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Rufai SB, Kumar P, Singh A, Prajapati S, Balooni V, Singh S. Comparison of Xpert MTB/RIF with line probe assay for detection of rifampin-monoresistant Mycobacterium tuberculosis. J Clin Microbiol 2014; 52:1846-52. [PMID: 24648554 PMCID: PMC4042801 DOI: 10.1128/jcm.03005-13] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The MTBDRplus line probe assay (LPA) and Xpert MTB/RIF have been endorsed by the World Health Organization for the rapid diagnosis of drug-resistant tuberculosis. However, there is no clarity regarding the superiority of one over the other. In a double-blinded prospective study, we evaluated the efficacy of the Xpert MTB/RIF on samples that were first tested by LPA under the revised national tuberculosis control program of India. A total of 405 sputum samples from suspected drug-resistant tuberculosis patients were included. Of these, 285 smear-positive samples were subjected to LPA. Seventy-two (25.8%) samples showed multidrug resistance, 62 (22.2%) showed rifampin monoresistance, 29 (10.3%) showed isoniazid monoresistance, and 116 (41.5%) were pan-susceptible. Six (2.1%) of the samples gave invalid results. Of the 62 rifampin-monoresistant samples by LPA, 38 (61.4%) showed rifampin resistance, while 21 (33.8%) were found susceptible to rifampin by Xpert MTB/RIF using cartridge version G4. Three (4.8%) samples gave an error. Of the 116 pan-susceptible samples, only 83 were available for Xpert MTB/RIF testing; 4 (5.1%) were rifampin resistant, 74 (94.8%) were susceptible, and 5 (6.0%) showed an error. The 25 discrepant samples were further subjected to MGIT960 drug susceptibility testing. The MGIT960 results showed 100% agreement with LPA results but only 64.4% agreement with Xpert MTB/RIF results. Sequencing analysis of discrepant samples showed 91.3% concordance with LPA but only 8.7% concordance with the Xpert MTB/RIF assay. These findings indicate that by using Xpert MTB/RIF testing we might be underestimating the burden of drug-resistant tuberculosis and indicate that country-specific probes need to be designed to increase the sensitivity of the Xpert MTB/RIF.
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Affiliation(s)
- Syed Beenish Rufai
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Parveen Kumar
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Amit Singh
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Suneel Prajapati
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Veena Balooni
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
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Ferreira Junior SLM, Dalla Costa ER, Santos PGD, Gomes HM, Silva MSN, Esteves LS, Oliveira MM, Maschmann RDA, Kritski AL, Suffys PN, Rossetti MLR. In house reverse membrane hybridisation assay versus GenoType MTBDRplus and their performance to detect mutations in the genes rpoB, katG and inhA. Mem Inst Oswaldo Cruz 2014; 109:307-14. [PMID: 24821057 PMCID: PMC4131782 DOI: 10.1590/0074-0276130469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 01/15/2014] [Indexed: 02/04/2023] Open
Abstract
Drug-resistant tuberculosis (TB) threatens global TB control and is a major public
health concern in several countries. We therefore developed a multiplex assay
(LINE-TB/MDR) that is able to identify the most frequent mutations related to
rifampicin (RMP) and isoniazid (INH) resistance. The assay is based on multiplex
polymerase chain reaction, membrane hybridisation and colorimetric detection
targeting of rpoB and katG genes, as well as the
inhA promoter, which are all known to carry specific mutations
associated with multidrug-resistant TB (MDR-TB). The assay was validated on a
reference panel of 108 M. tuberculosis isolates that were characterised by the
proportion method and by DNA sequencing of the targets. When comparing the
performance of LINE-TB/MDR with DNA sequencing, the sensitivity, specificity and
agreement were 100%, 100% and 100%, respectively, for RMP and 77.6%, 90.6% and 88.9%,
respectively, for INH. Using drug sensibility testing as a reference standard, the
performance of LINE-TB/MDR regarding sensitivity, specificity and agreement was 100%,
100% and 100% (95%), respectively, for RMP and 77%, 100% and 88.7% (82.2-95.1),
respectively, for INH. LINE-TB/MDR was compared with GenoType MTBDRplus for 65
isolates, resulting in an agreement of 93.6% (86.7-97.5) for RIF and 87.4%
(84.3-96.2) for INH. LINE-TB/MDR warrants further clinical validation and may be an
affordable alternative for MDR-TB diagnosis.
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Affiliation(s)
| | - Elis Regina Dalla Costa
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil
| | - Paula Gonçalves dos Santos
- Instituto de Doenças do Tórax, Hospital Universitário Clementino Fraga Filho, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Harrison Magdinier Gomes
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Marcia Susana Nunes Silva
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil
| | - Leonardo Souza Esteves
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil
| | - Martha Maria Oliveira
- Instituto de Doenças do Tórax, Hospital Universitário Clementino Fraga Filho, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Raquel de Abreu Maschmann
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil
| | - Afrânio Lineu Kritski
- Instituto de Doenças do Tórax, Hospital Universitário Clementino Fraga Filho, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Maria Lucia Rosa Rossetti
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil
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Sequence analysis for detection of drug resistance in Mycobacterium tuberculosis complex isolates from the Central Region of Cameroon. BMC Microbiol 2014; 14:113. [PMID: 24884632 PMCID: PMC4017682 DOI: 10.1186/1471-2180-14-113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/29/2014] [Indexed: 11/22/2022] Open
Abstract
Background The potential of genetic testing to rapidly diagnose drug resistance has lead to the development of new diagnostic assays. However, prior to implementation in a given setting, the association of specific mutations with specific drug resistance phenotypes should be evaluated. The purpose of this study was to evaluate molecular markers in predicting drug resistance in the Central Region of Cameroon. Results From April 2010 and March 2011, 725 smear positive pulmonary tuberculosis patients were enrolled and all positive cultures were tested for drug susceptibility. A total of 63 drug resistant and 100 drug sensitive Mycobacterium tuberculosis complex clinical isolates were screened for genetic mutations in katG, inhA, ahpC, rpoB, rpsL, rrs, gidB and embCAB loci using DNA sequencing. Of the 44 isoniazid resistant (INHR) isolates (24 high level, 1 μg/ml and 20 low level, 0.2 μg/ml), 73% (32/44) carried the katG315 and/or the -15 inhA promoter mutations. Of the 24 high level INHR, 17 (70.8%) harbored katG315 mutation, 1 a point mutation (-15C → T) in the inhA promoter and 6 were (25.0%) wild types. Thus, for INHR high level detection, katG315 mutation had a specificity and a sensitivity of 100% and 70.8% respectively. Of the 20 low level INHR, 10 (50.0%) had a -15C → T mutation in the inhA promoter region, and 1 (2.2%) a -32G → A mutation in the ahpC promoter region. All of the 7 rifampicin resistant (RIFR) isolates carried mutations in the rpoB gene (at codons Ser531Leu (71.4%), His526Asp (14.3%), and Asp516Val (14.3%)). Of the 27 streptomycin resistant (SMR) isolates, 7 carried mutations at the rpsL and the gidB genes. 1 of the 2 ethambutol resistant (EMBR) isolates displayed a mutation in embB gene. Conclusion This study provided the first molecular investigation assessing the correlation of phenotypic to genotypic characteristics on MTB isolates from the Central Region of Cameroon using DNA sequencing. Mutations on rpoB, katG315 and -15 point mutations in inhA promoter loci could be used as markers for RIF and INH -resistance detection respectively.
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Wang H, Zhang X, Luo T, Li X, Tian P, Xu Y, Gao Q. Prediction of XDR/pre-XDR tuberculosis by genetic mutations among MDR cases from a hospital in Shandong, China. Tuberculosis (Edinb) 2014; 94:277-81. [DOI: 10.1016/j.tube.2014.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/10/2014] [Accepted: 03/20/2014] [Indexed: 11/17/2022]
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Zimenkov DV, Kulagina EV, Antonova OV, Surzhikov SA, Bespyatykh YA, Shitikov EA, Ilina EN, Mikhailovich VM, Zasedatelev AS, Gryadunov DA. Analysis of the genetic determinants of multidrug and extensive drug resistance in Mycobacterium tuberculosis with the use of an oligonucleotide microchip. Mol Biol 2014. [DOI: 10.1134/s0026893314020186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Moure R, Espanol M, Tudo G, Vicente E, Coll P, Gonzalez-Martin J, Mick V, Salvado M, Alcaide F. Characterization of the embB gene in Mycobacterium tuberculosis isolates from Barcelona and rapid detection of main mutations related to ethambutol resistance using a low-density DNA array--authors' response. J Antimicrob Chemother 2014; 69:2299-300. [DOI: 10.1093/jac/dku134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Köser CU, Bryant JM, Comas I, Feuerriegel S, Niemann S, Gagneux S, Parkhill J, Peacock SJ. Comment on: characterization of the embB gene in Mycobacterium tuberculosis isolates from Barcelona and rapid detection of main mutations related to ethambutol resistance using a low-density DNA array. J Antimicrob Chemother 2014; 69:2298-9. [PMID: 24752956 PMCID: PMC4100706 DOI: 10.1093/jac/dku101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Claudio U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Iñaki Comas
- Genomics and Health Unit, FISABIO, Valencia, Spain CIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Barcelona, Spain
| | - Silke Feuerriegel
- Molecular Mycobacteriology, Borstel, Germany German Centre for Infection Research, Research Centre Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular Mycobacteriology, Borstel, Germany German Centre for Infection Research, Research Centre Borstel, Borstel, Germany
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland University of Basel, Basel, Switzerland
| | | | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Hinxton, UK Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Aubry A, Sougakoff W, Bodzongo P, Delcroix G, Armand S, Millot G, Jarlier V, Courcol R, Lemaître N. First evaluation of drug-resistant Mycobacterium tuberculosis clinical isolates from Congo revealed misdetection of fluoroquinolone resistance by line probe assay due to a double substitution T80A-A90G in GyrA. PLoS One 2014; 9:e95083. [PMID: 24743770 PMCID: PMC3990612 DOI: 10.1371/journal.pone.0095083] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/21/2014] [Indexed: 11/26/2022] Open
Abstract
Background Tuberculosis (TB) is one of the major public health problems in Congo. However, data concerning Mycobacterium tuberculosis drug resistance are lacking because of the insufficient processing capacity. So, the aim of this study was to investigate for the first time the resistance patterns and the strain lineages of a sample of M. tuberculosis complex (MTBC) isolates collected in the two main cities of Congo. Methods Over a 9-day period, 114 smear-positive sputa isolated from 114 patients attending centers for the diagnosis and treatment of TB in Brazzaville and Pointe Noire were collected for culture and drug susceptibility testing (DST). Detection of mutations conferring drug resistance was performed by using line probe assays (GenoType MTBDRplus and MTBDRsl) and DNA sequencing. Strain lineages were determined by MIRU-VNTR genotyping. Results Of the 114 sputa, 46 were culture positive for MTBC. Twenty-one (46%) were resistant to one or more first-line antiTB drugs. Of these, 15 (71%) were multidrug resistant (MDR). The most prevalent mutations involved in rifampin and isoniazid resistance, D516V (60%) in rpoB and S315T (87%) in katG respectively, were well detected by MTBDRplus assay. All the 15 MDR strains were susceptible to fluoroquinolone and injectable second-line drug. No mutation was detected in the rrs locus involved in resistance to amikacin and capreomycin by both the MTBDRsl assay and DNA sequencing. By contrast, 9 MDR strains belonging to the same cluster related to T-family were identified as being falsely resistant to fluoroquinolone by the MTBDRsl assay due to the presence of a double substitution T80A-A90G in GyrA. Conclusions Taken together, these data revealed a possible spread of a particular MDR clone in Congo, misidentified as fluoroquinolone resistant by MTBDRsl assay. Thus, this test cannot replace gold-standard culture method and should be interpreted carefully in view of the patient's native land.
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Affiliation(s)
- Alexandra Aubry
- UPMC Université, Paris, France
- INSERM U1135, Paris, France
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Wladimir Sougakoff
- UPMC Université, Paris, France
- INSERM U1135, Paris, France
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | | | - Guy Delcroix
- Laboratoire de Bactériologie-Hygiène du CHRU, Lille, France
| | - Sylvie Armand
- Laboratoire de Bactériologie-Hygiène du CHRU, Lille, France
| | - Gérald Millot
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Vincent Jarlier
- UPMC Université, Paris, France
- INSERM U1135, Paris, France
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - René Courcol
- Laboratoire de Bactériologie-Hygiène du CHRU, Lille, France
- Université Lille Nord de France, Lille, France
- UDSL, F-59000 Lille, France
- INSERM U1019-UMR8204, Lille, France
| | - Nadine Lemaître
- Laboratoire de Bactériologie-Hygiène du CHRU, Lille, France
- Université Lille Nord de France, Lille, France
- UDSL, F-59000 Lille, France
- INSERM U1019-UMR8204, Lille, France
- * E-mail:
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Flandrois JP, Lina G, Dumitrescu O. MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis. BMC Bioinformatics 2014; 15:107. [PMID: 24731071 PMCID: PMC4021062 DOI: 10.1186/1471-2105-15-107] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/07/2014] [Indexed: 11/29/2022] Open
Abstract
Background Tuberculosis is an infectious bacterial disease caused by Mycobacterium tuberculosis. It remains a major health threat, killing over one million people every year worldwide. An early antibiotic therapy is the basis of the treatment, and the emergence and spread of multidrug and extensively drug-resistant mutant strains raise significant challenges. As these bacteria grow very slowly, drug resistance mutations are currently detected using molecular biology techniques. Resistance mutations are identified by sequencing the resistance-linked genes followed by a comparison with the literature data. The only online database is the TB Drug Resistance Mutation database (TBDReaM database); however, it requires mutation detection before use, and its interrogation is complex due to its loose syntax and grammar. Description The MUBII-TB-DB database is a simple, highly structured text-based database that contains a set of Mycobacterium tuberculosis mutations (DNA and proteins) occurring at seven loci: rpoB, pncA, katG; mabA(fabG1)-inhA, gyrA, gyrB, and rrs. Resistance mutation data were extracted after the systematic review of MEDLINE referenced publications before March 2013. MUBII analyzes the query sequence obtained by PCR-sequencing using two parallel strategies: i) a BLAST search against a set of previously reconstructed mutated sequences and ii) the alignment of the query sequences (DNA and its protein translation) with the wild-type sequences. The post-treatment includes the extraction of the aligned sequences together with their descriptors (position and nature of mutations). The whole procedure is performed using the internet. The results are graphs (alignments) and text (description of the mutation, therapeutic significance). The system is quick and easy to use, even for technicians without bioinformatics training. Conclusion MUBII-TB-DB is a structured database of the mutations occurring at seven loci of major therapeutic value in tuberculosis management. Moreover, the system provides interpretation of the mutations in biological and therapeutic terms and can evolve by the addition of newly described mutations. Its goal is to provide easy and comprehensive access through a client–server model over the Web to an up-to-date database of mutations that lead to the resistance of M. tuberculosis to antibiotics.
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Affiliation(s)
- Jean-Pierre Flandrois
- Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd, du 11 Novembre 1918, 69622 Villeurbanne Cedex, France.
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Prevalence and molecular characteristics of drug-resistant Mycobacterium tuberculosis in Hunan, China. Antimicrob Agents Chemother 2014; 58:3475-80. [PMID: 24733464 DOI: 10.1128/aac.02426-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To determine the prevalence and molecular characteristics of drug-resistant tuberculosis in Hunan province, drug susceptibility testing and spoligotyping methods were performed among 171 M. tuberculosis isolates. In addition, the mutated characteristics of 12 loci, including katG, inhA, rpoB, rpsL, nucleotides 388 to 1084 of the rrs gene [rrs(388-1084)], embB, pncA, tlyA, eis, nucleotides 1158 to 1674 of the rrs gene [rrs(1158-1674)], gyrA, and gyrB, among drug-resistant isolates were also analyzed by DNA sequencing. Our results indicated that the prevalences of isoniazid (INH), rifampin (RIF), streptomycin (SM), ethambutol (EMB), pyrazinamide (PZA), capreomycin (CAP), kanamycin (KAN), amikacin (AKM), and ofloxacin (OFX) resistance in Hunan province were 35.7%, 26.9%, 20.5%, 9.9% 15.2%, 2.3%, 1.8%, 1.2%, and 10.5%, respectively. The previously treated patients presented significantly increased risks for developing drug resistance. The majority of M. tuberculosis isolates belonged to the Beijing family. Almost all the drug resistance results demonstrated no association with genotype. The most frequent mutations of drug-resistant isolates were katG codon 315 (katG315), inhA15, rpoB531, rpoB526, rpoB516, rpsL43, rrs514, embB306, pncA96, rrs1401, gyrA94, and gyrA90. These results contribute to the knowledge of the prevalence of drug resistance in Hunan province and also expand the molecular characteristics of drug resistance in China.
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Zhdanova S, Heysell SK, Ogarkov O, Boyarinova G, Alexeeva G, Pholwat S, Zorkaltseva E, Houpt ER, Savilov E. Primary multidrug-resistant Mycobacterium tuberculosis in 2 regions, Eastern Siberia, Russian Federation. Emerg Infect Dis 2014; 19:1649-52. [PMID: 24047678 PMCID: PMC3810730 DOI: 10.3201/eid1910.121108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Of 235 Mycobacterium tuberculosis isolates from patients who had not received tuberculosis treatment in the Irkutsk oblast and the Sakha Republic (Yakutia), eastern Siberia, 61 (26%) were multidrug resistant. A novel strain, S 256, clustered among these isolates and carried eis-related kanamycin resistance, indicating a need for locally informed diagnosis and treatment strategies.
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213
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Tsodikov OV, Green KD, Garneau-Tsodikova S. A random sequential mechanism of aminoglycoside acetylation by Mycobacterium tuberculosis Eis protein. PLoS One 2014; 9:e92370. [PMID: 24699000 PMCID: PMC3974725 DOI: 10.1371/journal.pone.0092370] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 02/20/2014] [Indexed: 11/17/2022] Open
Abstract
An important cause of bacterial resistance to aminoglycoside antibiotics is the enzymatic acetylation of their amino groups by acetyltransferases, which abolishes their binding to and inhibition of the bacterial ribosome. Enhanced intracellular survival (Eis) protein from Mycobacterium tuberculosis (Mt) is one of such acetyltransferases, whose upregulation was recently established as a cause of resistance to aminoglycosides in clinical cases of drug-resistant tuberculosis. The mechanism of aminoglycoside acetylation by MtEis is not completely understood. A systematic analysis of steady-state kinetics of acetylation of kanamycin A and neomycin B by Eis as a function of concentrations of these aminoglycosides and the acetyl donor, acetyl coenzyme A, reveals that MtEis employs a random-sequential bisubstrate mechanism of acetylation and yields the values of the kinetic parameters of this mechanism. The implications of these mechanistic properties for the design of inhibitors of Eis and other aminoglycoside acetyltransferases are discussed.
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Affiliation(s)
- Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, BioPharm Complex, Lexington, Kentucky, United States of America
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, BioPharm Complex, Lexington, Kentucky, United States of America
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, BioPharm Complex, Lexington, Kentucky, United States of America
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Concordance between molecular and phenotypic testing of Mycobacterium tuberculosis complex isolates for resistance to rifampin and isoniazid in the United States. J Clin Microbiol 2014; 52:1932-7. [PMID: 24648563 DOI: 10.1128/jcm.00417-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug-resistant (MDR) isolates of Mycobacterium tuberculosis complex (MTBC) are defined by resistance to at least rifampin (RMP) and isoniazid (INH). Rapid and accurate detection of multidrug resistance is essential for effective treatment and interruption of disease transmission of tuberculosis (TB). Overdiagnosis of MDR TB may result in treatment with second-line drugs that are more costly, less effective, and more poorly tolerated than first-line drugs. CDC offers rapid confirmation of MDR TB by the molecular detection of drug resistance (MDDR) for mutations associated with resistance to RMP and INH along with analysis for resistance to other first-line and second-line drugs. Simultaneously, CDC does growth-based phenotypic drug susceptibility testing (DST) by the indirect agar proportion method for a panel of first-line and second-line antituberculosis drugs. We reviewed discordance between molecular and phenotypic DST for INH and RMP for 285 isolates submitted as MTBC to CDC from September 2009 to February 2011. We compared CDC's results with those from the submitting public health laboratories (PHL). Concordances between molecular and phenotypic testing at CDC were 97.4% for RMP and 92.5% for INH resistance. Concordances between CDC's molecular testing and PHL DST results were 93.9% for RMP and 90.0% for INH. Overall concordance between CDC molecular and PHL DST results was 91.7% for RMP and INH collectively. Discordance was primarily attributable to the absence of known INH resistance mutations in isolates found to be INH resistant by DST and detection of mutations associated with low-level RMP resistance in isolates that were RMP susceptible by phenotypic DST. Both molecular and phenotypic test results should be considered for the diagnosis of MDR TB.
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Lu J, Liu M, Wang Y, Pang Y, Zhao Z. Mechanisms of fluoroquinolone monoresistance inMycobacterium tuberculosis. FEMS Microbiol Lett 2014; 353:40-8. [DOI: 10.1111/1574-6968.12401] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jie Lu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery; Beijing Pediatric Research Institute; Beijing Children's Hospital affiliated to Capital Medical University; Beijing China
- National Center for Tuberculosis Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing China
| | - Min Liu
- Liaoning Provincial Center for Disease Control and Prevention; Shenyang China
| | - Yufeng Wang
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery; Beijing Pediatric Research Institute; Beijing Children's Hospital affiliated to Capital Medical University; Beijing China
| | - Yu Pang
- National Center for Tuberculosis Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing China
| | - Zhuo Zhao
- Liaoning Provincial Center for Disease Control and Prevention; Shenyang China
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Rodwell TC, Valafar F, Douglas J, Qian L, Garfein RS, Chawla A, Torres J, Zadorozhny V, Kim MS, Hoshide M, Catanzaro D, Jackson L, Lin G, Desmond E, Rodrigues C, Eisenach K, Victor TC, Ismail N, Crudu V, Gler MT, Catanzaro A. Predicting extensively drug-resistant Mycobacterium tuberculosis phenotypes with genetic mutations. J Clin Microbiol 2014; 52:781-9. [PMID: 24353002 PMCID: PMC3957771 DOI: 10.1128/jcm.02701-13] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/12/2013] [Indexed: 01/20/2023] Open
Abstract
Molecular diagnostic methods based on the detection of mutations conferring drug resistance are promising technologies for rapidly detecting multidrug-/extensively drug-resistant tuberculosis (M/XDR TB), but large studies of mutations as markers of resistance are rare. The Global Consortium for Drug-Resistant TB Diagnostics analyzed 417 Mycobacterium tuberculosis isolates from multinational sites with a high prevalence of drug resistance to determine the sensitivities and specificities of mutations associated with M/XDR TB to inform the development of rapid diagnostic methods. We collected M/XDR TB isolates from regions of high TB burden in India, Moldova, the Philippines, and South Africa. The isolates underwent standardized phenotypic drug susceptibility testing (DST) to isoniazid (INH), rifampin (RIF), moxifloxacin (MOX), ofloxacin (OFX), amikacin (AMK), kanamycin (KAN), and capreomycin (CAP) using MGIT 960 and WHO-recommended critical concentrations. Eight genes (katG, inhA, rpoB, gyrA, gyrB, rrs, eis, and tlyA) were sequenced using Sanger sequencing. Three hundred seventy isolates were INHr, 356 were RIFr, 292 were MOXr/OFXr, 230 were AMKr, 219 were CAPr, and 286 were KANr. Four single nucleotide polymorphisms (SNPs) in katG/inhA had a combined sensitivity of 96% and specificities of 97 to 100% for the detection of INHr. Eleven SNPs in rpoB had a combined sensitivity of 98% for RIFr. Eight SNPs in gyrA codons 88 to 94 had sensitivities of 90% for MOXr/OFXr. The rrs 1401/1484 SNPs had 89 to 90% sensitivity for detecting AMKr/CAPr but 71% sensitivity for KANr. Adding eis promoter SNPs increased the sensitivity to 93% for detecting AMKr and to 91% for detecting KANr. Approximately 30 SNPs in six genes predicted clinically relevant XDR-TB phenotypes with 90 to 98% sensitivity and almost 100% specificity.
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Affiliation(s)
- Timothy C. Rodwell
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Faramarz Valafar
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - James Douglas
- Department of Microbiology, University of Hawaii Manoa, Honolulu, Hawaii, USA
| | - Lishi Qian
- Department of Microbiology, University of Hawaii Manoa, Honolulu, Hawaii, USA
| | - Richard S. Garfein
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Ashu Chawla
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Jessica Torres
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Victoria Zadorozhny
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Min Soo Kim
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Matt Hoshide
- Department of Microbiology, University of Hawaii Manoa, Honolulu, Hawaii, USA
| | - Donald Catanzaro
- Department of Bioinformatics and Medical Informatics, San Diego State University, San Diego, California, USA
| | - Lynn Jackson
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Grace Lin
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | - Edward Desmond
- California Department of Public Health, Microbial Diseases Laboratory, Richmond, California, USA
| | | | - Kathy Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Thomas C. Victor
- Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nazir Ismail
- National Tuberculosis Reference Laboratory, Johannesburg, South Africa
| | - Valeru Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | | | - Antonino Catanzaro
- Department of Medicine, University of California San Diego, San Diego, California, USA
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217
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Evidence of Clonal Expansion in the Genome of a Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolate from Peru. GENOME ANNOUNCEMENTS 2014; 2:2/1/e00089-14. [PMID: 24578270 PMCID: PMC3937606 DOI: 10.1128/genomea.00089-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report the genome sequence of Mycobacterium tuberculosis INS-MDR from Peru, a multidrug-resistant tuberculosis (MDR-TB) and Latin American-Mediterranean (LAM) lineage strain. Our analysis showed mutations related to drug resistance in the rpoB (D516V), katG (S315T), kasA (G269S), and pncA (Q10R) genes. Our evidence suggests that INS-MDR may be a clonal expansion related to the African strain KZN 1435.
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218
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Molecular characterization of multidrug-resistant Mycobacterium tuberculosis isolates from China. Antimicrob Agents Chemother 2014; 58:1997-2005. [PMID: 24419342 DOI: 10.1128/aac.01792-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To investigate the molecular characterization of multidrug-resistant tuberculosis (MDR-TB) isolates from China and the association of specific mutations conferring drug resistance with strains of different genotypes, we performed spoligotyping and sequenced nine loci (katG, inhA, the oxyR-ahpC intergenic region, rpoB, tlyA, eis, rrs, gyrA, and gyrB) for 128 MDR-TB isolates. Our results showed that 108 isolates (84.4%) were Beijing family strains, 64 (59.3%) of which were identified as modern Beijing strains. Compared with the phenotypic data, the sensitivity and specificity of DNA sequencing were 89.1% and 100.0%, respectively, for isoniazid (INH) resistance, 93.8% and 100.0% for rifampin (RIF) resistance, 60.0% and 99.4% for capreomycin (CAP) resistance, 84.6% and 99.4% for kanamycin (KAN) resistance, and 90.0% and 100.0% for ofloxacin (OFX) resistance. The most prevalent mutations among the MDR-TB isolates were katG315, inhA15, rpoB531, -526, and -516, rrs1401, eis-10, and gyrA94, -90, and -91. Furthermore, there was no association between specific resistance-conferring mutations and the strain genotype. These findings will be helpful for the establishment of rapid molecular diagnostic methods to be implemented in China.
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219
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Kim CK, Lee BS, Choi MJ, Kim HJ, Lee K. Molecular Detection of Fluoroquinolone Resistance in Multidrug-ResistantMycobacterium tuberculosisIsolates. ANNALS OF CLINICAL MICROBIOLOGY 2014. [DOI: 10.5145/acm.2014.17.3.80] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Chang-Ki Kim
- Korean Institute of Tuberculosis, Yonsei University College of Medicine, Seoul, Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Byung Soo Lee
- Korean Institute of Tuberculosis, Yonsei University College of Medicine, Seoul, Korea
| | - Myung Joon Choi
- Korean Institute of Tuberculosis, Yonsei University College of Medicine, Seoul, Korea
| | - Hee Jin Kim
- Korean Institute of Tuberculosis, Yonsei University College of Medicine, Seoul, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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220
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Pholwat S, Stroup S, Gratz J, Trangan V, Foongladda S, Kumburu H, Juma SP, Kibiki G, Houpt E. Pyrazinamide susceptibility testing of Mycobacterium tuberculosis by high resolution melt analysis. Tuberculosis (Edinb) 2014; 94:20-5. [PMID: 24246607 PMCID: PMC3877170 DOI: 10.1016/j.tube.2013.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/19/2013] [Accepted: 10/24/2013] [Indexed: 11/17/2022]
Abstract
Pyrazinamide (PZA) plays the important role in shortening the tuberculosis treatment period and in treating MDR-TB. Phenotypic PZA susceptibility methods are limited because they require specialized acidified media, which increases costs and complexity. In this study we developed a genotypic high resolution melt (HRM) analysis technique to detect pncA mutations associated with PZA resistant Mycobacterium tuberculosis. Seven overlapping primer pairs were designed to cover the entire pncA gene and upstream regions. Each gene segment was individually amplified by real-time PCR followed by HRM analysis. The assay was evaluated on 98 clinical M. tuberculosis isolates (41 PZA susceptible by MGIT method, 55 PZA resistant, 2 undetermined). HRM was 94% concordant to full-length sequencing results, with most discrepancies attributable to mixed populations per HRM or transversions. Sequencing and HRM yielded 82% and 84% concordance, respectively, to phenotypic PZA susceptibilities by MGIT, with most discrepancies attributable to isolates with wild-type pncA but phenotypic PZA resistance. This HRM technique is a simple and high-throughput method for screening clinical M. tuberculosis samples for PZA resistance.
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Affiliation(s)
- Suporn Pholwat
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Suzanne Stroup
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jean Gratz
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Varittha Trangan
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suporn Foongladda
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
| | - Saumu Pazia Juma
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
| | - Gibson Kibiki
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
| | - Eric Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
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221
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Kumar P, Balooni V, Sharma BK, Kapil V, Sachdeva KS, Singh S. High degree of multi-drug resistance and hetero-resistance in pulmonary TB patients from Punjab state of India. Tuberculosis (Edinb) 2014; 94:73-80. [PMID: 24184256 DOI: 10.1016/j.tube.2013.10.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 10/03/2013] [Accepted: 10/14/2013] [Indexed: 02/07/2023]
Abstract
Line Probe Assays (LPAs) have been recommended for rapid screening of MDR-TB. Aims of this study were (1) to compare the performance of LPA with standard Bactec MGIT 960 system and (2) to ascertain the pattern of genetic mutations in the resistance isolates. In phase I, a total of 141 Mycobacterium tuberculosis isolates from our routine laboratory were tested by LPA and Bactec MGIT 960 for DST. In phase II, 578 sputum specimens of suspected DR-TB patients were received from the Punjab state of India. Of them 438 specimens or their cultures were subjected to LPA. The presence of mutant bands with their corresponding wild type band was identified as "hetero-resistance". In phase I, LPA showed high concordance with 96.4% positive agreement and 97.6% negative agreement with Bactec MGIT 960-DST. In phase II, 12 (2.7%) specimens were detected as invalid by LPA. Of the remaining 426 specimens, 184 (43.1%) had resistance to RIF and 142 (33.3%) to INH while 103 (24.1%) specimens showed resistance to both INH and RIF (MDR-TB) by LPA. Of the 142 INH resistant, 113 (79.5%) showed mutations in katG and 29 (20.4%) in inhA. A high rate of hetero-resistance pattern was observed in rpoB gene (28.8%) and katG gene (9.8%). The most frequent mutation was S531L (81.1%) in rpoB region and S315T1 (100%) in katG gene.
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MESH Headings
- Antitubercular Agents/pharmacology
- Bacterial Proteins/genetics
- Catalase/genetics
- DNA-Directed RNA Polymerases
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Drug Resistance, Multiple, Bacterial/immunology
- Female
- Humans
- India
- Male
- Microbial Sensitivity Tests
- Molecular Diagnostic Techniques
- Mutation
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Sequence Analysis, DNA
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/genetics
- Tuberculosis, Multidrug-Resistant/immunology
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/genetics
- Tuberculosis, Pulmonary/immunology
- White People/genetics
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Affiliation(s)
- Parveen Kumar
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Veena Balooni
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Brijesh Kumar Sharma
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Virender Kapil
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - K S Sachdeva
- Central TB Division, Directorate General of Health Services, Ministry of Health and Family Welfare, Government of India, New Delhi, India
| | - Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi 110 029, India.
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222
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Ethambutol resistance as determined by broth dilution method correlates better than sequencing results with embB mutations in multidrug-resistant Mycobacterium tuberculosis isolates. J Clin Microbiol 2013; 52:638-41. [PMID: 24478502 DOI: 10.1128/jcm.02713-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated the correlation of phenotypic ethambutol (EMB) susceptibility as determined by two drug susceptibility methods with embB mutations in multidrug-resistant (MDR) Mycobacterium tuberculosis strains. The concordance rate for EMB resistance between broth dilution method and sequencing results (83.6%) was significantly higher than between the proportion method and sequencing results (61.7%) (P = 0.004). Of the embB mutants, 75.4% (46/61) possessed a mutation at embB306. Our results demonstrated that ethambutol resistance determined by broth dilution method reveals better correlation with embB mutations than the proportion method in MDR isolates.
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223
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Pyrosequencing for rapid detection of extensively drug-resistant Mycobacterium tuberculosis in clinical isolates and clinical specimens. J Clin Microbiol 2013; 52:475-82. [PMID: 24478476 DOI: 10.1128/jcm.01821-13] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Treating extensively drug-resistant (XDR) tuberculosis (TB) is a serious challenge. Culture-based drug susceptibility testing (DST) may take 4 weeks or longer from specimen collection to the availability of results. We developed a pyrosequencing (PSQ) assay including eight subassays for the rapid identification of Mycobacterium tuberculosis complex (MTBC) and concurrent detection of mutations associated with resistance to drugs defining XDR TB. The entire procedure, from DNA extraction to the availability of results, was accomplished within 6 h. The assay was validated for testing clinical isolates and clinical specimens, which improves the turnaround time for molecular DST and maximizes the benefit of using molecular testing. A total of 130 clinical isolates and 129 clinical specimens were studied. The correlations between the PSQ results and the phenotypic DST results were 94.3% for isoniazid, 98.7% for rifampin, 97.6% for quinolones (ofloxacin, levofloxacin, or moxifloxacin), 99.2% for amikacin, 99.2% for capreomycin, and 96.4% for kanamycin. For testing clinical specimens, the PSQ assay yielded a 98.4% sensitivity for detecting MTBC and a 95.8% sensitivity for generating complete sequencing results from all subassays. The PSQ assay was able to rapidly and accurately detect drug resistance mutations with the sequence information provided, which allows further study of the association of drug resistance or susceptibility with each mutation and the accumulation of such knowledge for future interpretation of results. Thus, reporting of false resistance for mutations known not to confer resistance can be prevented, which is a significant benefit of the assay over existing molecular diagnostic methods endorsed by the World Health Organization.
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224
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Houghton JL, Biswas T, Chen W, Tsodikov OV, Garneau-Tsodikova S. Chemical and structural insights into the regioversatility of the aminoglycoside acetyltransferase Eis. Chembiochem 2013; 14:2127-35. [PMID: 24106131 PMCID: PMC3947475 DOI: 10.1002/cbic.201300359] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Indexed: 11/08/2022]
Abstract
A recently discovered cause of tuberculosis resistance to a drug of last resort, the aminoglycoside kanamycin, results from modification of this drug by the enhanced intracellular survival (Eis) protein. Eis is a structurally and functionally unique acetyltransferase with an unusual capability of acetylating aminoglycosides at multiple positions. The extent of this regioversatility and its defining protein features are unclear. Herein, we determined the positions and order of acetylation of five aminoglycosides by NMR spectroscopy. This analysis revealed unprecedented acetylation of the 3''-amine of kanamycin, amikacin, and tobramycin, and the γ-amine of the 4-amino-2-hydroxybutyryl group of amikacin. A crystal structure of Eis in complex with coenzyme A and tobramycin revealed how tobramycin can be accommodated in the Eis active site in two binding modes, consistent with its diacetylation. These studies, describing chemical and structural details of acetylation, will guide future efforts towards designing aminoglycosides and Eis inhibitors to overcome resistance in tuberculosis.
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Affiliation(s)
- Jacob L. Houghton
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tapan Biswas
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wenjing Chen
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536-0596
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225
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Prevalence and molecular characterization of fluoroquinolone-resistant Mycobacterium tuberculosis isolates in China. Antimicrob Agents Chemother 2013; 58:364-9. [PMID: 24165186 DOI: 10.1128/aac.01228-13] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
China is one of the countries with the highest burdens of multidrug-resistant (MDR) and fluoroquinolone (FQ)-resistant tuberculosis (TB) globally. Nevertheless, knowledge about the prevalence and molecular characterization of FQ-resistant Mycobacterium tuberculosis isolates from this region remains scant. In this study, 138 M. tuberculosis isolates determined by the agar proportion susceptibility method to be resistant to ofloxacin (OFX) were enrolled from a national drug resistance survey of China. All these strains were tested for susceptibility to ofloxacin, levofloxacin, moxifloxacin, gatifloxacin, and sparfloxacin using liquid Middlebrook 7H9 medium. The entire gyrA and gyrB genes conferring FQ resistance were sequenced, and spoligotyping was performed to distinguish different genotypes. Overall, the prevalence of resistance in China was highest for ofloxacin (3.76%), intermediate for levofloxacin (3.18%) and moxifloxacin (3.12%), and lowest for sparfloxacin (1.91%) and gatifloxacin (1.33%). Mutations in the gyrA gene were observed in 89 (64.5%) out of the 138 OFX-resistant M. tuberculosis strains. Positions 94 and 90 were the most frequent sites of mutation conferring FQ resistance on these strains, accounting for high-level FQ resistance. Furthermore, the Beijing genotype showed no association with high-level FQ resistance or distribution in hot spots in the quinolone resistance-determining region (QRDR) of gyrA. Our findings provide essential implications for the feasibility of genotypic tests relying on detection of mutations in the QRDR of gyrA and the shorter first-line treatment regimens based on FQs in China.
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226
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Kurbatova EV, Cavanaugh JS, Dalton T, Click ES, Cegielski JP. Epidemiology of pyrazinamide-resistant tuberculosis in the United States, 1999-2009. Clin Infect Dis 2013; 57:1081-93. [PMID: 23840002 PMCID: PMC4578633 DOI: 10.1093/cid/cit452] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Pyrazinamide (PZA) is essential in tuberculosis treatment. We describe the prevalence, trends, and predictors of PZA resistance in Mycobacterium tuberculosis complex (MTBC) in the United States. METHODS We analyzed culture-positive MTBC cases with reported drug susceptibility tests for PZA in 38 jurisdictions routinely testing for PZA susceptibility from 1999 to 2009. National Tuberculosis Genotyping Service data for 2004-2009 were used to distinguish M. tuberculosis from Mycobacterium bovis and determine phylogenetic lineage. RESULTS Overall 2.7% (2167/79 321) of MTBC cases had PZA resistance, increasing annually from 2.0% to 3.3% during 1999-2009 (P < .001), largely because of an increase in PZA monoresistance. PZA-monoresistant MTBC (vs drug-susceptible) was associated with an age of 0-24 years (adjusted prevalence ratio [aPR],1.50; 95% confidence interval [CI], 1.31-1.71), Hispanic ethnicity (aPR, 3.52; 95% CI, 2.96-4.18), human immunodeficiency virus infection (aPR, 1.43; 95% CI, 1.15-1.77), extrapulmonary disease (aPR, 3.02; 95% CI, 2.60-3.52), and normal chest radiograph (aPR, 1.88; 95% CI, 1.63-2.16) and was inversely associated with Asian (aPR, 0.59; 95% CI, .47-.73) and black (aPR, 0.37; 95% CI, .29-.49) race. Among multidrug-resistant (MDR) cases, 38.0% were PZA-resistant; PZA resistance in MDR MTBC was associated with female sex (aPR, 1.25; 95% CI, 1.08-1.46) and previous tuberculosis diagnosis (aPR, 1.37; 95% CI, 1.16-1.62). Of 28 080 cases with genotyping data, 925 (3.3%) had PZA resistance; 465 of 925 (50.3%) were M. bovis. In non-MDR M. tuberculosis cases, PZA resistance was higher in the Indo-Oceanic than the East Asian lineage (2.2% vs 0.9%, respectively; aPR, 2.26; 95% CI, 1.53-3.36), but in MDR cases it was lower in the Indo-Oceanic lineage (22.0% vs 43.4%, respectively; aPR, 0.54; 95% CI, .32-.90). CONCLUSIONS Specific human and mycobacterial characteristics were associated with PZA-resistant MTBC, reflecting both specific subgroups of the population and phylogenetic lineages of the mycobacteria.
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Affiliation(s)
- Ekaterina V Kurbatova
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
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227
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Du Q, Dai G, Long Q, Yu X, Dong L, Huang H, Xie J. Mycobacterium tuberculosis rrs A1401G mutation correlates with high-level resistance to kanamycin, amikacin, and capreomycin in clinical isolates from mainland China. Diagn Microbiol Infect Dis 2013; 77:138-42. [DOI: 10.1016/j.diagmicrobio.2013.06.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 05/29/2013] [Accepted: 06/23/2013] [Indexed: 10/26/2022]
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228
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Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PKC, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet 2013; 45:1183-9. [PMID: 23995135 PMCID: PMC3887553 DOI: 10.1038/ng.2747] [Citation(s) in RCA: 292] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 08/08/2013] [Indexed: 11/09/2022]
Abstract
M. tuberculosis is evolving antibiotic resistance, threatening attempts at tuberculosis epidemic control. Mechanisms of resistance, including genetic changes favored by selection in resistant isolates, are incompletely understood. Using 116 newly sequenced and 7 previously sequenced M. tuberculosis whole genomes, we identified genome-wide signatures of positive selection specific to the 47 drug-resistant strains. By searching for convergent evolution--the independent fixation of mutations in the same nucleotide position or gene--we recovered 100% of a set of known resistance markers. We also found evidence of positive selection in an additional 39 genomic regions in resistant isolates. These regions encode components in cell wall biosynthesis, transcriptional regulation and DNA repair pathways. Mutations in these regions could directly confer resistance or compensate for fitness costs associated with resistance. Functional genetic analysis of mutations in one gene, ponA1, demonstrated an in vitro growth advantage in the presence of the drug rifampicin.
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Affiliation(s)
- Maha R Farhat
- Pulmonary and Critical Care Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114
| | - B Jesse Shapiro
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA 02115
- Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
| | - Karen J Kieser
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115
| | - Razvan Sultana
- Dana Farber Cancer Institute, Department of Bioinformatics and Computational Biology, Boston, MA, 02115
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, MA 02118
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Thomas C Victor
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Elizabeth M Streicher
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Alistair Calver
- Anglogold Ashanti Health West Vaal Hospital, Orkney, North West, South Africa
| | - Alex Sloutsky
- University of Massachusetts Medical School, Massachusetts Supranational TB Reference Laboratory, 305 South St., Boston MA 01230
| | - Devinder Kaur
- University of Massachusetts Medical School, Massachusetts Supranational TB Reference Laboratory, 305 South St., Boston MA 01230
| | - Jamie E Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333
| | - Bonnie Plikaytis
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333
| | - Marco R Oggioni
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Jennifer L Gardy
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver V5Z 4R4, Canada
| | - James C Johnston
- Clinical Prevention Services, British Columbia Centre for Disease Control, Vancouver V5Z 4R4, Canada
| | - Mabel Rodrigues
- Mycobacteriology/TB Laboratory, BCCDC Public Health Microbiology and Reference Laboratory, Provincial Health Services Authority Laboratories, Vancouver V5Z 4R4, Canada
| | - Patrick K C Tang
- Mycobacteriology/TB Laboratory, BCCDC Public Health Microbiology and Reference Laboratory, Provincial Health Services Authority Laboratories, Vancouver V5Z 4R4, Canada
| | - Midori Kato-Maeda
- Division of Pulmonary and Critical Care, University of California, San Francisco, San Francisco CA 94043
| | - Mark L Borowsky
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Harvard University, Boston MA 02115
| | - Bhavana Muddukrishna
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Harvard University, Boston MA 02115
| | - Barry N Kreiswirth
- Public Health Research Institute Tuberculosis Center, Rutgers, The State University of NJ, Newark, NJ 07103
| | - Natalia Kurepina
- Public Health Research Institute Tuberculosis Center, Rutgers, The State University of NJ, Newark, NJ 07103
| | - James Galagan
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142
- Departments of Biomedical Engineering, Boston University, Boston, MA 02215
- Department of Microbiology, Boston University, Boston, MA 02215
- Bioinformatics Program, Boston University, Boston, MA 02215
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland
- University of Basel, 4002 Basel, Switzerland
| | - Bruce Birren
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115
| | - Eric S Lander
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142
| | - Pardis C Sabeti
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA 02115
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA 02115
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115
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229
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Rifampin heteroresistance in Mycobacterium tuberculosis cultures as detected by phenotypic and genotypic drug susceptibility test methods. J Clin Microbiol 2013; 51:4220-2. [PMID: 24068005 DOI: 10.1128/jcm.01602-13] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis patients may harbor both drug-susceptible and -resistant bacteria, i.e., heteroresistance. We used mixtures of rifampin-resistant and -susceptible Mycobacterium tuberculosis strains to simulate heteroresistance in patient samples. Molecular tests can be used for earlier discovery of multidrug resistance (MDR), but the sensitivity to detect heteroresistance is unknown. Conventional phenotypic drug susceptibility testing was the most sensitive, whereas two line probe assays and sequencing were unable to detect the clinically important 1% resistant bacteria.
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230
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Detection of heteroresistant Mycobacterium tuberculosis by pyrosequencing. J Clin Microbiol 2013; 51:4210-2. [PMID: 24048543 DOI: 10.1128/jcm.01761-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of pyrosequencing to detect a resistant minority population of a heteroresistant Mycobacterium tuberculosis strain was investigated by performing a titration study. A mutant signal was noted only when the proportion of mutant DNA in the DNA target was 35 to 50%, showing that the sensitivity is significantly lower than that of phenotypic drug susceptibility test methods.
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231
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Mpagama SG, Houpt ER, Stroup S, Kumburu H, Gratz J, Kibiki GS, Heysell SK. Application of quantitative second-line drug susceptibility testing at a multidrug-resistant tuberculosis hospital in Tanzania. BMC Infect Dis 2013; 13:432. [PMID: 24034230 PMCID: PMC3848720 DOI: 10.1186/1471-2334-13-432] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/13/2013] [Indexed: 11/19/2022] Open
Abstract
Background Lack of rapid and reliable susceptibility testing for second-line drugs used in the treatment of multidrug-resistant tuberculosis (MDR-TB) may limit treatment success. Methods Mycobacterium tuberculosis isolates from patients referred to Kibong’oto National TB Hospital in Tanzania for second-line TB treatment underwent confirmatory speciation and susceptibility testing. Minimum inhibitory concentration (MIC) testing on MYCOTB Sensititre plates was performed for all drugs available in the second-line formulary. We chose to categorize isolates as borderline susceptible if the MIC was at or one dilution lower than the resistance breakpoint. M. tuberculosis DNA was sequenced for resistance mutations in rpoB (rifampin), inhA (isoniazid, ethionamide), katG (isoniazid), embB (ethambutol), gyrA (fluoroquinolones), rrs (amikacin, kanamycin, capreomycin), eis (kanamycin) and pncA (pyrazinamide). Results Of 22 isolates from patients referred for second-line TB treatment, 13 (59%) were MDR-TB and the remainder had other resistance patterns. MIC testing identified 3 (14%) isolates resistant to ethionamide and another 8 (36%) with borderline susceptibility. No isolate had ofloxacin resistance, but 10 (45%) were borderline susceptible. Amikacin was fully susceptible in 15 (68%) compared to only 11 (50%) for kanamycin. Resistance mutations were absent in gyrA, rrs or eis for all 13 isolates available for sequencing, but pncA mutation resultant in amino acid change or stop codon was present in 6 (46%). Ten (77%) of MDR-TB patients had at least one medication that could have logically been modified based on these results (median 2; maximum 4). The most common modifications were a change from ethioniamide to para-aminosalicylic acid, and the use of higher dose levofloxacin. Conclusions In Tanzania, quantitative second-line susceptibility testing could inform and alter MDR-TB management independent of drug-resistance mutations. Further operational studies are warranted.
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Affiliation(s)
- Stellah G Mpagama
- Division of Infectious Diseases and International Health, University of Virginia, PO Box 801340, Charlottesville, Virginia 22908, USA.
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232
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Identification of Mycobacterium species and Mycobacterium tuberculosis complex resistance determinants by use of PCR-electrospray ionization mass spectrometry. J Clin Microbiol 2013; 51:3492-8. [PMID: 23946518 DOI: 10.1128/jcm.01408-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
PCR coupled with electrospray ionization mass spectrometry (PCR-ESI-MS) is a novel technology that has recently been used to identify pathogens from clinical specimens or after culture within about 6 h. We evaluated the MDR-TB (multidrug-resistant tuberculosis) assay, which uses PCR-ESI-MS for detection and identification of Mycobacterium spp. and Mycobacterium tuberculosis complex (MTBC) resistance determinants from solid and broth Middlebrook culture media. The performance of the MDR-TB assay was compared to identification using nucleic acid hybridization probes and 16S rRNA gene sequencing for 68 MTBC and 97 nontuberculous mycobacterial (NTM) isolates grown on agar and 107 cultures grown in Bactec MGIT broth. MTBC resistance profiles from the MDR-TB assay were compared to results with the agar proportion method. The PCR-ESI-MS system correctly identified all MTBC isolates and 97.9% and 95.8% of the NTM isolates from characterized agar cultures and MGIT broth cultures to the species level, respectively. In comparison to the agar proportion method, the sensitivity and specificity for the detection of drug resistance using the MDR-TB assay were 100% and 92.3% for rifampin, 100% and 93.8% for isoniazid, 91.6% and 94.4% for ethambutol, and 100% and 100% for fluoroquinolones, respectively. The MDR-TB assay appears to be a rapid and accurate method for the simultaneous detection and identification of mycobacterial species and resistance determinants of MTBC from culture.
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233
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Jennings BC, Labby KJ, Green KD, Garneau-Tsodikova S. Redesign of substrate specificity and identification of the aminoglycoside binding residues of Eis from Mycobacterium tuberculosis. Biochemistry 2013; 52:5125-32. [PMID: 23837529 DOI: 10.1021/bi4002985] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The upsurge in drug-resistant tuberculosis (TB) is an emerging global problem. The increased expression of the enhanced intracellular survival (Eis) protein is responsible for the clinical resistance to aminoglycoside (AG) antibiotics of Mycobacterium tuberculosis . Eis from M. tuberculosis (Eis_Mtb) and M. smegmatis (Eis_Msm) function as acetyltransferases capable of acetylating multiple amines of many AGs; however, these Eis homologues differ in AG substrate preference and in the number of acetylated amine groups per AG. The AG binding cavity of Eis_Mtb is divided into two narrow channels, whereas Eis_Msm contains one large cavity. Five bulky residues lining one of the AG binding channels of Eis_Mtb, His119, Ile268, Trp289, Gln291, and Glu401, have significantly smaller counterparts in Eis_Msm, Thr119, Gly266, Ala287, Ala289, and Gly401, respectively. To identify the residue(s) responsible for AG binding in Eis_Mtb and for the functional differences from Eis_Msm, we have generated single, double, triple, quadruple, and quintuple mutants of these residues in Eis_Mtb by mutating them into their Eis_Msm counterparts, and we tested their acetylation activity with three structurally diverse AGs: kanamycin A (KAN), paromomyin (PAR), and apramycin (APR). We show that penultimate C-terminal residue Glu401 plays a critical role in the overall activity of Eis_Mtb. We also demonstrate that the identities of residues Ile268, Trp289, and Gln291 (in Eis_Mtb nomenclature) dictate the differences between the acetylation efficiencies of Eis_Mtb and Eis_Msm for KAN and PAR. Finally, we show that the mutation of Trp289 in Eis_Mtb into Ala plays a role in APR acetylation.
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Affiliation(s)
- Benjamin C Jennings
- Life Sciences Institute, 210 Washtenaw Avenue, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
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234
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Rifampin resistance missed in automated liquid culture system for Mycobacterium tuberculosis isolates with specific rpoB mutations. J Clin Microbiol 2013; 51:2641-5. [PMID: 23761146 DOI: 10.1128/jcm.02741-12] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
WHO-endorsed phenotypic drug susceptibility testing (DST) methods for Mycobacterium tuberculosis are assumed to be the gold standard for identifying rifampin (RMP) resistance. However, previous results indicated that low-level, yet probably clinically relevant, RMP resistance linked to specific rpoB mutations is easily missed by some growth-based methods. We aimed to compare the level of resistance detected on Löwenstein-Jensen (LJ) medium with resistance detected by the Bactec MGIT 960 automated DST (MGIT-DST) system for various rpoB mutants. Full agreement between LJ and MGIT-DST was observed for mutations located at codons 513 (Lys or Pro) and 531 (Leu, Trp), which were always resistant by both methods. For mutations 511Pro, 516Tyr, 533Pro, 572Phe, and several 526 mutations, LJ and MGIT results were highly discordant, with MGIT-DST failing to give a result or declaring the strains susceptible. Our data show that phenotypic RMP resistance testing of M. tuberculosis is not a binary phenomenon for some rpoB mutations and that the widely used automated MGIT 960 system is prone to miss some RMP resistance-conferring mutations, while careful DST on LJ missed hardly any. Given the association of these mutations with poor clinical outcome, our findings suggest that the gold standard for rifampin resistance should be reconsidered, in order to address the present confusion caused by discrepancies between phenotypic and genotypic results. The impacts of these mutations will depend on the frequency of their occurrence, which may vary from one setting to another.
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235
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Zimenkov DV, Antonova OV, Kuz'min AV, Isaeva YD, Krylova LY, Popov SA, Zasedatelev AS, Mikhailovich VM, Gryadunov DA. Detection of second-line drug resistance in Mycobacterium tuberculosis using oligonucleotide microarrays. BMC Infect Dis 2013; 13:240. [PMID: 23705640 PMCID: PMC3671172 DOI: 10.1186/1471-2334-13-240] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 05/21/2013] [Indexed: 11/17/2022] Open
Abstract
Background The steady rise in the spread of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) requires rapid and reliable methods to identify resistant strains. The current molecular methods to detect MTB resistance to second-line drugs either do not cover an extended spectrum of mutations to be identified or are not easily implemented in clinical laboratories. A rapid molecular technique for the detection of resistance to second-line drugs in M. tuberculosis has been developed using hybridisation analysis on microarrays. Methods The method allows the identification of mutations within the gyrA and gyrB genes responsible for fluoroquinolones resistance and mutations within the rrs gene and the eis promoter region associated with the resistance to injectable aminoglycosides and a cyclic peptide, capreomycin. The method was tested on 65 M. tuberculosis clinical isolates with different resistance spectra that were characterised by their resistance to ofloxacin, levofloxacin, moxifloxacin, kanamycin and capreomycin. Also, a total of 61 clinical specimens of various origin (e.g., sputum, bronchioalveolar lavage) were tested. Results The sensitivity and specificity of the method in the detection of resistance to fluoroquinolones were 98% and 100%, respectively, 97% and 94% for kanamycin, and 100% and 94% for capreomycin. The analytical sensitivity of the method was approximately 300 genome copies per assay. The diagnostic sensitivity of the assay ranging from 67% to 100%, depending on the smear grade, and the method is preferable for analysis of smear-positive specimens. Conclusions The combined use of the developed microarray test and the previously described microarray-based test for the detection of rifampin and isoniazid resistance allows the simultaneous identification of the causative agents of MDR and XDR and the detection of their resistance profiles in a single day.
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Affiliation(s)
- Danila V Zimenkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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236
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Wells WA, Boehme CC, Cobelens FG, Daniels C, Dowdy D, Gardiner E, Gheuens J, Kim P, Kimerling ME, Kreiswirth B, Lienhardt C, Mdluli K, Pai M, Perkins MD, Peter T, Zignol M, Zumla A, Schito M. Alignment of new tuberculosis drug regimens and drug susceptibility testing: a framework for action. THE LANCET. INFECTIOUS DISEASES 2013; 13:449-58. [PMID: 23531393 PMCID: PMC4012744 DOI: 10.1016/s1473-3099(13)70025-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
New tuberculosis drug regimens are creating new priorities for drug susceptibility testing (DST) and surveillance. To minimise turnaround time, rapid DST will need to be prioritised, but developers of these assays will need better data about the molecular mechanisms of resistance. Efforts are underway to link mutations with drug resistance and to develop strain collections to enable assessment of new diagnostic assays. In resource-limited settings, DST might not be appropriate for all patients with tuberculosis. Surveillance data and modelling will help country stakeholders to design appropriate DST algorithms and to decide whether to change drug regimens. Finally, development of practical DST assays is needed so that, in countries where surveillance and modelling show that DST is advisable, these assays can be used to guide clinical decisions for individual patients. If combined judiciously during both development and implementation, new tuberculosis regimens and new DST assays have enormous potential to improve patient outcomes and reduce the burden of disease.
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Affiliation(s)
| | | | - Frank G.J. Cobelens
- Department of Global Health, Academic Medical Center; and Amsterdam Institute of Global Health and Development, Amsterdam, The Netherlands
| | | | - David Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Jan Gheuens
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Peter Kim
- National Institutes of Allergy and Infectious Disease, Bethesda, MD, USA
| | | | - Barry Kreiswirth
- University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | | | - Khisi Mdluli
- Global Alliance for TB Drug Development, New York, NY, USA
| | - Madhukar Pai
- Department of Epidemiology and Biostatistics, McGill University, Montreal, Canada
| | - Mark D. Perkins
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Trevor Peter
- Clinton Health Access Initiative, Boston, MA, USA
| | - Matteo Zignol
- Stop TB Department, World Health Organization, Geneva, Switzerland
| | | | - Marco Schito
- HJF-DAIDS, a Division of The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Contractor to NIAID, NIH, DHHS, Bethesda, MD, USA
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237
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Cegielski P, Nunn P, Kurbatova EV, Weyer K, Dalton TL, Wares DF, Iademarco MF, Castro KG, Raviglione M. Challenges and controversies in defining totally drug-resistant tuberculosis. Emerg Infect Dis 2013; 18:e2. [PMID: 23092736 PMCID: PMC3559144 DOI: 10.3201/eid1811.120526] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In March 2012, in response to reports of tuberculosis (TB) resistant to all anti-TB drugs, the World Health Organization convened an expert consultation that identified issues to be resolved before defining a new category of highly drug-resistant TB. Proposed definitions are ambiguous, and extensive drug resistance is encompassed by the already defined extensively drug-resistant (XDR) TB. There is no evidence that proposed totally resistant TB differs from strains encompassed by XDR TB. Susceptibility tests for several drugs are poorly reproducible. Few laboratories can test all drugs, and there is no consensus list of all anti-TB drugs. Many drugs are used off-label for highly drug resistant TB, and new drugs formulated to combat resistant strains would render the proposed category obsolete. Labeling TB strains as totally drug resistant might lead providers to think infected patients are untreatable. These challenges must be addressed before defining a new category for highly drug-resistant TB.
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Affiliation(s)
- Peter Cegielski
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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238
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Jnawali HN, Hwang SC, Park YK, Kim H, Lee YS, Chung GT, Choe KH, Ryoo S. Characterization of mutations in multi- and extensive drug resistance among strains of Mycobacterium tuberculosis clinical isolates in Republic of Korea. Diagn Microbiol Infect Dis 2013; 76:187-96. [PMID: 23561273 DOI: 10.1016/j.diagmicrobio.2013.02.035] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/25/2013] [Accepted: 02/26/2013] [Indexed: 10/27/2022]
Abstract
In order to characterize molecular mechanisms of first- and second-line drug resistance in Mycobacterium tuberculosis and to evaluate the use of molecular markers of resistance, we analyzed 62 multidrug-resistant, 100 extensively drug-resistant, and 30 pan-susceptible isolates from Korean tuberculosis patients. Twelve genome regions associated with drug resistance, including katG, ahpC, and inhA promoter for isoniazid (INH); embB for ethambutol (EMB), rpoB for rifampin (RIF), pncA for pyrazinamide (PZA), gyrA for fluoroquinolones; rpsL, gidB, and rrs for streptomycin; rrs and eis for kanamycin (KM); rrs and tylA for capreomycin (CAP); and rrs for amikacin (AMK) were amplified simultaneously by polymerase chain reaction, and the DNA sequences were determined. We found mutations in 140 of 160 INH-resistant isolates (87.5%), 159 of 162 RIF-resistant isolates (98.15%), 127 of 143 EMB-resistant isolates (88.8%), 108 of 123 ofloxacin-resistant isolates (87.8%), and 107 of 122 PZA-resistant isolates (87.7%); 43 of 51 STM-resistant isolates (84.3%), 15 of 17 KM-resistant isolates (88.2%), and 14 of 15 (AMK and CAP)-resistant isolates (93.3%) had mutations related to specific drug resistance. In addition, the sequence analyses of the study revealed many novel mutations involving these loci. This result suggests that mutations in the rpoB531, katGSer315Thr, and C-15T in the inhA promoter region, and gyrA94, embB306, pncA159, rpsL43, and A1401G in the rrs gene could serve as useful markers for rapid detection of resistance profile in the clinical isolates of M. tuberculosis in Korea, with potentials for the new therapeutic benefits in actual clinical practice.
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Affiliation(s)
- Hum Nath Jnawali
- Korean Institute of Tuberculosis, Osong Saengmyeong 4-ro 168-5, Cheongwon-gun, Chungcheongbuk-do, 363-954, Republic of Korea
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239
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Houghton JL, Green KD, Pricer RE, Mayhoub AS, Garneau-Tsodikova S. Unexpected N-acetylation of capreomycin by mycobacterial Eis enzymes. J Antimicrob Chemother 2013; 68:800-5. [PMID: 23233486 PMCID: PMC3594498 DOI: 10.1093/jac/dks497] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 11/14/2012] [Accepted: 11/16/2012] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The enhanced intracellular survival (Eis) protein from Mycobacterium tuberculosis (Eis_Mtb), a regio-versatile N-acetyltransferase active towards many aminoglycosides (AGs), confers resistance to kanamycin A in some cases of extensively drug-resistant tuberculosis (XDR-TB). We assessed the activity of Eis_Mtb and of its homologue from Mycobacterium smegmatis (Eis_Msm) against a panel of anti-tuberculosis (TB) drugs and lysine-containing compounds. METHODS AND RESULTS Both enzymes acetylated capreomycin and some lysine-containing compounds, but not other non-AG non-lysine-containing drugs tested. Modelling studies predicted the site of modification on capreomycin to be one of the two primary amines in its β-lysine side chain. Using Eis_Mtb, we established via nuclear magnetic resonance (NMR) spectroscopy that acetylation of capreomycin occurs on the ε-amine of the β-lysine side chain. Using Msm, we also demonstrated for the first time to our knowledge that acetylation of capreomycin results in deactivation of the drug. CONCLUSIONS Eis is a unique acetyltransferase capable of inactivating the anti-TB drug capreomycin, AGs and other lysine-containing compounds.
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Affiliation(s)
- Jacob L. Houghton
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Room 4437, Ann Arbor, MI 48109, USA
| | - Keith D. Green
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Room 4437, Ann Arbor, MI 48109, USA
| | - Rachel E. Pricer
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Room 4437, Ann Arbor, MI 48109, USA
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Abdelrahman S. Mayhoub
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Room 4437, Ann Arbor, MI 48109, USA
| | - Sylvie Garneau-Tsodikova
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Room 4437, Ann Arbor, MI 48109, USA
- Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109, USA
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240
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Digital PCR to detect and quantify heteroresistance in drug resistant Mycobacterium tuberculosis. PLoS One 2013; 8:e57238. [PMID: 23468945 PMCID: PMC3584134 DOI: 10.1371/journal.pone.0057238] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/18/2013] [Indexed: 12/03/2022] Open
Abstract
Drug resistance in Mycobacterium tuberculosis presents an enormous public health threat. It is typically defined as >1% of drug resistant colonies using the agar proportion method. Detecting small numbers of drug resistant Tb in a population, also known as heteroresistance, is challenging with current methodologies. Here we have utilized digital PCR to detect heteroresistance within M. tuberculosis populations with excellent accuracy versus the agar proportion method. We designed dual TaqMan-MGB probes to detect wild-type and mutant sequences of katG (315), rpoB (531), gyrA (94,95) and rrs (1401), genes that associate with resistance to isoniazid, rifampin, fluoroquinolone, and aminoglycoside respectively. We generated heteroresistant mixtures of susceptible and extensively drug resistant Tb, followed by DNA extraction and digital PCR. Digital PCR yielded a close approximation to agar proportion's percentages of resistant colonies, and yielded 100% concordance with agar proportion's susceptible/resistant results. Indeed, the digital PCR method was able to identify mutant sequence in mixtures containing as little as 1000∶1 susceptible:resistant Tb. By contrast, real-time PCR or PCR followed by Sanger sequencing were less sensitive and had little resolution to detect heteroresistance, requiring fully 1∶1 or 10∶1 susceptible:resistant ratios in order to detect resistance. Our assay can also work in sputum so long as sufficient quantities of Tb are present (>1000 cfu/ml). This work demonstrates the utility of digital PCR to detect and quantify heteroresistance in drug resistant Tb, which may be useful to inform treatment decisions faster than agar proportion.
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241
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Evaluation of methods for testing the susceptibility of clinical Mycobacterium tuberculosis isolates to pyrazinamide. J Clin Microbiol 2013; 51:1374-80. [PMID: 23390285 DOI: 10.1128/jcm.03197-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyrazinamide (PZA) is a first-line antituberculosis (anti-TB) drug capable of killing nonreplicating, persistent Mycobacterium tuberculosis. However, reliable testing of the susceptibility of M. tuberculosis to PZA is challenging. Using 432 clinical M. tuberculosis isolates, we compared the performances of five methods for the determination of M. tuberculosis susceptibility to PZA: the MGIT 960 system, the molecular drug susceptibility test (mDST), the pyrazinamidase (PZase) activity assay, the resazurin microtiter assay (REMA), and the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction test. The sensitivities of the MGIT 960 system, the PZase activity assay, the mDST, the REMA, and the MTT assay were 98.8%, 88.8%, 90.5%, 98.8%, and 98.2%, respectively. The sensitivities of the PZase activity assay and the mDST were lower than those of the other three methods (P < 0.05). The specificities of the MGIT 960 system, the PZase activity assay, the mDST, the REMA and the MTT assays were 99.2%, 98.9%, 90.9%, 98.5%, and 100%, respectively. The specificity of the mDST was lower than those of the other four methods (P < 0.05). In conclusion, the MGIT 960 system, the MTT assay, and the REMA are superior to the PZase activity assay and the mDST in determining the susceptibility of M. tuberculosis to PZA. The MTT assay and the REMA might serve as alternative methods for clinical laboratories without access to the MGIT 960 system. For rapid testing in well-equipped laboratories, the mDST might be the best choice, particularly for small quantities of M. tuberculosis. The PZase activity assay has no obvious advantage in the assessment of M. tuberculosis susceptibility to PZA, as it is less accurate and requires larger quantities of bacteria.
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Aminoglycoside cross-resistance in Mycobacterium tuberculosis due to mutations in the 5' untranslated region of whiB7. Antimicrob Agents Chemother 2013; 57:1857-65. [PMID: 23380727 DOI: 10.1128/aac.02191-12] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since the discovery of streptomycin's bactericidal activity against Mycobacterium tuberculosis, aminoglycosides have been utilized to treat tuberculosis (TB). Today, the aminoglycosides kanamycin and amikacin are used to treat multidrug-resistant (MDR) TB, and resistance to any of the second-line injectable antibiotics, including kanamycin, amikacin, or capreomycin, is a defining characteristic of extensively drug-resistant (XDR) TB. Resistance to kanamycin and streptomycin is thought to be due to the acquisition of unlinked chromosomal mutations. However, we identified eight independent mutations in the 5' untranslated region of the transcriptional activator whiB7 that confer low-level resistance to both aminoglycosides. The mutations lead to 23- to 145-fold increases in whiB7 transcripts and subsequent increased expression of both eis (Rv2416c) and tap (Rv1258c). Increased expression of eis confers kanamycin resistance in these mutants, while increased expression of tap, which encodes an efflux pump, is a previously uncharacterized mechanism of low-level streptomycin resistance. Additionally, high-level resistance to streptomycin arose at a much higher frequency in whiB7 mutants than in a wild-type (WT) strain. Although whiB7 is typically associated with intrinsic antibiotic resistance in M. tuberculosis, these data suggest that mutations in an uncharacterized regulatory region of whiB7 contribute to cross-resistance against clinically used second-line antibiotics. As drug resistance continues to develop and spread, understanding the mechanisms and molecular basis of antibiotic resistance is critical for the development of rapid molecular tests to diagnose drug-resistant TB strains and ultimately for designing regimens to treat drug-resistant cases of TB.
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Molecular genetics of Mycobacterium tuberculosis resistant to aminoglycosides and cyclic peptide capreomycin antibiotics in Korea. World J Microbiol Biotechnol 2013; 29:975-82. [PMID: 23329063 DOI: 10.1007/s11274-013-1256-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/04/2013] [Indexed: 10/27/2022]
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Interpretation and Relevance of Advanced Technique Results. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2013. [PMCID: PMC7119927 DOI: 10.1007/978-1-4614-3970-7_47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past two decades due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation and user-friendly software have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, have benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods has lagged somewhat behind. The purpose of this chapter is to review and discuss the interpretation and relevance of results produced by these advanced molecular techniques. Moreover, this chapter will address the “myths” of NAATs, as these myths can markedly influence the interpretation and relevance of these results.
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Wang S, Zhao B, Song Y, Zhou Y, Pang Y, Ou X, Li Q, Xia H, Zhao Y. Molecular characterization of the rpoB gene mutations of Mycobacterium tuberculosis isolated from China. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/jtr.2013.11001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lu W, Chen C, Shao Y, Shi J, Zhong C, Yang D, Song H, Li G, Ding X, Peng H, Zhu L, Zhou Y, Zhu L. Evaluation of biochip system in determining isoniazid and rifampicin resistances of mycobacterium tuberculosis in sputum samples. PLoS One 2012; 7:e52953. [PMID: 23285233 PMCID: PMC3532416 DOI: 10.1371/journal.pone.0052953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 11/22/2012] [Indexed: 11/22/2022] Open
Abstract
Objective To evaluate a biochip system in determining isoniazid and rifampicin resistances of Mycobacterium tuberculosis in sputum samples in a Chinese population. Methods We assembled 907 sputum smeared positive specimens of tuberculosis patients in total. Each sample would be separated into two parts for culture and biochip assay simultaneously. And those cultured positive and having full drug resistance results would be used as reference. The McNemar χ2 test was adopted for evaluating the paired 2×2 table. Results Compared with drug sensitivity test, the agreement rates of the two methods in detecting rifampicin and isoniazid resistances were 93.37% and 94.49%, respectively. The sensitivity and specificity of biochip in detecting isoniazid were 74.31% and 96.92%, respectively. Meanwhile, the sensitivity and specificity for rifampicin were 79.76% and 96.53%, respectively. For multi-drug resistance, the sensitivity and specificity were 64.62% and 97.75%, respectively. Conclusions The biochip system is a rapid and accurate method for drug resistant tuberculosis diagnosis using sputum samples directly, especially for rifampicin resistance detection.
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Affiliation(s)
- Wei Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, People's Republic of China
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Tahmasebi P, Farnia P, Sheikholslami F, Velayati A. Rapid identification of extensively and extremely drug resistant tuberculosis from multidrug resistant strains; using PCR-RFLP and PCR-SSCP. IRANIAN JOURNAL OF MICROBIOLOGY 2012. [PMID: 23205246 DOI: pmid/23205246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND AND OBJECTIVES Resistance in Mycobacterium tuberculosis is caused by mutations in genes encoding drug targets. Investigators have already demonstrated the existence of mutations in codons 88 to 94 in the gyrA gene and also in codons 1400, 1401, and 1483 of rrs gene among extensively and extremely drug resistant tuberculosis (XDR & XXDR-TB) strains. The aim of this study was to identify the XDR and XXDR-TB stains based on their mutational analysis. MATERIALS AND METHODS Susceptibility testing against first and second-line anti-tuberculosis drugs was performed by the proportional method. Based on susceptibility results, samples were later analyzed, using PCR-SSCP and PCR-RFLP for detection of mutation in gyrA and rrs genes. RESULTS Overall, using proportional method, sixty-three strains (64.9%) were identified as MDR, 8(8.2%) as non-MDR and 26 strains (26.8%) were susceptible. Thirty-one cases (31.9%) were amikacin-resistant and 18 (18.5%) samples were ciprofloxacin-resistant. Using PCR-SSCP and PCR-RFLP, we identified 6(6.2%) and 7(7.2%) resistant strains, respectively. Discrepancy in strains was cross-checked by sequencing. The results showed no mutation in 66.6% and 77.4% of CIP and AMK- resistant strains. CONCLUSION Rapid detection of drug-resistant Mycobacterium tuberculosis using molecular techniques could be effective in determining therapeutic regimen and preventing the spread of XDR and MDR TB in the community. We should still keep in mind that a high number of resistant strains may have no mutation in proposed candidate genes.
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Affiliation(s)
- P Tahmasebi
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Disease (NRITLD), WHO & UNION Collaborating Centre for TB & Lung Diseases, Darabad, Tehran, Iran
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Jin J, Shen Y, Fan X, Diao N, Wang F, Wang S, Weng X, Zhang W. Underestimation of the resistance of Mycobacterium tuberculosis to second-line drugs by the new GenoType MTBDRsl test. J Mol Diagn 2012; 15:44-50. [PMID: 23159109 DOI: 10.1016/j.jmoldx.2012.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 07/25/2012] [Accepted: 08/07/2012] [Indexed: 11/25/2022] Open
Abstract
The GenoType MTBDRsl is a new-generation PCR-based line-probe assay for the detection of extensively drug-resistant tuberculosis (XDR-TB). This study evaluated the performance of MTBDRsl in detecting genotypic resistance to ethambutol, kanamycin, and ofloxacin in Mycobacterium tuberculosis (MTB) strains. The drug resistance of 262 unique clinical MTB isolates from China was analyzed with MTBDRsl, traditional TB drug susceptibility testing (DST), and sequencing. Sensitivity of MTBDRsl was 62.4% (93/149; 95% CI = 54.1 to 70.2) for detection of ethambutol resistance, 57.9% (55/95; 95% CI = 47.3 to 68) for kanamycin resistance, and 81% (111/137; 95% CI = 73.4 to 87.2) for ofloxacin resistance; specificity was 76.8% (86/112; 95% CI = 67.9 to 84.2), 98.8% (164/166; 95% CI = 95.7 to 99.9), and 91.1% (113/124; 95% CI = 84.7 to 95.5), respectively. Sequencing suggested that 36.9% (55/149) of ethambutol-resistant strains had no embB306 mutation and that 26.8% (40/149) had embB497 mutation not covered by MTBDRsl. Furthermore, MTBDRsl indicated ethambutol resistance in 23.2% (26/112) of ethambutol-susceptible strains, of which 92.3% (24/26) were confirmed resistant by sequencing. This study demonstrated that genotypic resistance to ethambutol, kanamycin, and ofloxacin in MTB can be quickly determined with the MTBDRsl. As a rapid and convenient genetic method, this assay could function as a supplement to traditional DST. More relevant genetic markers are needed to improve sensitivity.
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Affiliation(s)
- Jialin Jin
- Department of Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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Narayanaswamy VK, Nayak SK, Pillay M, Prasanna R, Coovadia YM, Odhav B. Synthesis and antitubercular activity of 2-(substituted phenyl/benzyl-amino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chlorides. Chem Biol Drug Des 2012; 81:219-27. [PMID: 23150983 DOI: 10.1111/cbdd.12065] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A series of 2-(substituted phenyl/benzyl-amino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chlorides 7-13 and 15 was synthesized in their hydrochloride salt form. The title compounds were characterized by FT-IR, NMR ((1)H and (13)C) and elemental analysis. They were evaluated for their in vitro antitubercular activity against Mycobacterium tuberculosis H37Rv, multidrug resistance tuberculosis and extensively drug resistance tuberculosis by agar diffusion method and tested for the cytotoxic action on peripheral blood mononuclear cells by MTT assay. Among all the tested compounds in the series, compounds 7 and 11 emerged as promising antitubercular agents at 16 μg/mL against multidrug resistance tuberculosis and over 64 μg/mL against extensively drug resistance tuberculosis. The conformational features and supramolecular assembly of the promising compounds 7 and 11 were determined by single crystal X-ray study.
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Affiliation(s)
- Venugopala K Narayanaswamy
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
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