Apartado 12, 2781-901 Oeiras, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5034-5494","authenticated-orcid":false,"given":"M\u00f3nica","family":"Nunes","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, Avenida da Rep\u00fablica, 2780-157 Oeiras, Portugal"},{"name":"iBET, Instituto de Biologia Experimental e Tecnol\u00f3gica, Apartado 12, 2781-901 Oeiras, Portugal"}]},{"given":"Ana","family":"Silva","sequence":"additional","affiliation":[{"name":"Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark"}]},{"given":"Maria","family":"Barreto Crespo","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica Ant\u00f3nio Xavier, Universidade Nova de Lisboa, Avenida da Rep\u00fablica, 2780-157 Oeiras, Portugal"},{"name":"iBET, Instituto de Biologia Experimental e Tecnol\u00f3gica, Apartado 12, 2781-901 Oeiras, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2021,9,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"S521","DOI":"10.1093\/cid\/ciz824","article-title":"Epidemiology and Diagnostics of Carbapenem Resistance in Gram-negative Bacteria","volume":"69","author":"Nordmann","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1016\/j.watres.2017.07.002","article-title":"Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements","volume":"123","author":"Guo","year":"2017","journal-title":"Water Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1016\/j.watres.2012.11.027","article-title":"Urban wastewater treatment plants as hotspots for the release of antibiotics in the environment: A review","volume":"47","author":"Michael","year":"2013","journal-title":"Water Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/j.scitotenv.2013.01.032","article-title":"Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: A review","volume":"447","author":"Rizzo","year":"2013","journal-title":"Sci. Total Environ."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.molmed.2012.03.003","article-title":"Carbapenem resistance in Enterobacteriaceae: Here is the storm!","volume":"18","author":"Nordmann","year":"2012","journal-title":"Trends Mol. Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"501","DOI":"10.2217\/17460913.2.5.501","article-title":"Carbapenemases: Molecular diversity and clinical consequences","volume":"2","author":"Poirel","year":"2007","journal-title":"Future Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1016\/S0924-8579(10)70004-2","article-title":"Emerging carbapenemases: A global perspective","volume":"36","author":"Walsh","year":"2010","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/j.ijmm.2010.04.005","article-title":"Resistance to cephalosporins and carbapenems in Gram-negative bacterial pathogens","volume":"300","author":"Pfeifer","year":"2010","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2165\/11597960-000000000-00000","article-title":"Plasmid-Mediated Resistance in Enterobacteriaceae: Changing Landscape and Implications for Therapy","volume":"72","author":"Schultsz","year":"2012","journal-title":"Drugs"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.watres.2019.06.039","article-title":"Antibiotic resistance genes in treated wastewater and in the receiving water bodies: A pan-European survey of urban settings","volume":"162","author":"Cacace","year":"2019","journal-title":"Water Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.chemosphere.2017.08.133","article-title":"Sewage treatment effluents in Delhi: A key contributor of \u0392-lactam resistant bacteria and genes to the environment","volume":"188","author":"Lamba","year":"2017","journal-title":"Chemosphere"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Mathys, D.A., Mollenkopf, D.F., Feicht, S.M., Adams, R.J., Albers, A.L., Stuever, D.M., Grooters, S.V., Ballash, G.A., Daniels, J.B., and Wittum, T.E. (2019). Carbapenemase-producing Enterobacteriaceae and Aeromonas spp. present in wastewater treatment plant effluent and nearby surface waters in the US. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0218650"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"116011","DOI":"10.1016\/j.watres.2020.116011","article-title":"The environmental contribution to the dissemination of carbapenem and (fluoro)quinolone resistance genes by discharged and reused wastewater effluents: The role of cellular and extracellular DNA","volume":"182","author":"Oliveira","year":"2020","journal-title":"Water Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"aau9124","DOI":"10.1126\/sciadv.aau9124","article-title":"Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence","volume":"5","author":"Kneis","year":"2019","journal-title":"Sci. Adv."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Yang, F., Mao, D., Zhou, H., and Luo, Y. (2016). Prevalence and Fate of Carbapenemase Genes in a Wastewater Treatment Plant in Northern China. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0156383"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"186","DOI":"10.4314\/wsa.v43i2.02","article-title":"Carbapenem-resistant bacteria in a secondary wastewater treatment plant","volume":"43","author":"Hrenovic","year":"2017","journal-title":"Water SA"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1016\/j.watres.2017.09.007","article-title":"The fate of carbapenem-resistant bacteria in a wastewater treatment plant","volume":"126","author":"Hrenovic","year":"2017","journal-title":"Water Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"55","DOI":"10.4314\/wsa.v45i1.07","article-title":"Untreated wastewater as a source of carbapenem-resistant bacteria to the riverine ecosystem","volume":"45","author":"Hrenovic","year":"2019","journal-title":"Water SA"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1080\/09603123.2018.1522423","article-title":"Presence of carbapenem-resistant bacteria in soils affected by illegal waste dumps","volume":"29","author":"Hrenovic","year":"2019","journal-title":"Int. J. Environ. Health Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1529","DOI":"10.1128\/JCM.02981-13","article-title":"Benchmarking of Methods for Genomic Taxonomy","volume":"52","author":"Larsen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1089\/mdr.2015.0072","article-title":"Low Prevalence of Carbapenem-Resistant Bacteria in River Water: Resistance is Mostly Related to Intrinsic Mechanisms","volume":"21","author":"Correia","year":"2015","journal-title":"Microb. Drug Resist."},{"key":"ref_22","unstructured":"WHO (2017). Prioritization of Pathogens to Guide Discovery, Research and Development of New Antibiotics for Drug-Resistant Bacterial Infections, Including Tuberculosis, WHO. WHO\/EMP\/IAU\/2017.12."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.3201\/eid2509.190656","article-title":"Epidemiology of Carbapenemase- Producing Klebsiella pneumoniae in a Hospital, Portugal","volume":"25","author":"Pereira","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3588","DOI":"10.1128\/AAC.05065-14","article-title":"Predominance of KPC-3 in a survey for carbapenemase-producing Enterobacteriaceae in Portugal","volume":"59","author":"Manageiro","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2834","DOI":"10.3389\/fmicb.2018.02834","article-title":"Molecular Epidemiology and Risk Factors of Carbapenemase-Producing Enterobacteriaceae Isolates in Portuguese Hospitals: Results from European Survey on Carbapenemase-Producing Enterobacteriaceae (EuSCAPE)","volume":"9","author":"Manageiro","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1017\/S0950268816002442","article-title":"Outbreak of KPC-3-producing ST15 and ST348 Klebsiella pneumoniae in a Portuguese hospital","volume":"145","author":"Vubil","year":"2017","journal-title":"Epidemiol. Infect."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.3389\/fmicb.2017.01143","article-title":"Insights into a Novel bla KPC-2 -Encoding IncP-6 Plasmid Reveal Carbapenem-Resistance Circulation in Several Enterobacteriaceae Species from Wastewater and a Hospital Source in Spain","volume":"8","author":"Yao","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Zhang, L., Ma, X., Luo, L., Hu, N., Duan, J., Tang, Z., Zhong, R., and Li, Y. (2020). The Prevalence and Characterization of Extended-Spectrum \u03b2-lactamase-and Carbapenemase-Producing Bacteria from Hospital Sewage, Treated Effluents and Receiving Rivers. Int. J. Environ. Res. Public Health, 17.","DOI":"10.3390\/ijerph17041183"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"8113","DOI":"10.1038\/s41598-020-65106-w","article-title":"Characterization of the global distribution and diversified plasmid reservoirs of the colistin resistance gene mcr-9","volume":"10","author":"Li","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_30","first-page":"557","article-title":"Polymyxins: Antibacterial Activity, Susceptibility Testing, and Resistance Mechanisms Encoded by Plasmids or Chromosomes","volume":"30","author":"Poirel","year":"2017","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1080\/10934529.2015.964602","article-title":"Antibiotic resistance in wastewater: Occurrence and fate of Enterobacteriaceae producers of Class A and Class C \u03b2-lactamases","volume":"50","author":"Amador","year":"2015","journal-title":"J. Environ. Sci. Health Part A"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1111\/j.1550-7408.1999.tb04612.x","article-title":"Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis","volume":"46","author":"Turner","year":"1999","journal-title":"J. Eukaryot. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_36","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_37","doi-asserted-by":"crossref","first-page":"2484","DOI":"10.1093\/jac\/dkw184","article-title":"Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data","volume":"71","author":"Clausen","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Clausen, P.T.L.C., Aarestrup, F.M., and Lund, O. (2018). Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinform., 19.","DOI":"10.1186\/s12859-018-2336-6"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1128\/JCM.03617-13","article-title":"Real-time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli","volume":"52","author":"Joensen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_41","unstructured":"EUCAST (2020, February 05). Disk Diffusion Method for Antimicrobial Susceptibility Testing. Available online: https:\/\/www.eucast.org\/fileadmin\/src\/media\/PDFs\/EUCAST_files\/Disk_test_documents\/2021_manuals\/Manual_v_9.0_EUCAST_Disk_Test_2021.pdf."},{"key":"ref_42","unstructured":"Kahlmeter, G. (2020, February 05). The EUCAST Steering Committee Redefining Susceptibility Testing Categories S, I and R. Available online: https:\/\/www.eucast.org\/fileadmin\/src\/media\/PDFs\/EUCAST_files\/EUCAST_Presentations\/2018\/EUCAST_-_Intermediate_category_-_information_for_all.pdf."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/10\/9\/1118\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:00:56Z","timestamp":1760166056000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/10\/9\/1118"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,16]]},"references-count":42,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2021,9]]}},"alternative-id":["antibiotics10091118"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics10091118","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,9,16]]}}}