{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T13:58:40Z","timestamp":1790344720639,"version":"4.1.0"},"reference-count":89,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Mycobacterium abscessus<\/jats:italic>\n                      has emerged as one of the most formidable pathogens affecting people with cystic fibrosis (pwCF), driven by intrinsic antimicrobial resistance, complex taxonomy, and substantial diagnostic uncertainty. Despite major technological advances, establishing a diagnosis of pulmonary disease remains challenging, as traditional culture-based workflows are constrained by limited sensitivity, prolonged turnaround times. However, recent progress in proteomic and genomic technologies has markedly improved organism detection and taxonomic resolution. This review examines the contemporary diagnostic architecture for\n                      <jats:italic toggle=\"yes\">M. abscessus<\/jats:italic>\n                      pulmonary infection in pwCF, identifying persistent gaps, and proposes a precision-oriented framework in which culture, proteomics, genomics, and host-response biomarkers converge to support earlier and more individualized clinical decision-making.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/jcm.00812-26","type":"journal-article","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T13:00:43Z","timestamp":1790341243000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Diagnostic challenges in\n                    <i>Mycobacterium abscessus<\/i>\n                    pulmonary disease, particularly in patients with cystic fibrosis: toward an integrated precision framework"],"prefix":"10.1128","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2012-1750","authenticated-orcid":true,"given":"Vincent","family":"Le Moigne","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, UVSQ, Inserm, Infection et inflammation","place":["Montigny-le-Bretonneux, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5579-9476","authenticated-orcid":true,"given":"Anne-Laure","family":"Roux","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, UVSQ, Inserm, Infection et inflammation","place":["Montigny-le-Bretonneux, France"]},{"id":[{"id":"https:\/\/ror.org\/03pef0w96","id-type":"ROR","asserted-by":"publisher"}],"name":"Assistance Publique-H\u00f4pitaux de Paris. GHU Paris-Saclay, Service de Microbiologie, Hopital Raymond-Poincare","place":["Garches, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6163-2947","authenticated-orcid":true,"given":"Cl\u00e9mence","family":"Beauruelle","sequence":"additional","affiliation":[{"name":"Center of Biome Analysis and Microbiota (CBAM), Brest University Hospital","place":["Brest, France"]},{"id":[{"id":"https:\/\/ror.org\/03befxt38","id-type":"ROR","asserted-by":"publisher"}],"name":"UnivBrest, Inserm, EFS, UMR 1078, GGB, Brest University","place":["Brest, France"]},{"name":"Department of Infectious Agents, Brest University Hospital","place":["Brest, France"]}],"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":[{"name":"Center of Biome Analysis and Microbiota (CBAM), Brest University Hospital","place":["Brest, France"]},{"id":[{"id":"https:\/\/ror.org\/03befxt38","id-type":"ROR","asserted-by":"publisher"}],"name":"UnivBrest, Inserm, EFS, UMR 1078, GGB, Brest University","place":["Brest, France"]},{"name":"Department of Infectious Agents, Brest University Hospital","place":["Brest, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2347-6418","authenticated-orcid":false,"given":"Jean-Louis","family":"Herrmann","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, UVSQ, Inserm, Infection et inflammation","place":["Montigny-le-Bretonneux, France"]},{"id":[{"id":"https:\/\/ror.org\/03pef0w96","id-type":"ROR","asserted-by":"publisher"}],"name":"Assistance Publique-H\u00f4pitaux de Paris. GHU Paris-Saclay, Service de Microbiologie, Hopital Raymond-Poincare","place":["Garches, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","published-online":{"date-parts":[[2026,9,25]]},"reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-020-0331-1"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00250-2019"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa1125"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.05030-11"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.00697-25"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.001376"},{"key":"e_1_3_2_8_2","first-page":"297","volume-title":"European manual of clinical microbiology","author":"Delogu G","year":"2012","unstructured":"Delogu G, Herrmann JL. 2012. Mycobacterium species, p 297\u2013307. In Cornaglia G, Courcol R, Herrmann JL, Kahlmeter G, Peigue-Lafeuille H, Vila J (ed), European manual of clinical microbiology. Vol. Soci\u00e9t\u00e9 Fran\u00e7aise de Microbiologie. Paris."},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00285-06"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2015.05.002"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02379-10"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00471-16"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02423-16"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00097-16"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jctube.2018.07.003"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01519-18"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2019.e02684"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02736-23"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijerph191710645"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.dib.2025.111358"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.00036-23"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/jid.1953.18"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-73-1-55"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1099\/00207713-42-2-240"},{"key":"e_1_3_2_25_2","first-page":"3697","volume-title":"Principles and practice of infectious diseases","author":"Brown-Elliott BA","year":"2014","unstructured":"Brown-Elliott BA, Wallace RJ. 2014. Infection caused by nontuberculous mycobacteria other than Mycobacterium avium complex, p 3697. In Principles and practice of infectious diseases. Elsevier Inc."},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00788-14"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00072-12"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00237-18"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.01110-22"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1111\/1751-7915.14545"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.5c00534"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.63969-0"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01688-08"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00037-09"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.resmic.2013.12.003"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01275-08"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2014.04.001"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01204-18"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf8156"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-021-00963-3"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(13)60632-7"},{"key":"e_1_3_2_42_2","unstructured":"CLSI. 2018. Susceptibility testing of mycobacteria nocardia spp. and other aerobic actinomycetes. 3rd ed. CLSI standard M24. Clinical and Laboratory Standards Institute Wayne PA"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.40.7.1676"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.00428-23"},{"key":"e_1_3_2_45_2","first-page":"136","volume-title":"CA-SFM \/ EUCAST: Soci\u00e9t\u00e9 Fran\u00e7aise de Microbiologie Ed","year":"2025","unstructured":"Soci\u00e9t\u00e9 Fran\u00e7aise de Microbiologie. Chapter 2.5: Tableaux des concentrations critiques: Mycobacterium abscessus complex, p 136\u2013137. 2025. In CA-SFM \/ EUCAST: Soci\u00e9t\u00e9 Fran\u00e7aise de Microbiologie Ed"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2016.10.004"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00147-16"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00516-19"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkx021"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0239146"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.00489-23"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1007\/s15010-022-01890-z"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1183\/16000617.0299-2020"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.01855-22"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.202303-0401OC"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.aca.2026.345085"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.0040202"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1001062"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1128\/CVI.05205-11"},{"key":"e_1_3_2_60_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-021-06825-x"},{"key":"e_1_3_2_61_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01257-09"},{"key":"e_1_3_2_62_2","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201709-727OC"},{"key":"e_1_3_2_63_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.200207-678OC"},{"key":"e_1_3_2_64_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccm.2015.11.001"},{"key":"e_1_3_2_65_2","doi-asserted-by":"publisher","DOI":"10.1183\/23120541.00082-2019"},{"key":"e_1_3_2_66_2","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2015-207360"},{"key":"e_1_3_2_67_2","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00535-2020"},{"key":"e_1_3_2_68_2","doi-asserted-by":"publisher","DOI":"10.7883\/yoken.67.329"},{"key":"e_1_3_2_69_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.resinv.2019.04.002"},{"key":"e_1_3_2_70_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2018.11.011"},{"key":"e_1_3_2_71_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.rmed.2020.106086"},{"key":"e_1_3_2_72_2","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00098212"},{"key":"e_1_3_2_73_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12931-020-01420-1"},{"key":"e_1_3_2_74_2","doi-asserted-by":"publisher","DOI":"10.4103\/ijmy.ijmy_14_20"},{"key":"e_1_3_2_75_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jctube.2020.100189"},{"key":"e_1_3_2_76_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0242598"},{"key":"e_1_3_2_77_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-45893-8"},{"key":"e_1_3_2_78_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chest.2024.10.029"},{"key":"e_1_3_2_79_2","doi-asserted-by":"publisher","DOI":"10.1086\/344277"},{"key":"e_1_3_2_80_2","doi-asserted-by":"publisher","DOI":"10.1111\/resp.12640"},{"key":"e_1_3_2_81_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00702-13"},{"key":"e_1_3_2_82_2","doi-asserted-by":"publisher","DOI":"10.1086\/426442"},{"key":"e_1_3_2_83_2","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00011815"},{"key":"e_1_3_2_84_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.00432"},{"key":"e_1_3_2_85_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2021.08.019"},{"key":"e_1_3_2_86_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00192-22"},{"key":"e_1_3_2_87_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01874-22"},{"key":"e_1_3_2_88_2","doi-asserted-by":"publisher","DOI":"10.1136\/thorax-2022-218800"},{"key":"e_1_3_2_89_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-58455-5"},{"key":"e_1_3_2_90_2","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2026.2678657"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/jcm.00812-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/jcm.00812-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T13:00:45Z","timestamp":1790341245000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/jcm.00812-26"}},"subtitle":[],"editor":[{"given":"Nathan A.","family":"Ledeboer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,25]]},"references-count":89,"alternative-id":["10.1128\/jcm.00812-26"],"URL":"https:\/\/doi.org\/10.1128\/jcm.00812-26","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,25]]},"assertion":[{"value":"2026-09-25","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00812-26"}}