{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T03:38:19Z","timestamp":1792640299262,"version":"4.5.0"},"reference-count":86,"publisher":"European Respiratory Society (ERS)","issue":"164","license":[{"start":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T00:00:00Z","timestamp":1653436800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":["publications.ersnet.org"],"crossmark-restriction":true},"short-container-title":["Eur Respir Rev"],"accepted":{"date-parts":[[2022,3,2]]},"published-print":{"date-parts":[[2022,6,30]]},"abstract":"<jats:p>\n                    The development of resistome analysis,\n                    <jats:italic>i.e.<\/jats:italic>\n                    the comprehensive analysis of antibiotic-resistance genes (ARGs), is enabling a better understanding of the mechanisms of antibiotic-resistance emergence. The respiratory microbiome is a dynamic and interactive network of bacteria, with a set of ARGs that could influence the response to antibiotics. Viruses such as bacteriophages, potential carriers of ARGs, may also form part of this respiratory resistome. Chronic respiratory diseases (CRDs) such as cystic fibrosis, severe asthma, chronic obstructive pulmonary disease and bronchiectasis, managed with long-term antibiotic therapies, lead to multidrug resistance. Antibiotic susceptibility testing provides a partial view of the bacterial response to antibiotics in the complex lung environment. Assessing the ARG network would allow personalised, targeted therapeutic strategies and suitable antibiotic stewardship in CRDs, depending on individual resistome and microbiome signatures. This review summarises the influence of pulmonary antibiotic protocols on the respiratory microbiome, detailing the variable consequences according to antibiotic class and duration of treatment. The different resistome-profiling methods are explained to clarify their respective place in antibiotic-resistance analysis in the lungs. Finally, this review details current knowledge on the respiratory resistome related to therapeutic strategies and provides insight into the application of resistome analysis to counter the emergence of multidrug-resistant respiratory pathogens.\n                  <\/jats:p>","DOI":"10.1183\/16000617.0259-2021","type":"journal-article","created":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T10:40:12Z","timestamp":1653475212000},"page":"210259","update-policy":"https:\/\/doi.org\/10.1183\/ers-crossmark-policy","source":"Crossref","is-referenced-by-count":36,"title":["Antibiotic resistance in chronic respiratory diseases: from susceptibility testing to the resistome"],"prefix":"10.1183","volume":"31","author":[{"given":"H\u00e9l\u00e8ne","family":"Pailhori\u00e8s","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Louis","family":"Herrmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lourdes","family":"Velo-Suarez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudie","family":"Lamoureux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cl\u00e9mence","family":"Beauruelle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0903-9828","authenticated-orcid":false,"given":"Pierre-R\u00e9gis","family":"Burgel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2089-3825","authenticated-orcid":false,"given":"Genevi\u00e8ve","family":"H\u00e9ry-Arnaud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"81","published-online":{"date-parts":[[2022,5,25]]},"reference":[{"key":"2024102404030264000_31.164.210259.1","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1016\/S2213-2600(18)30510-1","article-title":"Functional effects of the microbiota in chronic respiratory disease","volume":"7","author":"Budden","year":"2019","journal-title":"Lancet Respir Med"},{"key":"2024102404030264000_31.164.210259.2","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00202013"},{"key":"2024102404030264000_31.164.210259.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.jpeds.2016.09.064"},{"key":"2024102404030264000_31.164.210259.4","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1016\/j.mayocp.2018.05.026","article-title":"COPD guidelines: a review of the 2018 GOLD report","volume":"93","author":"Mirza","year":"2018","journal-title":"Mayo Clin Proc"},{"key":"2024102404030264000_31.164.210259.5","first-page":"CD010337","article-title":"Interventions for bronchiectasis: an overview of Cochrane systematic reviews","volume":"7","author":"Welsh","year":"2015","journal-title":"Cochrane Database Syst Rev"},{"key":"2024102404030264000_31.164.210259.6","doi-asserted-by":"publisher","DOI":"10.1002\/alr.21609"},{"key":"2024102404030264000_31.164.210259.7","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(17)31281-3"},{"key":"2024102404030264000_31.164.210259.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2012.02.006"},{"key":"2024102404030264000_31.164.210259.9","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00343-20"},{"key":"2024102404030264000_31.164.210259.10","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/j.jcf.2019.01.008","article-title":"Antimicrobial susceptibility testing (AST) and associated clinical outcomes in individuals with cystic fibrosis: a systematic review","volume":"18","author":"Somayaji","year":"2019","journal-title":"J Cyst Fibros"},{"key":"2024102404030264000_31.164.210259.11","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2017.14"},{"key":"2024102404030264000_31.164.210259.12","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1614"},{"key":"2024102404030264000_31.164.210259.13","doi-asserted-by":"publisher","DOI":"10.1126\/science.1176950"},{"key":"2024102404030264000_31.164.210259.14","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1051\/medsci\/20153111003","article-title":"Lung resistome","volume":"31","author":"Br\u00e9geon","year":"2015","journal-title":"Med Sci (Paris)"},{"key":"2024102404030264000_31.164.210259.15","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(14)61137-5"},{"key":"2024102404030264000_31.164.210259.16","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.jcf.2018.02.006","article-title":"ECFS best practice guidelines: the 2018 revision","volume":"17","author":"Castellani","year":"2018","journal-title":"J Cyst Fibros"},{"key":"2024102404030264000_31.164.210259.17","first-page":"CD001912","article-title":"Prophylactic anti-staphylococcal antibiotics for cystic fibrosis","volume":"9","author":"Rosenfeld","year":"2020","journal-title":"Cochrane Database Syst Rev"},{"key":"2024102404030264000_31.164.210259.18","doi-asserted-by":"crossref","first-page":"177","DOI":"10.5694\/mja17.01195","article-title":"Management of bronchiectasis in adults","volume":"209","author":"Visser","year":"2018","journal-title":"Med J Aust"},{"key":"2024102404030264000_31.164.210259.19","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00629-2017"},{"key":"2024102404030264000_31.164.210259.20","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.2217\/fmb-2021-0150","article-title":"Management of chronic Pseudomonas aeruginosa infection with inhaled levofloxacin in people with cystic fibrosis","volume":"16","author":"Elborn","year":"2021","journal-title":"Future Microbiol"},{"key":"2024102404030264000_31.164.210259.21","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201207-1160OE"},{"key":"2024102404030264000_31.164.210259.22","doi-asserted-by":"publisher","DOI":"10.1002\/ppul.21301"},{"key":"2024102404030264000_31.164.210259.23","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1097\/MCP.0000000000000730","article-title":"Treatment of pulmonary exacerbations in cystic fibrosis","volume":"26","author":"Ng","year":"2020","journal-title":"Curr Opin Pulm Med"},{"key":"2024102404030264000_31.164.210259.24","first-page":"CD009764","article-title":"Prophylactic antibiotic therapy for chronic obstructive pulmonary disease (COPD)","volume":"10","author":"Herath","year":"2018","journal-title":"Cochrane Database Syst Rev"},{"key":"2024102404030264000_31.164.210259.25","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.l4486"},{"key":"2024102404030264000_31.164.210259.26","unstructured":"National Institute for Health and Care Excellence . Bronchiectasis (Non-Cystic Fibrosis), Acute Exacerbation: Antimicrobial Prescribing . www.nice.org.uk\/guidance\/ng117\/chapter\/recommendations Date last accessed: April 14, 2021."},{"key":"2024102404030264000_31.164.210259.27","doi-asserted-by":"publisher","DOI":"10.1002\/14651858.CD002203.pub4"},{"key":"2024102404030264000_31.164.210259.28","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201204-0596PP"},{"key":"2024102404030264000_31.164.210259.29","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1186\/s13613-019-0584-x","article-title":"Management of severe asthma exacerbation: guidelines from the Soci\u00e9t\u00e9 Fran\u00e7aise de M\u00e9decine d'Urgence, the Soci\u00e9t\u00e9 de R\u00e9animation de Langue Fran\u00e7aise and the French Group for Pediatric Intensive Care and Emergencies","volume":"9","author":"Le Conte","year":"2019","journal-title":"Ann Intensive Care"},{"key":"2024102404030264000_31.164.210259.30","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1120577109"},{"key":"2024102404030264000_31.164.210259.31","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2015.198"},{"key":"2024102404030264000_31.164.210259.32","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-1-27"},{"key":"2024102404030264000_31.164.210259.33","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00103-18"},{"key":"2024102404030264000_31.164.210259.34","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-017-1022-6"},{"key":"2024102404030264000_31.164.210259.35","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201809-1739OC"},{"key":"2024102404030264000_31.164.210259.36","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2013-204517"},{"key":"2024102404030264000_31.164.210259.37","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1016\/S2213-2600(14)70213-9","article-title":"The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial","volume":"2","author":"Rogers","year":"2014","journal-title":"Lancet Respir Med"},{"key":"2024102404030264000_31.164.210259.38","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00035-14"},{"key":"2024102404030264000_31.164.210259.39","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1016\/S2213-2600(16)30081-9","article-title":"The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study","volume":"4","author":"Mika","year":"2016","journal-title":"Lancet Respir Med"},{"key":"2024102404030264000_31.164.210259.40","doi-asserted-by":"crossref","first-page":"2534","DOI":"10.1038\/s41598-019-38984-y","article-title":"Changes in microbiome diversity following \u03b2-lactam antibiotic treatment are associated with therapeutic versus subtherapeutic antibiotic exposure in cystic fibrosis","volume":"9","author":"Hahn","year":"2019","journal-title":"Sci Rep"},{"key":"2024102404030264000_31.164.210259.41","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0045001"},{"key":"2024102404030264000_31.164.210259.42","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00203013"},{"key":"2024102404030264000_31.164.210259.43","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2019.02.010"},{"key":"2024102404030264000_31.164.210259.44","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2019-214187"},{"key":"2024102404030264000_31.164.210259.45","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2019-214191"},{"key":"2024102404030264000_31.164.210259.46","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2014.00178"},{"key":"2024102404030264000_31.164.210259.47","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1016\/j.biocel.2011.05.009","article-title":"Macrolides: new therapeutic perspectives in lung diseases","volume":"43","author":"Guillot","year":"2011","journal-title":"Int J Biochem Cell Biol"},{"key":"2024102404030264000_31.164.210259.48","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1513\/AnnalsATS.202002-176OC","article-title":"Effect of concomitant azithromycin and tobramycin use on cystic fibrosis pulmonary exacerbation treatment","volume":"18","author":"Cogen","year":"2021","journal-title":"Ann Am Thorac Soc"},{"key":"2024102404030264000_31.164.210259.49","doi-asserted-by":"publisher","DOI":"10.1136\/jim-2021-001824"},{"key":"2024102404030264000_31.164.210259.50","doi-asserted-by":"publisher","DOI":"10.4161\/viru.28196"},{"key":"2024102404030264000_31.164.210259.51","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx199"},{"key":"2024102404030264000_31.164.210259.52","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2019-213485"},{"key":"2024102404030264000_31.164.210259.53","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s40248-018-0140-9","article-title":"Understanding the impact of antibiotic therapies on the respiratory tract resistome: a novel pooled-template metagenomic sequencing strategy","volume":"13","author":"Taylor","year":"2018","journal-title":"Multidiscip Respir Med"},{"key":"2024102404030264000_31.164.210259.54","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1007\/s00109-016-1478-0","article-title":"Translational metagenomics and the human resistome: confronting the menace of the new millennium","volume":"95","author":"Willmann","year":"2017","journal-title":"J Mol Med Berl Ger"},{"key":"2024102404030264000_31.164.210259.55","doi-asserted-by":"publisher","DOI":"10.1111\/nyas.13268"},{"key":"2024102404030264000_31.164.210259.56","doi-asserted-by":"publisher","DOI":"10.1080\/14737159.2019.1592678"},{"key":"2024102404030264000_31.164.210259.57","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0234-1"},{"key":"2024102404030264000_31.164.210259.58","doi-asserted-by":"publisher","DOI":"10.1111\/1758-2229.12735"},{"key":"2024102404030264000_31.164.210259.59","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01324-19"},{"key":"2024102404030264000_31.164.210259.60","doi-asserted-by":"crossref","first-page":"212","DOI":"10.3389\/fmicb.2019.00212","article-title":"Nasal resistome development in infants with cystic fibrosis in the first year of life","volume":"10","author":"Allemann","year":"2019","journal-title":"Front Microbiol"},{"key":"2024102404030264000_31.164.210259.61","first-page":"e61","article-title":"Rapid resistome mapping using nanopore sequencing","volume":"45","author":"van der Helm","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2024102404030264000_31.164.210259.62","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2017.28"},{"key":"2024102404030264000_31.164.210259.63","doi-asserted-by":"publisher","DOI":"10.2217\/fmb.11.135"},{"key":"2024102404030264000_31.164.210259.64","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/s41564-018-0292-6","article-title":"Prediction of the intestinal resistome by a three-dimensional structure-based method","volume":"4","author":"Rupp\u00e9","year":"2019","journal-title":"Nat Microbiol"},{"key":"2024102404030264000_31.164.210259.65","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.3390\/ijms18081654","article-title":"A different microbiome gene repertoire in the airways of cystic fibrosis patients with severe lung disease","volume":"18","author":"Bacci","year":"2017","journal-title":"Int J Mol Sci"},{"key":"2024102404030264000_31.164.210259.66","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1164\/rccm.201911-2202OC","article-title":"Metagenomics reveals a core macrolide resistome related to microbiota in chronic respiratory disease","volume":"202","author":"Mac Aog\u00e1in","year":"2020","journal-title":"Am J Respir Crit Care Med"},{"key":"2024102404030264000_31.164.210259.67","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02204-13"},{"key":"2024102404030264000_31.164.210259.68","doi-asserted-by":"crossref","first-page":"2102730","DOI":"10.1183\/13993003.02730-2021","article-title":"Global Initiative for Asthma Strategy 2021: executive summary and rationale for key changes","volume":"59","author":"Reddel","year":"2022","journal-title":"Eur Respir J"},{"key":"2024102404030264000_31.164.210259.69","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2015-207194"},{"key":"2024102404030264000_31.164.210259.70","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkr315"},{"key":"2024102404030264000_31.164.210259.71","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00856"},{"key":"2024102404030264000_31.164.210259.72","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01845-09"},{"key":"2024102404030264000_31.164.210259.73","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-015-2480-0"},{"key":"2024102404030264000_31.164.210259.74","doi-asserted-by":"publisher","DOI":"10.2147\/COPD.S77562"},{"key":"2024102404030264000_31.164.210259.75","doi-asserted-by":"publisher","DOI":"10.1016\/j.rmed.2013.04.006"},{"key":"2024102404030264000_31.164.210259.76","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00211311"},{"key":"2024102404030264000_31.164.210259.77","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1186\/s13756-020-00783-w","article-title":"Prevalence and abundance of selected genes conferring macrolide resistance genes in COPD patients during maintenance treatment with azithromycin","volume":"9","author":"Djamin","year":"2020","journal-title":"Antimicrob Resist Infect Control"},{"key":"2024102404030264000_31.164.210259.78","doi-asserted-by":"publisher","DOI":"10.1136\/bmjresp-2018-000321"},{"key":"2024102404030264000_31.164.210259.79","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1016\/S2213-2600(13)70185-1","article-title":"Long-term azithromycin for Indigenous children with non-cystic-fibrosis bronchiectasis or chronic suppurative lung disease (Bronchiectasis Intervention Study): a multicentre, double-blind, randomised controlled trial","volume":"1","author":"Valery","year":"2013","journal-title":"Lancet Respir Med"},{"key":"2024102404030264000_31.164.210259.80","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00965-10"},{"key":"2024102404030264000_31.164.210259.81","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1016\/j.cmi.2021.05.011","article-title":"Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence resistome analysis","volume":"27","author":"Cortes-Lara","year":"2021","journal-title":"Clin Microbiol Infect"},{"key":"2024102404030264000_31.164.210259.82","doi-asserted-by":"crossref","first-page":"e10264","DOI":"10.15252\/emmm.201910264","article-title":"Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics","volume":"12","author":"Khaledi","year":"2020","journal-title":"EMBO Mol Med"},{"key":"2024102404030264000_31.164.210259.83","doi-asserted-by":"publisher","DOI":"10.1165\/rcmb.2019-0273TR"},{"key":"2024102404030264000_31.164.210259.84","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2019.03.086"},{"key":"2024102404030264000_31.164.210259.85","doi-asserted-by":"crossref","first-page":"213","DOI":"10.3389\/fcimb.2020.00213","article-title":"Bacterial community interactions during chronic respiratory disease","volume":"10","author":"Welp","year":"2020","journal-title":"Front Cell Infect Microbiol"},{"key":"2024102404030264000_31.164.210259.86","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2015.12.004"}],"container-title":["European Respiratory Review"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1183\/16000617.0259-2021","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,24]],"date-time":"2025-02-24T00:05:05Z","timestamp":1740355505000},"score":1,"resource":{"primary":{"URL":"https:\/\/publications.ersnet.org\/lookup\/doi\/10.1183\/16000617.0259-2021"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,25]]},"references-count":86,"journal-issue":{"issue":"164","published-online":{"date-parts":[[2022,5,25]]},"published-print":{"date-parts":[[2022,6,30]]}},"alternative-id":["10.1183\/16000617.0259-2021"],"URL":"https:\/\/doi.org\/10.1183\/16000617.0259-2021","relation":{},"ISSN":["0905-9180","1600-0617"],"issn-type":[{"value":"0905-9180","type":"print"},{"value":"1600-0617","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,5,25]]}}}