{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T01:25:49Z","timestamp":1790558749301,"version":"4.1.0"},"reference-count":37,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2022,8,12]],"date-time":"2022-08-12T00:00:00Z","timestamp":1660262400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Research Affairs of the Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran","award":["OG- 9915"],"award-info":[{"award-number":["OG- 9915"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:sec id=\"sec001\">\n<jats:title>Background<\/jats:title>\n<jats:p>Among Non-tuberculous mycobacteria (NTM) which generally cause opportunistic infections, especially in immunocompromised hosts, <jats:italic>Mycobacterium simiae<\/jats:italic> (<jats:italic>M<\/jats:italic>. <jats:italic>simiae<\/jats:italic>) is one of the most important NTM, associated with pulmonary disease. The main concern about <jats:italic>M<\/jats:italic>. <jats:italic>simiae<\/jats:italic> infections is the extreme resistance of this NTM to antibiotics. There are limited studies about drug susceptibility testing (DST) and the causes of drug resistance in <jats:italic>M<\/jats:italic>. <jats:italic>simiae<\/jats:italic>. Hence, the current study aimed to identify the <jats:italic>M<\/jats:italic>. <jats:italic>simiae<\/jats:italic> isolates and to assess the drug resistance of the isolates using phenotypic and molecular methods.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec002\">\n<jats:title>Materials and methods<\/jats:title>\n<jats:p>In this study, 50 clinical pulmonary isolates suspected of NTM were collected from regional tuberculosis reference laboratories in Iran. The isolates were identified as <jats:italic>M<\/jats:italic>. <jats:italic>simiae<\/jats:italic> by using standard biochemical tests and molecular methods. DST was performed for identified <jats:italic>M<\/jats:italic>. <jats:italic>simiae<\/jats:italic> isolates and additional 35 <jats:italic>M<\/jats:italic>. <jats:italic>simiae<\/jats:italic> isolates from the department archive, against eight drugs. The mutations in <jats:italic>gyrA<\/jats:italic>, <jats:italic>gyrB<\/jats:italic>, and <jats:italic>rrl<\/jats:italic> genes in clarithromycin and moxifloxacin resistant isolates were investigated by polymerase chain reaction (PCR) followed by sequencing.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec003\">\n<jats:title>Results<\/jats:title>\n<jats:p>Out of 50 suspected NTM isolates, 25 isolates were detected as <jats:italic>M<\/jats:italic>. <jats:italic>simiae<\/jats:italic> species based on the biochemical tests, and 18 isolates were verified based on the <jats:italic>rpoB<\/jats:italic> gene sequence analysis to achieve a total of 53 isolates when the archive isolates were included. DST results showed that all 53 isolates were resistant to isoniazid, rifampin, and clofazimine. The rate of resistance to ethambutol and linezolid were 34 (64%), and 40 (76%) respectively. The highest susceptibility rate was demonstrated for amikacin 53 (100%) and clarithromycin 45(85%), followed by moxifloxacin 35(66%). Sequence analysis showed mutations in positions 2058 and 2059 of the <jats:italic>rrl<\/jats:italic> gene, as well non-synonymous mutation at codons 389, 444, and 571 of the <jats:italic>gyrB<\/jats:italic> gene. Sequence analysis showed no mutation in the <jats:italic>gyrA<\/jats:italic> gene. drug-resistant isolates with mutations showed higher MICs compared to non-mutant resistant isolates.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec004\">\n<jats:title>Conclusions<\/jats:title>\n<jats:p>This study revealed amikacin, clarithromycin, and moxifloxacin as the most effective antibiotics. However, since <jats:italic>M<\/jats:italic>. <jats:italic>simiae<\/jats:italic> exhibited a high level of antibiotic resistance <jats:italic>in vitro<\/jats:italic>, therefore, species identification and determining the antibiotic susceptibility pattern of the isolates are essential before treatment.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pone.0267320","type":"journal-article","created":{"date-parts":[[2022,8,12]],"date-time":"2022-08-12T17:44:46Z","timestamp":1660326286000},"page":"e0267320","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Drug susceptibility profiling and genetic determinants of drug resistance in Mycobacterium simiae isolates obtained from regional tuberculosis reference laboratories of Iran"],"prefix":"10.1371","volume":"17","author":[{"given":"Sara","family":"Daneshfar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7852-6868","authenticated-orcid":true,"given":"Azar Dokht","family":"Khosravi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8090-2332","authenticated-orcid":true,"given":"Mohammad","family":"Hashemzadeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,8,12]]},"reference":[{"key":"pone.0267320.ref001","article-title":"Non tuberculous mycobacteria pulmonary disease: patients and clinicians working together to improve the evidence base for care","author":"M Lipman","year":"2021","journal-title":"Int J Infect Dis"},{"issue":"3","key":"pone.0267320.ref002","doi-asserted-by":"crossref","first-page":"365","DOI":"10.3201\/eid2203.151643","article-title":"Leveraging advances in tuberculosis diagnosis and treatment to address nontuberculous mycobacterial disease","volume":"22","author":"RM Raju","year":"2016","journal-title":"Emerging Infect Dis"},{"key":"pone.0267320.ref003","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.nmni.2018.09.008","article-title":"Mycobacterium simiae pulmonary disease in Iran: systematic review and meta-analysis","volume":"26","author":"MJ Nasiri","year":"2018","journal-title":"New Microbes New Infect"},{"key":"pone.0267320.ref004","doi-asserted-by":"crossref","first-page":"2324","DOI":"10.1007\/s00284-021-02486-w","article-title":"Characterization of clinical isolates of Mycobacterium simiae using drug susceptibility tests and molecular analyses","volume":"78","author":"H Dezhkhi","year":"2021","journal-title":"Curr Microbiol"},{"issue":"3","key":"pone.0267320.ref005","doi-asserted-by":"crossref","first-page":"e00715","DOI":"10.1002\/rcr2.715","article-title":"A case of multidrug-resistant Mycobacterium simiae in an elderly woman.","volume":"9","author":"H Lotfi","year":"2021","journal-title":"Respirol Case Rep"},{"issue":"46","key":"pone.0267320.ref006","doi-asserted-by":"crossref","first-page":"e01185","DOI":"10.1128\/MRA.01185-20","article-title":"Draft genome sequence of Mycobacterium simiae, a potential pathogen isolated from the normal human oral cavity","volume":"9","author":"V Chauhan","year":"2020","journal-title":"Microbiol Resour Announc"},{"issue":"1","key":"pone.0267320.ref007","article-title":"Mycobacterium simiae infection in an immunocompetent elderly woman: case report in Roraima state of brasil. sa\u00fade (Santa Maria).","volume":"47","author":"BJ Sequeira","year":"2021","journal-title":"Revista Sa\u00fade (Sta. Maria)."},{"key":"pone.0267320.ref008","doi-asserted-by":"crossref","first-page":"6913564","DOI":"10.1155\/2017\/6913564","article-title":"Computed tomography findings of pulmonary Mycobacterium simiae infection","volume":"2017","author":"A Baghizadeh","year":"2017","journal-title":"Can Respir J"},{"issue":"3","key":"pone.0267320.ref009","doi-asserted-by":"crossref","first-page":"e00719","DOI":"10.1002\/rcr2.719","article-title":"Mycobacterium simiae pulmonary infection: a case series and literature review.","volume":"9","author":"H Lotfi","year":"2021","journal-title":"Respirol Case Rep"},{"issue":"6","key":"pone.0267320.ref010","doi-asserted-by":"crossref","first-page":"475","DOI":"10.7883\/yoken.66.475","article-title":"Mycobacterium simiae: a possible emerging pathogen in iran","volume":"66","author":"A Hashemi-Shahraki","year":"2013","journal-title":"Jpn J Infect Dis"},{"key":"pone.0267320.ref011","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.meegid.2019.01.017","article-title":"Nontuberculous mycobacteria: insights on taxonomy and evolution","volume":"72","author":"CY Turenne","year":"2019","journal-title":"Infect Genet Evol"},{"issue":"4","key":"pone.0267320.ref012","doi-asserted-by":"crossref","first-page":"e1008418","DOI":"10.1371\/journal.ppat.1008418","article-title":"Mycobacterium simiae: Harmless colonizer or deadly pathogen?.","volume":"16","author":"JF Jabbour","year":"2020","journal-title":"PLoS Pathog"},{"issue":"4","key":"pone.0267320.ref013","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0195390","article-title":"Emergence of Mycobacterium simiae: a retrospective study from a tertiary care center in lebanon","volume":"13","author":"A Hamieh","year":"2018","journal-title":"PLoS One"},{"issue":"2","key":"pone.0267320.ref014","doi-asserted-by":"crossref","first-page":"96","DOI":"10.3390\/biology10020096","article-title":"Drug resistance in nontuberculous mycobacteria: mechanisms and models","volume":"10","author":"S Saxena","year":"2021","journal-title":"Biol"},{"key":"pone.0267320.ref015","volume-title":"Textbook of Diagn Microbiol -e-book","author":"CR Mahon","year":"2018"},{"issue":"5","key":"pone.0267320.ref016","doi-asserted-by":"crossref","first-page":"180","DOI":"10.17221\/5538-VETMED","article-title":"Methods of mycobacterial DNA isolation from different biological material: a review","volume":"51","author":"J Hosek","year":"2006","journal-title":"Vet Med (Praha)."},{"issue":"12","key":"pone.0267320.ref017","doi-asserted-by":"crossref","first-page":"5699","DOI":"10.1128\/JCM.41.12.5699-5708.2003","article-title":"rpoB-based identification of nonpigmented and late pigmenting rapidly growing mycobacteria","volume":"41","author":"T Ad\u00e9kambi","year":"2003","journal-title":"J Clin Microbiol"},{"issue":"62","key":"pone.0267320.ref018","first-page":"1","article-title":"Agarose gel electrophoresis for the separation of DNA fragments","author":"PY Lee","year":"2012","journal-title":"J Vis Exp"},{"issue":"6","key":"pone.0267320.ref019","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: molecular evolutionary genetics analysis across computing platforms","volume":"35","author":"S Kumar","year":"2018","journal-title":"Mol Biol Evol"},{"key":"pone.0267320.ref020","first-page":"2011","article-title":"M24-A2 Susceptibility testing of Mycobacteria, Nocardiae and other aerobic Actinomycetes; Approved standard-\/Clinical and laboratory standard institute","volume":"65","author":"GL Woods","year":"2011","journal-title":"NLCSI"},{"issue":"4","key":"pone.0267320.ref021","doi-asserted-by":"crossref","first-page":"e01788","DOI":"10.1128\/AAC.01788-17","article-title":"Drug susceptibility profiling and genetic determinants of drug resistance in Mycobacterium kansasii","volume":"62","author":"Z Baku\u0142a","year":"2018","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"pone.0267320.ref022","doi-asserted-by":"crossref","first-page":"e22184","DOI":"10.1002\/jcla.22184","article-title":"Identification of nontuberculous mycobacteria using multilocus sequence analysis of 16S rRNA, hsp65, and rpoB","volume":"32","author":"SH Kim","year":"2018","journal-title":"J Clin Lab Anal"},{"issue":"1","key":"pone.0267320.ref023","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1128\/microbiolspec.TNMI7-0029-2016","article-title":"The role of therapeutic drug monitoring in mycobacterial infections","volume":"5","author":"C. Peloquin","year":"2017","journal-title":"Microbiol Spectr"},{"key":"pone.0267320.ref024","doi-asserted-by":"crossref","first-page":"S32","DOI":"10.1016\/j.jfma.2020.05.002","article-title":"Identification and drug susceptibility testing for nontuberculous mycobacteria","volume":"119","author":"WC Huang","year":"2020","journal-title":"J Formos Med Assoc"},{"issue":"7","key":"pone.0267320.ref025","doi-asserted-by":"crossref","first-page":"e00395","DOI":"10.1128\/AAC.00395-18","article-title":"Clinical, radiological, and microbiological characteristics of Mycobacterium simiae infection in 97 patients","volume":"62","author":"N Coolen-Allou","year":"2018","journal-title":"Antimicrob Agents Chemother"},{"issue":"2","key":"pone.0267320.ref026","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1089\/mdr.2015.0134","article-title":"In vitro antimicrobial susceptibility of nontuberculous mycobacteria in Iran","volume":"22","author":"P Heidarieh","year":"2016","journal-title":"Microb Drug Resist"},{"key":"pone.0267320.ref027","first-page":"42","article-title":"Prevalence of non-tuberculous mycobacteria in hospital waters of major cities of Khuzestan Province","volume":"6","author":"AD Khosravi","year":"2016","journal-title":"Iran. Front Cell Infect Microbiol"},{"key":"pone.0267320.ref028","doi-asserted-by":"crossref","first-page":"2171","DOI":"10.2147\/IDR.S245295","article-title":"Molecular identification, and characterization of Mycobacterium kansasii strains isolated from four tuberculosis regional reference laboratories in iran during 2016\u20132018.","volume":"13","author":"AD Khosravi","year":"2020","journal-title":"Infect Drug Resist"},{"issue":"7","key":"pone.0267320.ref029","doi-asserted-by":"crossref","first-page":"2544","DOI":"10.1128\/JCM.00233-14","article-title":"Utility of rpoB gene sequencing for identification of nontuberculous mycobacteria in the Netherlands","volume":"52","author":"R de Zwaan","year":"2014","journal-title":"J Clin Microbiol"},{"issue":"5","key":"pone.0267320.ref030","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1164\/ajrccm.152.5.7582293","article-title":"Clinical isolates of Mycobacterium simiae in San Antonio, Texas. An 11-yr review","volume":"152","author":"G Valero","year":"1995","journal-title":"Am J Respir Crit Care Med"},{"issue":"4","key":"pone.0267320.ref031","doi-asserted-by":"crossref","first-page":"619","DOI":"10.2174\/1871526520999200727114148","article-title":"Drug susceptibility testing of Mycobacterium simiae: An emerging pathogen in Iran.","volume":"21","author":"MJ Nasiri","year":"2021","journal-title":"Infect Disord Drug Targets"},{"issue":"4","key":"pone.0267320.ref032","first-page":"375","article-title":"Identification of non-tuberculosis mycobacteria by line probe assay and determination of drug resistance patterns of isolates in iranian patients","volume":"74","author":"M Karami-Zarandi","year":"2019","journal-title":"Arch Razi Inst."},{"issue":"3","key":"pone.0267320.ref033","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/j.jinf.2015.12.007","article-title":"The antimicrobial susceptibility of non-tuberculous mycobacteria","volume":"72","author":"S Cowman","year":"2016","journal-title":"J Infect"},{"issue":"2","key":"pone.0267320.ref034","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.ijantimicag.2009.09.023","article-title":"In vitro drug susceptibility of 2275 clinical non-tuberculous Mycobacterium isolates of 49 species in The Netherlands","volume":"35","author":"J Van Ingen","year":"2010","journal-title":"Int J Antimicrob Agents"},{"issue":"2","key":"pone.0267320.ref035","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.ijantimicag.2011.09.019","article-title":"Drug susceptibility testing and pharmacokinetics question current treatment regimens in Mycobacterium simiae complex disease.","volume":"39","author":"J van Ingen","year":"2012","journal-title":"Int J Antimicrob Agents"},{"key":"pone.0267320.ref036","doi-asserted-by":"crossref","first-page":"S215","DOI":"10.1016\/j.ijmyco.2016.11.006","article-title":"Molecular drug susceptibility testing against the first-line (rifampin and isoniazid) and second-line (ciprofloxacin\u2013amikacin and kanamycin) treatment in different subtypes of Mycobacterium simiae.","volume":"5","author":"P Farnia","year":"2016","journal-title":"Int J Mycobacteriol."},{"issue":"6","key":"pone.0267320.ref037","doi-asserted-by":"crossref","first-page":"1669","DOI":"10.1093\/jac\/dkx021","article-title":"Evaluation of the new GenoType NTM-DR kit for the molecular detection of antimicrobial resistance in non-tuberculous mycobacteria","volume":"72","author":"F Mougari","year":"2017","journal-title":"J Antimicrob Chemother"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0267320","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,12]],"date-time":"2022-08-12T17:45:38Z","timestamp":1660326338000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0267320"}},"subtitle":[],"editor":[{"given":"Yatin N.","family":"Dholakia","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,8,12]]},"references-count":37,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2022,8,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0267320","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,8,12]]}}}