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Bhanushali A, Atre S, Nair P, Thandaseery GA, Shah S, Kuruwa S, Zade A, Nikam C, Gomare M, Chatterjee A. Whole-genome sequencing of clinical isolates from tuberculosis patients in India: real-world data indicates a high proportion of pre-XDR cases. Microbiol Spectr 2024; 12:e0277023. [PMID: 38597637 PMCID: PMC11064594 DOI: 10.1128/spectrum.02770-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
Treatment decisions for tuberculosis (TB) in the absence of full drug-susceptibility data can result in amplifying resistance and may compromise treatment outcomes. Genomics of Mycobacterium tuberculosis (M.tb) from clinical samples enables detection of drug resistance to multiple drugs. We performed whole-genome sequencing (WGS) for 600 clinical samples from patients with tuberculosis to identify the drug-resistance profile and mutation spectrum. We documented the reasons reported by clinicians for referral. WGS identified a high proportion (51%) of pre-extensively drug-resistant (pre-XDR) cases followed by multidrug-resistant tuberculosis (MDR-TB) (15.5%). This correlates with the primary reason for referral, as non-response to the first-line treatment (67%) and treatment failure or rifampicin resistance (14%). Multivariate analysis indicated that all young age groups (P < 0.05), male gender (P < 0.05), and Beijing strain (P < 0.01) were significant independent predictors of MDR-TB or MDR-TB+ [pre-extensively drug-resistant tuberculosis (XDR-TB) and XDR-TB]. Ser315Thr (72.5%) in the inhA gene and Ser450Leu in the rpoB gene (65.5%) were the most prevalent mutations, as were resistance-conferring mutations to pyrazinamide (41%) and streptomycin (61.33%). Mutations outside the rifampicin resistance-determining region (RRDR), Ile491Phe and Val170Phe, were seen in 1.3% of cases; disputed mutations in rpoB (Asp435Tyr, His445Asn, His445Leu, and Leu430Pro) were seen in 6% of cases, and mutations to newer drugs such as bedaquiline and linezolid in 1.0% and 7.5% of cases, respectively. This study on clinical samples highlights that there is a high proportion of pre-XDR cases and emerging resistance to newer drugs; ongoing transmission of these strains can cause serious threat to public health; and whole-genome sequencing can effectively identify and support precision medicine for TB. IMPORTANCE The current study is based on real-world data on the TB drug-resistance profile by whole-genome sequencing of 600 clinical samples from patients with TB in India. This study indicates the clinicians' reasons for sending samples for WGS, which is for difficult-to-treat cases and/or relapse and treatment failure. The study reports a significant proportion of cases with pre-XDR-TB strains that warrant policy makers' attention. It reflects the current iterative nature of the diagnostic tests under programmatic conditions that leads to delays in appropriate diagnosis and empirical treatment. India had an estimated burden of 2.95 million TB cases in 2020 and 135,000 multidrug-resistant cases. However, WGS profiles of M.tb from India remains disproportionately poorly represented. This study adds a significant body of data on the mutation profiles seen in M.tb isolated from patients with TB in India, mutations outside the RRDR, disputed mutations, and resistance-conferring mutations to newer drugs such as bedaquiline and linezolid.
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Affiliation(s)
| | - Sachin Atre
- Dr. D.Y. Patil Medical College Hospital and Research Centre, Pune, India
| | - Preethi Nair
- HaystackAnalytics Pvt. Ltd., IIT Bombay, Mumbai, India
| | | | - Sanchi Shah
- HaystackAnalytics Pvt. Ltd., IIT Bombay, Mumbai, India
| | | | - Amrutraj Zade
- HaystackAnalytics Pvt. Ltd., IIT Bombay, Mumbai, India
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Liu B, Su P, Hu P, Yan M, Li W, Yi S, Chen Z, Zhang X, Guo J, Wan X, Wang J, Gong D, Bai H, Wan K, Liu H, Li G, Tan Y. Prevalence, Transmission and Genetic Diversity of Pyrazinamide Resistance Among Multidrug-Resistant Mycobacterium tuberculosis Isolates in Hunan, China. Infect Drug Resist 2024; 17:403-416. [PMID: 38328339 PMCID: PMC10849141 DOI: 10.2147/idr.s436161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Background China is a country with a burden of high rates of both TB and multidrug-resistant TB (MDR-TB). However, published data on pyrazinamide (PZA) resistance are still limited in Hunan province, China. This study investigated the prevalence, transmission, and genetic diversity of PZA resistance among multidrug-resistant Mycobacterium tuberculosis isolates in Hunan province. Methods Drug susceptibility testing (DST) with the Bactec MGIT 960 PZA kit and pyrazinamidase (PZase) testing were conducted on all 298 MDR clinical isolates. Moreover, 24-locus MIRU-VNTR and DNA sequencing of pncA, rpsA, and panD genes were conducted on 180 PZA-resistant (PZA-R) isolates. Results The prevalence of PZA resistance among MDR-TB strains reached 60.4%. Newly diagnosed PZA-R TB patients and clustered isolates with identical pncA, rpsA, and panD mutations showed that transmission of PZA-R isolates played a significant role in the formation of PZA-R TB. Ninety-eight mutation patterns were observed in the pncA among 180 PZA-R isolates, and seventy-one (72.4%) were point mutations. Twenty-four of these mutations are new, including 2 base substitutions (V93G and T153S) and 22 nucleotide deletions or insertions. The W119C was found in PZA-S isolates, on the other hand, F94L and V155A mutations were found in both PZA resistant and susceptible isolates with positive PZase activity, indicating that they were not associated with PZA resistance. This is not entirely in line with the WHO catalogue. Ten novel rpsA mutations were found in 10 PZA-R isolates, which all combined with mutations in pncA. Thus, it is unpredictable whether these mutations in rpsA can impact PZA resistance. No panD mutation was found in all PZA-R isolates. Conclusion DNA sequencing of pncA and PZase activity testing have great potential in predicting PZA resistance.
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Affiliation(s)
- Binbin Liu
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Pan Su
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Peilei Hu
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Mi Yan
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Wenbin Li
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Songlin Yi
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Zhenhua Chen
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Xiaoping Zhang
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Jingwei Guo
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Xiaojie Wan
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Jue Wang
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Daofang Gong
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Hua Bai
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
| | - Kanglin Wan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Haican Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Guilian Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yunhong Tan
- Clinical Laboratory, Hunan Chest Hospital, Changsha, People’s Republic of China
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Wang Z, Tang Z, Heidari H, Molaeipour L, Ghanavati R, Kazemian H, Koohsar F, Kouhsari E. Global status of phenotypic pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates: an updated systematic review and meta-analysis. J Chemother 2023; 35:583-595. [PMID: 37211822 DOI: 10.1080/1120009x.2023.2214473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/01/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
Pyrazinamide (PZA) is an essential first-line tuberculosis drug for its unique mechanism of action active against multidrug-resistant-TB (MDR-TB). Thus, the aim of updated meta-analysis was to estimate the PZA weighted pooled resistance (WPR) rate in M. tuberculosis isolates based on publication date and WHO regions. We systematically searched the related reports in PubMed, Scopus, and Embase (from January 2015 to July 2022). Statistical analyses were performed using STATA software. The 115 final reports in the analysis investigated phenotypic PZA resistance data. The WPR of PZA was 57% (95% CI 48-65%) in MDR-TB cases. According to the WHO regions, the higher WPRs of PZA were reported in the Western Pacific (32%; 95% CI 18-46%), South East Asian region (37%; 95% CI 31-43%), and the Eastern Mediterranean (78%; 95% CI 54-95%) among any-TB patients, high risk of MDR-TB patients, and MDR-TB patients, respectively. A negligible increase in the rate of PZA resistance were showed in MDR-TB cases (55% to 58%). The rate of PZA resistance has been rising in recent years among MDR-TB cases, underlines the essential for both standard and novel drug regimens development.
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Affiliation(s)
- Zheming Wang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, China
| | - Zhihua Tang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, China
| | - Hamid Heidari
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Leila Molaeipour
- Department of Epidemiology, School of Public Health, University of Medical Sciences, Tehran, Iran
| | | | - Hossein Kazemian
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Faramarz Koohsar
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran
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Nasiri MJ, Fardsanei F, Arshadi M, Deihim B, Khalili F, Dadashi M, Goudarzi M, Mirsaeidi M. Performance of Wayne assay for detection of pyrazinamide resistance in Mycobacterium tuberculosis: a meta-analysis study. New Microbes New Infect 2021; 42:100886. [PMID: 34141437 PMCID: PMC8184659 DOI: 10.1016/j.nmni.2021.100886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022] Open
Abstract
Conventional culture-based drug susceptibility testing (DST) of Mycobacterium tuberculosis to pyrazinamide (PZA) is time-consuming and difficult to perform. The current systematic review and meta-analysis was aimed to evaluate the diagnostic accuracy of Wayne assay against culture-based DSTs as the reference standard. We searched the MEDLINE/Pubmed, Embase, and Web of Science databases for the relevant records. The QUADAS-2 tool was used to assess the quality of the studies. Diagnostic accuracy measures (i.e., sensitivity and specificity) were pooled with a random-effects model. Statistical analyses were performed with STATA (version 14, Stata Corporation, College Station, TX, USA), RevMan (version 5.3; The Nordic Cochrane Centre, the Cochrane Collaboration, Copenhagen, Denmark), and Meta-DiSc (version 1.4, Cochrane Colloquium, Barcelona, Spain). A total of 31 articles comprising data for 2457 isolates of M. tuberculosis were included in the final analysis. The pooled sensitivity and specificity of the Wayne assay against all reference tests (the combination of BACTEC MGIT 960, BACTEC 460, and proportion method) were 86.6% (95% CI: 84.3-88.7) and 96.0% (95% CI: 94.8-97). The positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and the area under the curve (AUC) estimates were found to be 17.6 (95% CI: 10.5-29.3), 0.11 (95% CI: 0.06-0.20), 164 (95% CI: 83-320) and 97%, respectively. Deek's test result indicated no evidence for publication bias (P > 0.05). Although the current study shows that the Wayne test is sensitive and specific for detecting PZA resistance, it may be used in combination with conventional DSTs to diagnose PZA resistance accurately.
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Affiliation(s)
- M J Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - F Fardsanei
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - M Arshadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - B Deihim
- Department of Bacteriology and Virology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Farima Khalili
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - M Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M Mirsaeidi
- Department of Pulmonary and Critical Care, University of Miami Miller School of Medicine, Miami, FL, USA
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High prevalence of phenotypic pyrazinamide resistance and its association with pncA gene mutations in Mycobacterium tuberculosis isolates from Uganda. PLoS One 2020; 15:e0232543. [PMID: 32413052 PMCID: PMC7228079 DOI: 10.1371/journal.pone.0232543] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/16/2020] [Indexed: 12/20/2022] Open
Abstract
Introduction Susceptibility testing for pyrazinamide (PZA), a cornerstone anti-TB drug is not commonly done in Uganda because it is expensive and characterized with technical difficulties thus resistance to this drug is less studied. Resistance is commonly associated with mutations in the pncA gene and its promoter region. However, these mutations vary geographically and those conferring phenotypic resistance are unknown in Uganda. This study determined the prevalence of PZA resistance and its association with pncA mutations. Materials and methods Using a cross-sectional design, archived isolates collected during the Uganda national drug resistance survey between 2008–2011 were sub-cultured. PZA resistance was tested by BACTEC Mycobacterial Growth Indicator Tube (MGIT) 960 system. Sequence reads were downloaded from the NCBI Library and bioinformatics pipelines were used to screen for PZA resistance–conferring mutations. Results The prevalence of phenotypic PZA resistance was found to be 21%. The sensitivity and specificity of pncA sequencing were 24% (95% CI, 9.36–45.13%) and 100% (73.54% - 100.0%) respectively. We identified four mutations associated with PZA phenotypic resistance in Uganda; K96R, T142R, R154G and V180F. Conclusion There is a high prevalence of phenotypic PZA resistance among TB patients in Uganda. The low sensitivity of pncA gene sequencing confirms the already documented discordances suggesting other mechanisms of PZA resistance in Mycobacterium tuberculosis.
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Dixit A, Freschi L, Vargas R, Calderon R, Sacchettini J, Drobniewski F, Galea JT, Contreras C, Yataco R, Zhang Z, Lecca L, Kolokotronis SO, Mathema B, Farhat MR. Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting. Sci Rep 2019; 9:5602. [PMID: 30944370 PMCID: PMC6447560 DOI: 10.1038/s41598-019-41967-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/20/2019] [Indexed: 11/09/2022] Open
Abstract
Whole genome sequencing (WGS) can elucidate Mycobacterium tuberculosis (Mtb) transmission patterns but more data is needed to guide its use in high-burden settings. In a household-based TB transmissibility study in Peru, we identified a large MIRU-VNTR Mtb cluster (148 isolates) with a range of resistance phenotypes, and studied host and bacterial factors contributing to its spread. WGS was performed on 61 of the 148 isolates. We compared transmission link inference using epidemiological or genomic data and estimated the dates of emergence of the cluster and antimicrobial drug resistance (DR) acquisition events by generating a time-calibrated phylogeny. Using a set of 12,032 public Mtb genomes, we determined bacterial factors characterizing this cluster and under positive selection in other Mtb lineages. Four of the 61 isolates were distantly related and the remaining 57 isolates diverged ca. 1968 (95%HPD: 1945-1985). Isoniazid resistance arose once and rifampin resistance emerged subsequently at least three times. Emergence of other DR types occurred as recently as within the last year of sampling. We identified five cluster-defining SNPs potentially contributing to transmissibility. In conclusion, clusters (as defined by MIRU-VNTR typing) may be circulating for decades in a high-burden setting. WGS allows for an enhanced understanding of transmission, drug resistance, and bacterial fitness factors.
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Affiliation(s)
- Avika Dixit
- Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | | | | | | | | | | | | | | | | | - Zibiao Zhang
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Leonid Lecca
- Harvard Medical School, Boston, MA, USA
- Socios En Salud, Lima, Peru
| | | | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Maha R Farhat
- Harvard Medical School, Boston, MA, USA
- Massachussetts General Hospital, Boston, MA, USA
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MODS-Wayne, a Colorimetric Adaptation of the Microscopic-Observation Drug Susceptibility (MODS) Assay for Detection of Mycobacterium tuberculosis Pyrazinamide Resistance from Sputum Samples. J Clin Microbiol 2019; 57:JCM.01162-18. [PMID: 30429257 PMCID: PMC6355525 DOI: 10.1128/jcm.01162-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/27/2018] [Indexed: 02/03/2023] Open
Abstract
Although pyrazinamide (PZA) is a key component of first- and second-line tuberculosis treatment regimens, there is no gold standard to determine PZA resistance. Approximately 50% of multidrug-resistant tuberculosis (MDR-TB) and over 90% of extensively drug-resistant tuberculosis (XDR-TB) strains are also PZA resistant. Although pyrazinamide (PZA) is a key component of first- and second-line tuberculosis treatment regimens, there is no gold standard to determine PZA resistance. Approximately 50% of multidrug-resistant tuberculosis (MDR-TB) and over 90% of extensively drug-resistant tuberculosis (XDR-TB) strains are also PZA resistant. pncA sequencing is the endorsed test to evaluate PZA susceptibility. However, molecular methods have limitations for their wide application. In this study, we standardized and evaluated a new method, MODS-Wayne, to determine PZA resistance. MODS-Wayne is based on the detection of pyrazinoic acid, the hydrolysis product of PZA, directly in the supernatant of sputum cultures by detecting a color change following the addition of 10% ferrous ammonium sulfate. Using a PZA concentration of 800 µg/ml, sensitivity and specificity were evaluated at three different periods of incubation (reading 1, reading 2, and reading 3) using a composite reference standard (MGIT-PZA, pncA sequencing, and the classic Wayne test). MODS-Wayne was able to detect PZA resistance, with a sensitivity and specificity of 92.7% and 99.3%, respectively, at reading 3. MODS-Wayne had an agreement of 93.8% and a kappa index of 0.79 compared to the classic Wayne test, an agreement of 95.3% and kappa index of 0.86 compared to MGIT-PZA, and an agreement of 96.9% and kappa index of 0.90 compared to pncA sequencing. In conclusion, MODS-Wayne is a simple, fast, accurate, and inexpensive approach to detect PZA resistance, making this an attractive assay especially for low-resource countries, where TB is a major public health problem.
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Duarte R, Silva DR, Rendon A, Alves TG, Rabahi MF, Centis R, Kritski A, Migliori GB. Eliminating tuberculosis in Latin America: making it the point. J Bras Pneumol 2018; 44:73-76. [PMID: 29791551 PMCID: PMC6044666 DOI: 10.1590/s1806-37562017000000449] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Raquel Duarte
- Serviço de Pneumologia, Centro Hospitalar de Vila Nova de Gaia-Espinho, Porto, Portugal
| | - Denise Rossato Silva
- Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Adrian Rendon
- Centro de Investigación, Prevención y Tratamiento de Infecciones Respiratorias, Hospital Universitario, Universidad Autonoma de Nuevo Leon, Monterrey, México
| | - Tatiana Galvẫo Alves
- Hospital Especializado Octávio Mangabeira, Secretaria de Saúde do Estado da Bahia, Salvador, BA, Brasil
| | | | - Rosella Centis
- WHO Collaborating Centre for TB and Lung Diseases, Fondazione Salvatore Maugeri, Istituto di Ricovero e Cura a Carattere Scientifico, Tradate, Italia
| | - Afrânio Kritski
- Instituto de Doenças do Tórax, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Giovanni Battista Migliori
- WHO Collaborating Centre for TB and Lung Diseases, Fondazione Salvatore Maugeri, Istituto di Ricovero e Cura a Carattere Scientifico, Tradate, Italia
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