{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T15:17:34Z","timestamp":1786979854623,"version":"build-2736575974"},"reference-count":243,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T00:00:00Z","timestamp":1774483200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Hainan Province Higher Education Scientific Research Project","award":["Hnky2025ZC-3"],"award-info":[{"award-number":["Hnky2025ZC-3"]}]},{"name":"Hainan Medical University Talent Research Launch Fund","award":["RZ2300006042"],"award-info":[{"award-number":["RZ2300006042"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microb Ecol"],"DOI":"10.1007\/s00248-026-02740-3","type":"journal-article","created":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T02:17:13Z","timestamp":1774491433000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Assessing the Ecological Roles of Resistomes within Microbial Communities in Antibiotic-contaminated Ecosystems"],"prefix":"10.1007","volume":"89","author":[{"given":"Malama","family":"Chewe","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tilahun kefyalew","family":"Shembo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel Patrick","family":"Dumfeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanji","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel Stephen","family":"Odinga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guojing","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Okugbe Ebiotubo","family":"Ohore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,3,26]]},"reference":[{"key":"2740_CR1","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1016\/J.CHOM.2024.05.015","volume":"32","author":"A Abbas","year":"2024","unstructured":"Abbas A, Barkhouse A, Hackenberger D, Wright GD (2024) Antibiotic resistance: a key microbial survival mechanism that threatens public health. Cell Host Microbe 32:837\u2013851. https:\/\/doi.org\/10.1016\/J.CHOM.2024.05.015","journal-title":"Cell Host Microbe"},{"key":"2740_CR2","doi-asserted-by":"publisher","DOI":"10.3389\/FPUBH.2024.1422137\/BIBTEX","volume":"12","author":"TA Abebe","year":"2024","unstructured":"Abebe TA, Gebreyes DS, Abebe BA, Yitayew B (2024) Antibiotic-resistant bacteria and resistance-genes in drinking water source in North Shoa zone, Amhara region, Ethiopia. Front Public Health 12:1422137. https:\/\/doi.org\/10.3389\/FPUBH.2024.1422137\/BIBTEX","journal-title":"Front Public Health"},{"key":"2740_CR3","doi-asserted-by":"publisher","DOI":"10.3390\/IJERPH22081273","volume":"22","author":"A Abraham","year":"2025","unstructured":"Abraham A, Mtewa AG, Chiutula C, Mvula RLS, Maluwa A, Eregno FE, Njalam\u2019mano J (2025) Prevalence of antibiotic resistance bacteria in manure, soil, and vegetables in urban Blantyre, Malawi, from a farm-to-fork perspective. Int J Environ Res Public Health 22:1273. https:\/\/doi.org\/10.3390\/IJERPH22081273","journal-title":"Int J Environ Res Public Health"},{"issue":"6","key":"2740_CR4","doi-asserted-by":"publisher","first-page":"1173","DOI":"10.1007\/S12223-025-01355-4","volume":"70","author":"K Abuelhaded","year":"2025","unstructured":"Abuelhaded K, Mohamed HH, Faraag AHI, Basiouny MS, El-Mongy MA, Mohammed OA, Doghish AS (2025) Pseudomonas spp. and antimicrobial resistance: unlocking new horizons with 1-hydroxyphenazine. Folia Microbiol 70(6):1173\u20131199. https:\/\/doi.org\/10.1007\/S12223-025-01355-4","journal-title":"Folia Microbiol"},{"key":"2740_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12866-020-01983-5\/FIGURES\/5","volume":"20","author":"H Acar Kirit","year":"2020","unstructured":"Acar Kirit H, Lagator M, Bollback JP (2020) Experimental determination of evolutionary barriers to horizontal gene transfer. BMC Microbiol 20:1\u201313. https:\/\/doi.org\/10.1186\/S12866-020-01983-5\/FIGURES\/5","journal-title":"BMC Microbiol"},{"key":"2740_CR6","doi-asserted-by":"publisher","first-page":"047","DOI":"10.30574\/WJBPHS.2025.22.3.0504","volume":"22","author":"H Agboro","year":"2025","unstructured":"Agboro H, Iyiola AT, Ohaekwe CC, Adebowale MT, Lawal M, Ali VE, Philips OA (2025) Antibiotic resistance genes (ARGs) in wastewater: environmental fate and risk mitigation strategies. World Journal of Biology Pharmacy and Health Sciences 22:047\u2013063. https:\/\/doi.org\/10.30574\/WJBPHS.2025.22.3.0504","journal-title":"World Journal of Biology Pharmacy and Health Sciences"},{"key":"2740_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.15244\/PJOES\/185701","volume":"34","author":"KF Alabbosh","year":"2025","unstructured":"Alabbosh KF (2025) Leveraging the potential of environmental microorganisms: an extensive examination of their capacity in tackling global and local environmental and ecological challenges. Pol J Environ Stud 34:1\u201311. https:\/\/doi.org\/10.15244\/PJOES\/185701","journal-title":"Pol J Environ Stud"},{"key":"2740_CR8","doi-asserted-by":"publisher","first-page":"11512","DOI":"10.1073\/PNAS.0801925105","volume":"105","author":"SD Allison","year":"2008","unstructured":"Allison SD, Martiny JBH (2008) Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci U S A 105:11512\u201311519. https:\/\/doi.org\/10.1073\/PNAS.0801925105","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2740_CR9","doi-asserted-by":"publisher","DOI":"10.3390\/BIOLOGY14020165","volume":"14","author":"A Almatroudi","year":"2025","unstructured":"Almatroudi A (2025) Biofilm resilience: molecular mechanisms driving antibiotic resistance in clinical contexts. Biology (Basel) 14:165. https:\/\/doi.org\/10.3390\/BIOLOGY14020165","journal-title":"Biology (Basel)"},{"key":"2740_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S41467-021-22849-Y","volume":"12","author":"A del Alonso- Valle","year":"2021","unstructured":"del Alonso- Valle A, Le\u00f3n-Sampedro R, Rodr\u00edguez-Beltr\u00e1n J, DelaFuente J, Hern\u00e1ndez-Garc\u00eda M, Ruiz-Garbajosa P, Cant\u00f3n R, Pe\u00f1a-Miller R, San Mill\u00e1n A (2021) Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities. Nat Commun 12:1\u201314. https:\/\/doi.org\/10.1038\/S41467-021-22849-Y","journal-title":"Nat Commun"},{"key":"2740_CR11","doi-asserted-by":"publisher","first-page":"2016","DOI":"10.1080\/10643389.2019.1692611","volume":"50","author":"M Amarasiri","year":"2020","unstructured":"Amarasiri M, Sano D, Suzuki S (2020) Understanding human health risks caused by antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) in water environments: current knowledge and questions to be answered. Crit Rev Environ Sci Technol 50:2016\u20132059. https:\/\/doi.org\/10.1080\/10643389.2019.1692611","journal-title":"Crit Rev Environ Sci Technol"},{"key":"2740_CR12","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2013.00241\/XML","volume":"4","author":"RI Aminov","year":"2013","unstructured":"Aminov RI (2013) Biotic acts of antibiotics. Front Microbiol 4:60635. https:\/\/doi.org\/10.3389\/FMICB.2013.00241\/XML","journal-title":"Front Microbiol"},{"key":"2740_CR13","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1038\/nrmicro3270","volume":"12","author":"DI Andersson","year":"2014","unstructured":"Andersson DI, Hughes D (2014) Microbiological effects of sublethal levels of antibiotics. Nature Reviews Microbiology 2014 12:7 12:465\u2013478. https:\/\/doi.org\/10.1038\/nrmicro3270","journal-title":"Nature Reviews Microbiology 2014 12:7"},{"key":"2740_CR14","doi-asserted-by":"publisher","DOI":"10.1186\/S12915-024-01937-7","volume":"22","author":"SG Babajanyan","year":"2024","unstructured":"Babajanyan SG, Garushyants SK, Wolf YI, Koonin EV (2024) Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model. BMC Biology 2024 22:1 22:148-. https:\/\/doi.org\/10.1186\/S12915-024-01937-7","journal-title":"BMC Biology 2024 22:1"},{"issue":"7773","key":"2740_CR15","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41586-019-1521-8","volume":"573","author":"E Bakkeren","year":"2019","unstructured":"Bakkeren E, Huisman JS, Fattinger SA, Hausmann A, Furter M, Egli A, Slack E, Sellin ME, Bonhoeffer S, Regoes RR, Diard M, Hardt WD (2019) Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut. Nature 573(7773):276\u2013280. https:\/\/doi.org\/10.1038\/s41586-019-1521-8","journal-title":"Nature"},{"key":"2740_CR16","doi-asserted-by":"publisher","DOI":"10.1038\/S41564-025-02162-W","author":"E Bakkeren","year":"2025","unstructured":"Bakkeren E, Piskovsky V, Lee MNY, Jahn MT, Foster KR (2025) Strain displacement in microbiomes via ecological competition. Nat Microbiol. https:\/\/doi.org\/10.1038\/S41564-025-02162-W","journal-title":"Nat Microbiol"},{"key":"2740_CR17","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2015.01216\/BIBTEX","volume":"6","author":"JL Balc\u00e1zar","year":"2015","unstructured":"Balc\u00e1zar JL, Subirats J, Borrego CM (2015) The role of biofilms as environmental reservoirs of antibiotic resistance. Front Microbiol 6:155551. https:\/\/doi.org\/10.3389\/FMICB.2015.01216\/BIBTEX","journal-title":"Front Microbiol"},{"key":"2740_CR18","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1016\/j.bpj.2017.11.3739","volume":"114","author":"E Ban","year":"2018","unstructured":"Ban E, Franklin JM, Nam S, Smith LR, Wang H, Wells RG, Chaudhuri O, Liphardt JT, Shenoy VB (2018) Mechanisms of plastic deformation in collagen networks induced by cellular forces. Biophys J 114:450\u2013461. https:\/\/doi.org\/10.1016\/j.bpj.2017.11.3739","journal-title":"Biophys J"},{"key":"2740_CR19","doi-asserted-by":"publisher","DOI":"10.3389\/FEVO.2020.00021\/FULL","volume":"8","author":"T Banitz","year":"2020","unstructured":"Banitz T, Chatzinotas A, Worrich A (2020) Prospects for integrating disturbances, biodiversity and ecosystem functioning using microbial systems. Front Ecol Evol 8:480992. https:\/\/doi.org\/10.3389\/FEVO.2020.00021\/FULL","journal-title":"Front Ecol Evol"},{"key":"2740_CR21","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00050-19","author":"F Baquero","year":"2021","unstructured":"Baquero F, Mart\u00ednez JL, Lanza VF, Rodr\u00edguez-Beltr\u00e1n J, Gal\u00e1n JC, San Mill\u00e1n A, Cant\u00f3n R, Coque TM (2021) Evolutionary pathways and trajectories in antibiotic resistance. Clin Microbiol Rev. https:\/\/doi.org\/10.1128\/CMR.00050-19","journal-title":"Clin Microbiol Rev"},{"key":"2740_CR22","doi-asserted-by":"publisher","first-page":"798","DOI":"10.3390\/ANTIBIOTICS14080798\/S1","volume":"14","author":"K Barrantes-Jim\u00e9nez","year":"2025","unstructured":"Barrantes-Jim\u00e9nez K, Mendoza-Guido B, Morales-Mora E, Rivera-Montero L, Montiel-Mora J, Chac\u00f3n-Jim\u00e9nez L, Rojas-Jim\u00e9nez K, Arias-Andr\u00e9s M (2025) Influence of seasonality and pollution on the presence of antibiotic resistance genes and potentially pathogenic bacteria in a tropical urban river. Antibiotics 14:798. https:\/\/doi.org\/10.3390\/ANTIBIOTICS14080798\/S1","journal-title":"Antibiotics"},{"issue":"1","key":"2740_CR23","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09058-4","volume":"10","author":"TC Barrett","year":"2019","unstructured":"Barrett TC, Mok WWK, Murawski AM, Brynildsen MP (2019) Enhanced antibiotic resistance development from fluoroquinolone persisters after a single exposure to antibiotic. Nat Commun (1):1177. https:\/\/doi.org\/10.1038\/s41467-019-09058-4","journal-title":"Nat Commun"},{"key":"2740_CR24","doi-asserted-by":"publisher","first-page":"1612","DOI":"10.1080\/09593330.2024.2394719","volume":"46","author":"D Basiry","year":"2025","unstructured":"Basiry D, Kommedal R, Kaster KM (2025) Effect of subinhibitory concentrations on the spreading of the ampicillin resistance gene blaCMY-2 in an activated sludge microcosm. Environ Technol 46:1612\u20131624. https:\/\/doi.org\/10.1080\/09593330.2024.2394719","journal-title":"Environ Technol"},{"key":"2740_CR25","doi-asserted-by":"publisher","DOI":"10.3402\/IEE.V5.28564","volume":"5","author":"B Berglund","year":"2015","unstructured":"Berglund B (2015) Environmental dissemination of antibiotic resistance genes and correlation to anthropogenic contamination with antibiotics. Infection Ecology & Epidemiology 5:28564. https:\/\/doi.org\/10.3402\/IEE.V5.28564","journal-title":"Infection Ecology & Epidemiology"},{"key":"2740_CR26","doi-asserted-by":"publisher","first-page":"4368","DOI":"10.1016\/J.MOLCEL.2022.10.024","volume":"82","author":"S Bhattacharyya","year":"2022","unstructured":"Bhattacharyya S, Bhattacharyya M, Pfannenstiel DM, Nandi AK, Hwang YS, Ho K, Harshey RM (2022) Efflux-linked accelerated evolution of antibiotic resistance at a population edge. Mol Cell 82:4368-4385e.e6. https:\/\/doi.org\/10.1016\/J.MOLCEL.2022.10.024","journal-title":"Mol Cell"},{"key":"2740_CR27","doi-asserted-by":"publisher","DOI":"10.1093\/FEMSEC\/FIAD027","volume":"99","author":"SM Bird","year":"2023","unstructured":"Bird SM, Ford S, Thompson CMA, Little R, Hall Jacob Malone JPJ, Harrison E, Brockhurst MA, Jackson RW (2023) Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities. FEMS Microbiol Ecol 99:fiad027. https:\/\/doi.org\/10.1093\/FEMSEC\/FIAD027","journal-title":"FEMS Microbiol Ecol"},{"issue":"1","key":"2740_CR28","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-56425-5","volume":"2025","author":"KS Blake","year":"2025","unstructured":"Blake KS, Xue YP, Gillespie VJ, Fishbein SRS, Tolia NH, Wencewicz TA, Dantas G (2025) The tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation. Nat Commun 2025(1):1452. https:\/\/doi.org\/10.1038\/s41467-025-56425-5","journal-title":"Nat Commun"},{"key":"2740_CR29","doi-asserted-by":"publisher","DOI":"10.1128\/MSYSTEMS.01018-23","author":"A Bogri","year":"2024","unstructured":"Bogri A, Jensen EEB, Borchert AV, Brinch C, Otani S, Aarestrup FM (2024) Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations. mSystems. https:\/\/doi.org\/10.1128\/MSYSTEMS.01018-23","journal-title":"mSystems"},{"key":"2740_CR30","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1111\/RAQ.12786","volume":"15","author":"MG Bondad-Reantaso","year":"2023","unstructured":"Bondad-Reantaso MG, MacKinnon B, Karunasagar I, Fridman S, Alday-Sanz V, Brun E, Le Groumellec M, Li A, Surachetpong W, Karunasagar I, Hao B, Dall\u2019Occo A, Urbani R, Caputo A (2023) Review of alternatives to antibiotic use in aquaculture. Rev Aquac 15:1421\u20131451. https:\/\/doi.org\/10.1111\/RAQ.12786","journal-title":"Rev Aquac"},{"key":"2740_CR31","doi-asserted-by":"publisher","DOI":"10.1016\/J.MIB.2022.102152","volume":"68","author":"MJ Bottery","year":"2022","unstructured":"Bottery MJ (2022) Ecological dynamics of plasmid transfer and persistence in microbial communities. Curr Opin Microbiol 68:102152. https:\/\/doi.org\/10.1016\/J.MIB.2022.102152","journal-title":"Curr Opin Microbiol"},{"key":"2740_CR32","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2022.883081\/BIBTEX","volume":"13","author":"E Bourdonnais","year":"2022","unstructured":"Bourdonnais E, Colcanap D, Le Bris C, Brauge T, Midelet G (2022) Occurrence of indicator genes of antimicrobial resistance contamination in the English Channel and North Sea sectors and interactions with environmental variables. Front Microbiol 13:883081. https:\/\/doi.org\/10.3389\/FMICB.2022.883081\/BIBTEX","journal-title":"Front Microbiol"},{"key":"2740_CR33","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2024.1305148\/BIBTEX","volume":"15","author":"NL Bragazzi","year":"2024","unstructured":"Bragazzi NL, Woldegerima WA, Siri A (2024) Economic microbiology: exploring microbes as agents in economic systems. Front Microbiol 15:1305148. https:\/\/doi.org\/10.3389\/FMICB.2024.1305148\/BIBTEX","journal-title":"Front Microbiol"},{"key":"2740_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12879-019-4268-9\/FIGURES\/1","volume":"19","author":"L Brescini","year":"2019","unstructured":"Brescini L, Morroni G, Valeriani C, Castelletti S, Mingoia M, Simoni S, Masucci A, Montalti R, Vivarelli M, Giacometti A, Barchiesi F (2019) Clinical and epidemiological characteristics of KPC-producing Klebsiella pneumoniae from bloodstream infections in a tertiary referral center in Italy. BMC Infect Dis 19:1\u20139. https:\/\/doi.org\/10.1186\/S12879-019-4268-9\/FIGURES\/1","journal-title":"BMC Infect Dis"},{"issue":"7","key":"2740_CR35","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1038\/s41579-021-00534-7","volume":"19","author":"IL Brito","year":"2021","unstructured":"Brito IL (2021) Examining horizontal gene transfer in microbial communities. Nat Rev Microbiol 19(7):442\u2013453. https:\/\/doi.org\/10.1038\/s41579-021-00534-7","journal-title":"Nat Rev Microbiol"},{"key":"2740_CR36","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1016\/j.tim.2021.11.001","volume":"30","author":"MA Brockhurst","year":"2022","unstructured":"Brockhurst MA, Harrison E (2022) Ecological and evolutionary solutions to the plasmid paradox. Trends Microbiol 30:534\u2013543. https:\/\/doi.org\/10.1016\/j.tim.2021.11.001","journal-title":"Trends Microbiol"},{"issue":"1","key":"2740_CR37","doi-asserted-by":"publisher","DOI":"10.1186\/S40168-022-01321-Z","volume":"10","author":"E Broman","year":"2022","unstructured":"Broman E, Izabel-Shen D, Rodr\u00edguez-Gij\u00f3n A, Bonaglia S, Garcia SL, Nascimento FJA (2022) Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem. Microbiome 10(1):126. https:\/\/doi.org\/10.1186\/S40168-022-01321-Z","journal-title":"Microbiome"},{"key":"2740_CR38","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1016\/j.tree.2018.09.008","volume":"33","author":"JM Bullock","year":"2018","unstructured":"Bullock JM, Bonte D, Pufal G, da Silva Carvalho C, Chapman DS, Garc\u00eda C, Garc\u00eda D, Matthysen E, Delgado MM (2018) Human-mediated dispersal and the rewiring of spatial networks. Trends Ecol Evol 33:958\u2013970. https:\/\/doi.org\/10.1016\/j.tree.2018.09.008","journal-title":"Trends Ecol Evol"},{"key":"2740_CR39","doi-asserted-by":"publisher","DOI":"10.1093\/GBE\/EVAD089","author":"CL Burch","year":"2023","unstructured":"Burch CL, Romanchuk A, Kelly M, Wu Y, Jones CD (2023) Empirical evidence that complexity limits horizontal gene transfer. Genome Biol Evol. https:\/\/doi.org\/10.1093\/GBE\/EVAD089","journal-title":"Genome Biol Evol"},{"key":"2740_CR40","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/s41579-022-00833-7","volume":"21","author":"G Caballero-Flores","year":"2022","unstructured":"Caballero-Flores G, Pickard JM, N\u00fa\u00f1ez G (2022) Microbiota-mediated colonization resistance: mechanisms and regulation. Nature Reviews Microbiology 2022 21:6 21:347\u2013360. https:\/\/doi.org\/10.1038\/s41579-022-00833-7","journal-title":"Nature Reviews Microbiology 2022 21:6"},{"issue":"1","key":"2740_CR41","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-018-0041-7","volume":"1","author":"J Cairns","year":"2018","unstructured":"Cairns J, Ruokolainen L, Hultman J, Tamminen M, Virta M, Hiltunen T (2018) Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes. Commun Biol 1(1):1\u20138. https:\/\/doi.org\/10.1038\/s42003-018-0041-7","journal-title":"Commun Biol"},{"issue":"5","key":"2740_CR42","doi-asserted-by":"publisher","DOI":"10.1073\/PNAS.2309575121","volume":"121","author":"J Camacho-Mateu","year":"2024","unstructured":"Camacho-Mateu J, Lampo A, Sireci M, Mu\u00f1oz MA, Cuesta JA (2024) Sparse species interactions reproduce abundance correlation patterns in microbial communities. Proc Natl Acad Sci U S A 121(5):e2309575121. https:\/\/doi.org\/10.1073\/PNAS.2309575121","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2740_CR43","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2012.00110\/XML","volume":"3","author":"R Cant\u00f3n","year":"2012","unstructured":"Cant\u00f3n R, Gonz\u00e1lez-Alba JM, Gal\u00e1n JC (2012) CTX-M enzymes: origin and diffusion. Front Microbiol 3:20597. https:\/\/doi.org\/10.3389\/FMICB.2012.00110\/XML","journal-title":"Front Microbiol"},{"issue":"1","key":"2740_CR44","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1038\/s41579-023-00926-x","volume":"22","author":"S Casta\u00f1eda-Barba","year":"2023","unstructured":"Casta\u00f1eda-Barba S, Top EM, Stalder T (2023) Plasmids, a molecular cornerstone of antimicrobial resistance in the one health era. Nat Rev Microbiol 22(1):18\u201332. https:\/\/doi.org\/10.1038\/s41579-023-00926-x","journal-title":"Nat Rev Microbiol"},{"key":"2740_CR45","doi-asserted-by":"publisher","DOI":"10.1016\/J.ENVINT.2020a.105538","volume":"137","author":"H Chen","year":"2020","unstructured":"Chen H, Li Y, Sun W, Song L, Zuo R, Teng Y (2020a) Characterization and source identification of antibiotic resistance genes in the sediments of an interconnected river-lake system. Environ Int 137:105538. https:\/\/doi.org\/10.1016\/J.ENVINT.2020a.105538","journal-title":"Environ Int"},{"key":"2740_CR47","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/S42832-019-0011-0","volume":"1","author":"QL Chen","year":"2019","unstructured":"Chen QL, An XL, Zheng BX, Gillings M, Pe\u00f1uelas J, Cui L, Su JQ, Zhu YG (2019) Loss of soil microbial diversity exacerbates spread of antibiotic resistance. Soil Ecol Lett 1:3\u201313. https:\/\/doi.org\/10.1007\/S42832-019-0011-0","journal-title":"Soil Ecol Lett"},{"key":"2740_CR48","doi-asserted-by":"crossref","unstructured":"Chen X, Crocker K, Kuehn S, Walczak AM, Mora T (2025) Inferring resource competition in microbial communities from time series","DOI":"10.1101\/2025.01.08.631910"},{"issue":"10","key":"2740_CR49","doi-asserted-by":"publisher","first-page":"2696","DOI":"10.1038\/s41564-024-01775-x","volume":"9","author":"Y Cherrak","year":"2024","unstructured":"Cherrak Y, Salazar MA, N\u00e4pflin N, Malfertheiner L, Herzog MKM, Schubert C, von Mering C, Hardt WD (2024) Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut. Nat Microbiol 9(10):2696\u20132709. https:\/\/doi.org\/10.1038\/s41564-024-01775-x","journal-title":"Nat Microbiol"},{"key":"2740_CR50","doi-asserted-by":"publisher","DOI":"10.1177\/1178636119889629","author":"N Chowdhury","year":"2019","unstructured":"Chowdhury N, Suhani S, Purkaystha A, Begum MK, Raihan T, Alam M, Islam K, Azad AK (2019) Identification of AcrAB-TolC efflux pump genes and detection of mutation in efflux repressor AcrR from omeprazole responsive multidrug-resistant Escherichia coli isolates causing urinary tract infections. Microbiol Insights. https:\/\/doi.org\/10.1177\/1178636119889629","journal-title":"Microbiol Insights"},{"key":"2740_CR51","doi-asserted-by":"publisher","DOI":"10.1128\/MSPHERE.00718-24","author":"M Chua","year":"2024","unstructured":"Chua M, Collins J (2024) Mice colonized with the defined microbial community OMM19.1 are susceptible to Clostridioides difficile infection without prior antibiotic treatment. mSphere. https:\/\/doi.org\/10.1128\/MSPHERE.00718-24","journal-title":"mSphere"},{"issue":"1","key":"2740_CR52","doi-asserted-by":"publisher","first-page":"1231-","DOI":"10.1038\/s41467-022-28188-w","volume":"13","author":"H Chung","year":"2022","unstructured":"Chung H, Merakou C, Schaefers MM, Flett KB, Martini S, Lu R, Blumenthal JA, Webster SS, Cross AR, Al Ahmar R, Halpin E, Anderson M, Moore NS, Snesrud EC, Yu HD, Goldberg JB, O\u2019Toole GA, McGann P, Stam JA, Hinkle M, McAdam AJ, Kishony R, Priebe GP (2022) Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections. Nat Commun 13(1):1231-. https:\/\/doi.org\/10.1038\/s41467-022-28188-w","journal-title":"Nat Commun"},{"key":"2740_CR53","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PBIO.3002329","volume":"21","author":"CH Connor","year":"2023","unstructured":"Connor CH, Zucoloto AZ, Munnoch JT, Yu IL, Corander J, Hoskisson PA, McDonald B, McNally A (2023) Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract. PLoS Biol 21:e3002329. https:\/\/doi.org\/10.1371\/JOURNAL.PBIO.3002329","journal-title":"PLoS Biol"},{"key":"2740_CR54","doi-asserted-by":"publisher","first-page":"2190","DOI":"10.1038\/S41396-023-01512-Y","volume":"17","author":"I Cordero","year":"2023","unstructured":"Cordero I, Leizeaga A, Hicks LC, Rousk J, Bardgett RD (2023) High intensity perturbations induce an abrupt shift in soil microbial state. ISME J 17:2190\u20132199. https:\/\/doi.org\/10.1038\/S41396-023-01512-Y","journal-title":"ISME J"},{"key":"2740_CR55","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PBIO.3001847","volume":"20","author":"KZ Coyte","year":"2022","unstructured":"Coyte KZ, Stevenson C, Knight CG, Harrison E, Hall JPJ, Brockhurst MA (2022) Horizontal gene transfer and ecological interactions jointly control microbiome stability. PLoS Biol 20:e3001847. https:\/\/doi.org\/10.1371\/JOURNAL.PBIO.3001847","journal-title":"PLoS Biol"},{"key":"2740_CR56","doi-asserted-by":"publisher","DOI":"10.1002\/BIES.202400164","author":"HD Curtsinger","year":"2025","unstructured":"Curtsinger HD, Mart\u00ednez-Absal\u00f3n S, Liu Y, Lopatkin AJ (2025) The metabolic burden associated with plasmid acquisition: an assessment of the unrecognized benefits to host cells. Bioessays. https:\/\/doi.org\/10.1002\/BIES.202400164","journal-title":"Bioessays"},{"key":"2740_CR57","doi-asserted-by":"publisher","DOI":"10.3389\/FGENE.2020.575592\/XML","volume":"11","author":"VAC de Abreu","year":"2021","unstructured":"de Abreu VAC, Perdig\u00e3o J, Almeida S (2021) Metagenomic approaches to analyze antimicrobial resistance: an overview. Front Genet 11:575592. https:\/\/doi.org\/10.3389\/FGENE.2020.575592\/XML","journal-title":"Front Genet"},{"key":"2740_CR58","doi-asserted-by":"publisher","unstructured":"de Vries FT, Griffiths RI, Bailey M, Craig H, Girlanda M, Gweon HS, Hallin S, Kaisermann A, Keith AM, Kretzschmar M, Lemanceau P, Lumini E, Mason KE, Oliver A, Ostle N, Prosser JI, Thion C, Thomson B, Bardgett RD (2018) Soil bacterial networks are less stable under drought than fungal networks. Nat Commun. https:\/\/doi.org\/10.1038\/s41467-018-05516-7","DOI":"10.1038\/s41467-018-05516-7"},{"key":"2740_CR59","doi-asserted-by":"publisher","DOI":"10.1186\/S40168-022-01405-W","author":"M Delgado-Baquerizo","year":"2022","unstructured":"Delgado-Baquerizo M, Hu HW, Maestre FT, Guerra CA, Eisenhauer N, Eldridge DJ, Zhu YG, Chen QL, Trivedi P, Du S, Makhalanyane TP, Verma JP, Gozalo B, Ochoa V, Asensio S, Wang L, Zaady E, Ill\u00e1n JG, Siebe C, Grebenc T, Zhou X, Liu YR, Bamigboye AR, Blanco-Pastor JL, Duran J, Rodr\u00edguez A, Mamet S, Alfaro F, Abades S, Teixido AL, Pe\u00f1aloza-Bojac\u00e1 GF, Molina-Montenegro MA, Torres-D\u00edaz C, Perez C, Gallardo A, Garc\u00eda-Vel\u00e1zquez L, Hayes PE, Neuhauser S, He JZ (2022) The global distribution and environmental drivers of the soil antibiotic resistome. Microbiome. https:\/\/doi.org\/10.1186\/S40168-022-01405-W","journal-title":"Microbiome"},{"key":"2740_CR60","doi-asserted-by":"publisher","DOI":"10.1038\/S41467-023-42998-6","author":"PJ Diebold","year":"2023","unstructured":"Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, Ahmed S, Kulkarni V, Deshpande P, Alexander M, Thi Hoa N, Christakis NA, Iqbal NT, Ali SA, Mathad JS, Brito IL (2023) Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nat Commun. https:\/\/doi.org\/10.1038\/S41467-023-42998-6","journal-title":"Nat Commun"},{"key":"2740_CR61","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2023.1207441\/FULL","volume":"14","author":"Y Ding","year":"2023","unstructured":"Ding Y, Hao J, Xiao W, Ye C, Xiao X, Jian C, Tang M, Li G, Liu J, Zeng Z (2023) Role of efflux pumps, their inhibitors, and regulators in colistin resistance. Front Microbiol 14:1207441. https:\/\/doi.org\/10.3389\/FMICB.2023.1207441\/FULL","journal-title":"Front Microbiol"},{"key":"2740_CR62","doi-asserted-by":"publisher","first-page":"e70042","DOI":"10.1111\/1758-2229.70042","volume":"16","author":"Y Ding","year":"2024","unstructured":"Ding Y, Ma RA, Zhang R, Zhang H, Zhang J, Li S, Zhang SY (2024) Increased antibiotic resistance gene abundance linked to intensive bacterial competition in the phyllosphere across an elevational gradient. Environ Microbiol Rep 16:e70042. https:\/\/doi.org\/10.1111\/1758-2229.70042;WEBSITE:WEBSITE:SFAMJOURNALS;WGROUP:STRING:PUBLICATION","journal-title":"Environ Microbiol Rep"},{"key":"2740_CR63","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1038\/S41559-024-02357-0","volume":"8","author":"M Dmitrijeva","year":"2024","unstructured":"Dmitrijeva M, Tackmann J, Matias Rodrigues JF, Huerta-Cepas J, Coelho LP, von Mering C (2024) A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer. Nat. Ecol. Evol. 8:986\u2013998. https:\/\/doi.org\/10.1038\/S41559-024-02357-0","journal-title":"Nat. Ecol. Evol."},{"key":"2740_CR64","doi-asserted-by":"publisher","first-page":"4681","DOI":"10.3390\/IJERPH16234681","volume":"16","author":"B Du","year":"2019","unstructured":"Du B, Yang Q, Wang R, Wang R, Wang Q, Xin Y (2019) Evolution of antibiotic resistance and the relationship between the antibiotic resistance genes and microbial compositions under long-term exposure to tetracycline and sulfamethoxazole. Int J Environ Res Public Health 16:4681\u20134681. https:\/\/doi.org\/10.3390\/IJERPH16234681","journal-title":"Int J Environ Res Public Health"},{"key":"2740_CR65","doi-asserted-by":"publisher","DOI":"10.1128\/MSYSTEMS.00726-24","author":"S Duller","year":"2024","unstructured":"Duller S, Kumpitsch C, Moissl-Eichinger C, Wink L, Koskinen Mora K, Mahnert A (2024) In-hospital areas with distinct maintenance and staff\/patient traffic have specific microbiome profiles, functions, and resistomes. mSystems. https:\/\/doi.org\/10.1128\/MSYSTEMS.00726-24","journal-title":"mSystems"},{"issue":"1","key":"2740_CR66","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-025-98498-8","volume":"15","author":"A El Badawy","year":"2025","unstructured":"El Badawy A, Hamza D, Ahmed Z, Sabry MA (2025) Seasonal and environmental drivers of antibiotic resistance and virulence in Escherichia coli from aquaculture and their public health implications. Sci Rep 15(1):16100. https:\/\/doi.org\/10.1038\/s41598-025-98498-8","journal-title":"Sci Rep"},{"key":"2740_CR67","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PCBI.1006179","volume":"14","author":"S Estrela","year":"2018","unstructured":"Estrela S, Brown SP (2018) Community interactions and spatial structure shape selection on antibiotic resistant lineages. PLoS Comput. Biol. 14:e1006179. https:\/\/doi.org\/10.1371\/JOURNAL.PCBI.1006179","journal-title":"PLoS Comput. Biol."},{"key":"2740_CR68","doi-asserted-by":"publisher","DOI":"10.1016\/J.SCITOTENV.2023.164265","volume":"889","author":"Y Fan","year":"2023","unstructured":"Fan Y, Li Z, Li B, Ke B, Zhao W, Lu P, Li Z, Zhang T, Lu X, Kan B (2023) Metagenomic profiles of planktonic bacteria and resistome along a salinity gradient in the Pearl River estuary, South China. Sci Total Environ 889:164265. https:\/\/doi.org\/10.1016\/J.SCITOTENV.2023.164265","journal-title":"Sci Total Environ"},{"issue":"4","key":"2740_CR69","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1111\/J.1469-185X.2008.00054.X","volume":"83","author":"T Fenchel","year":"2008","unstructured":"Fenchel T, Finlay B (2008) Oxygen and the spatial structure of microbial communities. Biol Rev 83(4):553\u2013569. https:\/\/doi.org\/10.1111\/J.1469-185X.2008.00054.X","journal-title":"Biol Rev"},{"key":"2740_CR70","doi-asserted-by":"publisher","first-page":"539","DOI":"10.3390\/ANTIBIOTICS13060539\/S1","volume":"13","author":"G Flores-Vargas","year":"2024","unstructured":"Flores-Vargas G, Bergsveinson J, Korber DR (2024) Environmentally relevant antibiotic concentrations exert stronger selection pressure on river biofilm resistomes than AMR-reservoir effluents. Antibiotics 13:539. https:\/\/doi.org\/10.3390\/ANTIBIOTICS13060539\/S1","journal-title":"Antibiotics"},{"key":"2740_CR71","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2016.175","author":"Y Gerardin","year":"2016","unstructured":"Gerardin Y, Springer M, Kishony R (2016) A competitive trade-off limits the selective advantage of increased antibiotic production. Nat Microbiol. https:\/\/doi.org\/10.1038\/nmicrobiol.2016.175","journal-title":"Nat Microbiol"},{"key":"2740_CR72","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2024.1338026\/BIBTEX","volume":"15","author":"TM Ghaly","year":"2024","unstructured":"Ghaly TM, Gillings MR, Rajabal V, Paulsen IT, Tetu SG (2024) Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange. Front Microbiol 15:1338026. https:\/\/doi.org\/10.3389\/FMICB.2024.1338026\/BIBTEX","journal-title":"Front Microbiol"},{"key":"2740_CR73","doi-asserted-by":"publisher","DOI":"10.1093\/FEMSRE\/FUAE017","author":"BF Gillieatt","year":"2024","unstructured":"Gillieatt BF, Coleman NV (2024) Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria. FEMS Microbiol Rev. https:\/\/doi.org\/10.1093\/FEMSRE\/FUAE017","journal-title":"FEMS Microbiol Rev"},{"key":"2740_CR74","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1111\/j.1462-2920.2005.00695.x","volume":"7","author":"MS Girvan","year":"2005","unstructured":"Girvan MS, Campbell CD, Killham K, Prosser JI, Glover LA (2005) Bacterial diversity promotes community stability and functional resilience after perturbation. Environ Microbiol 7:301\u2013313. https:\/\/doi.org\/10.1111\/j.1462-2920.2005.00695.x","journal-title":"Environ Microbiol"},{"key":"2740_CR75","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PBIO.3002907","volume":"22","author":"EM Glass","year":"2024","unstructured":"Glass EM, Dillard LR, Kolling GL, Warren AS, Papin JA (2024) Niche-specific metabolic phenotypes can be used to identify antimicrobial targets in pathogens. PLoS Biol 22:e3002907. https:\/\/doi.org\/10.1371\/JOURNAL.PBIO.3002907","journal-title":"PLoS Biol"},{"key":"2740_CR76","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevLett.120.158102","volume":"120","author":"A Goyal","year":"2018","unstructured":"Goyal A, Maslov S (2018) Diversity, stability, and reproducibility in stochastically assembled microbial ecosystems. Phys Rev Lett 120:158102. https:\/\/doi.org\/10.1103\/PhysRevLett.120.158102","journal-title":"Phys Rev Lett"},{"key":"2740_CR77","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1111\/J.1574-6976.2012.00343.X","volume":"37","author":"BS Griffiths","year":"2013","unstructured":"Griffiths BS, Philippot L (2013) Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol Rev 37:112\u2013129. https:\/\/doi.org\/10.1111\/J.1574-6976.2012.00343.X","journal-title":"FEMS Microbiol Rev"},{"key":"2740_CR78","doi-asserted-by":"publisher","DOI":"10.1016\/J.AQUATOX.2022.106221","volume":"249","author":"Y Guan","year":"2022","unstructured":"Guan Y, Jia J, Fan X, Li K, Wang Z (2022) Anthropogenic impacts on antibiotic resistance genes and their hosts from pristine to urban river using metagenomic and binning approaches. Aquat Toxicol 249:106221. https:\/\/doi.org\/10.1016\/J.AQUATOX.2022.106221","journal-title":"Aquat Toxicol"},{"key":"2740_CR79","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2022.972267\/BIBTEX","volume":"13","author":"F Guill\u00e9n-Chable","year":"2022","unstructured":"Guill\u00e9n-Chable F, Avila Castro LA, Rodr\u00edguez-Escamilla Z, Mart\u00ednez-N\u00fa\u00f1ez MA (2022) Insights into coastal microbial antibiotic resistome through a meta-transcriptomic approach in Yucatan. Front Microbiol 13:972267. https:\/\/doi.org\/10.3389\/FMICB.2022.972267\/BIBTEX","journal-title":"Front Microbiol"},{"key":"2740_CR80","doi-asserted-by":"publisher","DOI":"10.1016\/J.ECOENV.2020.111362","volume":"205","author":"X Guo","year":"2020","unstructured":"Guo X, Zhong H, Li P, Zhang C (2020) Microbial communities responded to tetracyclines and Cu(II) in constructed wetlands microcosms with Myriophyllum aquaticum. Ecotoxicol Environ Saf 205:111362. https:\/\/doi.org\/10.1016\/J.ECOENV.2020.111362","journal-title":"Ecotoxicol Environ Saf"},{"key":"2740_CR81","doi-asserted-by":"publisher","unstructured":"Bhat H, Tandel RA, Pandey RS (2022) P.K., Alternatives to antibiotics for combating the antimicrobial resistance in aquaculture 1\u201318. https:\/\/doi.org\/10.36062\/ijah.2022.spl.01322","DOI":"10.36062\/ijah.2022.spl.01322"},{"key":"2740_CR82","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2025.1529157","volume":"16","author":"B Han","year":"2025","unstructured":"Han B, Feng C, Jiang Y, Ye C, Wei Y, Liu J, Zeng Z (2025) Mobile genetic elements encoding antibiotic resistance genes and virulence genes in Klebsiella pneumoniae: important pathways for the acquisition of virulence and resistance. Front Microbiol 16:1529157. https:\/\/doi.org\/10.3389\/FMICB.2025.1529157","journal-title":"Front Microbiol"},{"key":"2740_CR83","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2022.976657","volume":"13","author":"B Han","year":"2022","unstructured":"Han B, Ma L, Yu Q, Yang J, Su W, Hilal MG, Li X, Zhang S, Li H (2022) The source, fate and prospect of antibiotic resistance genes in soil: a review. Front Microbiol 13:976657. https:\/\/doi.org\/10.3389\/FMICB.2022.976657","journal-title":"Front Microbiol"},{"issue":"1","key":"2740_CR84","doi-asserted-by":"publisher","DOI":"10.3390\/ANTIBIOTICS11010040","volume":"11","author":"CM Hasan","year":"2021","unstructured":"Hasan CM, Dutta D, Nguyen ANT (2021) Revisiting antibiotic resistance: mechanistic foundations to evolutionary outlook. Antibiotics 11(1):40. https:\/\/doi.org\/10.3390\/ANTIBIOTICS11010040","journal-title":"Antibiotics"},{"key":"2740_CR85","doi-asserted-by":"publisher","first-page":"i3","DOI":"10.1093\/JAC\/DKP256","volume":"64","author":"PM Hawkey","year":"2009","unstructured":"Hawkey PM, Jones AM (2009) The changing epidemiology of resistance. J Antimicrob Chemother 64:i3\u2013i10. https:\/\/doi.org\/10.1093\/JAC\/DKP256","journal-title":"J Antimicrob Chemother"},{"issue":"1","key":"2740_CR86","doi-asserted-by":"publisher","DOI":"10.1038\/s41545-020-0051-0","volume":"3","author":"Y He","year":"2020","unstructured":"He Y, Yuan Q, Mathieu J, Stadler L, Senehi N, Sun R, Alvarez PJJ (2020) Antibiotic resistance genes from livestock waste: occurrence, dissemination, and treatment. NPJ Clean Water 3(1):4. https:\/\/doi.org\/10.1038\/s41545-020-0051-0","journal-title":"NPJ Clean Water"},{"key":"2740_CR87","doi-asserted-by":"publisher","first-page":"5417","DOI":"10.1021\/ACS.CHEMREV.0C01226","volume":"121","author":"PJF Henderson","year":"2021","unstructured":"Henderson PJF, Maher C, Elbourne LDH, Eijkelkamp BA, Paulsen IT, Hassan KA (2021) Physiological functions of bacterial multidrug efflux pumps. Chem Rev 121:5417\u20135478. https:\/\/doi.org\/10.1021\/ACS.CHEMREV.0C01226","journal-title":"Chem Rev"},{"issue":"1","key":"2740_CR88","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1038\/nrmicro2259","volume":"8","author":"ME Hibbing","year":"2009","unstructured":"Hibbing ME, Fuqua C, Parsek MR, Peterson SB (2009) Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 8(1):15\u201325. https:\/\/doi.org\/10.1038\/nrmicro2259","journal-title":"Nat Rev Microbiol"},{"key":"2740_CR89","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/J.TRSL.2012.02.008","volume":"160","author":"RJ Hickey","year":"2012","unstructured":"Hickey RJ, Zhou X, Pierson JD, Ravel J, Forney LJ (2012) Understanding vaginal microbiome complexity from an ecological perspective. Transl Res 160:267\u2013282. https:\/\/doi.org\/10.1016\/J.TRSL.2012.02.008","journal-title":"Transl Res"},{"key":"2740_CR90","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1126\/SCIENCE.ADE2516","volume":"378","author":"M Huelsmann","year":"2022","unstructured":"Huelsmann M, Ackermann M (2022) Community instability in the microbial world. Science (1979) 378:29\u201330. https:\/\/doi.org\/10.1126\/SCIENCE.ADE2516","journal-title":"Science (1979)"},{"key":"2740_CR91","doi-asserted-by":"publisher","DOI":"10.1016\/J.MICPATH.2021.105040","volume":"158","author":"HI Hussain","year":"2021","unstructured":"Hussain HI, Aqib AI, Seleem MN, Shabbir MA, Hao H, Iqbal Z, Kulyar MF, Zaheer T, Li K (2021) Genetic basis of molecular mechanisms in \u03b2-lactam resistant gram-negative bacteria. Microb Pathog 158:105040. https:\/\/doi.org\/10.1016\/J.MICPATH.2021.105040","journal-title":"Microb Pathog"},{"key":"2740_CR92","doi-asserted-by":"publisher","first-page":"5031","DOI":"10.3390\/SU13095031\/S1","volume":"13","author":"AA Ivanova","year":"2021","unstructured":"Ivanova AA, Miroshnikov KK, Oshkin IY (2021) Exploring antibiotic susceptibility, resistome and mobilome structure of Planctomycetes from Gemmataceae family. Sustain (Switzerland) 13:5031. https:\/\/doi.org\/10.3390\/SU13095031\/S1","journal-title":"Sustain (Switzerland)"},{"key":"2740_CR93","doi-asserted-by":"publisher","unstructured":"Ivanova M, Svensmark B, Jensen EEB, Aarestrup FM, Vigre H, Otani S (2025) Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods. https:\/\/doi.org\/10.21203\/RS.3.RS-8285969\/V1","DOI":"10.21203\/RS.3.RS-8285969\/V1"},{"key":"2740_CR94","unstructured":"Jahn LJ (2019) Characterizing and exploiting genetic trajectories towards antibiotic resistance"},{"key":"2740_CR95","doi-asserted-by":"publisher","first-page":"12271","DOI":"10.1021\/ACS.EST.5B03521\/SUPPL_FILE\/ES5B03521_SI_001.PDF","volume":"49","author":"S Jia","year":"2015","unstructured":"Jia S, Shi P, Hu Q, Li B, Zhang T, Zhang XX (2015) Bacterial community shift drives antibiotic resistance promotion during drinking water chlorination. Environ Sci Technol 49:12271\u201312279. https:\/\/doi.org\/10.1021\/ACS.EST.5B03521\/SUPPL_FILE\/ES5B03521_SI_001.PDF","journal-title":"Environ Sci Technol"},{"key":"2740_CR96","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/J.WATRES.2017.07.061","volume":"124","author":"S Jia","year":"2017","unstructured":"Jia S, Zhang XX, Miao Y, Zhao Y, Ye L, Li B, Zhang T (2017) Fate of antibiotic resistance genes and their associations with bacterial community in livestock breeding wastewater and its receiving river water. Water Res 124:259\u2013268. https:\/\/doi.org\/10.1016\/J.WATRES.2017.07.061","journal-title":"Water Res"},{"issue":"1","key":"2740_CR97","doi-asserted-by":"publisher","DOI":"10.1186\/S40168-024-01803-2","volume":"12","author":"B Joannard","year":"2024","unstructured":"Joannard B, Sanchez-Cid C (2024) Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution. Microbiome 12(1):97. https:\/\/doi.org\/10.1186\/S40168-024-01803-2","journal-title":"Microbiome"},{"key":"2740_CR98","doi-asserted-by":"publisher","DOI":"10.1128\/SPECTRUM.05179-22","author":"EL Johnston","year":"2023","unstructured":"Johnston EL, Zavan L, Bitto NJ, Petrovski S, Hill AF, Kaparakis-Liaskos M (2023) Planktonic and biofilm-derived Pseudomonas aeruginosa outer membrane vesicles facilitate horizontal gene transfer of plasmid DNA. Microbiol Spectr. https:\/\/doi.org\/10.1128\/SPECTRUM.05179-22","journal-title":"Microbiol Spectr"},{"issue":"1","key":"2740_CR99","doi-asserted-by":"publisher","DOI":"10.1186\/S12862-022-02091-W","volume":"22","author":"CT Jones","year":"2022","unstructured":"Jones CT, Susko E, Bielawski JP (2022) Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis. BMC Ecol Evol 22(1):140. https:\/\/doi.org\/10.1186\/S12862-022-02091-W","journal-title":"BMC Ecol Evol"},{"key":"2740_CR100","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2023.1270999\/FULL","volume":"14","author":"E Jordana-Lluch","year":"2023","unstructured":"Jordana-Lluch E, Barcel\u00f3 IM, Escobar-Salom M, Est\u00e9vez MA, Zamorano L, G\u00f3mez-Zorrilla S, Sendra E, Oliver A, Juan C (2023) The balance between antibiotic resistance and fitness\/virulence in Pseudomonas aeruginosa: an update on basic knowledge and fundamental research. Front Microbiol 14:1270999. https:\/\/doi.org\/10.3389\/FMICB.2023.1270999\/FULL","journal-title":"Front Microbiol"},{"key":"2740_CR101","doi-asserted-by":"publisher","DOI":"10.1126\/SCIADV.1600124","author":"A Jousset","year":"2016","unstructured":"Jousset A, Eisenhauer N, Merker M, Mouquet N, Scheu S (2016) High functional diversity stimulates diversification in experimental microbial communities. Sci Adv. https:\/\/doi.org\/10.1126\/SCIADV.1600124","journal-title":"Sci Adv"},{"key":"2740_CR102","doi-asserted-by":"publisher","unstructured":"Jurburg SD, Blowes S, Shade A, Eisenhauer N, Chase JM (2023) Synthesis of recovery patterns in microbial communities across environments. https:\/\/doi.org\/10.21203\/RS.3.RS-3725330\/V1","DOI":"10.21203\/RS.3.RS-3725330\/V1"},{"key":"2740_CR103","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/J.SCITOTENV.2016.01.044","volume":"548","author":"J Jutkina","year":"2016","unstructured":"Jutkina J, Rutgersson C, Flach CF, Joakim Larsson DG (2016) An assay for determining minimal concentrations of antibiotics that drive horizontal transfer of resistance. Sci Total Environ 548:131\u2013138. https:\/\/doi.org\/10.1016\/J.SCITOTENV.2016.01.044","journal-title":"Sci Total Environ"},{"key":"2740_CR104","doi-asserted-by":"publisher","first-page":"7549","DOI":"10.1002\/ECE3.5286","volume":"9","author":"K Kawamura","year":"2019","unstructured":"Kawamura K, Yamaura Y, Senzaki M, Ueta M, Nakamura F (2019) Seasonality in spatial distribution: climate and land use have contrasting effects on the species richness of breeding and wintering birds. Ecol Evol 9:7549. https:\/\/doi.org\/10.1002\/ECE3.5286","journal-title":"Ecol Evol"},{"key":"2740_CR105","doi-asserted-by":"publisher","first-page":"11430","DOI":"10.1021\/ACS.EST.3C01980\/SUPPL_FILE\/ES3C01980_SI_001.PDF","volume":"57","author":"Y Ke","year":"2023","unstructured":"Ke Y, Sun W, Chen X, Zhu Y, Guo X, Yan W, Xie S (2023) Seasonality determines the variations of biofilm microbiome and antibiotic resistome in a pilot-scale chlorinated drinking water distribution system deciphered by metagenome assembly. Environ Sci Technol 57:11430\u201311441. https:\/\/doi.org\/10.1021\/ACS.EST.3C01980\/SUPPL_FILE\/ES3C01980_SI_001.PDF","journal-title":"Environ Sci Technol"},{"key":"2740_CR106","doi-asserted-by":"publisher","DOI":"10.3390\/AGRONOMY14051021","volume":"14","author":"L Khmelevtsova","year":"2024","unstructured":"Khmelevtsova L, Azhogina T, Karchava S, Klimova M, Polienko E, Litsevich A, Chernyshenko E, Khammami M, Sazykin I, Sazykina M (2024) Effect of mineral fertilizers and pesticides application on bacterial community and antibiotic-resistance genes distribution in agricultural soils. Agronomy 2024, Vol. 14, Page 1021 14:1021. https:\/\/doi.org\/10.3390\/AGRONOMY14051021","journal-title":"Agronomy 2024, Vol. 14, Page 1021"},{"key":"2740_CR107","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1038\/S12276-021-00569-Z","volume":"53","author":"DW Kim","year":"2021","unstructured":"Kim DW, Cha CJ (2021) Antibiotic resistome from the one-Health perspective: understanding and controlling antimicrobial resistance transmission. Exp Mol Med 53:301\u2013309. https:\/\/doi.org\/10.1038\/S12276-021-00569-Z","journal-title":"Exp Mol Med"},{"key":"2740_CR108","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-48221-2","volume":"13","author":"J Kim","year":"2023","unstructured":"Kim J, Cho Y, Lim SK, Seo MR, Sohn JW, Kim B, Rho M, Pai H (2023) Comparative analyses of the faecal resistome against \u03b2-lactam and quinolone antibiotics in humans and livestock using metagenomic sequencing. Scientific Reports 2023 13:1 13:20993-. https:\/\/doi.org\/10.1038\/s41598-023-48221-2","journal-title":"Scientific Reports 2023 13:1"},{"key":"2740_CR109","doi-asserted-by":"publisher","unstructured":"Klawe JJ, Tafil-Klawe M (2003) Antibiotic-resistant bacteria. Encyclopedia of Food Sciences and Nutrition. pp 247\u2013249. https:\/\/doi.org\/10.1016\/B0-12-227055-X\/01389-4","DOI":"10.1016\/B0-12-227055-X\/01389-4"},{"key":"2740_CR110","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S42003-024-06338-8","volume":"7","author":"U Kl\u00fcmper","year":"2024","unstructured":"Kl\u00fcmper U, Gionchetta G, Cat\u00e3o E, Bellanger X, Dielacher I, Elena AX, Fang P, Galazka S, Goryluk-Salmonowicz A, Kneis D, Okoroafor U, Radu E, Szadziul M, Szekeres E, Teban-Man A, Coman C, Kreuzinger N, Popowska M, Vierheilig J, Walsh F, Woegerbauer M, B\u00fcrgmann H, Merlin C, Berendonk TU (2024) Environmental microbiome diversity and stability is a barrier to antimicrobial resistance gene accumulation. Commun Biol 7:1\u201313. https:\/\/doi.org\/10.1038\/S42003-024-06338-8","journal-title":"Commun Biol"},{"key":"2740_CR111","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PONE.0205202","volume":"13","author":"J Kosakowski","year":"2018","unstructured":"Kosakowski J, Verma P, Sengupta S, Higgs PG (2018) The evolution of antibiotic production rate in a spatial model of bacterial competition. PLoS One 13:e0205202. https:\/\/doi.org\/10.1371\/JOURNAL.PONE.0205202","journal-title":"PLoS One"},{"key":"2740_CR112","doi-asserted-by":"publisher","first-page":"2244","DOI":"10.1038\/s41564-023-01511-x","volume":"8","author":"C Kost","year":"2023","unstructured":"Kost C, Patil KR, Friedman J, Garcia SL, Ralser M (2023) Metabolic exchanges are ubiquitous in natural microbial communities. Nature Microbiology 2023 8:12 8:2244\u20132252. https:\/\/doi.org\/10.1038\/s41564-023-01511-x","journal-title":"Nature Microbiology 2023 8:12"},{"key":"2740_CR113","doi-asserted-by":"publisher","DOI":"10.3389\/FSYSB.2025.1557413\/FULL","volume":"5","author":"R Kumavath","year":"2025","unstructured":"Kumavath R, Gupta P, Tatta ER, Mohan MS, Salim SA, Busi S (2025) Unraveling the role of mobile genetic elements in antibiotic resistance transmission and defense strategies in bacteria. Front Syst Biol 5:1557413. https:\/\/doi.org\/10.3389\/FSYSB.2025.1557413\/FULL","journal-title":"Front Syst Biol"},{"key":"2740_CR114","doi-asserted-by":"publisher","DOI":"10.3389\/BJBS.2024.12958\/FULL","volume":"81","author":"AP Kunnath","year":"2024","unstructured":"Kunnath AP, Suodha Suoodh M, Chellappan DK, Chellian J, Palaniveloo K (2024) Bacterial persister cells and development of antibiotic resistance in chronic infections: an update. Br J Biomed Sci 81:12958. https:\/\/doi.org\/10.3389\/BJBS.2024.12958\/FULL","journal-title":"Br J Biomed Sci"},{"key":"2740_CR115","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S13073-016-0294-Z","volume":"8","author":"A Langdon","year":"2016","unstructured":"Langdon A, Crook N, Dantas G (2016) The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Medicine 2016 8:1 8:1\u201316. https:\/\/doi.org\/10.1186\/S13073-016-0294-Z","journal-title":"Genome Medicine 2016 8:1"},{"key":"2740_CR116","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1038\/s41579-021-00649-x","volume":"20","author":"DGJ Larsson","year":"2021","unstructured":"Larsson DGJ, Flach CF (2021) Antibiotic resistance in the environment. Nature Reviews Microbiology 2021 20:5 20:257\u2013269. https:\/\/doi.org\/10.1038\/s41579-021-00649-x","journal-title":"Nature Reviews Microbiology 2021 20:5"},{"key":"2740_CR117","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2022.897905\/BIBTEX","volume":"13","author":"K Lawther","year":"2022","unstructured":"Lawther K, Santos FG, Oyama LB, Rubino F, Morrison S, Creevey CJ, McGrath JW, Huws SA (2022) Resistome analysis of global livestock and soil microbiomes. Front Microbiol 13:897905. https:\/\/doi.org\/10.3389\/FMICB.2022.897905\/BIBTEX","journal-title":"Front Microbiol"},{"key":"2740_CR118","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12879-019-4265-Z\/TABLES\/5","volume":"19","author":"HF Leal","year":"2019","unstructured":"Leal HF, Azevedo J, Silva GEO, Amorim AML, De Roma LRC, Arraes ACP, Gouveia EL, Reis MG, Mendes AV, De Oliveira Silva M, Barberino MG, Martins IS, Reis JN (2019) Bloodstream infections caused by multidrug-resistant gram-negative bacteria: epidemiological, clinical and microbiological features. BMC Infect Dis 19:1\u201311. https:\/\/doi.org\/10.1186\/S12879-019-4265-Z\/TABLES\/5","journal-title":"BMC Infect Dis"},{"key":"2740_CR119","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12866-021-02129-X\/FIGURES\/5","volume":"21","author":"RM Lebeaux","year":"2021","unstructured":"Lebeaux RM, Coker MO, Dade EF, Palys TJ, Morrison HG, Ross BD, Baker ER, Karagas MR, Madan JC, Hoen AG (2021) The infant gut resistome is associated with E. coli and early-life exposures. BMC Microbiol 21:1\u201318. https:\/\/doi.org\/10.1186\/S12866-021-02129-X\/FIGURES\/5","journal-title":"BMC Microbiol"},{"key":"2740_CR120","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PCBI.1009584","volume":"17","author":"P Lech\u00f3n-Alonso","year":"2021","unstructured":"Lech\u00f3n-Alonso P, Clegg T, Cook J, Smith TP, Pawar S (2021) The role of competition versus cooperation in microbial community coalescence. PLoS Comput Biol 17:e1009584. https:\/\/doi.org\/10.1371\/JOURNAL.PCBI.1009584","journal-title":"PLoS Comput Biol"},{"key":"2740_CR121","doi-asserted-by":"publisher","unstructured":"Lerminiaux NA, Cameron ADS (2018) Horizontal transfer of antibiotic resistance genes in clinical environments. https:\/\/doi.org\/10.1139\/cjm-2018-0275 65, 34\u201344. https:\/\/doi.org\/10.1139\/CJM-2018-0275","DOI":"10.1139\/cjm-2018-0275"},{"key":"2740_CR122","doi-asserted-by":"publisher","unstructured":"Lesani SS, Soleimani M, Shakib P, Zolfaghari MR, Lesani SS, Soleimani M, Shakib P, Zolfaghari MR, Lesani SS, Soleimani M, Shakib P, Zolfaghari MR, Lesani SS, Soleimani M, Shakib P, Zolfaghari MR, Lesani SS, Soleimani M, Shakib P, Zolfaghari MR (2020) Prevalence of blaCTX-M, blaSHV, and blaTEM genes in Escherichia coli strains isolated from urinary tract infection samples of patients in the intensive care unit in Qom, Iran. Gene, Cell and Tissue 2020 7:2 7. https:\/\/doi.org\/10.5812\/GCT.102700","DOI":"10.5812\/GCT.102700"},{"issue":"4","key":"2740_CR123","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1038\/s41559-020-01385-w","volume":"5","author":"AD Letten","year":"2021","unstructured":"Letten AD, Hall AR, Levine JM (2021) Using ecological coexistence theory to understand antibiotic resistance and microbial competition. Nat Ecol Evol 5(4):431\u2013441. https:\/\/doi.org\/10.1038\/s41559-020-01385-w","journal-title":"Nat Ecol Evol"},{"key":"2740_CR124","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1128\/CMR.00117-14\/ASSET\/583856BD-C6B1-4341-8AD4-B1826C00FE4C\/ASSETS\/GRAPHIC\/ZCM0021525060008.JPEG","volume":"28","author":"XZ Li","year":"2015","unstructured":"Li XZ, Pl\u00e9siat P, Nikaido H (2015) The challenge of efflux-mediated antibiotic resistance in gram-negative bacteria. Clin Microbiol Rev 28:337\u2013418. https:\/\/doi.org\/10.1128\/CMR.00117-14\/ASSET\/583856BD-C6B1-4341-8AD4-B1826C00FE4C\/ASSETS\/GRAPHIC\/ZCM0021525060008.JPEG","journal-title":"Clin Microbiol Rev"},{"key":"2740_CR125","doi-asserted-by":"publisher","DOI":"10.5772\/62942","author":"Y-H Li","year":"2016","unstructured":"Li Y-H, Tian X-L (2016) Microbial interactions in biofilms: impacts on homeostasis and pathogenesis. Microb Biofilms - Importance Appl. https:\/\/doi.org\/10.5772\/62942","journal-title":"Microb Biofilms - Importance Appl"},{"issue":"1","key":"2740_CR126","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s43247-025-02610-9","volume":"6","author":"H Liao","year":"2025","unstructured":"Liao H, Wang YZ, Duan CS, Zhu YG, Su JQ (2025) Nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundance. Communications Earth & Environment 6(1):1\u201316. https:\/\/doi.org\/10.1038\/s43247-025-02610-9","journal-title":"Communications Earth & Environment"},{"key":"2740_CR127","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S42003-022-04187-X","volume":"5","author":"Q Lin","year":"2022","unstructured":"Lin Q, Xavier BB, Alako BTF, Mitchell AL, Rajakani SG, Glupczynski Y, Finn RD, Cochrane G, Malhotra-Kumar S (2022) Screening of global microbiomes implies ecological boundaries impacting the distribution and dissemination of clinically relevant antimicrobial resistance genes. Commun Biol 5:1\u20139. https:\/\/doi.org\/10.1038\/S42003-022-04187-X","journal-title":"Commun Biol"},{"key":"2740_CR128","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2021.660566\/BIBTEX","volume":"12","author":"RB Linke","year":"2021","unstructured":"Linke RB, Zeki S, Mayer R, Keiblinger K, Savio D, Kirschner AKT, Reischer GH, Mach RL, Sommer R, Farnleitner AH (2021) Identifying inorganic turbidity in water samples as potential loss factor during nucleic acid extraction: implications for molecular fecal pollution diagnostics and source tracking. Front Microbiol 12:660566. https:\/\/doi.org\/10.3389\/FMICB.2021.660566\/BIBTEX","journal-title":"Front Microbiol"},{"issue":"1","key":"2740_CR129","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-020-65031-y","volume":"10","author":"F Lira","year":"2020","unstructured":"Lira F, Vaz-Moreira I, Tamames J, Manaia CM, Mart\u00ednez JL (2020) Metagenomic analysis of an urban resistome before and after wastewater treatment. Sci Rep 10(1):1\u20139. https:\/\/doi.org\/10.1038\/s41598-020-65031-y","journal-title":"Sci Rep"},{"key":"2740_CR130","doi-asserted-by":"publisher","DOI":"10.1016\/J.ENVPOL.2024.125018","volume":"362","author":"K Liu","year":"2024","unstructured":"Liu K, Li Y, Ge Z, Huang D, Zhang J (2024) 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. Environ Pollut 362:125018. https:\/\/doi.org\/10.1016\/J.ENVPOL.2024.125018","journal-title":"Environ Pollut"},{"key":"2740_CR132","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2015.00285\/BIBTEX","volume":"6","author":"S Liu","year":"2015","unstructured":"Liu S, Ren H, Shen L, Lou L, Tian G, Zheng P, Hu B (2015) pH levels drive bacterial community structure in the Qiantang River as determined by 454 pyrosequencing. Front Microbiol 6:133339. https:\/\/doi.org\/10.3389\/FMICB.2015.00285\/BIBTEX","journal-title":"Front Microbiol"},{"key":"2740_CR133","doi-asserted-by":"publisher","unstructured":"Liu Z, Zhao Y, Zhang B, Hangzhou Z, Environment E, Center M, Wang HJ, Zhu L, Hu B (2022) Deterministic effects of pH in shaping soil resistome revealed by metagenomic analysis. https:\/\/doi.org\/10.21203\/RS.3.RS-1673295\/V1","DOI":"10.21203\/RS.3.RS-1673295\/V1"},{"key":"2740_CR134","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1021\/ACS.EST.2C06684","volume":"57","author":"Z Liu","year":"2023","unstructured":"Liu Z, Zhao Y, Zhang B, Wang J, Zhu L, Hu B (2023) Deterministic effect of pH on shaping soil resistome revealed by metagenomic analysis. Environ Sci Technol 57:985\u2013996. https:\/\/doi.org\/10.1021\/ACS.EST.2C06684","journal-title":"Environ Sci Technol"},{"key":"2740_CR135","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41522-024-00489-6","volume":"10","author":"B Lories","year":"2024","unstructured":"Lories B, Belpaire TER, Smeets B, Steenackers HP (2024) Competition quenching strategies reduce antibiotic tolerance in polymicrobial biofilms. NPJ Biofilms Microbiomes 10:1\u201311. https:\/\/doi.org\/10.1038\/S41522-024-004896;SUBJMETA=22,2565,326,421,46,631,855;KWRD=ANTIMICROBIALS,BIOFILMS,MICROBIAL+ECOLOGY,PATHOGENS","journal-title":"NPJ Biofilms Microbiomes"},{"key":"2740_CR136","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1111\/RAQ.12344","volume":"12","author":"R Lulijwa","year":"2020","unstructured":"Lulijwa R, Rupia EJ, Alfaro AC (2020) Antibiotic use in aquaculture, policies and regulation, health and environmental risks: a review of the top 15 major producers. Rev Aquac 12:640\u2013663. https:\/\/doi.org\/10.1111\/RAQ.12344","journal-title":"Rev Aquac"},{"issue":"1","key":"2740_CR137","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/S00248-024-02484-Y","volume":"87","author":"H Luo","year":"2025","unstructured":"Luo H, Xie K, Dong P, Zhang Y, Ren T, Sui C, Ma C, Zhao C, Dewangan NK, Gong Z (2025) Assessing the risks of potential pathogens and antibiotic resistance genes among heterogeneous habitats in a temperate estuary wetland: a meta-analysis. Microb Ecol 87(1):1\u201317. https:\/\/doi.org\/10.1007\/S00248-024-02484-Y","journal-title":"Microb Ecol"},{"key":"2740_CR138","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2021.738629\/EPUB","volume":"12","author":"E Lyautey","year":"2021","unstructured":"Lyautey E, Bonnineau C, Billard P, Loizeau JL, Naffrechoux E, Tlili A, Topp E, Ferrari BJD, Pesce S (2021) Diversity, functions and antibiotic resistance of sediment microbial communities from Lake Geneva are driven by the spatial distribution of anthropogenic contamination. Front Microbiol 12:738629. https:\/\/doi.org\/10.3389\/FMICB.2021.738629\/EPUB","journal-title":"Front Microbiol"},{"issue":"1","key":"2740_CR139","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-021-27904-2","volume":"13","author":"H Maan","year":"2022","unstructured":"Maan H, Itkin M, Malitsky S, Friedman J, Kolodkin-Gal I (2022) Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors. Nat Commun 13(1):1\u201315. https:\/\/doi.org\/10.1038\/s41467-021-27904-2","journal-title":"Nat Commun"},{"issue":"6","key":"2740_CR140","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1038\/s41558-018-0161-6","volume":"8","author":"DR MacFadden","year":"2018","unstructured":"MacFadden DR, McGough SF, Fisman D, Santillana M, Brownstein JS (2018) Antibiotic resistance increases with local temperature. Nat Clim Chang 8(6):510\u2013514. https:\/\/doi.org\/10.1038\/s41558-018-0161-6","journal-title":"Nat Clim Chang"},{"issue":"2","key":"2740_CR141","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/s41559-020-01353-4","volume":"5","author":"D Machado","year":"2021","unstructured":"Machado D, Maistrenko OM, Andrejev S, Kim Y, Bork P, Patil KR, Patil KR (2021) Polarization of microbial communities between competitive and cooperative metabolism. Nat Ecol Evol 5(2):195\u2013203. https:\/\/doi.org\/10.1038\/s41559-020-01353-4","journal-title":"Nat Ecol Evol"},{"key":"2740_CR142","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S41467-024-45638-9","volume":"15","author":"R Maddamsetti","year":"2024","unstructured":"Maddamsetti R, Yao Y, Wang T, Gao J, Huang VT, Hamrick GS, Son HI, You L (2024) Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria. Nat Commun 15:1\u201315. https:\/\/doi.org\/10.1038\/S41467-024-45638-9","journal-title":"Nat Commun"},{"key":"2740_CR143","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1016\/J.JTBI.2018.08.040","volume":"457","author":"L Marrec","year":"2018","unstructured":"Marrec L, Bitbol AF (2018) Quantifying the impact of a periodic presence of antimicrobial on resistance evolution in a homogeneous microbial population of fixed size. J Theor Biol 457:190\u2013198. https:\/\/doi.org\/10.1016\/J.JTBI.2018.08.040","journal-title":"J Theor Biol"},{"issue":"1","key":"2740_CR144","doi-asserted-by":"publisher","first-page":"10278-","DOI":"10.1038\/s41467-025-66070-7","volume":"16","author":"HM Martiny","year":"2025","unstructured":"Martiny HM, Munk P, Fuschi A, Becsei \u00c1, Pyrounakis N, Brinch C, Larsson DGJ, Koopmans M, Remondini D, Csabai I, Aarestrup FM (2025) Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes. Nat Commun 16(1):10278-. https:\/\/doi.org\/10.1038\/s41467-025-66070-7","journal-title":"Nat Commun"},{"key":"2740_CR145","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1093\/ICB\/ICAC055","volume":"62","author":"AA Mauro","year":"2022","unstructured":"Mauro AA, Shah AA, Martin PR, Ghalambor CK (2022) An integrative perspective on the mechanistic basis of context-dependent species interactions. Integr Comp Biol 62:164\u2013178. https:\/\/doi.org\/10.1093\/ICB\/ICAC055","journal-title":"Integr Comp Biol"},{"key":"2740_CR146","doi-asserted-by":"publisher","first-page":"3348","DOI":"10.1128\/aac.00419-13","volume":"57","author":"AG McArthur","year":"2013","unstructured":"McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O\u2019Brien JS, Pawlowski AC, Piddock LJV, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57:3348\u20133357. https:\/\/doi.org\/10.1128\/aac.00419-13","journal-title":"Antimicrob Agents Chemother"},{"key":"2740_CR147","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1111\/EVA.12196","volume":"8","author":"AH Melnyk","year":"2015","unstructured":"Melnyk AH, Wong A, Kassen R (2015) The fitness costs of antibiotic resistance mutations. Evol Appl 8:273\u2013283. https:\/\/doi.org\/10.1111\/EVA.12196","journal-title":"Evol Appl"},{"issue":"2","key":"2740_CR148","doi-asserted-by":"publisher","DOI":"10.3390\/ANTIBIOTICS12020328","volume":"12","author":"C Michaelis","year":"2023","unstructured":"Michaelis C, Grohmann E (2023) Horizontal gene transfer of antibiotic resistance genes in biofilms. Antibiotics 12(2):328. https:\/\/doi.org\/10.3390\/ANTIBIOTICS12020328","journal-title":"Antibiotics"},{"key":"2740_CR149","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PONE.0024552","volume":"6","author":"A Michon","year":"2011","unstructured":"Michon A, Allou N, Chau F, Podglajen I, Fantin B, Cambau E (2011) Plasmidic qnrA3 enhances Escherichia coli fitness in absence of antibiotic exposure. PLoS One 6:e24552. https:\/\/doi.org\/10.1371\/JOURNAL.PONE.0024552","journal-title":"PLoS One"},{"key":"2740_CR150","doi-asserted-by":"publisher","DOI":"10.1073\/PNAS.2209043119","volume":"120","author":"SP Mizrahi","year":"2023","unstructured":"Mizrahi SP, Goyal A, Gore J (2023) Community interactions drive the evolution of antibiotic tolerance in bacteria. Proc Natl Acad Sci U S A 120:e2209043119. https:\/\/doi.org\/10.1073\/PNAS.2209043119","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2740_CR151","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12879-024-09023-7\/TABLES\/3","volume":"24","author":"MIA Mohammedkheir","year":"2024","unstructured":"Mohammedkheir MIA, Gaafar EM, AbdAlla EGAE (2024) Assessment of Bla TEM, Bla SHV, and Bla CTX-M genes of antibiotic resistance in gram-negative bacilli causing urinary tract infections in Khartoum State: a cross-sectional study. BMC Infect Dis 24:1\u20137. https:\/\/doi.org\/10.1186\/S12879-024-09023-7\/TABLES\/3","journal-title":"BMC Infect Dis"},{"key":"2740_CR152","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1016\/J.CHOM.2023.03.017","volume":"31","author":"J Moura de Sousa","year":"2023","unstructured":"Moura de Sousa J, Louren\u00e7o M, Gordo I (2023) Horizontal gene transfer among host-associated microbes. Cell Host Microbe 31:513\u2013527. https:\/\/doi.org\/10.1016\/J.CHOM.2023.03.017","journal-title":"Cell Host Microbe"},{"issue":"1","key":"2740_CR153","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1186\/S40168-025-02231-6","volume":"13","author":"AM Muhummed","year":"2025","unstructured":"Muhummed AM, Lanker KC, Yersin S, Zinsstag J, Vonaesch P (2025) One health, one microbiome. Microbiome 13(1):216. https:\/\/doi.org\/10.1186\/S40168-025-02231-6","journal-title":"Microbiome"},{"issue":"1","key":"2740_CR154","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S44259-024-00026-7","volume":"2","author":"LM Murray","year":"2024","unstructured":"Murray LM, Hayes A, Snape J, Kasprzyk-Hordern B, Gaze WH, Murray AK (2024) Co-selection for antibiotic resistance by environmental contaminants. NPJ Antimicrob Resist 2(1):1\u201313. https:\/\/doi.org\/10.1038\/S44259-024-00026-7","journal-title":"NPJ Antimicrob Resist"},{"key":"2740_CR155","unstructured":"Musovic S, Kl\u00fcmper U, Lundin ALN, S\u00f8rensen SJ, Smets BF (2012) Permissiveness of soil microbial communities toward receipt of mobile genetic elements"},{"key":"2740_CR156","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2020.548793\/BIBTEX","volume":"11","author":"S Muszynski","year":"2021","unstructured":"Muszynski S, Maurer F, Henjes S, Horn MA, Noll M (2021) Fungal and bacterial diversity patterns of two diversity levels retrieved from a late decaying Fagus sylvatica under two temperature regimes. Front Microbiol 11:548793. https:\/\/doi.org\/10.3389\/FMICB.2020.548793\/BIBTEX","journal-title":"Front Microbiol"},{"key":"2740_CR157","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S41598-018-20077-X","volume":"8","author":"G Na","year":"2018","unstructured":"Na G, Lu Z, Gao H, Zhang L, Li Q, Li R, Yang F, Huo C, Yao Z (2018) The effect of environmental factors and migration dynamics on the prevalence of antibiotic-resistant Escherichia coli in estuary environments. Sci Rep 8:1\u20139. https:\/\/doi.org\/10.1038\/S41598-018-20077-X","journal-title":"Sci Rep"},{"issue":"1","key":"2740_CR158","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-023-04716-2","volume":"6","author":"RR Nair","year":"2023","unstructured":"Nair RR, Andersson DI (2023) Interspecies interaction reduces selection for antibiotic resistance in Escherichia coli. Commun Biol 6(1):1\u20139. https:\/\/doi.org\/10.1038\/s42003-023-04716-2","journal-title":"Commun Biol"},{"key":"2740_CR159","doi-asserted-by":"publisher","DOI":"10.1016\/J.MICROB.2025.100386","volume":"7","author":"F Naznine","year":"2025","unstructured":"Naznine F, Shafi Z, Aafreen U, Shahid M, Parveen S, Ansari MI (2025) Tracking antimicrobial resistance in river waters: sources, key microbes, and detection techniques. The Microbe 7:100386. https:\/\/doi.org\/10.1016\/J.MICROB.2025.100386","journal-title":"The Microbe"},{"key":"2740_CR160","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S41598-023-35402-2","volume":"13","author":"AA Negeri","year":"2023","unstructured":"Negeri AA, Mamo H, Gahlot DK, Gurung JM, Seyoum ET, Francis MS (2023) Characterization of plasmids carrying bla CTX-M genes among extra-intestinal Escherichia coli clinical isolates in Ethiopia. Sci Rep 13:1\u201314. https:\/\/doi.org\/10.1038\/S41598-023-35402-2","journal-title":"Sci Rep"},{"key":"2740_CR161","doi-asserted-by":"publisher","first-page":"899","DOI":"10.33314\/JNHRC.V20I4.4257","volume":"20","author":"L Neupane","year":"2023","unstructured":"Neupane L, Sah AK, Rayamajhee B, Pokhrel A, Singh A (2023) Detection of blaoxa-23 gene from carbapenem-resistant Acinetobacter baumannii. J Nepal Health Res Counc 20:899\u2013905. https:\/\/doi.org\/10.33314\/JNHRC.V20I4.4257","journal-title":"J Nepal Health Res Counc"},{"key":"2740_CR162","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2017.02200","volume":"8","author":"C Ng","year":"2017","unstructured":"Ng C, Tay M, Tan B, Le TH, Haller L, Chen H, Koh TH, Barkham TMS, Gin KYH (2017) Characterization of metagenomes in urban aquatic compartments reveals high prevalence of clinically relevant antibiotic resistance genes in wastewaters. Front Microbiol 8:298023. https:\/\/doi.org\/10.3389\/FMICB.2017.02200","journal-title":"Front Microbiol"},{"issue":"1","key":"2740_CR163","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1186\/S12879-025-11616-9","volume":"25","author":"Y Ni","year":"2025","unstructured":"Ni Y, Zhao J, Yuan Y, Feng B (2025) Climate change and antimicrobial resistance: a global-scale analysis. BMC Infect Dis 25(1):1191. https:\/\/doi.org\/10.1186\/S12879-025-11616-9","journal-title":"BMC Infect Dis"},{"key":"2740_CR164","doi-asserted-by":"publisher","first-page":"2966","DOI":"10.1111\/J.1462-2920.2008.01701.X","volume":"10","author":"GW Nicol","year":"2008","unstructured":"Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10:2966\u20132978. https:\/\/doi.org\/10.1111\/J.1462-2920.2008.01701.X","journal-title":"Environ Microbiol"},{"key":"2740_CR165","doi-asserted-by":"publisher","unstructured":"Noell SE, Abbaszadeh J, Richards H, Vincent MS, Lee CK, Herbold CW, Stott MB, Cary SC, McDonald IR (2024) Antarctic geothermal soils exhibit an absence of regional habitat generalist microorganisms. bioRxiv. https:\/\/doi.org\/10.1101\/2024.06.06.597824","DOI":"10.1101\/2024.06.06.597824"},{"key":"2740_CR166","doi-asserted-by":"publisher","DOI":"10.1016\/j.chemosphere.2022.135428","author":"OE Ohore","year":"2022","unstructured":"Ohore OE, Wei Y, Wang Y, Nwankwegu AS, Wang Z (2022) Tracking the influence of antibiotics, antibiotic resistomes, and salinity gradient in modulating microbial community assemblage of surface water and the ecological consequences. Chemosphere. https:\/\/doi.org\/10.1016\/j.chemosphere.2022.135428","journal-title":"Chemosphere"},{"key":"2740_CR167","doi-asserted-by":"publisher","DOI":"10.1016\/J.SOILBIO.2024.109644","volume":"200","author":"NJ Oram","year":"2025","unstructured":"Oram NJ, Brennan F, Praeg N, Bardgett RD, Illmer P, Ingrisch J, Bahn M (2025) Plant community composition and traits modulate the impacts of drought intensity on soil microbial community composition and function. Soil Biol Biochem 200:109644. https:\/\/doi.org\/10.1016\/J.SOILBIO.2024.109644","journal-title":"Soil Biol Biochem"},{"issue":"1","key":"2740_CR168","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-46571-7","volume":"15","author":"A Pal","year":"2024","unstructured":"Pal A, Andersson DI (2024) Bacteria can compensate the fitness costs of amplified resistance genes via a bypass mechanism. Nat Commun 15(1):2333. https:\/\/doi.org\/10.1038\/s41467-024-46571-7","journal-title":"Nat Commun"},{"issue":"1","key":"2740_CR169","doi-asserted-by":"publisher","DOI":"10.1186\/S40168-016-0199-5","volume":"4","author":"C Pal","year":"2016","unstructured":"Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ (2016) The structure and diversity of human, animal and environmental resistomes. Microbiome 4(1):54. https:\/\/doi.org\/10.1186\/S40168-016-0199-5","journal-title":"Microbiome"},{"key":"2740_CR170","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2022.1037389","volume":"13","author":"X Pan","year":"2022","unstructured":"Pan X, Zhou Z, Liu B, Wu Z (2022) A novel therapeutic concern: antibiotic resistance genes in common chronic diseases. Front Microbiol 13:1037389. https:\/\/doi.org\/10.3389\/FMICB.2022.1037389","journal-title":"Front Microbiol"},{"key":"2740_CR171","doi-asserted-by":"publisher","unstructured":"Parab A, Ghose M, Manohar CS (2025) Antibiotic-resistant bacteria in marine productive zones of the Eastern Arabian Sea: Insight from shotgun metagenomics and draft genome analysis. https:\/\/doi.org\/10.2139\/SSRN.5106600","DOI":"10.2139\/SSRN.5106600"},{"key":"2740_CR172","doi-asserted-by":"publisher","first-page":"1495","DOI":"10.1038\/S41396-023-01465-2","volume":"17","author":"A Pathak","year":"2023","unstructured":"Pathak A, Angst DC, Le\u00f3n-Sampedro R, Hall AR (2023) Antibiotic-degrading resistance changes bacterial community structure via species-specific responses. ISME J 17:1495\u20131503. https:\/\/doi.org\/10.1038\/S41396-023-01465-2","journal-title":"ISME J"},{"key":"2740_CR173","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PONE.0062814","volume":"8","author":"P Patra","year":"2013","unstructured":"Patra P, Klumpp S (2013) Population dynamics of bacterial persistence. PLoS One 8:e62814. https:\/\/doi.org\/10.1371\/JOURNAL.PONE.0062814","journal-title":"PLoS One"},{"key":"2740_CR174","doi-asserted-by":"publisher","DOI":"10.1128\/MBIO.01851-22","author":"E Pfeifer","year":"2022","unstructured":"Pfeifer E, Bonnin RA, Rocha EPC (2022) Phage-plasmids spread antibiotic resistance genes through infection and lysogenic conversion. mBio. https:\/\/doi.org\/10.1128\/MBIO.01851-22","journal-title":"mBio"},{"key":"2740_CR175","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00026-20","author":"L Philippot","year":"2021","unstructured":"Philippot L, Griffiths BS, Langenheder S (2021) Microbial community resilience across ecosystems and multiple disturbances. Microbiol Mol Biol Rev. https:\/\/doi.org\/10.1128\/MMBR.00026-20","journal-title":"Microbiol Mol Biol Rev"},{"key":"2740_CR176","doi-asserted-by":"publisher","unstructured":"Pillay S, Abeel T (2025) A comparative metagenomic analysis of antibiotic resistance in the fecal microbiome of pigs raised with and without antibiotics. bioRxiv. https:\/\/doi.org\/10.1101\/2025.01.20.633852","DOI":"10.1101\/2025.01.20.633852"},{"key":"2740_CR177","doi-asserted-by":"publisher","DOI":"10.3389\/FIMMU.2024.1371118\/BIBTEX","volume":"15","author":"F Pulvirenti","year":"2024","unstructured":"Pulvirenti F, Giufr\u00e8 M, Pentimalli TM, Camilli R, Milito C, Villa A, Sculco E, Cerquetti M, Pantosti A, Quinti I (2024) Oropharyngeal microbial ecosystem perturbations influence the risk for acute respiratory infections in common variable immunodeficiency. Front Immunol 15:1371118. https:\/\/doi.org\/10.3389\/FIMMU.2024.1371118\/BIBTEX","journal-title":"Front Immunol"},{"key":"2740_CR178","doi-asserted-by":"publisher","DOI":"10.1128\/MBIO.03552-21","author":"F Rajer","year":"2022","unstructured":"Rajer F, Sandegren L (2022) The role of antibiotic resistance genes in the fitness cost of multiresistance plasmids. mBio. https:\/\/doi.org\/10.1128\/MBIO.03552-21","journal-title":"mBio"},{"issue":"1","key":"2740_CR179","doi-asserted-by":"publisher","DOI":"10.1038\/s41545-020-0050-1","volume":"3","author":"B Ram","year":"2020","unstructured":"Ram B, Kumar M (2020) Correlation appraisal of antibiotic resistance with fecal, metal and microplastic contamination in a tropical Indian river, lakes and sewage. NPJ Clean Water 3(1):3. https:\/\/doi.org\/10.1038\/s41545-020-0050-1","journal-title":"NPJ Clean Water"},{"key":"2740_CR180","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2020.586050\/FULL","volume":"11","author":"R Raveau","year":"2020","unstructured":"Raveau R, Fontaine J, Hijri M, Loun\u00e8s-Hadj Sahraoui A (2020) The aromatic plant clary sage shaped bacterial communities in the roots and in the trace element-contaminated soil more than mycorrhizal inoculation \u2013 a two-year monitoring field trial. Front Microbiol 11:586050. https:\/\/doi.org\/10.3389\/FMICB.2020.586050\/FULL","journal-title":"Front Microbiol"},{"key":"2740_CR181","doi-asserted-by":"publisher","DOI":"10.1016\/J.GENREP.2024.102065","volume":"37","author":"L Razaq","year":"2024","unstructured":"Razaq L, Uddin F, Ali S, Ali S, Kausar R, Sohail M (2024) Extended-spectrum \u03b2-lactamase variants in Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis from community- and hospital-acquired urinary tract infections. Gene Rep 37:102065. https:\/\/doi.org\/10.1016\/J.GENREP.2024.102065","journal-title":"Gene Rep"},{"key":"2740_CR182","doi-asserted-by":"publisher","first-page":"15831","DOI":"10.1021\/ACS.EST.1C04641","volume":"55","author":"CY Ren","year":"2021","unstructured":"Ren CY, Wu EL, Hartmann EM, Zhao HP (2021) Biological mitigation of antibiotic resistance gene dissemination by antioxidant-producing microorganisms in activated sludge systems. Environ Sci Technol 55:15831\u201315842. https:\/\/doi.org\/10.1021\/ACS.EST.1C04641","journal-title":"Environ Sci Technol"},{"key":"2740_CR183","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PGEN.1011560","volume":"21","author":"J Rodriguez-Grande","year":"2025","unstructured":"Rodriguez-Grande J, Ortiz Y, Garcia-Lopez D, Garcill\u00e1n-Barcia PP, De La Cruz F, Fernandez-Lopez R (2025) Encounter rates and engagement times limit the transmission of conjugative plasmids. PLoS Genet 21:e1011560. https:\/\/doi.org\/10.1371\/JOURNAL.PGEN.1011560","journal-title":"PLoS Genet"},{"issue":"1","key":"2740_CR184","doi-asserted-by":"publisher","DOI":"10.1186\/S40793-024-00559-4","volume":"19","author":"S Romdhane","year":"2024","unstructured":"Romdhane S, Huet S, Spor A, Bru D, Breuil MC, Philippot L (2024) Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly. Environ Microbiol 19(1):18. https:\/\/doi.org\/10.1186\/S40793-024-00559-4","journal-title":"Environ Microbiol"},{"key":"2740_CR185","doi-asserted-by":"publisher","first-page":"136","DOI":"10.22038\/IJBMS.2020.48905.11208","volume":"24","author":"P Sabbagh","year":"2021","unstructured":"Sabbagh P, Rajabnia M, Maali A, Ferdosi-Shahandashti E (2021) Integron and its role in antimicrobial resistance: a literature review on some bacterial pathogens. Iran J Basic Med Sci 24:136. https:\/\/doi.org\/10.22038\/IJBMS.2020.48905.11208","journal-title":"Iran J Basic Med Sci"},{"key":"2740_CR186","doi-asserted-by":"publisher","DOI":"10.3390\/HEALTHCARE11131946","volume":"2023","author":"MA Salam","year":"2023","unstructured":"Salam MA, Al-Amin MY, Salam MT, Pawar JS, Akhter N, Rabaan AA, Alqumber MAA (2023) Antimicrobial resistance: a growing serious threat for global public health. Healthcare 2023:1946. https:\/\/doi.org\/10.3390\/HEALTHCARE11131946","journal-title":"Healthcare"},{"issue":"1","key":"2740_CR187","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S41598-023-35074-Y","volume":"13","author":"C Sanchez-Cid","year":"2023","unstructured":"Sanchez-Cid C, Ghaly TM, Gillings MR, Vogel TM (2023) Sub-inhibitory gentamicin pollution induces gentamicin resistance gene integration in class 1 integrons in the environment. Sci Rep 13(1):1\u20137. https:\/\/doi.org\/10.1038\/S41598-023-35074-Y","journal-title":"Sci Rep"},{"key":"2740_CR188","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/J.IJANTIMICAG.2018.03.010","volume":"52","author":"L Santos","year":"2018","unstructured":"Santos L, Ramos F (2018) Antimicrobial resistance in aquaculture: current knowledge and alternatives to tackle the problem. Int J Antimicrob Agents 52:135\u2013143. https:\/\/doi.org\/10.1016\/J.IJANTIMICAG.2018.03.010","journal-title":"Int J Antimicrob Agents"},{"key":"2740_CR189","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1126\/SCIENCE.ADF5121","volume":"381","author":"M Sch\u00e4fer","year":"2023","unstructured":"Sch\u00e4fer M, Pacheco AR, K\u00f6nzler R, Bortfeld-Miller M, Field CM, Vayena E, Hatzimanikatis V, Vorholt JA (2023) Metabolic interaction models recapitulate leaf microbiota ecology. Science (1979) 381:42\u201355. https:\/\/doi.org\/10.1126\/SCIENCE.ADF5121","journal-title":"Science (1979)"},{"key":"2740_CR190","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1111\/J.1365-2699.2010.02407.X","volume":"38","author":"D Scherrer","year":"2011","unstructured":"Scherrer D, K\u00f6rner C (2011) Topographically controlled thermal-habitat differentiation buffers alpine plant diversity against climate warming. J Biogeogr 38:406\u2013416. https:\/\/doi.org\/10.1111\/J.1365-2699.2010.02407.X","journal-title":"J Biogeogr"},{"key":"2740_CR191","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12862-015-0470-6\/TABLES\/2","volume":"15","author":"DC Schlatter","year":"2015","unstructured":"Schlatter DC, Kinkel LL (2015) Do tradeoffs structure antibiotic inhibition, resistance, and resource use among soil-borne Streptomyces? BMC Evol Biol 15:1\u201311. https:\/\/doi.org\/10.1186\/S12862-015-0470-6\/TABLES\/2","journal-title":"BMC Evol Biol"},{"issue":"1","key":"2740_CR193","doi-asserted-by":"publisher","DOI":"10.1186\/S40168-025-02086-X","volume":"13","author":"JM Serrana","year":"2025","unstructured":"Serrana JM, Nascimento FJA, Dessirier B, Broman E, Posselt M (2025) Environmental drivers of the resistome across the Baltic Sea. Microbiome 13(1):92. https:\/\/doi.org\/10.1186\/S40168-025-02086-X","journal-title":"Microbiome"},{"key":"2740_CR194","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2012.00417\/FULL","volume":"3","author":"A Shade","year":"2012","unstructured":"Shade A, Peter H, Allison SD, Baho DL, Berga M, B\u00fcrgmann H, Huber DH, Langenheder S, Lennon JT, Martiny JBH, Matulich KL, Schmidt TM, Handelsman J (2012) Fundamentals of microbial community resistance and resilience. Front Microbiol 3:37301. https:\/\/doi.org\/10.3389\/FMICB.2012.00417\/FULL","journal-title":"Front Microbiol"},{"key":"2740_CR195","doi-asserted-by":"publisher","DOI":"10.7554\/ELIFE.62719","author":"M Sheinman","year":"2021","unstructured":"Sheinman M, Arkhipova K, Arndt PF, Dutilh BE, Hermsen R, Massip F (2021) Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. Elife. https:\/\/doi.org\/10.7554\/ELIFE.62719","journal-title":"Elife"},{"key":"2740_CR196","doi-asserted-by":"publisher","DOI":"10.1073\/PNAS.2516722122","volume":"122","author":"LQ Shen","year":"2025","unstructured":"Shen LQ, Lin D, Ye YQ, Liu Y, Ni B, Wu D, Wang L, Zhu D (2025) Combined pesticide pollution enhances the dissemination of the phage-encoded antibiotic resistome in the soil under nitrogen deposition. Proc Natl Acad Sci U S A 122:e2516722122. https:\/\/doi.org\/10.1073\/PNAS.2516722122","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2740_CR197","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268821002260","volume":"149","author":"RP Smith","year":"2021","unstructured":"Smith RP, Sharma M, Gilson D, Anjum M, Teale CJ (2021) Livestock-associated methicillin-resistant Staphylococcus aureus in slaughtered pigs in England. Epidemiol Infect 149:e236. https:\/\/doi.org\/10.1017\/S0950268821002260","journal-title":"Epidemiol Infect"},{"issue":"8","key":"2740_CR198","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1038\/s41579-023-00877-3","volume":"21","author":"WPJ Smith","year":"2023","unstructured":"Smith WPJ, Wucher BR, Nadell CD, Foster KR (2023) Bacterial defences: mechanisms, evolution and antimicrobial resistance. Nat Rev Microbiol 21(8):519\u2013534. https:\/\/doi.org\/10.1038\/s41579-023-00877-3","journal-title":"Nat Rev Microbiol"},{"key":"2740_CR199","doi-asserted-by":"publisher","DOI":"10.3390\/ANTIBIOTICS12091461","volume":"12","author":"C Smoglica","year":"2023","unstructured":"Smoglica C, Farooq M, Ruffini F, Marsilio F, Di Francesco CE (2023) Microbial community and abundance of selected antimicrobial resistance genes in poultry litter from conventional and antibiotic-free farms. Antibiotics (Basel) 12:1461. https:\/\/doi.org\/10.3390\/ANTIBIOTICS12091461","journal-title":"Antibiotics (Basel)"},{"key":"2740_CR200","doi-asserted-by":"publisher","DOI":"10.3390\/GENES13020385","volume":"13","author":"T Song","year":"2022","unstructured":"Song T, Liang Q, Du Z, Wang X, Chen G, Du Z, Mu D (2022) Salinity gradient controls microbial community structure and assembly in coastal solar salterns. Genes (Basel). 13:385. https:\/\/doi.org\/10.3390\/GENES13020385","journal-title":"Genes (Basel)."},{"key":"2740_CR201","doi-asserted-by":"publisher","DOI":"10.1126\/SCIENCE.ADJ3502","author":"F Spragge","year":"2023","unstructured":"Spragge F, Bakkeren E, Jahn MT, Araujo EBN, Pearson CF, Wang X, Pankhurst L, Cunrath O, Foster KR (2023) Microbiome diversity protects against pathogens by nutrient blocking. Science (1979). https:\/\/doi.org\/10.1126\/SCIENCE.ADJ3502","journal-title":"Science (1979)"},{"key":"2740_CR202","doi-asserted-by":"publisher","unstructured":"Stachurov\u00e1 T, S\u00fdkorov\u00e1 N, Semer\u00e1d J, Malachov\u00e1 K (2022) Resistant genes and multidrug-resistant bacteria in wastewater: A study of their transfer to the water reservoir in the Czech Republic. 12 147. https:\/\/doi.org\/10.3390\/LIFE12020147\/S1","DOI":"10.3390\/LIFE12020147\/S1"},{"key":"2740_CR203","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2020.575707","volume":"11","author":"Z Su","year":"2020","unstructured":"Su Z, Huang B, Mu Q, Wen D (2020) Evaluating the potential antibiotic resistance status in environment based on the trait of microbial community. Front. Microbiol. 11:575707. https:\/\/doi.org\/10.3389\/FMICB.2020.575707","journal-title":"Front. Microbiol."},{"key":"2740_CR204","doi-asserted-by":"publisher","DOI":"10.1128\/aem.01047-23","author":"J Subirats","year":"2023","unstructured":"Subirats J, Sharpe H, Tai V, Fruci M, Topp E (2023) Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments. Appl Environ Microbiol. https:\/\/doi.org\/10.1128\/aem.01047-23","journal-title":"Appl Environ Microbiol"},{"key":"2740_CR205","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1089\/MDR.2022.0296","volume":"30","author":"PA Sudhakari","year":"2024","unstructured":"Sudhakari PA, Ramisetty BCM (2024) Resistome diversity in Escherichia coli isolates of global wastewaters. Microb Drug Resist 30:37\u201349. https:\/\/doi.org\/10.1089\/MDR.2022.0296","journal-title":"Microb Drug Resist"},{"key":"2740_CR206","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/J.JHAZMAT.2016.04.077","volume":"315","author":"M Sun","year":"2016","unstructured":"Sun M, Ye M, Schwab AP, Li X, Wan J, Wei Z, Wu J, Friman VP, Liu K, Tian D, Liu M, Li H, Hu F, Jiang X (2016) Human migration activities drive the fluctuation of ARGs: case study of landfills in Nanjing, eastern China. J Hazard Mater 315:93\u2013101. https:\/\/doi.org\/10.1016\/J.JHAZMAT.2016.04.077","journal-title":"J Hazard Mater"},{"key":"2740_CR207","doi-asserted-by":"publisher","first-page":"1765","DOI":"10.1038\/S41396-023-01487-W","volume":"17","author":"D S\u00fcnderhauf","year":"2023","unstructured":"S\u00fcnderhauf D, Kl\u00fcmper U, Gaze WH, Westra ER, van Houte S (2023) Interspecific competition can drive plasmid loss from a focal species in a microbial community. ISME J. 17:1765\u20131773. https:\/\/doi.org\/10.1038\/S41396-023-01487-W","journal-title":"ISME J."},{"key":"2740_CR208","doi-asserted-by":"publisher","first-page":"4134","DOI":"10.1128\/AEM.00359-12\/SUPPL_FILE\/AEM00359-12_SUPPLEMENTAL.PDF","volume":"78","author":"M Tac\u00e3o","year":"2012","unstructured":"Tac\u00e3o M, Correia A, Henriques I (2012) Resistance to broad-spectrum antibiotics in aquatic systems: anthropogenic activities modulate the dissemination of blaCTX-M-like genes. Appl Environ Microbiol 78:4134\u20134140. https:\/\/doi.org\/10.1128\/AEM.00359-12\/SUPPL_FILE\/AEM00359-12_SUPPLEMENTAL.PDF","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"2740_CR209","doi-asserted-by":"publisher","first-page":"93","DOI":"10.3390\/BIOM15010093","volume":"15","author":"H Tahmasebi","year":"2025","unstructured":"Tahmasebi H, Arjmand N, Monemi M, Babaeizad A, Alibabaei F, Alibabaei N, Bahar A, Oksenych V, Eslami M (2025) From cure to crisis: understanding the evolution of antibiotic-resistant bacteria in human microbiota. Biomolecules 15(1):93\u201393. https:\/\/doi.org\/10.3390\/BIOM15010093","journal-title":"Biomolecules"},{"key":"2740_CR210","doi-asserted-by":"publisher","DOI":"10.3389\/FRMBI.2023.1232571","volume":"2","author":"H Tammert","year":"2023","unstructured":"Tammert H, Kivistik C, Kisand V, K\u00e4iro K, Herlemann DPR (2023) Resistance of freshwater sediment bacterial communities to salinity disturbance and the implication for industrial salt discharge and climate change-based salinization. Front Microbiomes 2:1232571. https:\/\/doi.org\/10.3389\/FRMBI.2023.1232571","journal-title":"Front Microbiomes"},{"key":"2740_CR211","doi-asserted-by":"publisher","DOI":"10.1371\/JOURNAL.PONE.0156854","volume":"11","author":"W Tao","year":"2016","unstructured":"Tao W, Zhang XX, Zhao F, Huang K, Ma H, Wang Z, Ye L, Ren H (2016) High levels of antibiotic resistance genes and their correlations with bacterial community and mobile genetic elements in pharmaceutical wastewater treatment bioreactors. PLoS One 11:e0156854. https:\/\/doi.org\/10.1371\/JOURNAL.PONE.0156854","journal-title":"PLoS One"},{"key":"2740_CR212","doi-asserted-by":"publisher","DOI":"10.1111\/1751-7915.14408","volume":"17","author":"M Tokuda","year":"2024","unstructured":"Tokuda M, Shintani M (2024) Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 17:e14408. https:\/\/doi.org\/10.1111\/1751-7915.14408","journal-title":"Microb Biotechnol"},{"key":"2740_CR213","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1039\/C9EM00458K","volume":"22","author":"XN Tong","year":"2020","unstructured":"Tong XN, Wang XZ, He XJ, Wang Z, Li WX (2020) Effects of antibiotics on microbial community structure and microbial functions in constructed wetlands treated with artificial root exudates. Environ Sci Process Impacts 22:217\u2013226. https:\/\/doi.org\/10.1039\/C9EM00458K","journal-title":"Environ Sci Process Impacts"},{"key":"2740_CR214","doi-asserted-by":"publisher","DOI":"10.1101\/2024.06.03.597162","author":"KC Tracy","year":"2024","unstructured":"Tracy KC, McKaig J, Kinnear C, Millar J, King AA, Read AF, Woods RJ (2024) Reversion to sensitivity explains limited transmission of resistance in a hospital pathogen. bioRxiv. https:\/\/doi.org\/10.1101\/2024.06.03.597162","journal-title":"bioRxiv"},{"key":"2740_CR215","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1111\/ELE.12579","volume":"19","author":"KT Tuff","year":"2016","unstructured":"Tuff KT, Tuff T, Davies KF (2016) A framework for integrating thermal biology into fragmentation research. Ecol Lett 19:361\u2013374. https:\/\/doi.org\/10.1111\/ELE.12579","journal-title":"Ecol Lett"},{"key":"2740_CR216","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2021.717809\/FULL","volume":"12","author":"C Uluseker","year":"2021","unstructured":"Uluseker C, Kaster KM, Thorsen K, Basiry D, Shobana S, Jain M, Kumar G, Kommedal R, Pala-Ozkok I (2021) A review on occurrence and spread of antibiotic resistance in wastewaters and in wastewater treatment plants: mechanisms and perspectives. Front Microbiol 12:717809. https:\/\/doi.org\/10.3389\/FMICB.2021.717809\/FULL","journal-title":"Front Microbiol"},{"key":"2740_CR217","doi-asserted-by":"publisher","DOI":"10.1016\/J.GEOMORPH.2022.108244","volume":"408","author":"RP van Denderen","year":"2022","unstructured":"van Denderen RP, Kater E, Jans LH, Schielen RMJ (2022) Disentangling changes in the river bed profile: the morphological impact of river interventions in a managed river. Geomorphology 408:108244. https:\/\/doi.org\/10.1016\/J.GEOMORPH.2022.108244","journal-title":"Geomorphology"},{"key":"2740_CR218","doi-asserted-by":"publisher","DOI":"10.3389\/FIMMU.2021.712915\/FULL","volume":"12","author":"G Varricchi","year":"2021","unstructured":"Varricchi G, Poto R, Ianiro G, Punziano A, Marone G, Gasbarrini A, Spadaro G (2021) Gut microbiome and common variable immunodeficiency: few certainties and many outstanding questions. Front Immunol 12:712915. https:\/\/doi.org\/10.3389\/FIMMU.2021.712915\/FULL","journal-title":"Front Immunol"},{"key":"2740_CR219","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1111\/ECOG.01306","volume":"38","author":"D Vasudev","year":"2015","unstructured":"Vasudev D, Fletcher RJ, Goswami VR, Krishnadas M (2015) From dispersal constraints to landscape connectivity: lessons from species distribution modeling. Ecography 38:967\u2013978. https:\/\/doi.org\/10.1111\/ECOG.01306","journal-title":"Ecography"},{"key":"2740_CR220","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2016.00173\/XML","volume":"7","author":"CJH Von Wintersdorff","year":"2016","unstructured":"Von Wintersdorff CJH, Penders J, Van Niekerk JM, Mills ND, Majumder S, Van Alphen LB, Savelkoul PHM, Wolffs PFG (2016) Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front Microbiol 7:174871. https:\/\/doi.org\/10.3389\/FMICB.2016.00173\/XML","journal-title":"Front Microbiol"},{"key":"2740_CR221","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S13104-024-06890-W\/TABLES\/2","volume":"17","author":"M Wajid Odhafa","year":"2024","unstructured":"Wajid Odhafa M, Al-Kadmy I, Pourmand MR, Naderi G, Asadian M, Ghourchian S, Douraghi M (2024) The context of blaOXA\u2009\u2013\u200923 gene in Iraqi carbapenem-resistant Acinetobacter baumannii isolates belonging to global clone 1 and global clone 2. BMC Res Notes 17:1\u20137. https:\/\/doi.org\/10.1186\/S13104-024-06890-W\/TABLES\/2","journal-title":"BMC Res Notes"},{"key":"2740_CR222","doi-asserted-by":"publisher","DOI":"10.1016\/J.WATRES.2024.121253","volume":"253","author":"B Wang","year":"2024","unstructured":"Wang B, Ma B, Zhang Y, Stirling E, Yan Q, He Z, Liu Z, Yuan X, Zhang H (2024) Global diversity, coexistence and consequences of resistome in inland waters. Water Res 253:121253. https:\/\/doi.org\/10.1016\/J.WATRES.2024.121253","journal-title":"Water Res"},{"key":"2740_CR223","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1016\/j.cels.2023.09.002","volume":"14","author":"A Weiss","year":"2023","unstructured":"Weiss A, Wang T, You L (2023) Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities. Cell Syst 14:895-905.e5. https:\/\/doi.org\/10.1016\/j.cels.2023.09.002","journal-title":"Cell Syst"},{"key":"2740_CR224","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S40168-020-00982-Y\/FIGURES\/4","volume":"9","author":"WA Wicaksono","year":"2021","unstructured":"Wicaksono WA, Kusstatscher P, Erschen S, Reisenhofer-Graber T, Grube M, Cernava T, Berg G (2021) Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome. Microbiome 9:1\u201314. https:\/\/doi.org\/10.1186\/S40168-020-00982-Y\/FIGURES\/4","journal-title":"Microbiome"},{"key":"2740_CR225","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1038\/S41396-019-0344-9","volume":"13","author":"EM Windels","year":"2019","unstructured":"Windels EM, Michiels JE, Fauvart M, Wenseleers T, den Van Bergh B, Michiels J (2019) Bacterial persistence promotes the evolution of antibiotic resistance by increasing survival and mutation rates. ISME J 13:1239. https:\/\/doi.org\/10.1038\/S41396-019-0344-9","journal-title":"ISME J"},{"key":"2740_CR226","doi-asserted-by":"publisher","DOI":"10.1128\/MBIO.01349-22","volume":"14","author":"K Wollein Waldetoft","year":"2023","unstructured":"Wollein Waldetoft K, Sundius S, Kuske R, Brown SP (2023) Defining the benefits of antibiotic resistance in commensals and the scope for resistance optimization. mBio 14:e0134922. https:\/\/doi.org\/10.1128\/MBIO.01349-22","journal-title":"mBio"},{"issue":"2","key":"2740_CR227","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1007\/S00253-017-8665-Y","volume":"102","author":"D Wu","year":"2017","unstructured":"Wu D, Dolfing J, Xie B (2017) Bacterial perspectives on the dissemination of antibiotic resistance genes in domestic wastewater bio-treatment systems: beneficiary to victim. Appl Microbiol Biotechnol 102(2):597\u2013604. https:\/\/doi.org\/10.1007\/S00253-017-8665-Y","journal-title":"Appl Microbiol Biotechnol"},{"key":"2740_CR228","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12879-018-3263-X\/TABLES\/3","volume":"18","author":"M Xu","year":"2018","unstructured":"Xu M, Fu Y, Kong H, Chen X, Chen Y, Li L, Yang Q (2018) Bloodstream infections caused by Klebsiella pneumoniae: prevalence of bla KPC, virulence factors and their impacts on clinical outcome. BMC Infect Dis 18:1\u20139. https:\/\/doi.org\/10.1186\/S12879-018-3263-X\/TABLES\/3","journal-title":"BMC Infect Dis"},{"key":"2740_CR229","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1360\/SST-2024-0258","volume":"55","author":"YX Xu","year":"2025","unstructured":"Xu YX, Cheng H, Hu XJ, Qin C, Gao YZ (2025) Fitness costs of plasmids carrying antibiotic resistance genes. Sci Sin Technol 55:662\u2013680. https:\/\/doi.org\/10.1360\/SST-2024-0258","journal-title":"Sci Sin Technol"},{"key":"2740_CR230","doi-asserted-by":"publisher","DOI":"10.1016\/J.SCITOTENV.2022.153731","volume":"823","author":"P Yang","year":"2022","unstructured":"Yang P, Hao S, Han M, Xu J, Yu S, Chen C, Zhang H, Ning K (2022) Analysis of antibiotic resistance genes reveals their important roles in influencing the community structure of ocean microbiome. Sci Total Environ 823:153731. https:\/\/doi.org\/10.1016\/J.SCITOTENV.2022.153731","journal-title":"Sci Total Environ"},{"key":"2740_CR231","doi-asserted-by":"publisher","DOI":"10.1016\/J.DRUP.2024.101140","volume":"77","author":"X Yang","year":"2024","unstructured":"Yang X, Li M, Jia ZC, Liu Y, Wu SF, Chen MX, Hao GF, Yang Q (2024) Unraveling the secrets: evolution of resistance mediated by membrane proteins. Drug Resist Updat 77:101140. https:\/\/doi.org\/10.1016\/J.DRUP.2024.101140","journal-title":"Drug Resist Updat"},{"key":"2740_CR232","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2025.1595833\/BIBTEX","volume":"16","author":"Z Yao","year":"2025","unstructured":"Yao Z, Yang Y, Gong Y, Shi S, Ge Y, Zeng W, Zhao D, Cao J, Zhou T, Shen M (2025) The ecological security risks of bronopol: a focus on antibiotic resistance gene dissemination. Front Microbiol 16:1595833. https:\/\/doi.org\/10.3389\/FMICB.2025.1595833\/BIBTEX","journal-title":"Front Microbiol"},{"key":"2740_CR233","doi-asserted-by":"publisher","first-page":"5653","DOI":"10.1128\/AEM.01927-16\/SUPPL_FILE\/ZAM999117413SO1.PDF","volume":"82","author":"S Young","year":"2016","unstructured":"Young S, Nayak B, Sun S, Badgley BD, Rohr JR, Harwood VJ (2016) Vancomycin-resistant enterococci and bacterial community structure following a sewage spill into an aquatic environment. Appl Environ Microbiol 82:5653\u20135660. https:\/\/doi.org\/10.1128\/AEM.01927-16\/SUPPL_FILE\/ZAM999117413SO1.PDF","journal-title":"Appl Environ Microbiol"},{"key":"2740_CR234","doi-asserted-by":"publisher","DOI":"10.1016\/J.DRUP.2023.101036","volume":"73","author":"K Yu","year":"2024","unstructured":"Yu K, Huang Z, Xiao Y, Gao H, Bai X, Wang D (2024) Global spread characteristics of CTX-M-type extended-spectrum \u03b2-lactamases: a genomic epidemiology analysis. Drug Resist Updat 73:101036. https:\/\/doi.org\/10.1016\/J.DRUP.2023.101036","journal-title":"Drug Resist Updat"},{"key":"2740_CR235","doi-asserted-by":"publisher","DOI":"10.3389\/FMICB.2022.820920\/BIBTEX","volume":"13","author":"MF Yu","year":"2022","unstructured":"Yu MF, Shu B, Li Z, Liu G, Liu W, Yang Y, Ma L (2022) Co-selective pressure of cadmium and doxycycline on the antibiotic and heavy metal resistance genes in ditch wetlands. Front Microbiol 13:820920. https:\/\/doi.org\/10.3389\/FMICB.2022.820920\/BIBTEX","journal-title":"Front Microbiol"},{"key":"2740_CR236","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/J.JES.2022.09.002","volume":"129","author":"Q Yuan","year":"2023","unstructured":"Yuan Q, Wang X, Fang H, Cheng Y, Sun R, Luo Y (2023) Coastal mudflats as reservoirs of extracellular antibiotic resistance genes: studies in Eastern China. J Environ Sci 129:58\u201368. https:\/\/doi.org\/10.1016\/J.JES.2022.09.002","journal-title":"J Environ Sci"},{"key":"2740_CR237","doi-asserted-by":"publisher","DOI":"10.1016\/J.HAZADV.2025.100768","volume":"19","author":"M Zarean","year":"2025","unstructured":"Zarean M, Dave SH, Brar SK, Kwong RWM (2025) Environmental drivers of antibiotic resistance: synergistic effects of climate change, co-pollutants, and microplastics. J Hazard Mater Adv 19:100768. https:\/\/doi.org\/10.1016\/J.HAZADV.2025.100768","journal-title":"J Hazard Mater Adv"},{"key":"2740_CR238","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12941-024-00766-4\/FIGURES\/4","volume":"24","author":"P Zhang","year":"2025","unstructured":"Zhang P, Hao J, Zhang Y, Su J, Sun G, Xie J, Hu J, Li G (2025) Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching hospitals. Ann Clin Microbiol Antimicrob 24:1\u20138. https:\/\/doi.org\/10.1186\/S12941-024-00766-4\/FIGURES\/4","journal-title":"Ann Clin Microbiol Antimicrob"},{"key":"2740_CR239","doi-asserted-by":"publisher","DOI":"10.1016\/J.ENVINT.2019.104912","volume":"130","author":"YJ Zhang","year":"2019","unstructured":"Zhang YJ, Hu HW, Chen QL, Singh BK, Yan H, Chen D, He JZ (2019) Transfer of antibiotic resistance from manure-amended soils to vegetable microbiomes. Environ Int 130:104912. https:\/\/doi.org\/10.1016\/J.ENVINT.2019.104912","journal-title":"Environ Int"},{"issue":"2","key":"2740_CR240","doi-asserted-by":"publisher","first-page":"268","DOI":"10.3390\/MICROORGANISMS8020268","volume":"8","author":"Z Zhou","year":"2020","unstructured":"Zhou Z, Yao H (2020) Effects of composting different types of organic fertilizer on the microbial community structure and antibiotic resistance genes. Microorganisms 8(2):268\u2013268. https:\/\/doi.org\/10.3390\/MICROORGANISMS8020268","journal-title":"Microorganisms"},{"issue":"1","key":"2740_CR241","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-59019-3","volume":"16","author":"C Zhu","year":"2025","unstructured":"Zhu C, Wu L, Ning D, Tian R, Gao S, Zhang B, Zhao J, Zhang Y, Xiao N, Wang Y, Brown MR, Tu Q, Zhuang W, Zhou H, Zheng W, Zhang W, Zhang Q, Zhang C, Young M, Yang M, Yan T, Xi C, Wu L, Wu JH, Woo SG, West S, Weaver JE, Wang B, Wakelin S, Van Nostrand JD, Tooker NB, Sun C, Stephens K, de Sousa OV, Smith K, Sidhu J, Rossetti S, de los Reyes FL, Reginatto V, Parameswaran P, Palmer A, Meyers AJ, de Menezes FGR, Mendon\u00e7a-Hagler LC, Liu Y, Li M, Li Z, Li Y, Lee ZMP, Leal CD, Kumari S, Keucken A, Marcantini DG, Johnson DR, Hu Z, Horn H, Harmon M, Hale L, Habagil M, Gu AZ, Griffin JS, G\u00f3mez JS, Ford A, Etchebehere C, Chen S, Cabrol L, Cabezas A, Bux F, Brewster RK, Bovio-Winkler P, Bott CB, Bond P, Boehnke K, de Abreu Mac Conell \u00c9F, de Araujo JC, Agullo-Barcelo M, Acevedo D, Ju F, Wells GF, Guo J, He Z, Nielsen PH, Wang A, Zhang Y, Chen T, He Q, Criddle CS, Wagner M, Tiedje JM, Curtis TP, Wen X, Yang Y, Alvarez-Cohen L, Stahl DA, Alvarez PJJ, Rittmann BE, Zhou J (2025) Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems. Nat Commun 16(1):4006-. https:\/\/doi.org\/10.1038\/s41467-025-59019-3","journal-title":"Nat Commun"},{"issue":"1","key":"2740_CR242","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-023-36254-0","volume":"14","author":"M Zhu","year":"2023","unstructured":"Zhu M, Dai X (2023) Stringent response ensures the timely adaptation of bacterial growth to nutrient downshift. Nat Commun 14(1):1\u201315. https:\/\/doi.org\/10.1038\/s41467-023-36254-0","journal-title":"Nat Commun"},{"issue":"1","key":"2740_CR243","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-45154-w","volume":"15","author":"S Zhu","year":"2024","unstructured":"Zhu S, Hong J, Wang T (2024) Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species. Nat Commun 15(1):800. https:\/\/doi.org\/10.1038\/s41467-024-45154-w","journal-title":"Nat Commun"},{"key":"2740_CR244","doi-asserted-by":"publisher","DOI":"10.1093\/FEMSRE\/FUAB022","author":"I Zilber-Rosenberg","year":"2021","unstructured":"Zilber-Rosenberg I, Rosenberg E (2021) Microbial-driven genetic variation in holobionts. FEMS Microbiol Rev. https:\/\/doi.org\/10.1093\/FEMSRE\/FUAB022","journal-title":"FEMS Microbiol Rev"},{"issue":"1","key":"2740_CR245","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-024-48219-y","volume":"15","author":"PD Zongo","year":"2024","unstructured":"Zongo PD, Cabanel N, Royer G, Depardieu F, Hartmann A, Naas T, Glaser P, Rosinski-Chupin I (2024) An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages. Nat Commun 15(1):1\u201315. https:\/\/doi.org\/10.1038\/s41467-024-48219-y","journal-title":"Nat Commun"},{"key":"2740_CR246","doi-asserted-by":"publisher","first-page":"2184","DOI":"10.1038\/S41564-019-0567-6","volume":"4","author":"C Zu\u00f1iga","year":"2019","unstructured":"Zu\u00f1iga C, Li CT, Yu G, Al-Bassam MM, Li T, Jiang L, Zaramela LS, Guarnieri M, Betenbaugh MJ, Zengler K (2019) Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities. Nat Microbiol 4:2184\u20132191. https:\/\/doi.org\/10.1038\/S41564-019-0567-6","journal-title":"Nat Microbiol"},{"key":"2740_CR247","doi-asserted-by":"publisher","DOI":"10.1128\/MSYSTEMS.00186-18","author":"M Zwanzig","year":"2019","unstructured":"Zwanzig M, Harrison E, Brockhurst MA, Hall JPJ, Berendonk TU, Berger U (2019) Mobile compensatory mutations promote plasmid survival. mSystems. https:\/\/doi.org\/10.1128\/MSYSTEMS.00186-18","journal-title":"mSystems"}],"container-title":["Microbial Ecology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00248-026-02740-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00248-026-02740-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00248-026-02740-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T04:40:00Z","timestamp":1775536800000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00248-026-02740-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,26]]},"references-count":243,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["2740"],"URL":"https:\/\/doi.org\/10.1007\/s00248-026-02740-3","relation":{},"ISSN":["1432-184X"],"issn-type":[{"value":"1432-184X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,26]]},"assertion":[{"value":"22 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 March 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 March 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"95"}}