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Dakhave M, Rale T, Suryawanshi H, Patil N, Suryawanshi A, Kumar R, Gadekar S, Bhatnagar P, Khaire A, Wankhede G. Advanced integrative molecular platform for high-throughput screening of drug-resistant tuberculosis. Diagn Microbiol Infect Dis 2024; 109:116373. [PMID: 38815365 DOI: 10.1016/j.diagmicrobio.2024.116373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024]
Abstract
A real time-polymerase chain reaction-based test in lyophilized form, was developed to simultaneously identify Mycobacterium tuberculosis complex (MTC) by targeting IS6110, rrs as dual markers, as well as mutations causing rifampicin and isoniazid resistance. The test was evaluated for pulmonary and non-pulmonary specimens from sample isolation to PCR analysis. The test demonstrated limit of detection of 25 CFU/mL for MTB, 200 CFU/mL for rpoB and inhA/katG targets with >95 % CI. The specificity for MTC was supported by a comprehensive clinical validation (n = 100). This load-and-go molecular platform, with features of high throughput, long shelf-life, room temperature storage provides simultaneous detection of MTC and its drug-resistant mutations in minimal time. The test named "PathoDetect TM MTB-RIF and INH resistance detection kit" has been approved by Central Drugs Standard Control Organisation, Indian Council of Medical Research and would have implications for tuberculosis elimination programs.
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Affiliation(s)
- Minal Dakhave
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India.
| | - Trupti Rale
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | | | - Nikita Patil
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | | | - Raju Kumar
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | - Shruti Gadekar
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | - Payal Bhatnagar
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | - Amrita Khaire
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
| | - Gautam Wankhede
- R&D Department, Mylab Discovery Solutions Pvt. Ltd., Pune, Maharashtra, India
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2
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Morales-Durán N, León-Buitimea A, Morones-Ramírez JR. Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions. Heliyon 2024; 10:e27984. [PMID: 38510041 PMCID: PMC10950705 DOI: 10.1016/j.heliyon.2024.e27984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Antimicrobial resistance is a global health threat. Misuse and overuse of antimicrobials are the main drivers in developing drug-resistant bacteria. The emergence of the rapid global spread of multi-resistant bacteria requires urgent multisectoral action to generate novel treatment alternatives. Combination therapy offers the potential to exploit synergistic effects for enhanced antibacterial efficacy of drugs. Understanding the complex dynamics and kinetics of drug interactions in combination therapy is crucial. Therefore, this review outlines the current advances in antibiotic resistance's evolutionary and genetic dynamics in combination therapies-exposed bacteria. Moreover, we also discussed four pivotal future research areas to comprehend better the development of antibiotic resistance in bacteria treated with combination strategies.
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Affiliation(s)
- Nami Morales-Durán
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - José R. Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
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3
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Jain B, Kulkarni S. Molecular Detection of Multidrug Resistance and Characterizations of Mutations in Mycobacterium Tuberculosis Using Polycarbonate Track-Etched Membrane Based DNA Bio-Chip. Indian J Microbiol 2024; 64:92-99. [PMID: 38468745 PMCID: PMC10924865 DOI: 10.1007/s12088-023-01116-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/07/2023] [Indexed: 03/13/2024] Open
Abstract
With the widespread use of rifampicin (RMP) and isoniazid (INH), multidrug resistance (MDR) in Mycobacterium tuberculosis (M.tb) poses a threat to the success of tuberculosis (TB) control programs. We have developed a new polycarbonate track-etched membranes (PC-TEM) based DNA bio-chip designed for rapid detection of mutations conferring MDR in M.tb culture isolates. Bio-chips were designed to contain 14 specific probes for wild type and mutated allele of selected codons within 80 bp rifampicin resistance determining region of rpoB gene, katG gene and mabA-inhA regulatory region. RMP-resistance-associated gene mutation points rpoB 516, 526, 531 and 533, and the INH-resistance-associated gene mutation points katG315 and inhA-15 were targeted. Bio-chip signal was detected using enhanced chemiluminescence. A total of 50 culture isolates that were sensitive or resistant to RMP and/or INH were analyzed by bio-chip. The results of culture-based drug susceptibility testing (DST) were used as the gold standard and gene sequencing was performed to resolve the discordance. Amongst 50 culture isolates, we have detected 18 MDR, 9 RMP mono-resistant, 6 INH mono-resistant, and 17 fully susceptible isolates. The developed DNA bio-chip has a sensitivity of 90% for RMP and MDR and 100% for INH resistance. The bio-chip has a specificity of 100% for RMP and MDR and 88.8% for INH detection. The identification of mutations using the DNA bio-chip was 100% concordant with the sequencing data for the probes covered by the bio-chip. The detection of rpoB, katG and inhA gene mutation points by a DNA bio-chip may be used as a rapid, accurate, and economical, clinical detection method for MDR detection in M.tb. This is very valuable for the control of TB epidemics.
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Affiliation(s)
- Bharti Jain
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, Maharashtra India
- Homi Bhabha National Institute, Mumbai, Maharashtra India
| | - Savita Kulkarni
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, Maharashtra India
- Homi Bhabha National Institute, Mumbai, Maharashtra India
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Traoré AN, Rikhotso MC, Mphaphuli MA, Patel SM, Mahamud HA, Kachienga LO, Kabue JP, Potgieter N. Isoniazid and Rifampicin Resistance-Conferring Mutations in Mycobacterium tuberculosis Isolates from South Africa. Pathogens 2023; 12:1015. [PMID: 37623975 PMCID: PMC10458554 DOI: 10.3390/pathogens12081015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 08/26/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), remains a significant global health issue, with high morbidity and mortality rates. The emergence of drug-resistant strains, particularly multidrug-resistant TB (MDR-TB), poses difficult challenges to TB control efforts. This comprehensive review and meta-analysis investigated the prevalence of and molecular insights into isoniazid (INH) and rifampicin (RIF) resistance-conferring mutations in M. tb isolates from South Africa. Through systematic search and analysis of 11 relevant studies, we determined the prevalence of gene mutations associated with RIF and INH resistance, such as rpoB, katG, and inhA. The findings demonstrated a high prevalence of specific mutations, including S450L in rpoB, and S315T, which are linked to resistance against RIF and INH, respectively. These results contribute to the understanding of drug resistance mechanisms and provide valuable insights for the development of targeted interventions against drug-resistant TB.
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Affiliation(s)
- Afsatou Ndama Traoré
- Department of Biochemistry and Microbiology, Faculty of Sciences, Engineering & Agriculture, University of Venda, Thohoyandou 0950, South Africa; (M.C.R.); (M.A.M.); (S.M.P.); (H.A.M.); (L.O.K.); (J.-P.K.); (N.P.)
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5
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Augustin L, Agarwal N. Designing a Cas9/gRNA-assisted quantitative Real-Time PCR (CARP) assay for identification of point mutations leading to rifampicin resistance in the human pathogen Mycobacterium tuberculosis. Gene 2023; 857:147173. [PMID: 36627091 DOI: 10.1016/j.gene.2023.147173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/13/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
A simple, rapid and low-cost diagnostic test, which can detect both the drug-sensitive and the drug-resistant tuberculosis (TB) cases is the need of the hour. Here, we developed a Cas9/gRNA-assisted quantitative Real-Time PCR (qRT-PCR) (CARP) assay to detect single nucleotide mutations causing drug resistance in the TB pathogen, Mycobacterium tuberculosis (Mtb). Guide RNAs (gRNAs) were designed against S531 and H526 positions in the rifampicin (RIF)-resistance-determining region (RRDR) of the Mtb rpoB gene that exhibit frequent mutations in the RR clinical isolates of Mtb. Conditions were optimised for in vitro Cas9 cleavage such that single nucleotide changes at these positions can be recognised by Cas9/gRNA complex with high sensitivity and 100% specificity. Further estimation of Cas9/gRNA-based cleavage of target DNA by qRT-PCR led to rapid detection of drug-resistant sequences. The newly designed CARP assay holds a great deal of promise in the diagnosis and prognosis of patients suffering from TB, in a cost-effective manner.
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Affiliation(s)
- Linus Augustin
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India.
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6
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Frequency of rpoB, katG, and inhA Gene Polymorphisms Associated with Multidrug-Resistant Mycobacterium tuberculosis Complex Isolates among Ethiopian TB Patients: A Systematic Review. Interdiscip Perspect Infect Dis 2022; 2022:1967675. [PMID: 35757683 PMCID: PMC9225881 DOI: 10.1155/2022/1967675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/05/2022] [Accepted: 05/26/2022] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis (TB) is one of the top 10 causes of mortality and the first killer among infectious diseases of poverty (IDoPs) worldwide. It disproportionately affects on-third of the world's low-income countries including Ethiopia. One of the factors driving the TB epidemic is the global rise of MDR/XDR-TB and their low detection affect the global TB control progress. Recently, the resistance-associated genetic mutations in MTBC known to confer drug resistance have been detected by rapid molecular diagnostic tests and sequencing methods. In this article, the published literature searched by PubMed database from 2010 to 2021 and English language were considered. The aim of this systematic review was to assess the prevalence of the most common rpoB, katG, and inhA gene mutations associated with multidrug resistance in MTBC clinical strains among TB patients in Ethiopia. Though 22 studies met our eligibility criteria, only 6 studies were included in the final analysis. Using the molecular GenoType MTBDRplus and MTBDRsl line probe assay and sequencing procedures, a total of 932 culture-positive MTBC isolates were examined to determine RIF, INH, and MDR-TB resistance patterns along with rpoB, katG, and inhA gene mutation analysis. As a result, among the genotypically tested MTBC isolates, 119 (12.77%), 83 (8.91%), and 73 (7.32%) isolates were INH, RIF, and MDR-TB resistant, respectively. In any RIF-resistant MTBC strains, the most common single point mutations were in codon 531 (S531L) followed by codon 526 (H526Y) of the rpoB gene. Besides, the most common mutations in any INH-resistant MTBC were strains observed at codon 315 (S315T) and WT probe in the katG gene and at codon C15T and WT1 probe in the inhA promoter region. Detection of resistance allele in rpoB, KatG, and inhA genes for RIF and INH could serve as a marker for MDR-TB strains. Tracking the most common S531L, S315T, and C15T mutations in rpoB, katG, and inhA genes among RIF- and INH-resistant isolates would be valuable in TB diagnostics and treatment regimens, and could reduce the development and risk of MDR/XDR-TB drug-resistance patterns.
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Diriba G, Kebede A, Tola HH, Alemu A, Yenew B, Moga S, Addise D, Mohammed Z, Getahun M, Fantahun M, Tadesse M, Dagne B, Amare M, Assefa G, Abera D, Desta K. Utility of line probe assay in detecting drug resistance and the associated mutations in patients with extrapulmonary tuberculosis in Addis Ababa, Ethiopia. SAGE Open Med 2022; 10:20503121221098241. [PMID: 35646363 PMCID: PMC9130810 DOI: 10.1177/20503121221098241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/14/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Molecular tests allow rapid detection of Mycobacterium tuberculosis and drug resistance in a few days. Identifying the mutations in genes associated with drug resistance may contribute to the development of appropriate interventions to improve tuberculosis control. So far, there is little information in Ethiopia about the diagnostic performance of line probe assay (LPA) and the M. tuberculosis common gene mutations associated with drug resistance in extrapulmonary tuberculosis. Thus, this study aimed to assess the frequency of drug resistance-associated mutations in patients with extrapulmonary tuberculosis (EPTB) and to compare the agreement and determine the utility of the genotypic in the detection of drug resistance in Addis Ababa, Ethiopia. Methods A cross-sectional study was conducted on stored M. tuberculosis isolates. The genotypic and phenotypic drug susceptibility tests were performed using LPA and BACTEC-MGIT-960, respectively. The common mutations were noted, and the agreement and the utility of the LPA were determined using the BACTEC-MGIT-960 as a gold standard. Results Of the 151 isolates, the sensitivity and specificity of MTBDRplus in detecting isoniazid resistance were 90.9% and 100%, respectively. While for rifampicin, it was 100% and 99.3% for sensitivity and specificity, respectively. The katG S315Tl was the most common mutation observed in 85.7% of the isoniazid-resistant isolates. In the case of rifampicin, the most common mutation (61.9%) was observed at position rpoB S531L. Mutations in the gyrA promoter region were strongly associated with Levofloxacin and Moxifloxacin resistance. Conclusion Line probe assay has high test performance in detecting resistance to anti-TB drugs in EPTB isolates. The MTBDRplus test was slightly less sensitive for the detection of isoniazid resistance as compared to the detection of rifampicin. The most prevalent mutations associated with isoniazid and rifampicin resistance were observed at katG S315Tl and rpoB S531L respectively. Besides, all the fluoroquinolone-resistant cases were associated with gyrA gene. Finally, a validation study with DNA sequencing is recommended.
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Affiliation(s)
- Getu Diriba
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
- Department of Medical Laboratory
Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa,
Ethiopia
| | - Abebaw Kebede
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
- Department of Microbial, Cellular and
Molecular Biology, College of Natural and Computational Sciences, Addis Ababa
University, Addis Ababa, Ethiopia
| | | | - Ayinalem Alemu
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
- Aklilu Lemma Institute of Pathobiology,
Addis Ababa University, Addis Ababa, Ethiopia
| | - Bazezew Yenew
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | - Shewki Moga
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | | | | | | | - Mengistu Fantahun
- St. Paul’s Hospital Millennium Medical
College, Addis Ababa, Ethiopia
| | | | - Biniyam Dagne
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | - Misikir Amare
- Ethiopian Public Health Institute,
Addis Ababa, Ethiopia
| | | | - Dessie Abera
- Department of Medical Laboratory
Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa,
Ethiopia
| | - Kassu Desta
- Department of Medical Laboratory
Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa,
Ethiopia
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8
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Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach. Int J Mol Sci 2021; 22:ijms222413259. [PMID: 34948055 PMCID: PMC8703488 DOI: 10.3390/ijms222413259] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/09/2021] [Accepted: 11/14/2021] [Indexed: 12/12/2022] Open
Abstract
Developing new, more effective antibiotics against resistant Mycobacterium tuberculosis that inhibit its essential proteins is an appealing strategy for combating the global tuberculosis (TB) epidemic. Finding a compound that can target a particular cavity in a protein and interrupt its enzymatic activity is the crucial objective of drug design and discovery. Such a compound is then subjected to different tests, including clinical trials, to study its effectiveness against the pathogen in the host. In recent times, new techniques, which involve computational and analytical methods, enhanced the chances of drug development, as opposed to traditional drug design methods, which are laborious and time-consuming. The computational techniques in drug design have been improved with a new generation of software used to develop and optimize active compounds that can be used in future chemotherapeutic development to combat global tuberculosis resistance. This review provides an overview of the evolution of tuberculosis resistance, existing drug management, and the design of new anti-tuberculosis drugs developed based on the contributions of computational techniques. Also, we show an appraisal of available software and databases on computational drug design with an insight into the application of this software and databases in the development of anti-tubercular drugs. The review features a perspective involving machine learning, artificial intelligence, quantum computing, and CRISPR combination with available computational techniques as a prospective pathway to design new anti-tubercular drugs to combat resistant tuberculosis.
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9
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Drug-resistant Tuberculosis: First Line Drug Resistance Pattern among Mycobacterium Tuberculosis Strains Isolated from a Reference Laboratory in Kerala State, India. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Resistance to antimycobacterial agents consistently remains a major obstacle to end TB in India. Geographical prevalence data regarding drug-resistant evolutionary genetics of M. tuberculosis (MTB) remains sparse in India. Our objective was to determine the genotypic drug resistance mutation pattern for Rifampicin and Isoniazid of MTB isolates to gain an understanding of the prevailing molecular epidemiology of drug-resistant tuberculosis. In this study 2528 M. tuberculosis DNA isolates from presumptive DRTB suspects received at the nodal TB reference laboratory in Kerala were tested for Rifampicin and Isoniazid resistance by sequence-based diagnostic Line Probe assay (LPA). Geographical prevalence and associations of rpoB, katG, inhA resistance codons was analyzed from January 2019 to March 2020. Among the 2528 DNA samples subjected for Rifampicin and Isoniazid resistance determination by LPA, 146 (5.8%) isolates were resistant to both drugs. Isoniazid mono-resistance was found in 164 (6.5%) and Rifampicin mono-resistance in 38 (1.5%) isolates. The most frequent rpoB mutation was S531L (60.32%) followed by S531W/L533P mutations seen in 8.15% of the isolates. S315T1 KatG mutation was seen in 97.33% of Isoniazid resistant isolates. 84.68% isolates with rpoB S531L mutation were found to be multidrug-resistant. 82.9% of isolates with rpoB S531L mutation showed katG S315T1 mutation. Mono isoniazid-resistant isolates were significantly higher compared to mono rifampicin-resistant isolates among the DNA isolates studied in our region. The molecular epidemiological pattern most frequently associated with multidrug resistance was rpoB S531L which was significantly associated with the co-presence of S315T1 mutation.
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Bisimwa BC, Nachega JB, Warren RM, Theron G, Metcalfe JZ, Shah M, Diacon AH, Sam-Agudu NA, Yotebieng M, Bulabula ANH, Katoto PDMC, Chirambiza JP, Nyota R, Birembano FM, Musafiri EM, Byadunia S, Bahizire E, Kaswa MK, Callens S, Kashongwe ZM. Xpert Mycobacterium tuberculosis/Rifampicin-Detected Rifampicin Resistance is a Suboptimal Surrogate for Multidrug-resistant Tuberculosis in Eastern Democratic Republic of the Congo: Diagnostic and Clinical Implications. Clin Infect Dis 2021; 73:e362-e370. [PMID: 32590841 DOI: 10.1093/cid/ciaa873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/19/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Rifampicin (RIF) resistance is highly correlated with isoniazid (INH) resistance and used as proxy for multidrug-resistant tuberculosis (MDR-TB). Using MTBDRplus as a comparator, we evaluated the predictive value of Xpert MTB/RIF (Xpert)-detected RIF resistance for MDR-TB in eastern Democratic Republic of the Congo (DRC). METHODS We conducted a cross-sectional study involving data from new or retreatment pulmonary adult TB cases evaluated between July 2013 and December 2016. Separate, paired sputa for smear microscopy and MTBDRplus were collected. Xpert testing was performed subject to the availability of Xpert cartridges on sample remnants after microscopy. RESULTS Among 353 patients, 193 (54.7%) were previously treated and 224 (63.5%) were MTBDRplus TB positive. Of the 224, 43 (19.2%) were RIF monoresistant, 11 (4.9%) were INH monoresistant, 53 (23.7%) had MDR-TB, and 117 (52.2%) were RIF and INH susceptible. Overall, among the 96 samples detected by MTBDRplus as RIF resistant, 53 (55.2%) had MDR-TB. Xpert testing was performed in 179 (50.7%) specimens; among these, 163 (91.1%) were TB positive and 73 (44.8%) RIF resistant. Only 45/73 (61.6%) Xpert-identified RIF-resistant isolates had concomitant MTBDRplus-detected INH resistance. Xpert had a sensitivity of 100.0% (95% CI, 92.1-100.0) for detecting RIF resistance but a positive-predictive value of only 61.6% (95% CI, 49.5-72.8) for MDR-TB. The most frequent mutations associated with RIF and INH resistance were S531L and S315T1, respectively. CONCLUSIONS In this high-risk MDR-TB study population, Xpert had low positive-predictive value for the presence of MDR-TB. Comprehensive resistance testing for both INH and RIF should be performed in this setting.
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Affiliation(s)
- Bertin C Bisimwa
- Laboratoire de Recherche Biomédicale Professeur André Lurhuma, Université Catholique de Bukavu, Bukavu, Democratic Republic of Congo.,Institut Supérieur des Techniques Médicales, Bukavu, Democratic Republic of Congo
| | - Jean B Nachega
- Departments of Epidemiology, Infectious Diseases, and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA.,Department of Medicine and Center for Infectious Diseases, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Departments of Epidemiology and International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Robin M Warren
- Division of Science and Technology (DST) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Grant Theron
- Division of Science and Technology (DST) Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - John Z Metcalfe
- Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California, San Francisco, San Francisco, California, USA
| | - Maunank Shah
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Andreas H Diacon
- Task Foundation and Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nadia A Sam-Agudu
- International Research Center of Excellence, Institute of Human Virology Nigeria, Abuja, Nigeria.,Division of Epidemiology and Prevention, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marcel Yotebieng
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - André N H Bulabula
- Department of Pediatrics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Infection Control Africa Network, Cape Town, South Africa
| | - Patrick D M C Katoto
- Centre for Environment and Health, Department of Public Health and Primary Care, Laboratory of Pneumology, Katholieke Universiteit Leuven, Leuven, Belgium.,Department of Internal Medicine, Faculty of Medicine, Université Catholique de Bukavu, Bukavu, Democratic Republic of Congo
| | - Jean-Paul Chirambiza
- National TB Program, Provincial Anti-Leprosy and TB Coordination, Bukavu, Democratic Republic of Congo
| | - Rosette Nyota
- National TB Program, Provincial Anti-Leprosy and TB Coordination, Bukavu, Democratic Republic of Congo
| | - Freddy M Birembano
- National TB Program, Provincial Anti-Leprosy and TB Coordination, Bukavu, Democratic Republic of Congo
| | - Eric M Musafiri
- National TB Program, Provincial Anti-Leprosy and TB Coordination, Bukavu, Democratic Republic of Congo
| | - Sifa Byadunia
- Institut Supérieur des Techniques Médicales, Bukavu, Democratic Republic of Congo
| | - Esto Bahizire
- Center for Tropical Diseases and Global Health, Catholic University of Bukavu, Bukavu, Democratic Republic of the Congo.,Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya.,Centre of Research in Epidemiology, Biostatistics, and Clinical Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Michel K Kaswa
- National Tuberculosis Program, Ministry of Health, Kinshasa, Democratic Republic of Congo
| | - Steven Callens
- Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Zacharie M Kashongwe
- Laboratoire de Recherche Biomédicale Professeur André Lurhuma, Université Catholique de Bukavu, Bukavu, Democratic Republic of Congo.,Institut Supérieur des Techniques Médicales, Bukavu, Democratic Republic of Congo.,Cliniques Universitaire de Kinshasa, Université Nationale de Kinshasa, Kinshasa, Democratic Republic of Congo
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11
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Rapid Molecular Diagnosis of Tuberculosis and Its Resistance to Rifampicin and Isoniazid with Automated MDR/MTB ELITe MGB ® Assay. Antibiotics (Basel) 2021; 10:antibiotics10070797. [PMID: 34208899 PMCID: PMC8300793 DOI: 10.3390/antibiotics10070797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/22/2022] Open
Abstract
The MDR/MTB ELITe MGB® kit (ELITech) carried on the ELITe InGenius® platform is a new real-time PCR assay allowing automated extraction and detection of DNA of the Mycobacterium tuberculosis complex (MTB) and mutations in the rpoB and katG genes and inhA promoter region (pro-inhA) associated to resistance to rifampicin and isoniazid, the two markers of multidrug-resistant TB (MDR). We assessed the performances of the test on a collection of strains (n = 54) and a set of clinical samples (n = 242) from routine practice, comparatively to TB diagnosis and genotypic drug susceptibility testing (gDST) as references. Regarding the 242 clinical samples, the sensitivity and specificity of MTB detection by ELITe were 90.9% and 97.5%, respectively. For the detection of resistance-conferring mutations on positive clinical samples, we observed perfect agreement with gDST for katG and pro-inhA (κ = 1.0) and two discordant results for rpoB (κ = 0.82). Considering the 54 cultured strains, very good agreement with gDST was observed for the detection of the 25 distinct mutations in rpoB, katG, and pro-inhA, (κ = 0.95, 0.88, and 0.95, respectively). In conclusion, the automated MDR/MTB ELITe MGB® assay shows great promise and appears to be a valuable tool for rapid detection of pre-MDR- and MDR-TB directly from clinical specimens.
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12
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Reta MA, Alemnew B, Abate BB, Fourie PB. Prevalence of drug resistance-conferring mutations associated with isoniazid- and rifampicin-resistant Mycobacterium tuberculosis in Ethiopia: a systematic review and meta-analysis. J Glob Antimicrob Resist 2021; 26:207-218. [PMID: 34214698 DOI: 10.1016/j.jgar.2021.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVES Globally, the incidence and mortality of tuberculosis (TB) are declining; however, low detection of drug-resistant disease threatens to reverse current progress toward global TB control. Multiple rapid molecular diagnostic tests have recently been developed to detect genetic mutations in Mycobacterium tuberculosis (Mtb) known to confer drug resistance. However, their utility depends on the frequency and distribution of resistance-associated mutations in the pathogen population. This review aimed to assess the prevalence of gene mutations associated with rifampicin (RIF)- and isoniazid (INH)-resistant Mtb in Ethiopia. METHODS We searched the literature in PubMed/MEDLINE, Web of Science, Scopus and Cochrane Library. Data analysis was conducted in Stata 11. RESULTS Totally, 909 (95.8%) of 949 INH-resistant Mtb isolates had detectable gene mutations: 95.8% in katG315 and 5.9% in the inhA promoter region. Meta-analysis resulted in an estimated pooled prevalence of katGMUT1(S315T1) of 89.2% (95% CI 81.94-96.43%) and a pooled prevalence of inhAMUT1(C15T) of 77.5% (95% CI 57.84-97.13%). Moreover, 769 (90.8%) of 847 RIF-resistant strains had detectable rpoB gene mutations. Meta-analysis resulted in a pooled prevalence of rpoBMUT3(S531L) of 74.2% (95% CI 66.39-82.00%). CONCLUSION RIF-resistant Mtb were widespread, particularly those harbouring rpoB(S531L) mutation. Similarly, INH-resistant Mtb with katG(S315T1) and inhA(C15T) mutations were common. Tracking S531L, S315T1 and C15T mutations among RIF- and INH-resistant isolates, respectively, would be diagnostically and epidemiologically valuable. Rapid diagnosis of RIF- and INH-resistant Mtb would expedite modification of TB treatment regimens, and proper timely infection control interventions could reduce the risk of development and transmission of multidrug-resistant TB.
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Affiliation(s)
- Melese Abate Reta
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Department of Medical Laboratory Sciences, College of Health Sciences, Woldia University, Woldia, Ethiopia.
| | - Birhan Alemnew
- Department of Medical Laboratory Sciences, College of Health Sciences, Woldia University, Woldia, Ethiopia
| | - Biruk Beletew Abate
- Department of Nursing, College of Health Sciences, Woldia University, Woldia, Ethiopia
| | - P Bernard Fourie
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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13
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Sheikh BA, Bhat BA, Mehraj U, Mir W, Hamadani S, Mir MA. Development of New Therapeutics to Meet the Current Challenge of Drug Resistant Tuberculosis. Curr Pharm Biotechnol 2021; 22:480-500. [PMID: 32600226 DOI: 10.2174/1389201021666200628021702] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/01/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is a prominent infective disease and a major reason of mortality/ morbidity globally. Mycobacterium tuberculosis causes a long-lasting latent infection in a significant proportion of human population. The increasing burden of tuberculosis is mainly caused due to multi drug-resistance. The failure of conventional treatment has been observed in large number of cases. Drugs that are used to treat extensively drug-resistant tuberculosis are expensive, have limited efficacy, and have more side effects for a longer duration of time and are often associated with poor prognosis. To regulate the emergence of multidrug resistant tuberculosis, extensively drug-resistant tuberculosis and totally drug resistant tuberculosis, efforts are being made to understand the genetic/molecular basis of target drug delivery and mechanisms of drug resistance. Understanding the molecular approaches and pathology of Mycobacterium tuberculosis through whole genome sequencing may further help in the improvement of new therapeutics to meet the current challenge of global health. Understanding cellular mechanisms that trigger resistance to Mycobacterium tuberculosis infection may expose immune associates of protection, which could be an important way for vaccine development, diagnostics, and novel host-directed therapeutic strategies. The recent development of new drugs and combinational therapies for drug-resistant tuberculosis through major collaboration between industry, donors, and academia gives an improved hope to overcome the challenges in tuberculosis treatment. In this review article, an attempt was made to highlight the new developments of drug resistance to the conventional drugs and the recent progress in the development of new therapeutics for the treatment of drugresistant and non-resistant cases.
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Affiliation(s)
- Bashir A Sheikh
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Basharat A Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Umar Mehraj
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Wajahat Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Suhail Hamadani
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Manzoor A Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
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14
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Khawbung JL, Nath D, Chakraborty S. Drug resistant Tuberculosis: A review. Comp Immunol Microbiol Infect Dis 2020; 74:101574. [PMID: 33249329 DOI: 10.1016/j.cimid.2020.101574] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) was announced as a global emergency in 1993. There was an alarming counter attack of TB worldwide. However, when it was known that TB can be cured completely, the general public became ignorant towards the infection. The pathogenic organism Mycobacterium tuberculosis continuously evolved to resist the antagonist drugs. This has led to the outbreak of resistant strain that gave rise to "Multi Drug Resistant-Tuberculosis" and "Extensively Drug Resistant Tuberculosis" that can still be cured with a lower success rate. While the mechanism of resistance proceeds further, it ultimately causes unmanageable totally drug resistant TB (TDR-TB). Studying the molecular mechanisms underlying the resistance to drugs would help us grasp the genetics and pathophysiology of the disease. In this review, we present the molecular mechanisms behind Mycobacterium tolerance to drugs and their approach towards the development of multi-drug resistant, extremely drug resistant and totally drug resistant TB.
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Affiliation(s)
| | - Durbba Nath
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
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15
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Vale N, Duarte D, Correia A, Alves C, Figueiredo P, Santos HA. New insights into ethionamide metabolism: influence of oxidized methionine on its degradation path. RSC Med Chem 2020; 11:1423-1428. [PMID: 34095849 DOI: 10.1039/d0md00253d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/17/2020] [Indexed: 11/21/2022] Open
Abstract
Ethionamide (ETH) is a commercial drug, used as a second-line resource to neutralize Mycobacterium tuberculosis infections. It is proven that its metabolization in the organism leads to the formation of the active form of the drug, but some metabolic pathways may lead to the loss of its activity. Our work proved that the presence of oxidized methionine in cells could influence ETH's degradation, leading to the appearance of an inactive metabolite that is detectable by HPLC and mass spectrometry. In addition, it was found this process increases with the degree of methionine oxidation. This study contributes to a better understanding of ethionamide's metabolism in living organisms, and can help in the design of new drugs or ethionamide boosters for the combat of multidrug resistant tuberculosis.
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Affiliation(s)
- Nuno Vale
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS) Rua Dr. Plácido da Costa 4200-450 Porto Portugal.,Faculty of Medicine, University of Porto Al. Prof. Hernâni Monteiro 4200-319 Porto Portugal
| | - Diana Duarte
- OncoPharma Research Group, Center for Health Technology and Services Research (CINTESIS) Rua Dr. Plácido da Costa 4200-450 Porto Portugal.,Laboratory of Pharmacology, Department of Drug Sciences, Faculty of Pharmacy of University of Porto Rua Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Alexandra Correia
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki FI-00014 Helsinki Finland
| | - Cláudia Alves
- Department of Chemistry and Biochemistry, Faculty of Sciences, LAQV/REQUIMTE, University of Porto Rua do Campo Alegre, 687 4169-007 Porto Portugal
| | - Patrícia Figueiredo
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki FI-00014 Helsinki Finland
| | - Hélder A Santos
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki FI-00014 Helsinki Finland.,Helsinki Institute of Life science (HiLIFE), University of Helsinki FI-00014 Helsinki Finland
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16
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Hsu LY, Lai LY, Hsieh PF, Lin TL, Lin WH, Tasi HY, Lee WT, Jou R, Wang JT. Two Novel katG Mutations Conferring Isoniazid Resistance in Mycobacterium tuberculosis. Front Microbiol 2020; 11:1644. [PMID: 32760384 PMCID: PMC7374161 DOI: 10.3389/fmicb.2020.01644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/24/2020] [Indexed: 12/04/2022] Open
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis, is among the top 10 leading causes of death worldwide. The treatment course for TB is challenging; it requires antibiotic administration for at least 6 months, and bacterial drug resistance makes treatment even more difficult. Understanding the mechanisms of resistance is important for improving treatment. To investigate new mechanisms of isoniazid (INH) resistance, we obtained three INH-resistant (INH-R) M. tuberculosis clinical isolates collected by the Taiwan Centers for Disease Control (TCDC) and sequenced genes known to harbor INH resistance-conferring mutations. Then, the relationship between the mutations and INH resistance of these three INH-R isolates was investigated. Sequencing of the INH-R isolates identified three novel katG mutations resulting in R146P, W341R, and L398P KatG proteins, respectively. To investigate the correlation between the observed INH-R phenotypes of the clinical isolates and these katG mutations, wild-type katG from H37Rv was expressed on a plasmid (pMN437-katG) in the isolates, and their susceptibilities to INH were determined. The plasmid expressing H37Rv katG restored INH susceptibility in the two INH-R isolates encoding the W341R KatG and L398P KatG proteins. In contrast, no phenotypic change was observed in the KatG R146P isolate harboring pMN437-katG. H37Rv isogenic mutant with W341R KatG or L398P KatG was further generated. Both showed resistant to INH. In conclusion, W341R KatG and L398P KatG conferred resistance to INH in M. tuberculosis, whereas R146P KatG did not affect the INH susceptibility of M. tuberculosis.
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Affiliation(s)
- Li-Yu Hsu
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li-Yin Lai
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Fang Hsieh
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tzu-Lung Lin
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wan-Hsuan Lin
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Taipei, Taiwan.,Diagnostics and Vaccine Center, Taiwan Centers for Disease Control, Taipei, Taiwan
| | - Hsing-Yuan Tasi
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Taipei, Taiwan.,Diagnostics and Vaccine Center, Taiwan Centers for Disease Control, Taipei, Taiwan
| | - Wei-Ting Lee
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Taipei, Taiwan.,Diagnostics and Vaccine Center, Taiwan Centers for Disease Control, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Taipei, Taiwan.,Diagnostics and Vaccine Center, Taiwan Centers for Disease Control, Taipei, Taiwan
| | - Jin-Town Wang
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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17
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Advanced integrative sensing technologies for detection of drug-resistant tuberculosis in point-of-care settings. SENSORS INTERNATIONAL 2020. [DOI: 10.1016/j.sintl.2020.100036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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18
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Chang Y, Kim S, Kim Y, Ei PW, Hwang D, Lee J, Chang CL, Lee H. Evaluation of the QuantaMatrix Multiplexed Assay Platform for Molecular Diagnosis of Multidrug- and Extensively Drug-Resistant Tuberculosis Using Clinical Strains Isolated in Myanmar. Ann Lab Med 2019; 40:142-147. [PMID: 31650730 PMCID: PMC6821996 DOI: 10.3343/alm.2020.40.2.142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/06/2019] [Accepted: 10/11/2019] [Indexed: 11/25/2022] Open
Abstract
Background Although the incidence of tuberculosis (TB) is decreasing, cases of multidrug-resistant (MDR) TB and extensively drug-resistant (XDR) TB continue to increase. As conventional phenotype drug susceptibility testing (pDST) takes six to eight weeks, molecular assays are widely used to determine drug resistance. we developed QuantaMatrix Multiplexed Assay Platform (QMAP) MDR/XDR assay (QuantaMatrix Inc., Seoul, Korea) that can simultaneously detect mutations related to both first- and second-line drug resistance (rifampin, isoniazid, ethambutol, fluoroquinolones, second-line injectable drugs, and streptomycin). Methods We used 190 clinical Mycobacterium tuberculosis (MTB) strains isolated from Myanmar, compared QMAP and pDST results, and determined concordance rates. Additionally, we performed sequence analyses for discordant results. Results QMAP results were 87.9% (167/190) concordant with pDST results. In the 23 isolates with discordant results, the QMAP and DNA sequencing results completely matched. Conclusions The QMAP MDR/XDR assay can detect all known DNA mutations associated with drug resistance for both MDR- and XDR-MTB strains. It can be used for molecular diagnosis of MDR- and XDR-TB to rapidly initiate appropriate anti-TB drug therapy.
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Affiliation(s)
- Yunhee Chang
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Seoyong Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Yeun Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Phyu Win Ei
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Dasom Hwang
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Jongseok Lee
- International Tuberculosis Research Center, Changwon, Korea
| | - Chulhun L Chang
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea.
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19
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Nguyen TNA, Anton-Le Berre V, Bañuls AL, Nguyen TVA. Molecular Diagnosis of Drug-Resistant Tuberculosis; A Literature Review. Front Microbiol 2019; 10:794. [PMID: 31057511 PMCID: PMC6477542 DOI: 10.3389/fmicb.2019.00794] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/28/2019] [Indexed: 11/13/2022] Open
Abstract
Drug-resistant tuberculosis is a global health problem that hinders the progress of tuberculosis eradication programs. Accurate and early detection of drug-resistant tuberculosis is essential for effective patient care, for preventing tuberculosis spread, and for limiting the development of drug-resistant strains. Culture-based drug susceptibility tests are the gold standard method for the detection of drug-resistant tuberculosis, but they are time-consuming and technically challenging, especially in low- and middle-income countries. Nowadays, different nucleic acid-based assays that detect gene mutations associated with resistance to drugs used to treat tuberculosis are available. These tests vary in type and number of targets and in sensitivity and specificity. In this review, we will describe the available molecular tests for drug-resistant tuberculosis detection and discuss their advantages and limitations.
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Affiliation(s)
- Thi Ngoc Anh Nguyen
- UMR MIVEGEC, Institute of Research for Development, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France.,Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.,LMI Drug Resistance in South East Asia, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Anne-Laure Bañuls
- UMR MIVEGEC, Institute of Research for Development, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France.,LMI Drug Resistance in South East Asia, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thi Van Anh Nguyen
- Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.,LMI Drug Resistance in South East Asia, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
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20
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Advani J, Verma R, Chatterjee O, Pachouri PK, Upadhyay P, Singh R, Yadav J, Naaz F, Ravikumar R, Buggi S, Suar M, Gupta UD, Pandey A, Chauhan DS, Tripathy SP, Gowda H, Prasad TSK. Whole Genome Sequencing of Mycobacterium tuberculosis Clinical Isolates From India Reveals Genetic Heterogeneity and Region-Specific Variations That Might Affect Drug Susceptibility. Front Microbiol 2019; 10:309. [PMID: 30863380 PMCID: PMC6399466 DOI: 10.3389/fmicb.2019.00309] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/05/2019] [Indexed: 11/15/2022] Open
Abstract
Whole genome sequencing (WGS) of Mycobacterium tuberculosis has been constructive in understanding its evolution, genetic diversity and the mechanisms involved in drug resistance. A large number of sequencing efforts from across the globe have revealed genetic diversity among clinical isolates and the genetic determinants for their resistance to anti-tubercular drugs. Considering the high TB burden in India, the availability of WGS studies is limited. Here we present, WGS results of 200 clinical isolates of M. tuberculosis from North India which are categorized as sensitive to first-line drugs, mono-resistant, multi-drug resistant and pre-extensively drug resistant isolates. WGS revealed that 20% of the isolates were co-infected with M. tuberculosis and non-tuberculous mycobacteria species. We identified 12,802 novel genetic variations in M. tuberculosis isolates including 343 novel SNVs in 38 genes which are known to be associated with drug resistance and are not currently used in the diagnostic kits for detection of drug resistant TB. We also identified M. tuberculosis lineage 3 to be predominant in the northern region of India. Additionally, several novel SNVs, which may potentially confer drug resistance were found to be enriched in the drug resistant isolates sampled. This study highlights the significance of employing WGS in diagnosis and for monitoring further development of MDR-TB strains.
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Affiliation(s)
- Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bengaluru, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bengaluru, India
| | - Oishi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bengaluru, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.,School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Praveen Kumar Pachouri
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Prashant Upadhyay
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Rajesh Singh
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Jitendra Yadav
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Farah Naaz
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Raju Ravikumar
- Department of Neuromicrobiology, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Shashidhar Buggi
- Intermediate Reference Laboratory, State Tuberculosis Training and Demonstration Centre, Someshwaranagar, SDSTRC and RGICD Campus, Bengaluru, India.,Department of Cardio Thoracic Surgery, Super Specialty State Referral Hospital for Chest Diseases, Someshwaranagar First Main Road, Dharmaram College Post, Bengaluru, India
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India
| | - Umesh D Gupta
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bengaluru, India.,Manipal Academy of Higher Education, Manipal, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Devendra S Chauhan
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Srikanth Prasad Tripathy
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bengaluru, India.,Manipal Academy of Higher Education, Manipal, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bengaluru, India.,Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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21
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Wood HN, Venken T, Willems H, Jacobs A, Reis AJ, Almeida da Silva PE, Homolka S, Niemann S, Rohde KH, Hooyberghs J. Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization. PLoS One 2019; 14:e0212064. [PMID: 30730960 PMCID: PMC6366778 DOI: 10.1371/journal.pone.0212064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/25/2019] [Indexed: 11/19/2022] Open
Abstract
In Mycobacterium tuberculosis (Mtb) the detection of single nucleotide polymorphisms (SNPs) is of high importance both for diagnostics, since drug resistance is primarily caused by the acquisition of SNPs in multiple drug targets, and for epidemiological studies in which strain typing is performed by SNP identification. To provide the necessary coverage of clinically relevant resistance profiles and strain types, nucleic acid-based measurement techniques must be able to detect a large number of potential SNPs. Since the Mtb problem is pressing in many resource-poor countries, requiring low-cost point-of-care biosensors, this is a non-trivial technological challenge. This paper presents a proof-of-concept in which we chose simple DNA-DNA hybridization as a sensing principle since this can be transferred to existing low-cost hardware platforms, and we pushed the multiplex boundaries of it. With a custom designed probe set and a physicochemical-driven data analysis it was possible to simultaneously detect the presence of SNPs associated with first- and second-line drug resistance and Mtb strain typing. We have demonstrated its use for the identification of drug resistance and strain type from a panel of phylogenetically diverse clinical strains. Furthermore, reliable detection of the presence of a minority population (<5%) of drug-resistant Mtb was possible.
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Affiliation(s)
- Hillary N. Wood
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Tom Venken
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Hanny Willems
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - An Jacobs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Ana Júlia Reis
- Laboratory of Tuberculosis, Faculty of Medicine, Universidade Federal do Rio Grande- FURG, Rio Grande so Sul, RS, Brazil
| | - Pedro Eduardo Almeida da Silva
- Laboratory of Tuberculosis, Faculty of Medicine, Universidade Federal do Rio Grande- FURG, Rio Grande so Sul, RS, Brazil
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Borstel, Germany
| | - Kyle H. Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
- * E-mail:
| | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
- Theoretical Physics, Hasselt University, Diepenbeek, Belgium
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22
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Tavanaee Sani A, Ashna H, Kaffash A, Khaledi A, Ghazvini K. Mutations of rpob Gene Associated with Rifampin Resistance among Mycobacterium Tuberculosis Isolated in Tuberculosis Regional Reference Laboratory in Northeast of Iran during 2015-2016. Ethiop J Health Sci 2018; 28:299-304. [PMID: 29983529 PMCID: PMC6016358 DOI: 10.4314/ejhs.v28i3.7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Drug resistance is a leading concern in control of TB. Resistance against rifampin as one of the most important drugs in the treatment of Mycobacterium tuberculosis is caused by mutations in the 81-base pair region of the rpoB gene encoding the β-subunit of RNA polymerase. This study aimed to characterize the mutations in the rpoB gene associated with rifampin resistance among M. tuberculosis. Methods This study was conducted on referred samples of patients who did not respond to anti-TB treatment, in Tuberculosis Regional Reference Laboratory at Shariati Hospital. Drug susceptibility of M. tuberculosis isolates was surveyed using a proportional method on LJ medium. The isolates with resistant to rifampin were reconfirmed and then the rpoB gene was amplified and sequenced. Results Among 27 resistant cases, 8, 11 and 8 people were from Iran, Afghanistan, and Turkmenistan, respectively. In 26 out of 27 isolates, rpoB gene mutations were observed. The most prevalent mutations belonged to the codon 53. The most prevalent mutations belonged to the TCG (Ser) 531TTG (leu) with prevalence 51.8% (n=14), and GAC (Asp)516TAC (Tyr), CAC (His) 526GAC (Asp) and CAC (His) 526TAC(Tyr) mutations with prevalence 14.8%(n=4). Twenty-three isolates had just one mutation. Conclusion The use of rpoB gene sequencing led to the lack of the need for growth of the organism in the culture medium, the direct use of clinical samples, reduction of biological risks and a detection about 96.3% of MDR TB cases lowering the cost of the treatment.
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Affiliation(s)
- Ashraf Tavanaee Sani
- Infectious Diseases Department, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Habib Ashna
- Infectious Diseases Department, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Afsaneh Kaffash
- Infectious Diseases Department, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Azad Khaledi
- Infectious Diseases Research Center, Kashan University of Medical Sciences, Kashan, IR Iran.,Department of Microbiology and Immunology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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23
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Djemal SE, Camperio C, Armas F, Siala M, Smaoui S, Messadi-Akrout F, Gdoura R, Marianelli C. Detection of a streptomycin-resistant Mycobacterium bovis strain through antitubercular drug susceptibility testing of Tunisian Mycobacterium tuberculosis complex isolates from cattle. BMC Vet Res 2018; 14:296. [PMID: 30268120 PMCID: PMC6162935 DOI: 10.1186/s12917-018-1623-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/24/2018] [Indexed: 01/06/2023] Open
Abstract
Background A rising isolation trend of drug-resistant M. bovis from human clinical cases is documented in the literature. Here we assessed Mycobacterium tuberculosis complex isolates from cattle for drug susceptibility by the gold standard agar proportion method and a simplified resazurin microtitre assay (d-REMA). A total of 38 M. tuberculosis complex strains, including M. bovis (n = 36) and M. caprae (n = 2) isolates, from cattle in Tunisia were tested against isoniazid, rifampin, streptomycin, ethambutol, kanamycin and pyrazinamide. Results M. caprae isolates were found to be susceptible to all test drugs. All M. bovis strains were resistant to pyrazinamide, as expected. In addition, one M. bovis isolate showed high-level resistance to streptomycin (MIC > 500.0 μg/ml). Concordant results with the two methods were found. The most common target genes associated with streptomycin resistance, namely the rrs, rpsL and gidB genes, were DNA sequenced. A non-synonymous mutation at codon 43 (K43R) was found in the rpsL gene. To the best of our knowledge, this is the first report describing the isolation of a streptomycin-resistant M. bovis isolate from animal origin. Conclusions Antitubercular drug susceptibility testing of M. bovis isolates from animals should be performed in settings where bTB is endemic in order to estimate the magnitude of the risk of drug-resistant tuberculosis transmission to humans.
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Affiliation(s)
- Saif Eddine Djemal
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, University of Sfax, Sfax, Tunisia
| | - Cristina Camperio
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Federica Armas
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Mariam Siala
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, University of Sfax, Sfax, Tunisia.,Department of Biology, Preparatory Institute for Engineering Studies, University of Sfax, Sfax, Tunisia
| | - Salma Smaoui
- Department of Microbiology, Regional Hygiene Care Mycobacteriology Laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia.,Department of Microbiology, National Reference Laboratory of Mycobacteria, Research Unit (UR12SP18), A. Mami University Hospital of Pneumology, Ariana, Tunisia
| | - Feriele Messadi-Akrout
- Department of Biology, Preparatory Institute for Engineering Studies, University of Sfax, Sfax, Tunisia.,Department of Microbiology, Regional Hygiene Care Mycobacteriology Laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
| | - Radhouane Gdoura
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, University of Sfax, Sfax, Tunisia
| | - Cinzia Marianelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
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24
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Hegeto LA, Caleffi-Ferracioli KR, Perez de Souza J, Almeida ALD, Nakamura de Vasconcelos SS, Barros ILE, Canezin PH, Campanerut-Sá PAZ, Scodro RBDL, Siqueira VLD, Teixeira JJV, Cardoso RF. Promising Antituberculosis Activity of Piperine Combined with Antimicrobials: A Systematic Review. Microb Drug Resist 2018; 25:120-126. [PMID: 30096263 DOI: 10.1089/mdr.2018.0107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Piperine, a bioactive compound from Piper nigrum and Piper longum, has shown promising activity as efflux pump (EP) inhibitor and as adjunct in treatment of tuberculosis (TB). The present systematic review investigated scientific studies of the activity of piperine against mycobacteria, with a focus on its mechanism of action, drug interactions, and antimycobacterial activity. A broad and rigorous literature search of three electronic databases (PubMed, Web of Knowledge, and LILACS) was performed according to the PRISMA statement. We considered studies that were published up to December 1, 2017. Google Scholar was also searched to increase the number of publications. We searched for articles using the search terms "piperine" and "Mycobacterium spp." The search yielded a total of 225 articles. After removing duplicate publications, 208 publications remained. Of these, we evaluated the full text of 13 articles. After applying the inclusion criteria, eight studies were included in the present systematic review. The results of the systematic review showed that piperine has promising anti-TB activity, mainly when combined with antimicrobials, and plays an important role as an EP inhibitor.
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Affiliation(s)
- Laíse Adriane Hegeto
- 1 Postgraduate Program in Health Sciences, State University of Maringa , Maringa, Brazil
| | - Katiany R Caleffi-Ferracioli
- 2 Department of Clinical Analysis and Biomedicine, State University of Maringa , Maringa, Brazil
- 3 Postgraduate Program in Biosciences and Physiopathology, State University of Maringa , Maringa, Brazil
| | - JoãoVitor Perez de Souza
- 3 Postgraduate Program in Biosciences and Physiopathology, State University of Maringa , Maringa, Brazil
| | - Aryadne Larissa de Almeida
- 3 Postgraduate Program in Biosciences and Physiopathology, State University of Maringa , Maringa, Brazil
| | | | | | - Pedro Henrique Canezin
- 1 Postgraduate Program in Health Sciences, State University of Maringa , Maringa, Brazil
| | | | - Regiane Bertin de Lima Scodro
- 1 Postgraduate Program in Health Sciences, State University of Maringa , Maringa, Brazil
- 2 Department of Clinical Analysis and Biomedicine, State University of Maringa , Maringa, Brazil
| | - Vera Lucia Dias Siqueira
- 2 Department of Clinical Analysis and Biomedicine, State University of Maringa , Maringa, Brazil
- 3 Postgraduate Program in Biosciences and Physiopathology, State University of Maringa , Maringa, Brazil
| | - Jorge Juarez Vieira Teixeira
- 1 Postgraduate Program in Health Sciences, State University of Maringa , Maringa, Brazil
- 2 Department of Clinical Analysis and Biomedicine, State University of Maringa , Maringa, Brazil
- 3 Postgraduate Program in Biosciences and Physiopathology, State University of Maringa , Maringa, Brazil
| | - Rosilene Fressatti Cardoso
- 1 Postgraduate Program in Health Sciences, State University of Maringa , Maringa, Brazil
- 2 Department of Clinical Analysis and Biomedicine, State University of Maringa , Maringa, Brazil
- 3 Postgraduate Program in Biosciences and Physiopathology, State University of Maringa , Maringa, Brazil
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25
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Hegeto LA, Caleffi-Ferracioli KR, Nakamura-Vasconcelos SS, Almeida ALD, Baldin VP, Nakamura CV, Siqueira VLD, Scodro RBL, Cardoso RF. In vitro combinatory activity of piperine and anti-tuberculosis drugs in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2018; 111:35-40. [PMID: 30029912 DOI: 10.1016/j.tube.2018.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/07/2018] [Accepted: 05/12/2018] [Indexed: 01/14/2023]
Abstract
Tuberculosis (TB) is an important public health problem worldwide and the emergence of multidrug-resistant (MDR) TB and extensively drug-resistant (XDR) TB worsened the global context. The resistance in Mycobacterium tuberculosis, the causative agent of TB, can partially derive from efflux pumps (EPs) activity in plasma membrane. Due to the recent discovery of piperine (PIP), an organic alkaloid compound, increasing the bioavailability of various drugs, the current assay evaluated the combined activity of PIP and anti-TB drugs in susceptible and resistant M. tuberculosis clinical isolates. The minimum inhibitory concentrations for isoniazid, rifampicin, ethambutol, streptomycin and PIP were determined by resazurin microtiter assay and the combined effects of anti-TB drugs with PIP determined by resazurin drug combination microtiter assay and time-kill curve. The efflux pump inhibitor activity of PIP was determined by bromide accumulation assay and cytotoxicity carried out in VERO cells and J774. A1 macrophages. PIP showed to have EPI activity and RIF + PIP and SM + PIP combinations showed synergistic effect, but low effect in enhancing the killing in M. tuberculosis H37Rv and in the clinical isolates studied, which had different resistance profiles. Future studies are needed to further clarify the importance of PIP as an adjunctive drug in the therapy against TB.
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Affiliation(s)
- Laíse Adriane Hegeto
- Postgraduate Program in Health Science, State University of Maringa, Parana, Brazil; Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Parana, Brazil
| | - Katiany R Caleffi-Ferracioli
- Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Parana, Brazil.
| | - Sandra S Nakamura-Vasconcelos
- Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Parana, Brazil
| | - Aryadne Larissa de Almeida
- Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Parana, Brazil
| | - Vanessa Pietrowski Baldin
- Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Parana, Brazil
| | | | - Vera Lúcia D Siqueira
- Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Parana, Brazil
| | - Regiane B L Scodro
- Postgraduate Program in Health Science, State University of Maringa, Parana, Brazil; Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Parana, Brazil
| | - Rosilene Fressatti Cardoso
- Postgraduate Program in Health Science, State University of Maringa, Parana, Brazil; Laboratory of Medical Bacteriology, Department of Clinical Analysis and Biomedicine, State University of Maringa, Parana, Brazil
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26
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Analysis of isoniazid and rifampicin resistance in Mycobacterium tuberculosis isolates in Morocco using GenoType® MTBDRplus assay. J Glob Antimicrob Resist 2018; 12:197-201. [DOI: 10.1016/j.jgar.2017.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/18/2017] [Accepted: 09/23/2017] [Indexed: 01/13/2023] Open
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27
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Rapid Microarray-Based Detection of Rifampin, Isoniazid, and Fluoroquinolone Resistance in Mycobacterium tuberculosis by Use of a Single Cartridge. J Clin Microbiol 2018; 56:JCM.01249-17. [PMID: 29212699 PMCID: PMC5786735 DOI: 10.1128/jcm.01249-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/23/2017] [Indexed: 02/07/2023] Open
Abstract
The rapid and robust identification of mutations in Mycobacterium tuberculosis complex (MTBC) strains mediating multidrug-resistant (MDR) and extensively drug-resistant (XDR) phenotypes is crucial to combating the MDR tuberculosis (TB) epidemic. Currently available molecular anti-TB drug susceptibility tests either are restricted to a single target or drug (i.e., the Xpert MTB/RIF test) or present a risk of cross-contamination due to the design limitations of the open platform (i.e., line probe assays). With a good understanding of the technical and commercial boundaries, we designed a test cartridge based on an oligonucleotide array into which dried reagents are introduced and which has the ability to identify MTBC strains resistant to isoniazid, rifampin, and the fluoroquinolones. The melting curve assay interrogates 43 different mutations in the rifampin resistance-determining region (RRDR) of rpoB, rpoB codon 572, katG codon 315, the inhA promoter region, and the quinolone resistance-determining region (QRDR) of gyrA in a closed cartridge system within 90 min. Assay performance was evaluated with 265 clinical MTBC isolates, including MDR/XDR, non-MDR, and fully susceptible isolates, from a drug resistance survey performed in Swaziland in 2009 and 2010. In 99.5% of the cases, the results were consistent with data previously acquired utilizing Sanger sequencing. The assay, which uses a closed cartridge system in combination with a battery-powered Alere q analyzer and which has the potential to extend the current gene target panel, could serve as a rapid and robust point-of-care test in settings lacking a comprehensive molecular laboratory infrastructure to differentiate TB patients infected with MDR and non-MDR strains and to assist clinicians with their early treatment decisions.
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28
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Jeanes C, O'Grady J. Diagnosing tuberculosis in the 21st century - Dawn of a genomics revolution? Int J Mycobacteriol 2018; 5:384-391. [PMID: 27931678 DOI: 10.1016/j.ijmyco.2016.11.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Tuberculosis (TB) ranks alongside HIV as the leading cause of death worldwide, killing 1.5million people in 2014. Traditional laboratory techniques do not provide sufficiently rapid results to inform clinicians on appropriate treatment, especially in the face of increasingly prevalent drug-resistant TB. Rapid molecular methods such as PCR and LAMP are vital tools in the fight against TB, however, rapid advances in next generation sequencing (NGS) technology are allowing increasingly rapid and accurate sequencing of entire bacterial genomes at ever decreasing cost, providing unprecedented depth of information. These advances mean NGS stands to revolutionise the diagnosis and epidemiological study of Mycobacterium tuberculosis infection. This review focuses on current applications of NGS for TB diagnosis including sequencing cultured isolates to predict drug resistance and, more desirably, direct diagnostic metagenomic sequencing of clinical samples. Also discussed is the potential impact of NGS on the epidemiological study of TB and some of the key challenges that need to be overcome to enable this promising technology to be translated into routine use.
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Affiliation(s)
- Christopher Jeanes
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norfolk NR4 7TJ, United Kingdom.
| | - Justin O'Grady
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norfolk NR4 7TJ, United Kingdom.
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29
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Donnellan S, Stone V, Johnston H, Giardiello M, Owen A, Rannard S, Aljayyoussi G, Swift B, Tran L, Watkins C, Stevenson K. Intracellular delivery of nano-formulated antituberculosis drugs enhances bactericidal activity. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/jin2.27] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samantha Donnellan
- Moredun Research Institute; Pentlands Science Park; Bush Loan Penicuik EH26 0PZ UK
- School of Engineering and Physical Sciences, Institute of Biological Chemistry, Biophysics and Bioengineering; Heriot-Watt University; Riccarton Edinburgh EH14 4AS UK
- Research Centre for Drugs and Diagnostics; Liverpool School of Tropical Medicine; Liverpool L3 5QA UK
| | - Vicki Stone
- School of Engineering and Physical Sciences, Institute of Biological Chemistry, Biophysics and Bioengineering; Heriot-Watt University; Riccarton Edinburgh EH14 4AS UK
| | - Helinor Johnston
- School of Engineering and Physical Sciences, Institute of Biological Chemistry, Biophysics and Bioengineering; Heriot-Watt University; Riccarton Edinburgh EH14 4AS UK
| | - Marco Giardiello
- Department of Chemistry; University of Liverpool; Crown Street Liverpool L69 3BX UK
| | - Andrew Owen
- Department of Chemistry; University of Liverpool; Crown Street Liverpool L69 3BX UK
| | - Steve Rannard
- Department of Chemistry; University of Liverpool; Crown Street Liverpool L69 3BX UK
| | - Ghaith Aljayyoussi
- Research Centre for Drugs and Diagnostics; Liverpool School of Tropical Medicine; Liverpool L3 5QA UK
| | - Benjamin Swift
- School of Veterinary Medicine and Science; University of Nottingham; Loughborough LE12 5RD UK
| | - Lang Tran
- Institute of Occupational Medicine; Research Avenue North; Riccarton Edinburgh EH14 4AP UK
| | - Craig Watkins
- Moredun Research Institute; Pentlands Science Park; Bush Loan Penicuik EH26 0PZ UK
| | - Karen Stevenson
- Moredun Research Institute; Pentlands Science Park; Bush Loan Penicuik EH26 0PZ UK
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30
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Clinical implication of novel drug resistance-conferring mutations in resistant tuberculosis. Eur J Clin Microbiol Infect Dis 2017; 36:2021-2028. [PMID: 28593375 DOI: 10.1007/s10096-017-3027-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
Abstract
Evolving novel and/or unfamiliar mutations are revolutionizing the pathways of antibiotic resistance of clinical tuberculosis. The accumulation and interaction of these poorly characterized mutations augment the complexity of resistant pathogenic strains and raise public health concerns. This article reviews our current understanding of the genetic changes that characterize drug resistance in tuberculosis and highlights the imperative for further investigations focusing on the effects of an individual mutation and interacting mutations with detailed strain epidemiology, particularly as these pertain to technology-limited countries with high tuberculosis incidence rates. Concomitantly, there is a need for the development, testing, and uptake of new tools for studying the effects of these mutations in drug resistance and fitness cost of the pathogen. Such genetic data are critical for effective localized and global tuberculosis control interventions and for accurate epidemiological predictions.
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31
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Ahamad S, Rahman S, Khan FI, Dwivedi N, Ali S, Kim J, Imtaiyaz Hassan M. QSAR based therapeutic management of M. tuberculosis. Arch Pharm Res 2017; 40:676-694. [PMID: 28456911 DOI: 10.1007/s12272-017-0914-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/06/2017] [Indexed: 01/09/2023]
Abstract
Mycobacterium tuberculosis is responsible for severe mortality and morbidity worldwide but, under-developed and developing countries are more prone to infection. In search of effective and wide-spectrum anti-tubercular agents, interdisciplinary approaches are being explored. Of the several approaches used, computer based quantitative structure activity relationship (QSAR) have gained momentum. Structure-based drug design and discovery implies a combined knowledge of accurate prediction of ligand poses with the good prediction and interpretation of statistically validated models derived from the 3D-QSAR approach. The validated models are generally used to screen a small combinatorial library of potential synthetic candidates to identify hits which further subjected to docking to filter out compounds as novel potential emerging drug molecules to address multidrug-resistant tuberculosis. Several newer models are integrated to QSAR methods which include different types of chemical and biological data, and simultaneous prediction of pharmacological activities including toxicities and/or other safety profiles to get new compounds with desired activity. In the process, several newer molecules have been identified which are now being assessed for their clinical efficacy. Present review deals with the advances made in the field highlighting overall future prospects of the development of anti-tuberculosis drugs.
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Affiliation(s)
- Shahzaib Ahamad
- Department of Biotechnology, School of Engineering & Technology, IFTM University, Lodhipur-Rajput, Delhi Road, Moradabad, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Faez Iqbal Khan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, 450001, China.,Department of Chemistry, Rhodes University, Grahamstown, 6140, South Africa
| | - Neeraja Dwivedi
- Department of Biotechnology, School of Engineering & Technology, IFTM University, Lodhipur-Rajput, Delhi Road, Moradabad, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 10025, India
| | - Jihoe Kim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea.
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 10025, India.
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32
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Vale N, Correia A, Silva S, Figueiredo P, Mäkilä E, Salonen J, Hirvonen J, Pedrosa J, Santos HA, Fraga A. Preparation and biological evaluation of ethionamide-mesoporous silicon nanoparticles against Mycobacterium tuberculosis. Bioorg Med Chem Lett 2016; 27:403-405. [PMID: 28057421 DOI: 10.1016/j.bmcl.2016.12.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/16/2022]
Abstract
Ethionamide (ETH) is an important second-line antituberculosis drug used for the treatment of patients infected with multidrug-resistant Mycobacterium tuberculosis. Recently, we reported that the loading of ETH into thermally carbonized-porous silicon (TCPSi) nanoparticles enhanced the solubility and permeability of ETH at different pH-values and also increased its metabolization process. Based on these results, we synthesized carboxylic acid functionalized thermally hydrocarbonized porous silicon nanoparticles (UnTHCPSi NPs) conjugated with ETH and its antimicrobial effect was evaluated against Mycobacterium tuberculosis strain H37Rv. The activity of the conjugate was increased when compared to free-ETH, which suggests that the nature of the synergy between the NPs and ETH is likely due to the weakening of the bacterial cell wall that improves conjugate-penetration. These ETH-conjugated NPs have great potential in reducing dosing frequency of ETH in the treatment of multidrug-resistant tuberculosis (MDR-TB).
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Affiliation(s)
- Nuno Vale
- UCIBIO/REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal.
| | - Alexandra Correia
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, Finland
| | - Sara Silva
- UCIBIO/REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Patrícia Figueiredo
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ermei Mäkilä
- Laboratory of Industrial Physics, Department of Physics and Astronomy, University of Turku, FI-20014, Finland
| | - Jarno Salonen
- Laboratory of Industrial Physics, Department of Physics and Astronomy, University of Turku, FI-20014, Finland
| | - Jouni Hirvonen
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, Finland
| | - Jorge Pedrosa
- Microbiology and Infection Research Domain, Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Hélder A Santos
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, Finland
| | - Alexandra Fraga
- Microbiology and Infection Research Domain, Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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33
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Thirumurugan R, Kathirvel M, Vallayyachari K, Surendar K, Samrot AV, Muthaiah M. Molecular analysis of rpoB gene mutations in rifampicin resistant Mycobacterium tuberculosis isolates by multiple allele specific polymerase chain reaction in Puducherry, South India. J Infect Public Health 2016; 8:619-25. [PMID: 26117709 DOI: 10.1016/j.jiph.2015.05.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 05/16/2015] [Indexed: 10/23/2022] Open
Abstract
BACKGROUND rpoB gene mutations in Mycobacterium tuberculosis (MTB) make the bacteria resistant to rifampicin. Thus, these mutations are surrogate markers for multi-drug resistance (MDR). The objective of this study was to evaluate an allele-specific multiplex-polymerase chain reaction (MAS-PCR) assay to detect mutations at codons 516, 526 and 531 of the rpoB gene. METHODS In total, 127 M. tuberculosis clinical isolates were subjected to standard drug susceptibility tests. A MAS-PCR assay was then performed to detect mutations in the rpoB gene. Three different allele-specific PCR assays were performed (single-step MAS-PCR) and the amplified products were sequenced. RESULTS Of the 127 isolates, 69 (54.3%) were multidrug resistant M. tuberculosis (MDR-TB), 21 (16.5%) were rifampicin mono-resistant and 37 (29.1%) were drug susceptible. The frequency of mutations at codons 531, 526 and 516 was 54.4%, 18.9% and 5.6%, respectively. A triple mutation was found in 4 (4.4%) isolates. Mutations in regions other than the 81-bp region were observed at codons 413 (11.1%), 511 (12.2%) and 521 (15.6%) of the rpoB gene. CONCLUSIONS The simplicity and specificity of the MAS-PCR assay allows for easy implementation in clinical laboratories to detect rifampicin drug resistance in MDR-TB strains.
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Affiliation(s)
- Ravibalan Thirumurugan
- Department of Microbiology, Intermediate Reference Laboratory, State TB Training and Demonstration Centre, Government Hospital for Chest Diseases, Gorimedu, Puducherry 605006, India; Department of Biotechnology, Sathyabama University, Jeppiaar Nagar, Rajiv Gandhi Salai, Sholinganallur, Chennai 600119, Tamil Nadu, India
| | - Maruthai Kathirvel
- Department of Biotechnology, Sathyabama University, Jeppiaar Nagar, Rajiv Gandhi Salai, Sholinganallur, Chennai 600119, Tamil Nadu, India
| | - Kommoju Vallayyachari
- Department of Biotechnology, Sathyabama University, Jeppiaar Nagar, Rajiv Gandhi Salai, Sholinganallur, Chennai 600119, Tamil Nadu, India
| | - Kesavan Surendar
- Department of Biotechnology, Sathyabama University, Jeppiaar Nagar, Rajiv Gandhi Salai, Sholinganallur, Chennai 600119, Tamil Nadu, India
| | - Antony V Samrot
- Department of Microbiology, Intermediate Reference Laboratory, State TB Training and Demonstration Centre, Government Hospital for Chest Diseases, Gorimedu, Puducherry 605006, India
| | - Muthuraj Muthaiah
- Department of Biotechnology, Sathyabama University, Jeppiaar Nagar, Rajiv Gandhi Salai, Sholinganallur, Chennai 600119, Tamil Nadu, India.
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Multidrug-resistant tuberculosis in Lithuania - Still a long way ahead. MEDICINA-LITHUANIA 2016; 52:69-78. [PMID: 27170479 DOI: 10.1016/j.medici.2016.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 02/01/2016] [Accepted: 02/13/2016] [Indexed: 11/21/2022]
Abstract
Despite the recent advances in the diagnosis of tuberculosis, treatment of the disease, for the most part, remains the same as it was half a century ago. In recent years only two new anti-tuberculosis drugs have been approved by the European Medicines Agency and Food and Drug Administration. Though the prevalence of this disease is slowly decreasing all over Europe, new challenges appear. One of them is multidrug-resistant tuberculosis (MDR-TB). This problem is especially prominent in Lithuania, which is one of the 27 high MDR-TB burden countries in the world and falls behind neighboring countries in terms of the prevalence of the disease. The objective of this paper was to review the situation of tuberculosis and MDR-TB in Lithuania, and current available methods of treatment, control and diagnosis of this disease.
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MTBDRplus and MTBDRsl Assays: Absence of Wild-Type Probe Hybridization and Implications for Detection of Drug-Resistant Tuberculosis. J Clin Microbiol 2016; 54:912-8. [PMID: 26763971 DOI: 10.1128/jcm.02505-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/06/2016] [Indexed: 01/24/2023] Open
Abstract
Accurate identification of drug-resistantMycobacterium tuberculosisis imperative for effective treatment and subsequent reduction in disease transmission. Line probe assays rapidly detect mutations associated with resistance and wild-type sequences associated with susceptibility. Examination of molecular-level performance is necessary for improved assay result interpretation and for continued diagnostic development. Using data collected from a large, multisite diagnostic study, probe hybridization results from line probe assays, MTBDRplusand MTBDRsl, were compared to those of sequencing, and the diagnostic performance of each individual mutation and wild-type probe was assessed. Line probe assay results classified as resistant due to the absence of wild-type probe hybridization were compared to those of sequencing to determine if novel mutations were inhibiting wild-type probe hybridization. The contribution of absent wild-type probe hybridization to the detection of drug resistance was assessed via comparison to a phenotypic reference standard. In our study, mutation probes demonstrated significantly higher specificities than wild-type probes and wild-type probes demonstrated marginally higher sensitivities than mutation probes, an ideal combination for detecting the presence of resistance conferring mutations while yielding the fewest number of false-positive results. The absence of wild-type probe hybridization without mutation probe hybridization was determined to be primarily the result of failure of mutation probe hybridization and not the result of novel or rare mutations. Compared to phenotypic culture-based drug susceptibility testing, the absence of wild-type probe hybridization without mutation probe hybridization significantly contributed to the detection of phenotypic rifampin and fluoroquinolone resistance with negligible increases in false-positive results.
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Varghese B, Shoukri M, Memish Z, Abuljadayel N, Alhakeem R, Alrabiah F, Al-Hajoj S. Occurrence of diverse mutations in isoniazid- and rifampicin-resistant Mycobacterium tuberculosis isolates from autochthonous and immigrant populations of Saudi Arabia. Microb Drug Resist 2015; 20:623-31. [PMID: 25014484 DOI: 10.1089/mdr.2014.0065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
For the first time in Saudi Arabia, the impact of a patient's ethnic background on mutations conferring resistance to rifampicin (RIF) and isoniazid (INH) in Mycobacterium tuberculosis isolates was analyzed on a nationwide sample collection. Four hundred fifteen isolates were subjected to drug susceptibility testing, mutation analysis, spoligotyping, and 24 loci-based Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeat typing, respectively. Phenotypically, 41 (9.9%) isolates were resistant to RIF, 239 (57.6%) to INH, and 135 (32.5%) to both RIF and INH, respectively. Forty (9.6%), 236 (56.8%), and 133 (32%) isolates were determined as resistant to RIF, INH, and to both by molecular assay. Codon 531 (S531L) mutations (69.4%) in the rpoB gene and codon 315 (S315T) mutations (67.2%) in the katG gene were the most prominent among RIF- and INH-resistant isolates, respectively. The autochthonous population showed a predominance of rpoB codon 516 and 526 mutations, while the inhA promoter position -15 and -8 mutations were prominent among immigrants. A strain cluster ratio of 32% (30 clusters) was observed and 24 clusters displayed identical mutations. Overall, Euro-American lineages were predominant. However, Beijing (56.7%) and EAI (42.7%) were noticed with the highest cluster rate. In Saudi Arabia, the occurrence of mutations responsible for INH and RIF resistance was significantly associated with the ethnic origin of the patient.
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Affiliation(s)
- Bright Varghese
- 1 Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre , Riyadh, Saudi Arabia
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A microbiological revolution meets an ancient disease: improving the management of tuberculosis with genomics. Clin Microbiol Rev 2015; 28:523-39. [PMID: 25810419 DOI: 10.1128/cmr.00124-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis (TB) is an ancient disease with an enormous global impact. Despite declining global incidence, the diagnosis, phenotyping, and epidemiological investigation of TB require significant clinical microbiology laboratory resources. Current methods for the detection and characterization of Mycobacterium tuberculosis consist of a series of laboratory tests varying in speed and performance, each of which yields incremental information about the disease. Since the sequencing of the first M. tuberculosis genome in 1998, genomic tools have aided in the diagnosis, treatment, and control of TB. Here we summarize genomics-based methods that are positioned to be introduced in the modern clinical TB laboratory, and we highlight how recent advances in genomics will improve the detection of antibiotic resistance-conferring mutations and the understanding of M. tuberculosis transmission dynamics and epidemiology. We imagine the future TB clinic as one that relies heavily on genomic interrogation of the M. tuberculosis isolate, allowing for more rapid diagnosis of TB and real-time monitoring of outbreak emergence.
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Marianelli C, Armas F, Boniotti MB, Mazzone P, Pacciarini ML, Di Marco Lo Presti V. Multiple drug-susceptibility screening in Mycobacterium bovis: new nucleotide polymorphisms in the embB gene among ethambutol susceptible strains. Int J Infect Dis 2015; 33:39-44. [DOI: 10.1016/j.ijid.2014.12.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 10/24/2022] Open
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Seifert M, Catanzaro D, Catanzaro A, Rodwell TC. Genetic mutations associated with isoniazid resistance in Mycobacterium tuberculosis: a systematic review. PLoS One 2015; 10:e0119628. [PMID: 25799046 PMCID: PMC4370653 DOI: 10.1371/journal.pone.0119628] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 01/14/2015] [Indexed: 01/12/2023] Open
Abstract
Background Tuberculosis (TB) incidence and mortality are declining worldwide; however, poor detection of drug-resistant disease threatens to reverse current progress toward global TB control. Multiple, rapid molecular diagnostic tests have recently been developed to detect genetic mutations in Mycobacterium tuberculosis (Mtb) genes known to confer first-line drug resistance. Their utility, though, depends on the frequency and distribution of the resistance associated mutations in the pathogen population. Mutations associated with rifampicin resistance, one of the two first-line drugs, are well understood and appear to occur in a single gene region in >95% of phenotypically resistant isolates. Mutations associated with isoniazid, the other first-line drug, are more complex and occur in multiple Mtb genes. Objectives/Methodology A systematic review of all published studies from January 2000 through August 2013 was conducted to quantify the frequency of the most common mutations associated with isoniazid resistance, to describe the frequency at which these mutations co-occur, and to identify the regional differences in the distribution of these mutations. Mutation data from 118 publications were extracted and analyzed for 11,411 Mtb isolates from 49 countries. Principal Findings/Conclusions Globally, 64% of all observed phenotypic isoniazid resistance was associated with the katG315 mutation. The second most frequently observed mutation, inhA-15, was reported among 19% of phenotypically resistant isolates. These two mutations, katG315 and inhA-15, combined with ten of the most commonly occurring mutations in the inhA promoter and the ahpC-oxyR intergenic region explain 84% of global phenotypic isoniazid resistance. Regional variation in the frequency of individual mutations may limit the sensitivity of molecular diagnostic tests. Well-designed systematic surveys and whole genome sequencing are needed to identify mutation frequencies in geographic regions where rapid molecular tests are currently being deployed, providing a context for interpretation of test results and the opportunity for improving the next generation of diagnostics.
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Affiliation(s)
- Marva Seifert
- University of California San Diego, School of Medicine, La Jolla, California, United States of America
| | - Donald Catanzaro
- University of California San Diego, School of Medicine, La Jolla, California, United States of America
| | - Antonino Catanzaro
- University of California San Diego, School of Medicine, La Jolla, California, United States of America
| | - Timothy C. Rodwell
- University of California San Diego, School of Medicine, La Jolla, California, United States of America
- * E-mail:
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Hu X, Li X, Huang L, Chan J, Chen Y, Deng H, Mi K. Quantitative proteomics reveals novel insights into isoniazid susceptibility in mycobacteria mediated by a universal stress protein. J Proteome Res 2015; 14:1445-54. [PMID: 25664397 DOI: 10.1021/pr5011058] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tuberculosis (TB) is caused by the ancient pathogen, Mycobacterium tuberculosis, and is one of the most serious infectious diseases in the world. Isoniazid (INH) is an important first-line drug for the treatment of active and latent TB. INH resistance is an increasing problem in the treatment of TB. Phenotypic resistance to INH, however, is poorly understood. In this study, we constructed a strain of Mycobacterium bovis BCG that overexpresses the latency-related universal stress protein (USP), BCG_2013, and designated this strain BCG-2013. BCG_2013 overexpression increased susceptibility to INH compared with that of the wild-type strain, BCG-pMV261. Quantitative proteomic analysis revealed that BCG_2013 overexpression resulted in the upregulation of 50 proteins and the downregulation of 26 proteins among the 1500 proteins identified. Upregulation of catalase-peroxidase KatG expression in BCG-2013 was observed and confirmed by qPCR, whereas expression of other INH resistance-related proteins did not change. In addition, differential expression of the mycobacterial persistence regulator MprA and its regulatory proteins was observed. BCG_2013 and katG mRNA levels increased in a Wayne dormancy model, whereas MprA mRNA levels decreased. Taken together, our results suggest that the increase in KatG levels induced by increased BCG_2013 levels underlies the phenotypic susceptibility of mycobacteria to INH.
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Affiliation(s)
- Xinling Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS , Beijing 100101, China
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Mathematical Modelling and Tuberculosis: Advances in Diagnostics and Novel Therapies. Adv Med 2015; 2015:907267. [PMID: 26556559 PMCID: PMC4590968 DOI: 10.1155/2015/907267] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 02/18/2015] [Accepted: 02/26/2015] [Indexed: 11/18/2022] Open
Abstract
As novel diagnostics, therapies, and algorithms are developed to improve case finding, diagnosis, and clinical management of patients with TB, policymakers must make difficult decisions and choose among multiple new technologies while operating under heavy resource constrained settings. Mathematical modelling can provide helpful insight by describing the types of interventions likely to maximize impact on the population level and highlighting those gaps in our current knowledge that are most important for making such assessments. This review discusses the major contributions of TB transmission models in general, namely, the ability to improve our understanding of the epidemiology of TB. We focus particularly on those elements that are important to appropriately understand the role of TB diagnosis and treatment (i.e., what elements of better diagnosis or treatment are likely to have greatest population-level impact) and yet remain poorly understood at present. It is essential for modellers, decision-makers, and epidemiologists alike to recognize these outstanding gaps in knowledge and understand their potential influence on model projections that may guide critical policy choices (e.g., investment and scale-up decisions).
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Trauner A, Borrell S, Reither K, Gagneux S. Evolution of drug resistance in tuberculosis: recent progress and implications for diagnosis and therapy. Drugs 2014; 74:1063-72. [PMID: 24962424 PMCID: PMC4078235 DOI: 10.1007/s40265-014-0248-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug-resistant tuberculosis is a growing threat to global public health. Recent efforts to understand the evolution of drug resistance have shown that changes in drug-target interactions are only the first step in a longer adaptive process. The emergence of transmissible drug-resistant Mycobacterium tuberculosis is the result of a multitude of additional genetic mutations, many of which interact, a phenomenon known as epistasis. The varied effects of these epistatic interactions include compensating for the reduction of the biological cost associated with the development of drug resistance, increasing the level of resistance, and possibly accommodating broader changes in the physiology of resistant bacteria. Knowledge of these processes and our ability to detect them as they happen informs the development of diagnostic tools and better control strategies. In particular, the use of whole genome sequencing combined with surveillance efforts in the field could provide a powerful instrument to prevent future epidemics of drug-resistant tuberculosis.
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Affiliation(s)
- Andrej Trauner
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, Basel, Switzerland
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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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Xiao ZP, Wang XD, Wang PF, Zhou Y, Zhang JW, Zhang L, Zhou J, Zhou SS, Ouyang H, Lin XY, Mustapa M, Reyinbaike A, Zhu HL. Design, synthesis, and evaluation of novel fluoroquinolone-flavonoid hybrids as potent antibiotics against drug-resistant microorganisms. Eur J Med Chem 2014; 80:92-100. [PMID: 24769347 DOI: 10.1016/j.ejmech.2014.04.037] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 12/15/2022]
Abstract
Based on a rationally conceived pharmacophore model to build a multi-target bacterial topoisomerase inhibitor, twenty-one fluoroquinolone-flavonoid hybrids were synthesized. Some obtained hybrids show excellent antibacterial activity against drug-resistant microorganisms with narigenin-ciprofloxacin being the most active, showing 8, 43, 23 and 88 times better activity than ciprofloxacin against Escherichia coli ATCC 35218, Bacillus subtilis ATCC 6633, Staphylococcus aureus ATCC 25923 and Candida albicans ATCC 90873, respectively. Drug accumulation and DNA supercoiling assays of two active analogues revealed potent inhibition of both the DNA gyrase and efflux pump, confirming the desired dual mode of action. Molecular docking study disclosed that the introduced flavonoid moiety not only provides several additional interactions but also does not disturb the binding mode of the floxacin moiety. Our data also demonstrated that development of antifungals is possible from fluoroquinolones modified at C-7 position.
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Affiliation(s)
- Zhu-Ping Xiao
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China; State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China.
| | - Xu-Dong Wang
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China
| | - Peng-Fei Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China
| | - Yin Zhou
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China
| | - Jing-Wen Zhang
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China
| | - Lei Zhang
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China
| | - Jiao Zhou
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China
| | - Sha-Sha Zhou
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China
| | - Hui Ouyang
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China
| | - Xiao-Yi Lin
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China
| | - Manzira Mustapa
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China
| | - Asaimuguli Reyinbaike
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China
| | - Hai-Liang Zhu
- College of Chemistry and Chemical Engineering, Jishou University, Jishou 416000, PR China; State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China.
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Lange C, Abubakar I, Alffenaar JWC, Bothamley G, Caminero JA, Carvalho ACC, Chang KC, Codecasa L, Correia A, Crudu V, Davies P, Dedicoat M, Drobniewski F, Duarte R, Ehlers C, Erkens C, Goletti D, Günther G, Ibraim E, Kampmann B, Kuksa L, de Lange W, van Leth F, van Lunzen J, Matteelli A, Menzies D, Monedero I, Richter E, Rüsch-Gerdes S, Sandgren A, Scardigli A, Skrahina A, Tortoli E, Volchenkov G, Wagner D, van der Werf MJ, Williams B, Yew WW, Zellweger JP, Cirillo DM. Management of patients with multidrug-resistant/extensively drug-resistant tuberculosis in Europe: a TBNET consensus statement. Eur Respir J 2014; 44:23-63. [PMID: 24659544 PMCID: PMC4076529 DOI: 10.1183/09031936.00188313] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) substantially challenges TB control, especially in the European Region of the World Health Organization, where the highest prevalence of MDR/XDR cases is reported. The current management of patients with MDR/XDR-TB is extremely complex for medical, social and public health systems. The treatment with currently available anti-TB therapies to achieve relapse-free cure is long and undermined by a high frequency of adverse drug events, suboptimal treatment adherence, high costs and low treatment success rates. Availability of optimal management for patients with MDR/XDR-TB is limited even in the European Region. In the absence of a preventive vaccine, more effective diagnostic tools and novel therapeutic interventions the control of MDR/XDR-TB will be extremely difficult. Despite recent scientific advances in MDR/XDR-TB care, decisions for the management of patients with MDR/XDR-TB and their contacts often rely on expert opinions, rather than on clinical evidence. This document summarises the current knowledge on the prevention, diagnosis and treatment of adults and children with MDR/XDR-TB and their contacts, and provides expert consensus recommendations on questions where scientific evidence is still lacking. TBNET consensus statement on the management of patients with MDR/XDR-TB has been released in theEur Respir Jhttp://ow.ly/uizRD
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Affiliation(s)
- Christoph Lange
- For the authors' affiliations see the Acknowledgements section
| | | | | | | | - Jose A Caminero
- For the authors' affiliations see the Acknowledgements section
| | | | - Kwok-Chiu Chang
- For the authors' affiliations see the Acknowledgements section
| | - Luigi Codecasa
- For the authors' affiliations see the Acknowledgements section
| | - Ana Correia
- For the authors' affiliations see the Acknowledgements section
| | - Valeriu Crudu
- For the authors' affiliations see the Acknowledgements section
| | - Peter Davies
- For the authors' affiliations see the Acknowledgements section
| | - Martin Dedicoat
- For the authors' affiliations see the Acknowledgements section
| | | | - Raquel Duarte
- For the authors' affiliations see the Acknowledgements section
| | - Cordula Ehlers
- For the authors' affiliations see the Acknowledgements section
| | - Connie Erkens
- For the authors' affiliations see the Acknowledgements section
| | - Delia Goletti
- For the authors' affiliations see the Acknowledgements section
| | - Gunar Günther
- For the authors' affiliations see the Acknowledgements section
| | - Elmira Ibraim
- For the authors' affiliations see the Acknowledgements section
| | - Beate Kampmann
- For the authors' affiliations see the Acknowledgements section
| | - Liga Kuksa
- For the authors' affiliations see the Acknowledgements section
| | - Wiel de Lange
- For the authors' affiliations see the Acknowledgements section
| | - Frank van Leth
- For the authors' affiliations see the Acknowledgements section
| | - Jan van Lunzen
- For the authors' affiliations see the Acknowledgements section
| | | | - Dick Menzies
- For the authors' affiliations see the Acknowledgements section
| | | | - Elvira Richter
- For the authors' affiliations see the Acknowledgements section
| | | | | | - Anna Scardigli
- For the authors' affiliations see the Acknowledgements section
| | - Alena Skrahina
- For the authors' affiliations see the Acknowledgements section
| | - Enrico Tortoli
- For the authors' affiliations see the Acknowledgements section
| | | | - Dirk Wagner
- For the authors' affiliations see the Acknowledgements section
| | | | - Bhanu Williams
- For the authors' affiliations see the Acknowledgements section
| | - Wing-Wai Yew
- For the authors' affiliations see the Acknowledgements section
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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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Song T, Park Y, Shamputa IC, Seo S, Lee SY, Jeon HS, Choi H, Lee M, Glynne RJ, Barnes SW, Walker JR, Batalov S, Yusim K, Feng S, Tung CS, Theiler J, Via LE, Boshoff HIM, Murakami KS, Korber B, Barry CE, Cho SN. Fitness costs of rifampicin resistance in Mycobacterium tuberculosis are amplified under conditions of nutrient starvation and compensated by mutation in the β' subunit of RNA polymerase. Mol Microbiol 2014; 91:1106-19. [PMID: 24417450 DOI: 10.1111/mmi.12520] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2014] [Indexed: 12/31/2022]
Abstract
Rifampicin resistance, a defining attribute of multidrug-resistant tuberculosis, is conferred by mutations in the β subunit of RNA polymerase. Sequencing of rifampicin-resistant (RIF-R) clinical isolates of Mycobacterium tuberculosis revealed, in addition to RIF-R mutations, enrichment of potential compensatory mutations around the double-psi β-barrel domain of the β' subunit comprising the catalytic site and the exit tunnel for newly synthesized RNA. Sequential introduction of the resistance allele followed by the compensatory allele in isogenic Mycobacterium smegmatis showed that these mutations respectively caused and compensated a starvation enhanced growth defect by altering RNA polymerase activity. While specific combinations of resistance and compensatory alleles converged in divergent lineages, other combinations recurred among related isolates suggesting transmission of compensated RIF-R strains. These findings suggest nutrient poor growth conditions impose larger selective pressure on RIF-R organisms that results in the selection of compensatory mutations in a domain involved in catalysis and starvation control of RNA polymerase transcription.
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Affiliation(s)
- Taeksun Song
- International Tuberculosis Research Center, Changwon, South Korea
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Veigas B, Pedrosa P, Couto I, Viveiros M, Baptista PV. Isothermal DNA amplification coupled to Au-nanoprobes for detection of mutations associated to Rifampicin resistance in Mycobacterium tuberculosis. J Nanobiotechnology 2013; 11:38. [PMID: 24274610 PMCID: PMC4222569 DOI: 10.1186/1477-3155-11-38] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 11/22/2013] [Indexed: 11/17/2022] Open
Abstract
Background Tuberculosis accounted for 8.7 million new cases in 2011 and continues to be one of the leading human infectious diseases. Burdensome is the increasing rate of multi-drug resistant tuberculosis (MDRTB) and the difficulties created for treatment and public health control programs, especially in developing countries. Resistance to rifampicin (RIF), a first line antibiotic, is commonly associated with point mutations within the rpoB gene of Mycobacterium tuberculosis (Mtb) whose detection is considered the best early molecular predictor for MDRTB. Gold nanoparticles functionalized with thiol-modified oligonucleotides (Au-nanoprobes) have shown the potential to provide a rapid and sensitive detection method for Mtb and single base alterations associated with antibiotic resistance, namely in rpoB gene associated to RIF resistance. Results We developed a strategy based on the isothermal amplification of sample DNA (LAMP) coupled to specific Au-nanoprobes capable of identifying members of the Mtb complex (MTBC) and discriminating specific mutations within the rpoB gene. Integration of LAMP and Au-nanoprobe assay allowed to detect MTBC member and identify mutations linked to RIF resistance. A total of 12 biological samples were tested and a 100% specificity and sensitivity was attained. Conclusions There is an increasing demand for simple, fast and cheap methods for the molecular identification of Mtb and for the detection of molecular tags associated to drug resistance suitable for use at point-of-need. Here we describe such a method, that as the potential to get molecular diagnostic of tuberculosis to remote environments.
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Affiliation(s)
- Bruno Veigas
- Nanotheranostics@CIGMH, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica 2829-516, Caparica, Portugal.
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Zhang H, Li D, Zhao L, Fleming J, Lin N, Wang T, Liu Z, Li C, Galwey N, Deng J, Zhou Y, Zhu Y, Gao Y, Wang T, Wang S, Huang Y, Wang M, Zhong Q, Zhou L, Chen T, Zhou J, Yang R, Zhu G, Hang H, Zhang J, Li F, Wan K, Wang J, Zhang XE, Bi L. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat Genet 2013; 45:1255-60. [DOI: 10.1038/ng.2735] [Citation(s) in RCA: 348] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 07/30/2013] [Indexed: 12/29/2022]
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50
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Maharaj Y, Soliman MES. Identification of Novel Gyrase B Inhibitors as Potential Anti-TB drugs: Homology Modelling, Hybrid Virtual Screening and Molecular Dynamics Simulations. Chem Biol Drug Des 2013; 82:205-15. [DOI: 10.1111/cbdd.12152] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/15/2013] [Accepted: 04/18/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Yushir Maharaj
- School of Health Sciences; University of KwaZulu-Natal; Durban; 4001; South Africa
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