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Al-Mutairi NM, Ahmad S, Mokaddas E. Discordance in Phenotypic and Genotypic Susceptibility Testing for Streptomycin Due to Nonsynonymous/Nonsense/Deletion Frame-Shift Mutations in Gidb Among Clinical Mycobacterium tuberculosis Isolates in Kuwait. Med Princ Pract 2024; 33:000538584. [PMID: 38560979 PMCID: PMC11324218 DOI: 10.1159/000538584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVE Increasing reports of resistance to newer anti-tuberculosis drugs have prompted the search for other alternative drugs. Streptomycin could be used for the treatment of drug-resistant tuberculosis if susceptibility of Mycobacterium tuberculosis isolate to streptomycin could be accurately detected. We performed phenotypic and genotypic drug susceptibility testing (DST) of 118 M. tuberculosis isolates for streptomycin. MATERIALS AND METHODS Fifty pansusceptible and 68 multidrug-resistant M. tuberculosis (MDR-TB) isolates were used. Phenotypic DST for streptomycin, rifampicin, isoniazid and ethambutol was performed by mycobacteria growth indicator tube (MGIT) 960 System. Genotypic DST was done by GenoTypeMTBDRplus assay for rifampicin and isoniazid and by PCR-sequencing of rpsL, rrs and gidB genes for streptomycin. MDR-TB isolates were genotyped by spoligotyping. RESULTS Phenotypic DST identified 50 isolates susceptible to all four drugs (pansusceptible). Sixty-one of 68 MDR-TB isolates were resistant to streptomycin. Genotypic testing for rifampicin and isoniazid yielded expected results. Fifty pansusceptible and 7 streptomycin-susceptible MDR-TB isolates contained no mutation in rpsL or rrs, while 47, 2 and 1 STR-resistant isolate contained rpsL, rrs and rpsL + rrs mutations, respectively. Of the remaining 11 STR-resistant MDR-TB, 9 isolates contained deletion frame-shift/nonsynonymous mutations in gidB. Surprisingly, 13 pansusceptible isolates also contained deletion frame-shift/nonsense/nonsynonymous mutations in gidB. Also, 30 of 68 MDR-TB but only 2 of 50 pansusceptible isolates belonged to the Beijing genotype. CONCLUSIONS Our data show that, like ifampicin, ethambutol and pyrazinamide, streptomycin also exhibits discordant phenotypic and genotypic DST results for some M. tuberculosis isolates. Hence, streptomycin should be included in therapy regimens only if both phenotypic and genotypic resistance testing indicate susceptibility to avoid amplification of resistance and drug toxicity.
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Qadir M, Faryal R, Khan MT, Khan SA, Zhang S, Li W, Wei DQ, Tahseen S, McHugh TD. Phenotype versus genotype discordant rifampicin susceptibility testing in tuberculosis: implications for a diagnostic accuracy. Microbiol Spectr 2024; 12:e0163123. [PMID: 37982632 PMCID: PMC10783056 DOI: 10.1128/spectrum.01631-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE An accurate diagnosis of drug resistance in clinical isolates is an important step for better treatment outcomes. The current study observed a higher discordance rate of rifampicin resistance on Mycobacteria Growth Indicator Tube (MGIT) drug susceptibility testing (DST) than Lowenstein-Jenson (LJ) DST when compared with the rpoB sequencing. We detected a few novel mutations and their combination in rifampicin resistance isolates that were missed by MGIT DST and may be useful for the better management of tuberculosis (TB) treatment outcomes. Few novel deletions in clinical isolates necessitate the importance of rpoB sequencing in large data sets in geographic-specific locations, especially high-burden countries. We explored the discordance rate on MGIT and LJ, which is important for the clinical management of rifampicin resistance to avoid the mistreatment of drug-resistant TB. Furthermore, MGIT-sensitive isolates may be subjected to molecular methods of diagnosis for further confirmation and treatment options.
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Affiliation(s)
- Mehmood Qadir
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rani Faryal
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Tahir Khan
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, China
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | - Sajjad Ahmed Khan
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
| | - Shulin Zhang
- School of Medicine, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Weimin Li
- National Tuberculosis Clinical Lab of China, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Dong Qing Wei
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
| | - Sabira Tahseen
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, University College London, London, United Kingdom
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Lindsey JA, Easton AV, Modestil H, Dworkin F, Burzynski J, Nilsen D. Rifampin Mono-Resistant Tuberculosis in New York City, 2010-2021: A Retrospective Case Series. Open Forum Infect Dis 2023; 10:ofad534. [PMID: 38023554 PMCID: PMC10662657 DOI: 10.1093/ofid/ofad534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Background Although relatively rare, rifampin mono-resistant tuberculosis (RMR TB) poses important challenges to effective TB treatment and control. Information on the burden of RMR TB and treatment outcomes is needed to inform diagnosis and management. Methods Standardized variables were collected from the New York City (NYC) tuberculosis surveillance system for patients treated for RMR TB in NYC during 2010-2021. Results Of 7097 TB cases reported in 2010-2021, 31 (<1%) were treated clinically as RMR TB. Five (16%) of these patients had HIV. Seventeen patients (55%) had TB that was rifampin-resistant by both molecular and phenotypic drug susceptibility testing; 2 (6%) had rifampin resistance by phenotypic tests, and molecular tests were not done; and 12 (39%) were identified based only on molecular tests. Among these 12, 7 were rifampin-sensitive by phenotypic tests, and phenotypic testing could not be done for the other 5. Ten of the 31 (32%) were diagnosed in 2010-2015; the other 21 (including 10/12 diagnosed by molecular tests alone) were diagnosed in 2016-2021. Of the 31 patients, 21 (68%) completed treatment (median treatment duration of 18 months). Although the interval between tuberculosis treatment initiation and change to a non-rifamycin-containing regimen decreased significantly during the study period, the overall duration of treatment did not decrease significantly between 2010 and 2021. Conclusions Molecular drug susceptibility tests identified cases of RMR TB that were not detected by phenotypic testing and helped enable timely adjustment of tuberculosis treatment regimens. Short-course regimens are needed to reduce duration of treatment for RMR TB.
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Affiliation(s)
- Joseph A Lindsey
- Bureau of Tuberculosis Control, NewYork City Department of Health and Mental Hygiene, Long Island City, New York, USA
| | - Alice V Easton
- Bureau of Tuberculosis Control, NewYork City Department of Health and Mental Hygiene, Long Island City, New York, USA
| | - Herns Modestil
- Bureau of Tuberculosis Control, NewYork City Department of Health and Mental Hygiene, Long Island City, New York, USA
| | - Felicia Dworkin
- Bureau of Tuberculosis Control, NewYork City Department of Health and Mental Hygiene, Long Island City, New York, USA
| | - Joseph Burzynski
- Bureau of Tuberculosis Control, NewYork City Department of Health and Mental Hygiene, Long Island City, New York, USA
| | - Diana Nilsen
- Bureau of Tuberculosis Control, NewYork City Department of Health and Mental Hygiene, Long Island City, New York, USA
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Graciaa DS, Schechter MC, Fetalvero KB, Cranmer LM, Kempker RR, Castro KG. Updated considerations in the diagnosis and management of tuberculosis infection and disease: integrating the latest evidence-based strategies. Expert Rev Anti Infect Ther 2023; 21:595-616. [PMID: 37128947 PMCID: PMC10227769 DOI: 10.1080/14787210.2023.2207820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/24/2023] [Indexed: 05/03/2023]
Abstract
INTRODUCTION Tuberculosis (TB) is a leading infectious cause of global morbidity and mortality, affecting nearly a quarter of the human population and accounting for over 10 million deaths each year. Over the past several decades, TB incidence and mortality have gradually declined, but 2021 marked a threatening reversal of this trend highlighting the importance of accurate diagnosis and effective treatment of all forms of TB. AREAS COVERED This review summarizes advances in TB diagnostics, addresses the treatment of people with TB infection and TB disease including recent evidence for treatment regimens for drug-susceptible and drug-resistant TB, and draws attention to special considerations in children and during pregnancy. EXPERT OPINION Improvements in diagnosis and management of TB have expanded the available options for TB control. Molecular testing has enhanced the detection of TB disease, but better diagnostics are still needed, particularly for certain populations such as children. Novel treatment regimens have shortened treatment and improved outcomes for people with TB. However, important questions remain regarding the optimal management of TB. Work must continue to ensure the potential of the latest developments is realized for all people affected by TB.
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Affiliation(s)
- Daniel S. Graciaa
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Marcos Coutinho Schechter
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Krystle B. Fetalvero
- Angelo King Medical Research Center-De La Salle Medical and Health Science Institute, Cavite, Philippines
- Department of Family and Community Medicine, Calamba Medical Center, Laguna, Philippines
| | - Lisa Marie Cranmer
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Russell R. Kempker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kenneth G. Castro
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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5
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Ule Belotti NC, Madela NK, Tonelli Nardi SM, Mariano DC, de Souza NG, Oliveira RS, Paro Pedro HDS. Evaluation of xpert Mycobacterium tuberculosis rifampicin for tuberculosis diagnosis in a reference laboratory. Int J Mycobacteriol 2022; 11:435-441. [PMID: 36510931 DOI: 10.4103/ijmy.ijmy_195_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background The Xpert Mycobacterium tuberculosis Rifampicin (MTB-RIF) is a technological innovation that presents precision and speed in the diagnosis of tuberculosis (TB). The study aimed to evaluate the performance of Xpert MTB/RIF in the TB diagnosis and compare its results with those of culture, species identification, Antimicrobial Susceptibility Testing (AST), and rpoB gene sequencing of discordant results in AST, used for the diagnosis of TB in a reference laboratory. Methods Cross-sectional descriptive study of pulmonary and extrapulmonary samples requesting Xpert MTB/RIF and culture for TB diagnosis from 2015 to 2019 at Adolfo Lutz Institute-São Paulo/Brazil. The analysis was performed with Epi-Info 7.2.1, presenting the distribution of frequencies and, for comparative analyses, Pearson's Chi-square test and Fisher's exact test were used, considering P ≤ 0.05 as statistically significant. For variables agreement, the Kappa method was used. Results A total of 1575 pulmonary and extrapulmonary samples were analyzed using Xpert MTB/RIF and culture, of which 293 were positive for the MTB Complex in both methodologies with a sensitivity of 94.55%; specificity of 95.97%; accuracy 95.69%; positive predictive value 85.53%; negative predictive value 98.59%, substantial agreement by Kappa 0.87, and detection sensitivity even at lower levels of bacillary load (P < 0.05). The Xpert MTB/RIF and AST showed concordant results (P < 0.05). Conclusion The study brings forward that the Xpert MTB/RIF shows substantial agreement with the results of culture and AST, contributing to the diagnosis of TB and the rapid detection of resistance. The sequencing of resistant cultures in Xpert MTB/RIF and sensitivity in AST identified the H526N mutation, characterized by a low level of resistance to RIF.
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Affiliation(s)
| | - Naiady Konno Madela
- Biomedical Sciences Center, Adolfo Lutz Institute, São José do Rio Preto, São Paulo, Brazil
| | | | | | - Nilza Gomes de Souza
- Tuberculosis Department, Epidemiological Surveillance Group, São José do Rio Preto, São Paulo, Brazil
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Mvelase NR, Singh R, Swe Swe-Han K, Mlisana KP. Pyrazinamide resistance in rifampicin discordant tuberculosis. PLoS One 2022; 17:e0274688. [PMID: 36129921 PMCID: PMC9491533 DOI: 10.1371/journal.pone.0274688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction Mycobacterium tuberculosis strains with phenotypically susceptible rpoB mutations (rifampicin discordant) have emerged following implementation of rapid molecular drug resistance testing for tuberculosis. Whilst rifampicin resistance is known to be associated with resistance to other rifamycins (rifapentine and rifabutin) as well as isoniazid and pyrazinamide, rifampicin discordant strains have shown high rates of susceptibility to isoniazid and rifabutin. However, pyrazinamide susceptibly testing results have not been reported. Materials and methods We evaluated pyrazinamide resistance in 80 rifampicin discordant and 25 rifampicin and isoniazid susceptible isolates from KwaZulu-Natal in South Africa using Mycobacteria Growth Indicator Tube method and sequencing of the pncA. We also compared susceptibility of pyrazinamide with that of isoniazid. Results Pyrazinamide resistance was found in 6/80 (7.5%) rifampicin discordant isolates. All pyrazinamide resistant isolates were also resistant to isoniazid and pyrazinamide resistance was found to be associated with isoniazid resistance. No pyrazinamide resistance was found among the isoniazid susceptible isolates. Conclusion Given the low prevalence of pyrazinamide resistance in rifampicin discordant TB, this anti-TB drug still has a significant role in the treatment of these patients. Performing pyrazinamide susceptibility testing remains a challenge, our findings show that isoniazid susceptible isolates are unlikely to be resistant to pyrazinamide among the discordant TB isolates.
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Affiliation(s)
- Nomonde Ritta Mvelase
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
- * E-mail:
| | - Ravesh Singh
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
| | - Khine Swe Swe-Han
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
| | - Koleka Patience Mlisana
- Department of Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, Department of Medical Microbiology, University of KwaZulu-Natal, College of Health Sciences, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, Durban, South Africa
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7
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Hunt M, Letcher B, Malone KM, Nguyen G, Hall MB, Colquhoun RM, Lima L, Schatz MC, Ramakrishnan S, Iqbal Z. Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes. Genome Biol 2022; 23:147. [PMID: 35791022 PMCID: PMC9254434 DOI: 10.1186/s13059-022-02714-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/20/2022] [Indexed: 12/30/2022] Open
Abstract
There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance. We quantify the correlation with phenotypic resistance and then replicate in a second cohort (N=10k).
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Affiliation(s)
- Martin Hunt
- EMBL-EBI, Cambridge, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | - Rachel M Colquhoun
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | | | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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8
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Characterization of rifampicin-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan. Sci Rep 2021; 11:14194. [PMID: 34244539 PMCID: PMC8270973 DOI: 10.1038/s41598-021-93501-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/24/2021] [Indexed: 11/08/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, is endemic in Pakistan. Resistance to both firstline rifampicin and isoniazid drugs (multidrug-resistant TB; MDR-TB) is hampering disease control. Rifampicin resistance is attributed to rpoB gene mutations, but rpoA and rpoC loci may also be involved. To characterise underlying rifampicin resistance mutations in the TB endemic province of Khyber Pakhtunkhwa, we sequenced 51 M. tuberculosis isolates collected between 2016 and 2019; predominantly, MDR-TB (n = 44; 86.3%) and lineage 3 (n = 30, 58.8%) strains. We found that known mutations in rpoB (e.g. S405L), katG (e.g. S315T), or inhA promoter loci explain the MDR-TB. There were 24 unique mutations in rpoA, rpoB, and rpoC genes, including four previously unreported. Five instances of within-host resistance diversity were observed, where two were a mixture of MDR-TB strains containing mutations in rpoB, katG, and the inhA promoter region, as well as compensatory mutations in rpoC. Heteroresistance was observed in two isolates with a single lineage. Such complexity may reflect the high transmission nature of the Khyber Pakhtunkhwa setting. Our study reinforces the need to apply sequencing approaches to capture the full-extent of MDR-TB genetic diversity, to understand transmission, and to inform TB control activities in the highly endemic setting of Pakistan.
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Shah M, Paradis S, Betz J, Beylis N, Bharadwaj R, Caceres T, Gotuzzo E, Joloba M, Mave V, Nakiyingi L, Nicol MP, Pradhan N, King B, Armstrong D, Knecht D, Maus CE, Cooper CK, Dorman SE, Manabe YC. Multicenter Study of the Accuracy of the BD MAX Multidrug-resistant Tuberculosis Assay for Detection of Mycobacterium tuberculosis Complex and Mutations Associated With Resistance to Rifampin and Isoniazid. Clin Infect Dis 2021; 71:1161-1167. [PMID: 31560049 PMCID: PMC7442848 DOI: 10.1093/cid/ciz932] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/08/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) control is hindered by absence of rapid tests to identify Mycobacterium tuberculosis (MTB) and detect isoniazid (INH) and rifampin (RIF) resistance. We evaluated the accuracy of the BD MAX multidrug-resistant (MDR)-TB assay (BD MAX) in South Africa, Uganda, India, and Peru. METHODS Outpatient adults with signs/symptoms of pulmonary TB were prospectively enrolled. Sputum smear microscopy and BD MAX were performed on a single raw sputum, which was then processed for culture and phenotypic drug susceptibility testing (DST), BD MAX, and Xpert MTB/RIF (Xpert). RESULTS 1053 participants with presumptive TB were enrolled (47% female; 32% with human immunodeficiency virus). In patients with confirmed TB, BD MAX sensitivity was 93% (262/282 [95% CI, 89-95%]); specificity was 97% (593/610 [96-98%]) among participants with negative cultures on raw sputa. BD MAX sensitivity was 100% (175/175 [98-100%]) for smear-positive samples (fluorescence microscopy), and 81% (87/107 [73-88%]) in smear-negative samples. Among participants with both BD MAX and Xpert, sensitivity was 91% (249/274 [87-94%]) for BD MAX and 90% (246/274 [86-93%]) for Xpert on processed sputa. Sensitivity and specificity for RIF resistance compared with phenotypic DST were 90% (9/10 [60-98%]) and 95% (211/222 [91-97%]), respectively. Sensitivity and specificity for detection of INH resistance were 82% (22/27 [63-92%]) and 100% (205/205 [98-100%]), respectively. CONCLUSIONS The BD MAX MDR-TB assay had high sensitivity and specificity for detection of MTB and RIF and INH drug resistance and may be an important tool for rapid detection of TB and MDR-TB globally.
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Affiliation(s)
- Maunank Shah
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sonia Paradis
- Becton, Dickinson and Company, Sparks, Maryland, USA
| | - Joshua Betz
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Natalie Beylis
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.,Medical Microbiology Laboratory National Health Laboratory Services Groote Schuur Hospital, Cape Town, South Africa
| | - Renu Bharadwaj
- Byramjee Jeejeebhoy Government Medical College, Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Tatiana Caceres
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eduardo Gotuzzo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Moses Joloba
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Vidya Mave
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Byramjee Jeejeebhoy Government Medical College, Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Lydia Nakiyingi
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Mark P Nicol
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.,Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Neeta Pradhan
- Byramjee Jeejeebhoy Government Medical College, Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Bonnie King
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Derek Armstrong
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | - Susan E Dorman
- Medical University of South Carolina, Charleston, South Carolina, USA
| | - Yukari C Manabe
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
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10
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Al-Mutairi NM, Ahmad S, Mokaddas E. Increasing prevalence of resistance to second-line drugs among multidrug-resistant Mycobacterium tuberculosis isolates in Kuwait. Sci Rep 2021; 11:7765. [PMID: 33833390 PMCID: PMC8032671 DOI: 10.1038/s41598-021-87516-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/30/2021] [Indexed: 11/13/2022] Open
Abstract
Molecular methods detect genetic mutations associated with drug resistance. This study detected resistance-conferring mutations in gyrA/gyrB for fluoroquinolones and rrs/eis genes for second-line injectable drugs (SLIDs) among multidrug-resistant Mycobacterium tuberculosis (MDR-TB) isolates in Kuwait. Fifty pansusceptible M. tuberculosis and 102 MDR-TB strains were tested. Phenotypic susceptibility testing was performed by MGIT 960 system using SIRE drug kit. GenoType MTBDRsl version 1 (gMTBDRslv1) and GenoType MTBDRsl version 2 (gMTBDRslv2) tests were used for mutation detection. Results were validated by PCR-sequencing of respective genes. Fingerprinting was performed by spoligotyping. No mutations were detected in pansusceptible isolates. gMTBDRslv1 detected gyrA mutations in 12 and rrs mutations in 8 MDR-TB isolates. gMTBDRsl2 additionally detected gyrB mutations in 2 and eis mutation in 1 isolate. Mutations in both gyrA/gyrB and rrs/eis were not detected. gMTBDRslv1 also detected ethambutol resistance-conferring embB mutations in 59 isolates. Although XDR-TB was not detected, frequency of resistance-conferring mutations for fluoroquinolones or SLIDs was significantly higher among isolates collected during 2013–2019 versus 2006–2012. Application of both tests is warranted for proper management of MDR-TB patients in Kuwait as gMTBDRslv2 detected resistance to fluoroquinolones and/or SLIDs in 3 additional isolates while gMTBDRslv1 additionally detected resistance to ethambutol in 58% of MDR-TB isolates.
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Affiliation(s)
- Noura M Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.,Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
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11
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Low-Level Rifampin Resistance and rpoB Mutations in Mycobacterium tuberculosis: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New York. J Clin Microbiol 2021; 59:JCM.01885-20. [PMID: 32999007 DOI: 10.1128/jcm.01885-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/05/2020] [Indexed: 01/02/2023] Open
Abstract
Rapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis and treatment of drug-resistant and multidrug-resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to the presence of rpoB mutations that do not confer high levels of RIF resistance, as have been exhibited in strains with mutations such as Ser450Leu. These strains, termed low-level RIF resistant, exhibit elevated RIF MICs compared to fully susceptible strains but remain phenotypically susceptible by mycobacterial growth indicator tube (MGIT) testing and have been associated with poor patient outcomes. Here, we assess RIF resistance prediction by whole-genome sequencing (WGS) among a set of 1,779 prospectively tested strains by both prevalence of rpoB gene mutation and phenotype as part of routine clinical testing during a 2.5-year period. During this time, 139 strains were found to have nonsynonymous rpoB mutations, 53 of which were associated with RIF resistance, including both low-level and high-level resistance. Resistance to RIF (1.0 μg/ml in MGIT) was identified in 43 (81.1%) isolates. The remaining 10 (18.9%) strains were susceptible by MGIT but were confirmed to be low-level RIF resistant by MIC testing. Full rpoB gene sequencing overcame the limitations of critical concentration phenotyping, probe-based genotyping, and partial gene sequencing methods. Universal clinical WGS with concurrent phenotypic testing provided a more complete understanding of the prevalence and type of rpoB mutations and their association with RIF resistance in New York.
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12
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Tsang CA, Shah N, Armstrong LR, Marks SM. Eligibility for a Shorter Treatment Regimen for Multidrug-resistant Tuberculosis in the United States, 2011-2016. Clin Infect Dis 2021; 70:907-916. [PMID: 30944927 DOI: 10.1093/cid/ciz263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/26/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND In 2016, the World Health Organization (WHO) recommended a shorter (9-12 month) multidrug-resistant tuberculosis (MDR-TB) treatment regimen (as compared to the conventional 18-24 month regimen) for patients without extrapulmonary TB, pregnancy, a previous second-line TB medication exposure, or drug resistance to pyrazinamide, ethambutol, kanamycin, moxifloxacin, ethionamide, or clofazimine. The recommendation was based on successful clinical trials conducted in Asia and Africa, but studies, using mainly European data, have shown few patients in higher-resource settings would meet WHO eligibility criteria. METHODS We assessed eligibility for the shorter regimen among US MDR-TB cases that had full drug susceptibility testing (DST) results and were reported during 2011-2016 to the US National TB Surveillance System. We estimated costs by applying the eligibility criteria for the shorter regimen, and proportional inpatient/outpatient costs from a previous, population-based study, to all MDR-TB patients reported to the National TB Surveillance System. RESULTS Of 586 reported MDR-TB cases, 10% (59) were eligible for the shorter regimen. Of 527 ineligible patients, 386 had full DST, of which 246 were resistant to ethambutol and 217 were resistant to pyrazinamide. Compared with conventional MDR-TB treatment, implementing the shorter regimen would have reduced the US annual societal MDR-TB cost burden by 4%, but the cost burden for eligible individuals would have been reduced by 37-46%. CONCLUSIONS Relying on full DST use, our analysis found a minority of US MDR-TB patients would have been eligible for the shorter regimen. Cost reductions would have been minimal for society, but large for eligible individuals.
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Affiliation(s)
- Clarisse A Tsang
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Neha Shah
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lori R Armstrong
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Suzanne M Marks
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia
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Krishnakumariamma K, Ellappan K, Muthuraj M, Tamilarasu K, Kumar SV, Joseph NM. Molecular diagnosis, genetic diversity and drug sensitivity patterns of Mycobacterium tuberculosis strains isolated from tuberculous meningitis patients at a tertiary care hospital in South India. PLoS One 2020; 15:e0240257. [PMID: 33017455 PMCID: PMC7535050 DOI: 10.1371/journal.pone.0240257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberculous meningitis (TBM) is the most severe form of Mycobacterium tuberculosis (Mtb) infection in humans and is a public health concern worldwide. We evaluated the performance of GeneXpert MTB/RIF (GeneXpert) for the diagnosis of TBM. In addition, genetic diversity and drug susceptibility profiling of Mtb strains isolated from TBM patients were also investigated. A total of 293 TBM suspected cerebrospinal fluid (CSF) samples were collected and subjected to GeneXpert and Mycobacterial Growth Indicator Tube (MGIT 960) culture, respectively. Sensitivity and specificity of GeneXpert was 72.7% and 98.5%, respectively by using MGIT 960 as a gold standard (GeneXpert (n = 20, 6.8%) vs MGIT 960 (n = 22, 7.5%)). All Mtb positive cultures were subjected to 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing, Line probe assay (LPA) and MGIT 960- Drug Susceptibility Testing (DST). The rpoB gene was amplified and sequenced for selected isolates. Among our TBM patients, East African Indian (EAI) lineage (n = 16, 72.7%) was most predominant followed by Beijing (n = 3, 13.6%), S-family (n = 2, 9.1%) and Delhi/CAS (n = 1, 4.5%). Three Mtb strains were found to be Isoniazid (INH) resistant by MGIT 960; however LPA revealed that two strains were INH resistant and one strain was multi drug resistant (MDR) (Resistant to Isoniazid and Rifampicin (RIF)). We identified rifampicin resistant isolate with the mutation D516F in rifampicin resistance-determining region (RRDR) and observed discordant results between LPA, GeneXpert and MGIT 960. In addition, GeneXpert showing false RIF resistance was identified (no mutation in RRDR). We conclude that GeneXpert is useful for the diagnostic confirmation of TBM; however a GeneXpert negative sample should be subjected to MGIT 960 culture or LPA to rule out TBM. EAI lineage was the most predominant among TBM patients in South India and associated with drug resistance. The discordance between GeneXpert, MGIT 960 and LPA with respect to rifampicin resistance has to be ruled out to avoid TB treatment failure or relapse.
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Affiliation(s)
- Krishnapriya Krishnakumariamma
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Kalaiarasan Ellappan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Muthaiah Muthuraj
- Intermediate Reference Laboratory, Government Hospital for Chest Diseases, Pondicherry, India
| | - Kadhiravan Tamilarasu
- Department of Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Saka Vinod Kumar
- Department of Pulmonary Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Noyal Mariya Joseph
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
- * E-mail:
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14
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Brandao AP, Pinhata JMW, Simonsen V, Oliveira RS, Ghisi KT, Rabello MCS, Fukasava S, Ferrazoli L. Transmission of Mycobacterium tuberculosis presenting unusually high discordance between genotypic and phenotypic resistance to rifampicin in an endemic tuberculosis setting. Tuberculosis (Edinb) 2020; 125:102004. [PMID: 33017720 DOI: 10.1016/j.tube.2020.102004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/02/2023]
Abstract
BACKGROUND Since the implementation of the Xpert MTB/RIF in Sao Paulo, Brazil, numerous Mycobacterium tuberculosis isolates presenting "rifampicin-resistant genotype with rifampicin-susceptible phenotype" were observed. OBJECTIVE To evaluate the prevalence, rpoB mutations and transmission of M. tuberculosis resistant to rifampicin on Xpert MTB/RIF but susceptible on BACTEC MGIT system, in Sao Paulo state. METHODS Patients' isolates with this pattern of rifampicin discordance, collected from 2014 to 2017, had their rpoB predominant rifampicin-resistance-determining region sequenced and were genotyped by IS6110 restriction fragment-length polymorphism. FINDINGS The prevalence of rifampicin-discordant M. tuberculosis with genotypic resistance was 55.1% (156/283). Among the sequenced and genotyped isolates, 75.5% (111/147) were in clusters, largely associated with the type of rpoB mutation. Most isolates (98.6%; 72/73) harbouring the predominant mutation, His445Asn, were pooled into the two largest clusters, SP2ga (42/72; 58.3%) and SP5o (12/72; 16.7%). Ranking second, isolates carrying the silent mutation Phe433Phe were mostly (92.3%; 24/26) gathered into four groups of the family SP25. CONCLUSION These findings suggest that this unusual high rifampicin discrepancy proportion was greatly influenced by few actively circulating clusters. Further studies on many of the rpoB mutations identified in our setting are needed to elucidate their association with phenotypic rifampicin resistance.
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Affiliation(s)
- Angela Pires Brandao
- Instituto Adolfo Lutz, São Paulo, SP, Brazil; IOC/FIOCRUZ, Rio de Janeiro, RJ, Brazil.
| | | | | | | | | | | | - Suely Fukasava
- Centro de Vigilância Epidemiológica do Estado de São Paulo, São Paulo, SP, Brazil
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15
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Genotypic characterization of 'inferred' rifampin mutations in GenoType MTBDRplus assay and its association with phenotypic susceptibility testing of Mycobacterium tuberculosis. Diagn Microbiol Infect Dis 2020; 96:114995. [PMID: 32037037 DOI: 10.1016/j.diagmicrobio.2020.114995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/10/2019] [Accepted: 01/17/2020] [Indexed: 12/23/2022]
Abstract
In GenoType MTBDRplus assay [line probe assay (LPA)], when Mycobacterium tuberculosis (M. tuberculosis) sample DNA fails to hybridize to at least 1 rpoB wild-type probe and any mutation probe, it is inferred as rifampin (RIF)-resistant. In this study, we sought to identify such 'inferred' mutations in M. tuberculosis isolates (n = 203) by rpoB gene sequencing and determined their association with phenotypic resistance. D516Y, H526N, L511P mutations were associated with both phenotypically sensitive (59%, n = 38/64) and resistant (23.7%, n = 33/139) antimicrobial susceptibility testing (AST) results, whereas S531W mutation was associated with only RIF-resistant isolates (33%, n = 46/139). These results demonstrated that, at standard drug concentrations, some 'inferred' mutations may be missed by RIF-AST (phenotypically sensitive). The use of LPA permits identification of these RIF-resistant isolates, and incorporation of additional mutation probes (e.g., S531W) could further increase LPA specificity. Further studies are needed to establish the significance of the type of 'inferred' mutation with clinical/treatment outcomes.
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16
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Torrea G, Ng KCS, Van Deun A, André E, Kaisergruber J, Ssengooba W, Desmaretz C, Gabriels S, Driesen M, Diels M, Asnong S, Fissette K, Gumusboga M, Rigouts L, Affolabi D, Joloba M, De Jong BC. Variable ability of rapid tests to detect Mycobacterium tuberculosis rpoB mutations conferring phenotypically occult rifampicin resistance. Sci Rep 2019; 9:11826. [PMID: 31413308 PMCID: PMC6694172 DOI: 10.1038/s41598-019-48401-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 08/01/2019] [Indexed: 01/15/2023] Open
Abstract
We compared the ability of commercial and non-commercial, phenotypic and genotypic rapid drug susceptibility tests (DSTs) to detect rifampicin resistance (RR)-conferring ‘disputed’ mutations frequently missed by Mycobacterium Growth Indicator Tube (MGIT), namely L430P, D435Y, L452P, and I491F. Strains with mutation S450L served as positive control while wild-types were used as negative control. Of the 38 mutant strains, 5.7% were classified as RR by MGIT, 16.2% by Trek Sensititre MYCOTB MIC plate, 19.4% by resazurin microtiter plate assay (REMA), 50.0% by nitrate reductase assay (NRA), and 62.2% by microscopic observation direct susceptibility testing (MODS). Reducing MGIT rifampicin concentration to 0.5 µg/ml, and/or increasing incubation time, enhanced detection of disputed mutations from 5.7% to at least 65.7%, particularly for mutation I491F (from 0.0 to 75.0%). Compared with MGIT at standard pre-set time with 0.25 µg/ml ECOFF as breakpoint, we found a statistically significant increase in the ability of MGIT to resolve disputed mutants and WT strains at extended incubation period of 15 and 21 days, with 0.5 µg/ml and 1 µg/ml ECOFF respectively. MODS detected 75.0% of the I491F strains and NRA 62.5%, while it was predictably missed by all molecular assays. Xpert MTB/RIF, Xpert Ultra, and GenoscholarTB-NTM + MDRTB detected all mutations within the 81 bp RR determining region. Only GenoType MTBDRplus version 2 missed mutation L430P in 2 of 11 strains. Phenotypic and genotypic DSTs varied greatly in detecting occult rifampicin resistance. None of these methods detected all disputed mutations without misclassifying wild-type strains.
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Affiliation(s)
- Gabriela Torrea
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Kamela C S Ng
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Armand Van Deun
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Emmanuel André
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | - Willy Ssengooba
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Christel Desmaretz
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Siemon Gabriels
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michèle Driesen
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Maren Diels
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sylvie Asnong
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kristina Fissette
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mourad Gumusboga
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Moses Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Bouke C De Jong
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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17
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Mvelase NR, Pillay M, Sibanda W, Ngozo JN, Brust JCM, Mlisana KP. rpoB Mutations Causing Discordant Rifampicin Susceptibility in Mycobacterium tuberculosis: Retrospective Analysis of Prevalence, Phenotypic, Genotypic, and Treatment Outcomes. Open Forum Infect Dis 2019; 6:ofz065. [PMID: 31024968 PMCID: PMC6475586 DOI: 10.1093/ofid/ofz065] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/08/2019] [Indexed: 02/07/2023] Open
Abstract
Background Discordant genotypic/phenotypic rifampicin susceptibility testing in Mycobacterium tuberculosis is a significant challenge, yet there are limited data on its prevalence and how best to manage such patients. Whether to treat isolates with rpoB mutations not conferring phenotypic resistance as susceptible or multidrug-resistant tuberculosis (MDR-TB) is unknown. We describe phenotypic and genotypic characteristics of discordant isolates and clinical characteristics and treatment outcomes of affected patients in KwaZulu-Natal, South Africa. Methods We analyzed clinical isolates showing rifampicin resistance on GenoType MTBDRplus while susceptible on 1% agar proportion method. We measured rifampicin minimum inhibitory concentrations (MICs) using Middlebrook 7H10 agar dilution and BACTEC MGIT 960. Sensititre MYCOTB plates were used for drug-susceptibility testing, and rpoB gene sequencing was performed on all isolates. Local MDR-TB program data were reviewed for clinical information and patient outcomes. Results Discordant isolates constituted 4.6% (60) of 1302 rifampicin-resistant cases over the study period. Of these, 62% remained susceptible to isoniazid and 98% remained susceptible to rifabutin. Rifampicin MICs were close to the critical concentration of 1 µg/mL (0.5–2 µg/mL) for 83% of isolates. The most frequent rpoB mutations were Q513P (25.3%), D516V (19.2%), and D516Y (13.3%). Whereas 70% were human immunodeficiency virus infected, the mean CD4 count was 289 cells/mm3 and 87% were receiving antiretroviral therapy. Standard therapy for MDR-TB was used and 53% achieved successful treatment outcomes. Conclusions Rifampicin-discordant TB is not uncommon and sequencing is required to confirm results. The high susceptibility to rifabutin and isoniazid and poor treatment outcomes with the current regimen suggest a potential utility for rifabutin-based therapy.
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Affiliation(s)
- Nomonde R Mvelase
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Melendhran Pillay
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa
| | - Wilbert Sibanda
- Department of Biostatistics, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Jacqueline N Ngozo
- Department of Health, KwaZulu-Natal Province, Pietermaritzburg, South Africa
| | - James C M Brust
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York
| | - Koleka P Mlisana
- Department of Medical Microbiology, KwaZulu-Natal Academic Complex, National Health Laboratory Service, Durban, South Africa.,Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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18
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Kang JY, Hur J, Kim S, Jeon S, Lee J, Kim YJ, Kim SC, Park YJ, Kim YK, Moon HS. Clinical implications of discrepant results between genotypic MTBDR plus and phenotypic Löwenstein-Jensen method for isoniazid or rifampicin drug susceptibility tests in tuberculosis patients. J Thorac Dis 2019; 11:400-409. [PMID: 30962983 PMCID: PMC6409268 DOI: 10.21037/jtd.2019.01.58] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The widespread use of molecular, genotypic drug susceptibility tests (DSTs) for antituberculosis (anti-TB) drugs has led to the dilemma of interpreting discordant results between genotypic and conventional, phenotypic DSTs. We investigated the clinical characteristics, including treatment patterns and outcomes, of TB patients with a genotype-phenotype discrepancy in susceptibility to isoniazid (INH) or rifampicin (RIF). METHODS We retrospectively reviewed the medical records of TB patients who had results for 2 DSTs (genotypic method, MTBDRplus test for INH and RIF, and phenotypic method) treated between August 2010 and October 2016 in a tertiary university hospital. RESULTS Among 1,069 TB patients, 63 (5.9%) had discrepant results for the 2 DSTs. Of the 57 multidrug-resistant (MDR) TB cases diagnosed by either DST, 18 (31.6%) showed discordant results for INH or RIF. The most frequent pattern of discordance was genotypic susceptibility with phenotypic resistance to INH. RIF-discordant subjects with genotypic resistance were more likely to have been exposed previously to anti-TB drugs and to have an MDR TB diagnosis and concurrent INH resistance. Forty-five of the 54 patients managed in our hospital (83.3%) had a favorable outcome with a mean treatment duration of 14.0 months. Ten of the 16 INH-discrepant patients with a genotypic mutation continued taking INH, but more than half patients in the RIF-discrepant group (8/14) with a genotypic mutation discontinued taking RIF. CONCLUSIONS Despite the low frequency, discordant results were obtained between the genotypic and phenotypic DSTs for INH or RIF, especially for patients with MDR TB or INH resistance. Furthermore, it seemed that RIF discrepancy with a genotypic mutation might have a greater impact on the clinical outcome than INH discrepancy.
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Affiliation(s)
- Ji Young Kang
- Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Jung Hur
- Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Shinyoung Kim
- Department of Internal Medicine, College of Medicine, St. Vincent’s Hospital, The Catholic University of Korea, Republic of Korea
| | - Sanghoon Jeon
- Department of Internal Medicine, Inha University School of Medicine, Incheon, Republic of Korea
| | - Jaeha Lee
- Department of Internal Medicine, Inje University College of Medicine, Haeundae Paik Hospital, Busan, Republic of Korea
| | - Youn Jeong Kim
- Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Seok Chan Kim
- Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Yeon Joon Park
- Deparment of Laboratory Medicine, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Young Kyoon Kim
- Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Hwa Sik Moon
- Department of Internal Medicine, St. Paul’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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19
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Al-Mutairi NM, Ahmad S, Mokaddas E, Eldeen HS, Joseph S. Occurrence of disputed rpoB mutations among Mycobacterium tuberculosis isolates phenotypically susceptible to rifampicin in a country with a low incidence of multidrug-resistant tuberculosis. BMC Infect Dis 2019; 19:3. [PMID: 30606116 PMCID: PMC6318973 DOI: 10.1186/s12879-018-3638-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 12/19/2018] [Indexed: 11/17/2022] Open
Abstract
Background Accurate drug susceptibility testing (DST) of Mycobacterium tuberculosis in clinical specimens and culture isolates to first-line drugs is crucial for diagnosis and management of multidrug-resistant tuberculosis (MDR-TB). Resistance of M. tuberculosis to rifampicin is mainly due to mutations in hot-spot region of rpoB gene (HSR-rpoB). The prevalence of disputed (generally missed by rapid phenotypic DST methods) rpoB mutations, which mainly include L511P, D516Y, H526N, H526L, H526S, and L533P in HSR-rpoB and I572F in cluster II region of rpoB gene, is largely unknown. This study determined the occurrence of all disputed mutations in HSR-rpoB and at rpoB codon 572 in M. tuberculosis strains phenotypically susceptible to rifampicin in Kuwait. Methods A total of 242 M. tuberculosis isolates phenotypically susceptible to rifampicin were used. The DST against first-line drugs was performed by Mycobacteria growth indicator tube (MGIT) 960 system. Mutations in HSR-rpoB (and katG codon 315 and inhA-regulatory region for isoniazid resistance) were detected by GenoType MDBDRplus assay. The I572F mutation in cluster II region of rpoB was detected by developing a multiplex allele-specific (MAS)-PCR assay. Results were confirmed by PCR-sequencing of respective loci. Molecular detection of resistance for ethambutol and pyrazinamide and fingerprinting by spoligotyping were also performed for isolates with an rpoB mutation. Results Among 242 rifampicin-susceptible isolates, 0 of 130 pansusceptible/monodrug-resistant isolates but 4 of 112 polydrug-resistant isolates contained a disputed rpoB mutation. All 4 isolates were also resistant to isoniazid and molecular screening identified additional resistance to pyrazinamide and ethambutol in one isolate each. In final analysis, 2 of 4 isolates were resistant to all 4 first-line drugs. Spoligotyping showed that the isolates belonged to different M. tuberculosis lineages. Conclusions Four of 242 (1.7%) rifampicin-susceptible M. tuberculosis isolates contained a disputed rpoB mutation including 2 isolates resistant to all four first-line drugs. The occurrence of a disputed rpoB mutation in polydrug-resistant M. tuberculosis isolates resistant at least to isoniazid (MDR-TB) suggests that polydrug-resistant strains should be checked for genotypic rifampicin resistance for optimal patient management since the failure/relapse rates are nearly same in isolates with a canonical or disputed rpoB mutation.
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Affiliation(s)
- Noura M Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Health Sciences Centre, Kuwait University, P. O. Box 24923, 13110, Safat, Kuwait.,Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
| | | | - Susan Joseph
- Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
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20
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Role of Disputed Mutations in the rpoB Gene in Interpretation of Automated Liquid MGIT Culture Results for Rifampin Susceptibility Testing of Mycobacterium tuberculosis. J Clin Microbiol 2018. [PMID: 29540456 DOI: 10.1128/jcm.01599-17] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Low-level rifampin resistance associated with specific rpoB mutations (referred as "disputed") in Mycobacterium tuberculosis is easily missed by some phenotypic methods. To understand the mechanism by which some mutations are systematically missed by MGIT phenotypic testing, we performed an in silico analysis of their effect on the structural interaction between the RpoB protein and rifampin. We also characterized 24 representative clinical isolates by determining MICs on 7H10 agar and testing them by an extended MGIT protocol. We analyzed 2,097 line probe assays, and 156 (7.4%) cases showed a hybridization pattern referred to here as "no wild type + no mutation." Isolates harboring "disputed" mutations (L430P, D435Y, H445C/L/N/S, and L452P) tested susceptible in MGIT, with prevalence ranging from 15 to 57% (overall, 16 out of 55 isolates [29%]). Our in silico analysis did not highlight any difference between "disputed" and "undisputed" substitutions, indicating that all rpoB missense mutations affect the rifampin binding site. MIC testing showed that "undisputed" mutations are associated with higher MIC values (≥20 mg/liter) compared to "disputed" mutations (4 to >20 mg/liter). Whereas "undisputed" mutations didn't show any delay (Δ) in time to positivity of the test tube compared to the control tube on extended MGIT protocol, "disputed" mutations showed a mean Δ of 7.2 days (95% confidence interval [CI], 4.2 to 10.2 days; P < 0.05), providing evidence that mutations conferring low-level resistance are associated with a delay in growth on MGIT. Considering the proved relevance of L430P, D435Y, H445C/L/N, and L452P mutations in determining clinical resistance, genotypic drug susceptibility testing (DST) should be used to replace phenotypic results (MGIT) when such mutations are found.
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21
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Increased Tuberculosis Patient Mortality Associated with Mycobacterium tuberculosis Mutations Conferring Resistance to Second-Line Antituberculous Drugs. J Clin Microbiol 2017; 55:1928-1937. [PMID: 28404672 DOI: 10.1128/jcm.00152-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/04/2017] [Indexed: 12/22/2022] Open
Abstract
Rapid molecular diagnostics have great potential to limit the spread of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) (M/XDR-TB). These technologies detect mutations in the Mycobacterium tuberculosis genome that confer phenotypic drug resistance. However, there have been few data published regarding the relationships between the detected M. tuberculosis resistance mutations and M/XDR-TB treatment outcomes, limiting our current ability to exploit the full potential of molecular diagnostics. We analyzed clinical, microbiological, and sequencing data for 451 patients and their clinical isolates collected in a multinational, observational cohort study to determine if there was an association between M. tuberculosis resistance mutations and patient mortality. The presence of an rrs 1401G mutation was associated with significantly higher odds of patient mortality (adjusted odds ratio [OR] = 5.72; 95% confidence interval [CI], 1.65 to 19.84]) after adjusting for relevant patient clinical characteristics and all other resistance mutations. Further analysis of mutations, categorized by the associated resistance level, indicated that the detection of mutations associated with high-level fluoroquinolone (OR, 3.99 [95% CI, 1.10 to 14.40]) and kanamycin (OR, 5.47 [95% CI, 1.64 to 18.24]) resistance was also significantly associated with higher odds of patient mortality, even after accounting for clinical site, patient age, reported smoking history, body mass index (BMI), diabetes, HIV, and all other resistance mutations. Specific gyrA and rrs resistance mutations, associated with high-level resistance, were associated with patient mortality as identified in clinical M. tuberculosis isolates from a diverse M/XDR-TB patient population at three high-burden clinical sites. These results have important implications for the interpretation of molecular diagnostics, including identifying patients at increased risk for mortality during treatment. (This study has been registered at ClinicalTrials.gov under registration no. NCT02170441.).
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Isoniazid-resistant tuberculosis treatment with first-line drugs. THE LANCET. INFECTIOUS DISEASES 2017; 17:258-259. [DOI: 10.1016/s1473-3099(17)30075-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/10/2017] [Indexed: 11/18/2022]
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A Comparison of the Sensititre MycoTB Plate, the Bactec MGIT 960, and a Microarray-Based Molecular Assay for the Detection of Drug Resistance in Clinical Mycobacterium tuberculosis Isolates in Moscow, Russia. PLoS One 2016; 11:e0167093. [PMID: 27902737 PMCID: PMC5130259 DOI: 10.1371/journal.pone.0167093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/07/2016] [Indexed: 12/01/2022] Open
Abstract
Background The goal of this study was to compare the consistency of three assays for the determination of the drug resistance of Mycobacterium tuberculosis (MTB) strains with various resistance profiles isolated from the Moscow region. Methods A total of 144 MTB clinical isolates with a strong bias toward drug resistance were examined using Bactec MGIT 960, Sensititre MycoTB, and a microarray-based molecular assay TB-TEST to detect substitutions in the rpoB, katG, inhA, ahpC, gyrA, gyrB, rrs, eis, and embB genes that are associated with resistance to rifampin, isoniazid, fluoroquinolones, second-line injectable drugs and ethambutol. Results The average correlation for the identification of resistant and susceptible isolates using the three methods was approximately 94%. An association of mutations detected with variable resistance levels was shown. We propose a change in the breakpoint minimal inhibitory concentration for kanamycin to less than 5 μg/ml in the Sensititre MycoTB system. A pairwise comparison of the minimal inhibitory concentrations (MICs) of two different drugs revealed an increased correlation in the first-line drug group and a partial correlation in the second-line drug group, reflecting the history of the preferential simultaneous use of drugs from these groups. An increased correlation with the MICs was also observed for drugs sharing common resistance mechanisms. Conclusions The quantitative measures of phenotypic drug resistance produced by the Sensititre MycoTB and the timely detection of mutations using the TB-TEST assay provide guidance for clinicians for the choice of the appropriate drug regimen.
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