1
|
Munir S, Mahmood N, Shahid S, Khan MI. Molecular detection of Isoniazid, Rifampin and Ethambutol resistance to M. tuberculosis and M. bovis in multidrug resistant tuberculosis (MDR-TB) patients in Pakistan. Microb Pathog 2017; 110:262-274. [PMID: 28688981 DOI: 10.1016/j.micpath.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/29/2017] [Accepted: 07/03/2017] [Indexed: 11/27/2022]
Abstract
The various aspects of MDR-TB, type of pathogen, different drug sensitive methods and mutation (s) in specific genes were determined. The histone-like protein (hupB) gene of M. tuberculosis was targeted by using primer sets: N & S and M & S (produced 645 bp & 318 bp fragment respectively). The most significant risk factors were the poverty and male gender of ages 11-25 years. All samples were detected as M. tuberculosis. By Drug Proportion method, the highest percentage (37%) was found resistant to only Rifampin. By MGIT method, the highest percentage (82.2%) was found resistant with the triple combination (Rifampin-RIF + Isoniazid-INH + Ethambutol-EMB) of the drugs. The highest mutations (76.92%) were found in gene rpoB (codon 531) in MDR TB patients. By, MAS-PCR, the highest percentage (34%) were found resistant to combination (INH + RIF) of the drugs. Minimum samples were resistant to RIF and RIF + INH drugs by MGIT, while proportionate results were observed from MAS-PCR and DP. Moreover, by MAS-PCR mutation in gene embB (306) caused EMB resistance (51.64%). We found that M. tuberculosis was the main cause of MDR-TB. Our findings may further be used for an early diagnosis of multi-drug resistant tuberculosis.
Collapse
Affiliation(s)
- Saba Munir
- Department of Allied Health Sciences, University of Health Sciences (UHS), Lahore, Pakistan
| | - Nasir Mahmood
- Department of Allied Health Sciences and Chemical Pathology, Department of Human Genetics and Molecular Biology, University of Health Sciences (UHS), Lahore, Pakistan.
| | - Saman Shahid
- Department of Sciences and Humanities, National University of Computer & Emerging Sciences (NUCES), Foundation for Advancement of Science and Technology (FAST), Lahore, Pakistan
| | - Muhammad Idrees Khan
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| |
Collapse
|
2
|
Chang KC, Yew WW, Zhang Y. A systematic review of rapid drug susceptibility tests for multidrug-resistant tuberculosis using rifampin resistance as a surrogate. ACTA ACUST UNITED AC 2013; 3:99-122. [PMID: 23485158 DOI: 10.1517/17530050802665694] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND The emergence of multidrug-resistant tuberculosis (MDR-TB) has prompted the development of rapid drug susceptibility assays with a focus on rifampin in recent years. Systematic reviews with evaluation of predictive values for different assays are scarce. METHOD MEDLINE was searched on 6 September 2008 for English articles that contain concurrent original data for generating summary measures of sensitivity, specificity and likelihood ratios of rapid rifampin susceptibility assays. RESULTS/CONCLUSIONS Significant heterogeneity was found in likelihood ratios across studies of all assays except nitrate reductase assay and colorimetric assays. Although rapid assays are fairly reliable for ruling out MDR-TB, careful consideration of clinical risk factors is required before using these assays to rule in MDR-TB under different epidemiological settings.
Collapse
Affiliation(s)
- Kwok-Chiu Chang
- Senior Medical and Health Officer Tuberculosis and Chest Service, Wanchai Chest Clinic, Department of Health, 1st Floor, Wanchai Polyclinic, 99, Kennedy Road, Wanchai, Hong Kong, China +852 25911147 ; +852 28346627 ;
| | | | | |
Collapse
|
3
|
Garza-González E, González G, Rentería A, Cruz-Pulido W, Rivera G, Bocanegra-García V. A pyrosequencing method for molecular monitoring of regions in the inhA, ahpC and rpoB genes of Mycobacterium tuberculosis. Clin Microbiol Infect 2010; 16:607-12. [DOI: 10.1111/j.1469-0691.2009.02932.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
4
|
Yang Z, Durmaz R, Yang D, Gunal S, Zhang L, Foxman B, Sanic A, Marrs CF. Simultaneous detection of isoniazid, rifampin, and ethambutol resistance of Mycobacterium tuberculosis by a single multiplex allele-specific polymerase chain reaction (PCR) assay. Diagn Microbiol Infect Dis 2005; 53:201-8. [PMID: 16243477 DOI: 10.1016/j.diagmicrobio.2005.06.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Accepted: 06/08/2005] [Indexed: 11/26/2022]
Abstract
Prompt detection of drug resistance of Mycobacterium tuberculosis is essential for effective control of tuberculosis (TB). We developed a multiplex allele-specific polymerase chain reaction (MAS-PCR) that detects the most commonly observed isoniazid (INH), rifampin (RIF), and ethambutol resistance-associated mutations in a single assay. The usefulness of the newly developed method was evaluated with 174 clinical isolates of M. tuberculosis obtained from Turkey. Distinct PCR banding patterns were observed for different mutation profiles and the correlation between MAS-PCR results and DNA sequencing findings was 99.4%. With culture-based phenotypic drug susceptibility testing as a reference standard, the sensitivity and specificity of the newly developed MAS-PCR assay for drug resistance-related genetic mutation detection were determined to be 81.1% and 97.5% for INH, 93.0% and 98.9 % for RIF, and 54.5% and 68.0 % for ethambutol. MAS-PCR provides a rapid, potentially more cost-effective, method of detecting multidrug-resistant TB.
Collapse
Affiliation(s)
- Zhenhua Yang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, 48109-2029, USA.
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Jalava J, Marttila H. Application of molecular genetic methods in macrolide, lincosamide and streptogramin resistance diagnostics and in detection of drug-resistant Mycobacterium tuberculosis. APMIS 2005; 112:838-55. [PMID: 15638840 DOI: 10.1111/j.1600-0463.2004.apm11211-1209.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antimicrobial susceptibility testing has traditionally been based on measurements of minimal inhibitory concentrations of antimicrobials. Molecular genetic studies on antimicrobial resistance have produced a great deal of genetic information which can be used for diagnosis of antimicrobial resistance determinants. Bacteria can acquire resistance to macrolides, lincosamides and streptogramin antibiotics by modification of the target site of the drugs, by active efflux of the drugs, and by inactivation of the drugs. The genetic backgrounds of these resistance mechanisms are well known and several molecular methods for detection of resistance determinants have been developed. Outbreaks of multidrug-resistant tuberculosis have focused international attention on the emergence of Mycobacterium tuberculosis strains that are resistant to antimycobacterial agents. Knowledge of the antimycobacterial resistance genetics and progress in molecular methods has made it possible to develop rapid molecular methods for susceptibility testing. This review presents the genetic background of drug resistance and introduces some methods for genotypic susceptibility testing.
Collapse
Affiliation(s)
- Jari Jalava
- National Public Health Institute, Department of Human Microbial Ecology and Inflammation, Turku University Central Hospital, Turku, Finland.
| | | |
Collapse
|
6
|
Shamputa IC, Rigouts And L, Portaels F. Molecular genetic methods for diagnosis and antibiotic resistance detection of mycobacteria from clinical specimens. APMIS 2004; 112:728-52. [PMID: 15638836 DOI: 10.1111/j.1600-0463.2004.apm11211-1203.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mycobacteria comprise a diverse group of bacteria that are widespread in nature, some of which cause significant disease in humans. Members of the Mycobacterium tuberculosis complex (MTBC) are the most important human pathogens of the genus Mycobacterium. Traditional methods for detection and identification of mycobacteria include microscopy, culture and phenotypic tests. These methods either lack sensitivity, specificity, or are time consuming. Advances in the field of molecular biology have provided rapid diagnostic tools that have reduced the turnaround times for detecting MTBC and drug resistance in cultures and directly in clinical specimens from weeks to days. This review discusses the molecular genetic techniques for detecting and identifying MTBC as well as drug resistance of mycobacteria in clinical specimens.
Collapse
Affiliation(s)
- I C Shamputa
- Mycobacteriology Unit, Department of Microbiology, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | |
Collapse
|
7
|
Kim BJ, Lee KH, Yun YJ, Park EM, Park YG, Bai GH, Cha CY, Kook YH. Simultaneous identification of rifampin-resistant Mycobacterium tuberculosis and nontuberculous mycobacteria by polymerase chain reaction-single strand conformation polymorphism and sequence analysis of the RNA polymerase gene (rpoB). J Microbiol Methods 2004; 58:111-8. [PMID: 15177909 DOI: 10.1016/j.mimet.2004.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Revised: 03/11/2004] [Accepted: 03/15/2004] [Indexed: 10/26/2022]
Abstract
Interspecies variations and mutations associated with rifampin resistance in rpoB of Mycobacterium allow for the simultaneous identification of rifampin-resistant Mycobacterium tuberculosis and nontuberculous mycobacteria by PCR-SSCP analysis and PCR- sequencing. One hundred and ten strains of rifampin-susceptible M. tuberculosis, 14 strains of rifampin-resistant M. tuberculosis, and four strains of the M. avium complex were easily identified by PCR-SSCP. Of another seven strains, which showed unique SSCP patterns, three were identified as rifampin-resistant M. tuberculosis and four as M. terrae complex by subsequent sequence analysis of their rpoB DNAs (306 bp). These results were concordant with those obtained by susceptibility testing, biochemical identification, and 16S rDNA sequencing.
Collapse
Affiliation(s)
- Bum-Joon Kim
- Department of Microbiology and Cancer Research Institute, Institute of Endemic Diseases, SNUMRC, Seoul National University College of Medicine, and Clinical Research Institute, Seoul National University Hospital, Chongno-Gu, South Korea
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Abstract
Drug-resistant tuberculosis is becoming increasingly common and represents a worldwide threat. Therefore, new approaches for the rapid susceptibility testing of Mycobacterium tuberculosis are needed to replace traditional culture-based methods. This article presents the genetic background of drug resistance in tubercle bacillus, and the methods currently available for genotypic susceptibility testing.
Collapse
Affiliation(s)
- Harri J Marttila
- Mycobacterial Reference Laboratory, National Public Health Institute, Kiinamyllynkatu 13, 20520 Turku, Finland
| | | |
Collapse
|
9
|
García de Viedma D. Rapid detection of resistance in Mycobacterium tuberculosis: a review discussing molecular approaches. Clin Microbiol Infect 2003; 9:349-59. [PMID: 12848747 DOI: 10.1046/j.1469-0691.2003.00695.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The last few years have seen the development of several molecular designs to search for mutations encoding resistance to antituberculous drugs in Mycobacterium tuberculosis. Most of these are highly efficient for RIF-r detection and are well adapted to search for the most relevant INH-R mutations. In this review, these new molecular approaches are explained and are presented according to the molecular strategies on which they are based. In this sense, techniques based on DNA-sequencing, electrophoresis and hybridization are reviewed and the newer designs based on real-time PCR and microarrays are also included. Molecular methods are sure to transform standard approaches to the issue of resistance in the mycobacteriology laboratory. This will allow laboratories to speed up the performance of resistance assays and provide access to essential information for highly refined detection, follow-up and management of antibiotic resistance in M. tuberculosis.
Collapse
Affiliation(s)
- D García de Viedma
- Servicio de Microbiología clínica y enfermedades infecciosas, Hospital general universitario Gregorio Marañón, C/Dr Esquerdo 46, 28007 Madrid, Spain.
| |
Collapse
|
10
|
Liu E, Jelinek J, Pastore YD, Guan Y, Prchal JF, Prchal JT. Discrimination of polycythemias and thrombocytoses by novel, simple, accurate clonality assays and comparison with PRV-1 expression and BFU-E response to erythropoietin. Blood 2003; 101:3294-301. [PMID: 12515724 DOI: 10.1182/blood-2002-07-2287] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Essential thrombocythemia (ET) and polycythemia vera (PV) are clonal myeloproliferative disorders that are often difficult to distinguish from other causes of elevated blood cell counts. Assays that could reliably detect clonal hematopoiesis would therefore be extremely valuable for diagnosis. We previously reported 3 X-chromosome transcription-based clonality assays (TCAs) involving the G6PD, IDS, and MPP1 genes, which together were informative in about 65% of female subjects. To increase our ability to detect clonality, we developed simple TCA for detecting the transcripts of 2 additional X-chromosome genes: Bruton tyrosine kinase (BTK) and 4-and-a-half LIM domain 1 (FHL1). The combination of TCA established the presence or absence of clonal hematopoiesis in about 90% of female subjects. We show that both genes are subject to X-chromosome inactivation and are polymorphic in all major US ethnic groups. The 5 TCAs were used to examine clonality in 46 female patients along with assays for erythropoietin-independent erythroid colonies (EECs) and granulocyte PRV-1 mRNA levels to discriminate polycythemias and thrombocytoses. Of these, all 19 patients with familial polycythemia or thrombocytosis had polyclonal hematopoiesis, whereas 22 of 26 patients with clinical evidence of myeloproliferative disorder and 1 patient with clinically obscure polycythemia were clonal. Interestingly, interferon alpha therapy in 2 patients with PV was associated with reversion of clonal to polyclonal hematopoiesis. EECs were observed in 14 of 14 patients with PV and 4 of 12 with ET, and increased granulocyte PRV-1 mRNA levels were found in 9 of 13 patients with PV and 2 of 12 with ET. Thus, these novel clonality assays are useful in the diagnosis and follow-up of polycythemic conditions and disorders with increased platelet levels.
Collapse
MESH Headings
- Adolescent
- Adult
- Agammaglobulinaemia Tyrosine Kinase
- Aged
- Child
- Chromosomes, Human, X/genetics
- Clone Cells/pathology
- Colony-Forming Units Assay
- Diagnosis, Differential
- Dosage Compensation, Genetic
- Erythroid Precursor Cells/chemistry
- Erythroid Precursor Cells/drug effects
- Erythropoietin/pharmacology
- Exons/genetics
- Female
- GPI-Linked Proteins
- Genetic Markers
- Granulocytes/metabolism
- Hematopoiesis/genetics
- Homeodomain Proteins/blood
- Homeodomain Proteins/genetics
- Humans
- Interferon-alpha/pharmacology
- Isoantigens
- Membrane Glycoproteins
- Middle Aged
- Polycythemia/diagnosis
- Polycythemia/genetics
- Polycythemia/pathology
- Polycythemia Vera/diagnosis
- Polycythemia Vera/drug therapy
- Polycythemia Vera/genetics
- Polycythemia Vera/pathology
- Polymorphism, Genetic
- Polymorphism, Single-Stranded Conformational
- Protein-Tyrosine Kinases/blood
- Protein-Tyrosine Kinases/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/blood
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Thrombocytosis/diagnosis
- Thrombocytosis/genetics
- Thrombocytosis/pathology
Collapse
Affiliation(s)
- Enli Liu
- Department of Hematology/Oncology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | | | |
Collapse
|
11
|
Fluit AC, Visser MR, Schmitz FJ. Molecular detection of antimicrobial resistance. Clin Microbiol Rev 2001; 14:836-71, table of contents. [PMID: 11585788 PMCID: PMC89006 DOI: 10.1128/cmr.14.4.836-871.2001] [Citation(s) in RCA: 257] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The determination of antimicrobial susceptibility of a clinical isolate, especially with increasing resistance, is often crucial for the optimal antimicrobial therapy of infected patients. Nucleic acid-based assays for the detection of resistance may offer advantages over phenotypic assays. Examples are the detection of the methicillin resistance-encoding mecA gene in staphylococci, rifampin resistance in Mycobacterium tuberculosis, and the spread of resistance determinants across the globe. However, molecular assays for the detection of resistance have a number of limitations. New resistance mechanisms may be missed, and in some cases the number of different genes makes generating an assay too costly to compete with phenotypic assays. In addition, proper quality control for molecular assays poses a problem for many laboratories, and this results in questionable results at best. The development of new molecular techniques, e.g., PCR using molecular beacons and DNA chips, expands the possibilities for monitoring resistance. Although molecular techniques for the detection of antimicrobial resistance clearly are winning a place in routine diagnostics, phenotypic assays are still the method of choice for most resistance determinations. In this review, we describe the applications of molecular techniques for the detection of antimicrobial resistance and the current state of the art.
Collapse
Affiliation(s)
- A C Fluit
- Eijkman-Winkler Institute, University Medical Center Utrecht, Utrecht, The Netherlands.
| | | | | |
Collapse
|
12
|
Caws M, Wilson SM, Clough C, Drobniewski F. Role of IS6110-targeted PCR, culture, biochemical, clinical, and immunological criteria for diagnosis of tuberculous meningitis. J Clin Microbiol 2000; 38:3150-5. [PMID: 10970348 PMCID: PMC87341 DOI: 10.1128/jcm.38.9.3150-3155.2000] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An open prospective clinical, microbiological, and molecular analysis of a national molecular diagnostic service for tuberculous meningitis (TBM) using an in-house IS6110-targeted PCR for molecular "Fastrack" diagnosis was carried out. Between April 1997 and June 1998. Consecutive cerebrospinal fluid (CSF) samples from 131 patients were assessed. Against a culture on the same sample, PCR had a sensitivity of 75% and a specificity of 94%. Of samples from patients classified as definite or probable TBM cases based on clinical criteria, 81% had raised CSF protein levels and 73% had a lymphocytosis, although 57% of all submitted samples showed a raised lymphocyte count. While only 46% had a CSF glucose level below the normal range, the CSF glucose level was significantly lower (P = 0. 0281) than in cases of meningitis of other etiologies. Levels of tumor necrosis factor alpha were also found to be significantly raised in definite or probable TBM cases (P = 0.028), while adenosine deaminase levels were not. The study showed IS6110-targeted PCR to be a rapid, sensitive, and specific test in routine use for the diagnosis of TBM.
Collapse
Affiliation(s)
- M Caws
- PHLS Mycobacterium Reference Unit, Dulwich PHL and Department of Microbiology, Guy's King's and St. Thomas School of Medicine, King's College (Dulwich), London SE22 8QF, United Kingdom.
| | | | | | | |
Collapse
|
13
|
Valim AR, Rossetti ML, Ribeiro MO, Zaha A. Mutations in the rpoB gene of multidrug-resistant Mycobacterium tuberculosis isolates from Brazil. J Clin Microbiol 2000; 38:3119-22. [PMID: 10921994 PMCID: PMC87207 DOI: 10.1128/jcm.38.8.3119-3122.2000] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations in a 69-bp region of the rpoB gene associated with rifampin resistance (Rif(r)) in 100 isolates (82 Rif(r)) from three states of Brazil were studied. Twenty-one different kinds of mutations were identified in the Rif(r) isolates, and six new alleles are described.
Collapse
Affiliation(s)
- A R Valim
- Laboratório Central do Rio Grande do Sul, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre-Rio Grande do Sul CEP 90130-001, Brazil
| | | | | | | |
Collapse
|
14
|
|
15
|
Scarpellini P, Braglia S, Carrera P, Cedri M, Cichero P, Colombo A, Crucianelli R, Gori A, Ferrari M, Lazzarin A. Detection of rifampin resistance in Mycobacterium tuberculosis by double gradient-denaturing gradient gel electrophoresis. Antimicrob Agents Chemother 1999; 43:2550-4. [PMID: 10508043 PMCID: PMC89519 DOI: 10.1128/aac.43.10.2550] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We applied double gradient-denaturing gradient gel electrophoresis (DG-DGGE) for the rapid detection of rifampin (RMP) resistance from rpoB PCR products of Mycobacterium tuberculosis isolates and clinical samples. The results of this method were fully concordant with those of DNA sequencing and susceptibility testing analyses. DG-DGGE is a valid alternative to the other methods of detecting mutations for predicting RMP resistance.
Collapse
Affiliation(s)
- P Scarpellini
- Infectious Diseases Division, San Raffaele Scientific Institute, University of Milan, Milan, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|