{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T04:09:35Z","timestamp":1788926975644,"version":"build-2803163510"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T00:00:00Z","timestamp":1753142400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T00:00:00Z","timestamp":1753142400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100010108","name":"Zhongshan Hospital","doi-asserted-by":"publisher","award":["2024ZSFZ39"],"award-info":[{"award-number":["2024ZSFZ39"]}],"id":[{"id":"10.13039\/501100010108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003392","name":"Natural Science Foundation of Fujian Province","doi-asserted-by":"crossref","award":["2024J08352"],"award-info":[{"award-number":["2024J08352"]}],"id":[{"id":"10.13039\/501100003392","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Ann Clin Microbiol Antimicrob"],"DOI":"10.1186\/s12941-025-00804-9","type":"journal-article","created":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T11:20:40Z","timestamp":1753183240000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Whole-genome recombination and dynamic accessory genomes drive the phenotypic diversity of Mycobacterium abscessus subspecies"],"prefix":"10.1186","volume":"24","author":[{"given":"Yu","family":"Chen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rong","family":"Bao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Na","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyu","family":"Yin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le","family":"Qin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bijie","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing","family":"Miao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,7,22]]},"reference":[{"issue":"4","key":"804_CR1","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1093\/cid\/ciaa1125","volume":"71","author":"CL Daley","year":"2020","unstructured":"Daley CL, Iaccarino JM, Lange C, Cambau E, Wallace RJ, Andrejak C, et al. Treatment of nontuberculous mycobacterial pulmonary disease: an official ATS\/ERS\/ESCMID\/IDSA clinical practice guideline. Clin Infect Dis. 2020;71(4):905\u201313. https:\/\/doi.org\/10.1093\/cid\/ciaa1125.","journal-title":"Clin Infect Dis"},{"issue":"3","key":"804_CR2","doi-asserted-by":"publisher","first-page":"364","DOI":"10.3201\/eid2003.131106","volume":"20","author":"H Tettelin","year":"2014","unstructured":"Tettelin H, Davidson RM, Agrawal S, Aitken ML, Shallom S, Hasan NA, et al. High-level relatedness among Mycobacterium abscessus subsp. Massiliense strains from widely separated outbreaks. Emerg Infect Dis. 2014;20(3):364\u201371. https:\/\/doi.org\/10.3201\/eid2003.131106.","journal-title":"Emerg Infect Dis"},{"issue":"1","key":"804_CR3","doi-asserted-by":"publisher","first-page":"5145","DOI":"10.1038\/s41467-021-25484-9","volume":"12","author":"RA Bronson","year":"2021","unstructured":"Bronson RA, Gupta C, Manson AL, Nguyen JA, Bahadirli-Talbott A, Parrish NM, et al. Global phylogenomic analyses of Mycobacterium abscessus provide context for Non cystic fibrosis infections and the evolution of antibiotic resistance. Nat Commun. 2021;12(1):5145. https:\/\/doi.org\/10.1038\/s41467-021-25484-9.","journal-title":"Nat Commun"},{"issue":"10","key":"804_CR4","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1038\/s41564-021-00963-3","volume":"6","author":"C Ruis","year":"2021","unstructured":"Ruis C, Bryant JM, Bell SC, Thomson R, Davidson RM, Hasan NA, et al. Dissemination of Mycobacterium abscessus via global transmission networks. Nat Microbiol. 2021;6(10):1279\u201388. https:\/\/doi.org\/10.1038\/s41564-021-00963-3.","journal-title":"Nat Microbiol"},{"issue":"4","key":"804_CR5","doi-asserted-by":"publisher","first-page":"e0490822","DOI":"10.1128\/spectrum.04908-22","volume":"11","author":"K Komiya","year":"2023","unstructured":"Komiya K, Yoshida M, Uchida S, Takikawa S, Yamasue M, Matsumoto T, et al. Massive and lengthy clonal nosocomial expansion of Mycobacterium abscessus subsp. Massiliense among patients who are ventilator dependent without cystic fibrosis. Microbiol Spectr. 2023;11(4):e0490822. https:\/\/doi.org\/10.1128\/spectrum.04908-22.","journal-title":"Microbiol Spectr"},{"key":"804_CR6","doi-asserted-by":"publisher","unstructured":"Kwak N, Dalcolmo MP, Daley CL, Eather G, Gayoso R, Hasegawa N, et al. M Ycobacterium abscessus pulmonary disease: individual patient data meta-analysis. Eur Respir J. 2019;54(1). https:\/\/doi.org\/10.1183\/13993003.01991-2018.","DOI":"10.1183\/13993003.01991-2018"},{"issue":"3","key":"804_CR7","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1111\/mmi.12387","volume":"90","author":"A Pawlik","year":"2013","unstructured":"Pawlik A, Garnier G, Orgeur M, Tong P, Lohan A, Le Chevalier F, et al. Identification and characterization of the genetic changes responsible for the characteristic smooth-to-rough morphotype alterations of clinically persistent Mycobacterium abscessus. Mol Microbiol. 2013;90(3):612\u201329. https:\/\/doi.org\/10.1111\/mmi.12387.","journal-title":"Mol Microbiol"},{"key":"804_CR8","doi-asserted-by":"publisher","unstructured":"Sapriel G, Konjek J, Orgeur M, Bouri L, Fr\u00e9zal L, Roux AL, et al. Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications. BMC Genomics. 2016;17. https:\/\/doi.org\/10.1186\/s12864-016-2448-1.","DOI":"10.1186\/s12864-016-2448-1"},{"key":"804_CR9","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02042","author":"JL Tan","year":"2017","unstructured":"Tan JL, Ng KP, Ong CS, Ngeow YF. Genomic comparisons reveal microevolutionary differences in Mycobacterium abscessus subspecies. Front Microbiol. 2017. https:\/\/doi.org\/10.3389\/fmicb.2017.02042.","journal-title":"Front Microbiol"},{"issue":"11","key":"804_CR10","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1016\/j.tig.2024.07.008","volume":"40","author":"M Vos","year":"2024","unstructured":"Vos M, Buckling A, Kuijper B, Eyre-Walker A, Bontemps C, Leblond P, et al. Why do mobile genetic elements transfer DNA of their hosts? Trends Genet. 2024;40(11):927\u201338. https:\/\/doi.org\/10.1016\/j.tig.2024.07.008.","journal-title":"Trends Genet"},{"issue":"9","key":"804_CR11","doi-asserted-by":"publisher","first-page":"1431","DOI":"10.1038\/s41564-022-01204-x","volume":"7","author":"L Boeck","year":"2022","unstructured":"Boeck L, Burbaud S, Skwark M, Pearson WH, Sangen J, Wuest AW, et al. Mycobacterium abscessus pathogenesis identified by phenogenomic analyses. Nat Microbiol. 2022;7(9):1431\u201341. https:\/\/doi.org\/10.1038\/s41564-022-01204-x.","journal-title":"Nat Microbiol"},{"key":"804_CR12","doi-asserted-by":"publisher","unstructured":"Coluzzi C, Guillemet M, Mazzamurro F, Touchon M, Godfroid M, Achaz G, et al. Chance favors the prepared genomes: horizontal transfer shapes the emergence of antibiotic resistance mutations in core genes. Mol Biol Evol. 2023;40(10). https:\/\/doi.org\/10.1093\/molbev\/msad217.","DOI":"10.1093\/molbev\/msad217"},{"key":"804_CR13","volume-title":"CLSI standards: guidelines for health care excellence. Susceptibility testing of mycobacteria, nocardiae, and other aerobic actinomycetes","author":"GL Woods","year":"2011","unstructured":"Woods GL, Brown-Elliott BA, Conville PS, Desmond EP, Hall GS, Lin G, et al. CLSI standards: guidelines for health care excellence. Susceptibility testing of mycobacteria, nocardiae, and other aerobic actinomycetes. Wayne (PA): Clinical and Laboratory Standards Institute; 2011."},{"key":"804_CR14","doi-asserted-by":"publisher","unstructured":"Chen S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using Fastp. Imeta. 2023;2(2). https:\/\/doi.org\/10.1002\/imt2.107.","DOI":"10.1002\/imt2.107"},{"issue":"3","key":"804_CR15","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gku1196","volume":"43","author":"NJ Croucher","year":"2015","unstructured":"Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, et al. Rapid phylogenetic analysis of large samples of Recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015;43(3):e15. https:\/\/doi.org\/10.1093\/nar\/gku1196.","journal-title":"Nucleic Acids Res"},{"key":"804_CR16","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu033","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis A. Bioinformatics. 2014;30(9):1312\u20133. https:\/\/doi.org\/10.1093\/bioinformatics\/btu033. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies."},{"key":"804_CR17","doi-asserted-by":"publisher","unstructured":"Letunic I, Bork P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1). https:\/\/doi.org\/10.1093\/nar\/gkz239W256-w9.","DOI":"10.1093\/nar\/gkz239W256-w9"},{"issue":"5","key":"804_CR18","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455\u201377. https:\/\/doi.org\/10.1089\/cmb.2012.0021.","journal-title":"J Comput Biol"},{"issue":"8","key":"804_CR19","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","volume":"29","author":"A Gurevich","year":"2013","unstructured":"Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072\u20135. https:\/\/doi.org\/10.1093\/bioinformatics\/btt086.","journal-title":"Bioinformatics"},{"issue":"7","key":"804_CR20","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043\u201355. https:\/\/doi.org\/10.1101\/gr.186072.114.","journal-title":"Genome Res"},{"issue":"1","key":"804_CR21","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","volume":"9","author":"C Jain","year":"2018","unstructured":"Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114. https:\/\/doi.org\/10.1038\/s41467-018-07641-9.","journal-title":"Nat Commun"},{"issue":"2","key":"804_CR22","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/j.diagmicrobio.2013.06.023","volume":"77","author":"SY Kim","year":"2013","unstructured":"Kim SY, Kang YA, Bae IK, Yim JJ, Park MS, Kim YS, et al. Standardization of multilocus sequence typing scheme for Mycobacterium abscessus and Mycobacterium massiliense. Diagn Microbiol Infect Dis. 2013;77(2):143\u20139. https:\/\/doi.org\/10.1016\/j.diagmicrobio.2013.06.023.","journal-title":"Diagn Microbiol Infect Dis"},{"issue":"14","key":"804_CR23","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/btu153.","journal-title":"Bioinformatics"},{"issue":"1","key":"804_CR24","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1186\/s13059-020-02090-4","volume":"21","author":"G Tonkin-Hill","year":"2020","unstructured":"Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, et al. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol. 2020;21(1):180. https:\/\/doi.org\/10.1186\/s13059-020-02090-4.","journal-title":"Genome Biol"},{"issue":"1","key":"804_CR25","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-016-1108-8","volume":"17","author":"O Brynildsrud","year":"2016","unstructured":"Brynildsrud O, Bohlin J, Scheffer L, Eldholm V. Rapid scoring of genes in microbial pan-genome-wide association studies with scoary. Genome Biol. 2016;17(1):238. https:\/\/doi.org\/10.1186\/s13059-016-1108-8.","journal-title":"Genome Biol"},{"issue":"1","key":"804_CR26","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1186\/s12859-023-05363-4","volume":"24","author":"RS Mehta","year":"2023","unstructured":"Mehta RS, Petit RA 3rd, Read TD, Weissman DB. Detecting patterns of accessory genome Coevolution in Staphylococcus aureus using data from thousands of genomes. BMC Bioinformatics. 2023;24(1):243. https:\/\/doi.org\/10.1186\/s12859-023-05363-4.","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"804_CR27","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1093\/molbev\/msi103","volume":"22","author":"AJ Drummond","year":"2005","unstructured":"Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005;22(5):1185\u201392. https:\/\/doi.org\/10.1093\/molbev\/msi103.","journal-title":"Mol Biol Evol"},{"issue":"1","key":"804_CR28","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1101\/gr.277340.122","volume":"33","author":"G Tonkin-Hill","year":"2023","unstructured":"Tonkin-Hill G, Gladstone RA, P\u00f6ntinen AK, Arredondo-Alonso S, Bentley SD, Corander J. Robust analysis of prokaryotic pangenome gene gain and loss rates with panstripe. Genome Res. 2023;33(1):129\u201340. https:\/\/doi.org\/10.1101\/gr.277340.122.","journal-title":"Genome Res"},{"issue":"5","key":"804_CR29","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.1093\/molbev\/msx066","volume":"34","author":"R Mostowy","year":"2017","unstructured":"Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P. Efficient inference of recent and ancestral recombination within bacterial populations. Mol Biol Evol. 2017;34(5):1167\u201382. https:\/\/doi.org\/10.1093\/molbev\/msx066.","journal-title":"Mol Biol Evol"},{"issue":"14","key":"804_CR30","doi-asserted-by":"publisher","first-page":"2490","DOI":"10.1093\/bioinformatics\/bty121","volume":"34","author":"T Nakamura","year":"2018","unstructured":"Nakamura T, Yamada KD, Tomii K, Katoh K. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics. 2018;34(14):2490\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/bty121.","journal-title":"Bioinformatics"},{"key":"804_CR31","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2023.09.019","author":"S Tunesi","year":"2023","unstructured":"Tunesi S, Zelazny A, Awad Z, Mougari F, Buyck J, Cambau E. Antimicrobial susceptibility of Mycobacterium abscessus and treatment of pulmonary and extra-pulmonary infections. Clin Microbiol Infect. 2023. https:\/\/doi.org\/10.1016\/j.cmi.2023.09.019.","journal-title":"Clin Microbiol Infect"},{"key":"804_CR32","doi-asserted-by":"publisher","unstructured":"Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10. https:\/\/doi.org\/10.1186\/1471-2105-10-421.","DOI":"10.1186\/1471-2105-10-421"},{"issue":"9","key":"804_CR33","doi-asserted-by":"publisher","first-page":"2069","DOI":"10.1093\/molbev\/msz131","volume":"36","author":"SA Ishikawa","year":"2019","unstructured":"Ishikawa SA, Zhukova A, Iwasaki W, Gascuel O. A fast likelihood method to reconstruct and visualize ancestral scenarios. Mol Biol Evol. 2019;36(9):2069\u201385. https:\/\/doi.org\/10.1093\/molbev\/msz131.","journal-title":"Mol Biol Evol"},{"issue":"4","key":"804_CR34","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1093\/sysbio\/syab092","volume":"71","author":"A Behdenna","year":"2022","unstructured":"Behdenna A, Godfroid M, Petot P, Pothier J, Lambert A, Achaz G. A minimal yet flexible likelihood framework to assess correlated evolution. Syst Biol. 2022;71(4):823\u201338. https:\/\/doi.org\/10.1093\/sysbio\/syab092.","journal-title":"Syst Biol"},{"issue":"2","key":"804_CR35","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1046\/j.1365-2958.2001.02394.x","volume":"40","author":"C Stahl","year":"2001","unstructured":"Stahl C, Kubetzko S, Kaps I, Seeber S, Engelhardt H, Niederweis M. MspA provides the main hydrophilic pathway through the cell wall of Mycobacterium smegmatis. Mol Microbiol. 2001;40(2):451\u201364. https:\/\/doi.org\/10.1046\/j.1365-2958.2001.02394.x.","journal-title":"Mol Microbiol"},{"issue":"38","key":"804_CR36","doi-asserted-by":"publisher","first-page":"23794","DOI":"10.1073\/pnas.2010189117","volume":"117","author":"Z Hu","year":"2020","unstructured":"Hu Z, Cronan JE. The primary step of biotin synthesis in mycobacteria. Proc Natl Acad Sci U S A. 2020;117(38):23794\u2013801. https:\/\/doi.org\/10.1073\/pnas.2010189117.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"804_CR37","doi-asserted-by":"publisher","first-page":"e1011318","DOI":"10.1371\/journal.ppat.1011318","volume":"19","author":"S Parmar","year":"2023","unstructured":"Parmar S, Tocheva EI. The cell envelope of Mycobacterium abscessus and its role in pathogenesis. PLoS Pathog. 2023;19(5):e1011318. https:\/\/doi.org\/10.1371\/journal.ppat.1011318.","journal-title":"PLoS Pathog"},{"issue":"3","key":"804_CR38","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1016\/j.jcf.2021.02.002","volume":"20","author":"AV Guti\u00e9rrez","year":"2021","unstructured":"Guti\u00e9rrez AV, Baron SA, Sardi FS, Saad J, Coltey B, Reynaud-Gaubert M, et al. Beyond phenotype: the genomic heterogeneity of co-infecting Mycobacterium abscessus smooth and rough colony variants in cystic fibrosis patients. J Cyst Fibros. 2021;20(3):421\u20133. https:\/\/doi.org\/10.1016\/j.jcf.2021.02.002.","journal-title":"J Cyst Fibros"},{"key":"804_CR39","doi-asserted-by":"publisher","unstructured":"Guti\u00e9rrez AV, Viljoen A, Ghigo E, Herrmann JL, Kremer L. Glycopeptidolipids, a Double-Edged sword of the Mycobacterium abscessus complex. Front Microbiol. 2018;9. https:\/\/doi.org\/10.3389\/fmicb.2018.01145.","DOI":"10.3389\/fmicb.2018.01145"},{"issue":"8","key":"804_CR40","doi-asserted-by":"publisher","first-page":"e1010771","DOI":"10.1371\/journal.ppat.1010771","volume":"18","author":"M Lagune","year":"2022","unstructured":"Lagune M, Le Moigne V, Johansen MD, V\u00e1squez Sotomayor F, Daher W, Petit C, et al. The ESX-4 substrates, EsxU and esxt, modulate Mycobacterium abscessus fitness. PLoS Pathog. 2022;18(8):e1010771. https:\/\/doi.org\/10.1371\/journal.ppat.1010771.","journal-title":"PLoS Pathog"},{"key":"804_CR41","doi-asserted-by":"publisher","unstructured":"Bryant JM, Brown KP, Burbaud S, Everall I, Belardinelli JM, Rodriguez-Rincon D, et al. Stepwise pathogenic evolution of Mycobacterium abscessus. Science. 2021;372(6541). https:\/\/doi.org\/10.1126\/science.abb8699.","DOI":"10.1126\/science.abb8699"},{"issue":"1","key":"804_CR42","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1186\/s43556-022-00106-y","volume":"3","author":"W Yan","year":"2022","unstructured":"Yan W, Zheng Y, Dou C, Zhang G, Arnaout T, Cheng W. The pathogenic mechanism of Mycobacterium tuberculosis: implication for new drug development. Mol Biomed. 2022;3(1):48. https:\/\/doi.org\/10.1186\/s43556-022-00106-y.","journal-title":"Mol Biomed"}],"container-title":["Annals of Clinical Microbiology and Antimicrobials"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12941-025-00804-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12941-025-00804-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12941-025-00804-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,22]],"date-time":"2025-07-22T11:20:41Z","timestamp":1753183241000},"score":1,"resource":{"primary":{"URL":"https:\/\/ann-clinmicrob.biomedcentral.com\/articles\/10.1186\/s12941-025-00804-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,22]]},"references-count":42,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["804"],"URL":"https:\/\/doi.org\/10.1186\/s12941-025-00804-9","relation":{"references":[{"id-type":"doi","id":"10.1093\/bioinformatics\/btu033","asserted-by":"subject"}]},"ISSN":["1476-0711"],"issn-type":[{"value":"1476-0711","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,22]]},"assertion":[{"value":"14 February 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 June 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 July 2025","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 samples used in the study were passaged bacterial isolates, not patient specimens. Information regarding the infection sites and sources of the isolates was approved by the Ethics Committee of Zhongshan Hospital, Fudan University (Approval No.: B2022-513R).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"44"}}