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Jeon SM, Park S, Lim NR, Lee N, Jung J, Sung N, Kim S. Molecular Analysis of Anti-Tuberculosis Drug Resistance of Mycobacterium tuberculosis Isolated in the Republic of Korea. Antibiotics (Basel) 2023; 12:1324. [PMID: 37627744 PMCID: PMC10451913 DOI: 10.3390/antibiotics12081324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Rapid and accurate detection of tuberculosis (TB) drug resistance is critical for the successful treatment and control of TB. Here, we investigated resistance to anti-TB drugs and genetic variations in 215 drug-resistant Mycobacterium tuberculosis isolates in Korea. Genetic variations were observed in rpoB Ser531Leu, katG Ser315Thr, and gyrA Asp94Gly; however, the minimum inhibitory concentrations varied, which can be attributed to other resistance mechanisms. Examination of genetic relatedness among drug-resistant isolates revealed that the cluster size of resistant bacteria was less than six strains, suggesting no evidence of a large-scale epidemic caused by a specific strain. However, rpoC mutants of the rifampicin-resistant isolates were composed of five types of clusters, suggesting that these compensatory mutations advance propagation. In the present study, more than 90% of the resistance mechanisms to major anti-TB drugs were identified, and the effect of each mutation on drug resistance was estimated. With the clinical application of recent next-generation sequencing-based susceptibility testing, the present study is expected to improve the clinical utilization of genotype-based drug susceptibility testing for the diagnosis and treatment of patients with drug-resistant TB.
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Affiliation(s)
- Se-Mi Jeon
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Sanghee Park
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Na-Ra Lim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Noori Lee
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Jihee Jung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Nackmoon Sung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Seonghan Kim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
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2
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Yan M, Zhao Z, Wu T, Liu T, Xu G, Xu H, Ying B. Highly Sensitive Detection of Complicated Mutations of Drug Resistance in Mycobacterium tuberculosis Using a Simple, Accurate, Rapid, and Low-Cost Tailored-Design Competitive Wild-Type Blocking Assay. SMALL METHODS 2023; 7:e2201322. [PMID: 36683186 DOI: 10.1002/smtd.202201322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Establishing simple, rapid, and highly sensitive molecular assays is crucial for timely diagnosis and effective treatment of drug-resistant tuberculosis. However, current genotypic drug susceptibility testing (DST) still encounters enormous challenges including lower sensitivity than phenotypic DST and insufficient accuracy. Herein, a simple, low-cost, multiplex real-time polymerase chain reaction-based assay is established to achieve highly sensitive detection of low-abundant mutants through competitive wild-type blocking (COWTB). Analytical performance of the COWTB assay can achieve 1% or even 0.1% mutants under background of 10 000 wild-type genomes/test. Furthermore, clinical practice feasibility is evaluated to identify resistance to rifampicin (RIF), isoniazid (INH), and streptomycin (SM) on 92 actual clinical samples, its sensitivity is 93.8% for RIF and 100% for INH and SM, and specificity is 100% each for RIF, INH, and SM when using DNA sequencing as the reference standard. In comparison, the sensitivity of reverse dot blotting assay commonly used in clinics is 93.8%, 90.0%, and 84.6%, and the specificity is 96.1%, 98.6%, and 100% for RIF, INH, and SM, respectively. Importantly, the COWTB assay can also be applicable for other drug-resistant mutations and pave a promising detection strategy to fill the gap between phenotypic and genotypic DST for detecting low-abundant drug-resistant M. tuberculosis.
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Affiliation(s)
- Mengqiu Yan
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Tao Wu
- Department of Clinical Laboratory Medicine, People's Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest Minzu University), Yinchuan, 750002, P. R. China
| | - Tangyuheng Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Gaolian Xu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Hong Xu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
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3
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Nandlal L, Perumal R, Naidoo K. Rapid Molecular Assays for the Diagnosis of Drug-Resistant Tuberculosis. Infect Drug Resist 2022; 15:4971-4984. [PMID: 36060232 PMCID: PMC9438776 DOI: 10.2147/idr.s381643] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/20/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Louansha Nandlal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), South African Medical Research Council (SAMRC)-CAPRISA-TB-HIV Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal Nelson R Mandela School of Medicine, Durban, South Africa
| | - Rubeshan Perumal
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), South African Medical Research Council (SAMRC)-CAPRISA-TB-HIV Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal Nelson R Mandela School of Medicine, Durban, South Africa
- Correspondence: Rubeshan Perumal, Centre for the AIDS Programme of Research in South Africa (CAPRISA), South African Medical Research Council (SAMRC)-CAPRISA-TB-HIV Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal Nelson R Mandela School of Medicine, Durban, South Africa, Email
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), South African Medical Research Council (SAMRC)-CAPRISA-TB-HIV Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal Nelson R Mandela School of Medicine, Durban, South Africa
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Disputed rpoB Mutations in Mycobacterium tuberculosis and Tuberculosis Treatment Outcomes. Antimicrob Agents Chemother 2021; 65:e0157320. [PMID: 33846134 DOI: 10.1128/aac.01573-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Discordant results between genotypic drug susceptibility testing (gDST) and phenotypic DST (pDST) for Mycobacterium tuberculosis isolates with disputed (discordance between gDST and pDST results) mutations affect rifampin (RIF)-resistant (RR) and multidrug-resistant (MDR) tuberculosis (TB) treatments due to a lack of practical clinical guidelines. To investigate the role of disputed rpoB mutations in M. tuberculosis and TB treatment outcomes, initial isolates of 837 clinical RR- or MDR-TB cases confirmed during 2014 to 2018 were retested using agar-based RIF pDST and rpoB gene sequencing. MICs were determined for isolates with disputed rpoB mutations. Disputed rpoB mutations were identified in 77 (9.2%) M. tuberculosis isolates, including 50 (64.9%) and 14 (18.2%) phenotypically RIF- and rifabutin (RFB)-resistant isolates, respectively. The predominant single mutations were those encoding L533P (a change of L to P at position 533) (44.2%) and L511P (20.8%). Most of the isolates harboring mutations encoding L511P (87.5%), H526N (100%), D516Y (70.0%), and L533P (63.6%) had MICs of ≤1 mg/liter, whereas isolates harboring the mutation encoding H526L (75%) had a MIC of >1 mg/liter. Of the 63 cases with treatment outcomes available, 11 (17.5%) cases died, 1 (1.6%) case transferred out, and 51 (81%) cases had favorable outcomes, including 8 and 20 cases treated with standard-dose RIF- and RFB-containing regimens, respectively. Excluding cases that transferred out or received no or 1-day treatment, we observed statistically significant differences between the outcomes using active and inactive fluoroquinolones (FQs) (P = 0.008, odds ratio = 0.05 [95% confidence interval, 0.01 to 0.38]) in 57 cases (where active means a case susceptible to the drug and inactive means a case resistant to the drug or drug not used). We concluded that disputed rpoB mutations are not rare. Depending on the resources available, sequencing and/or MIC testing is recommended for better management of RR- and MDR-TB cases.
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Low-Level Rifampin Resistance and rpoB Mutations in Mycobacterium tuberculosis: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New York. J Clin Microbiol 2021; 59:JCM.01885-20. [PMID: 32999007 DOI: 10.1128/jcm.01885-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/05/2020] [Indexed: 01/02/2023] Open
Abstract
Rapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis and treatment of drug-resistant and multidrug-resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to the presence of rpoB mutations that do not confer high levels of RIF resistance, as have been exhibited in strains with mutations such as Ser450Leu. These strains, termed low-level RIF resistant, exhibit elevated RIF MICs compared to fully susceptible strains but remain phenotypically susceptible by mycobacterial growth indicator tube (MGIT) testing and have been associated with poor patient outcomes. Here, we assess RIF resistance prediction by whole-genome sequencing (WGS) among a set of 1,779 prospectively tested strains by both prevalence of rpoB gene mutation and phenotype as part of routine clinical testing during a 2.5-year period. During this time, 139 strains were found to have nonsynonymous rpoB mutations, 53 of which were associated with RIF resistance, including both low-level and high-level resistance. Resistance to RIF (1.0 μg/ml in MGIT) was identified in 43 (81.1%) isolates. The remaining 10 (18.9%) strains were susceptible by MGIT but were confirmed to be low-level RIF resistant by MIC testing. Full rpoB gene sequencing overcame the limitations of critical concentration phenotyping, probe-based genotyping, and partial gene sequencing methods. Universal clinical WGS with concurrent phenotypic testing provided a more complete understanding of the prevalence and type of rpoB mutations and their association with RIF resistance in New York.
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Chen S, Liu C, Liu Y, Liu Q, Lu M, Bi S, Jing Z, Yu Q, Peng W. Label-Free Near-Infrared Plasmonic Sensing Technique for DNA Detection at Ultralow Concentrations. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000763. [PMID: 33304743 PMCID: PMC7709993 DOI: 10.1002/advs.202000763] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 08/05/2020] [Indexed: 06/12/2023]
Abstract
Biomolecular detection at a low concentration is usually the most important criterion for biological measurement and early stage disease diagnosis. In this paper, a highly sensitive nanoplasmonic biosensing approach is demonstrated by achieving near-infrared plasmonic excitation on a continuous gold-coated nanotriangular array. Near-infrared incident light at a small incident angle excites surface plasmon resonance with much higher spectral sensitivity compared with traditional configuration, due to its greater interactive volume and the stronger electric field intensity. By introducing sharp nanotriangular metallic tips, intense localization of plasmonic near-fields is realized to enhance the molecular perception ability on sensing surface. This approach with an enhanced sensitivity (42103.8 nm per RIU) and a high figure of merit (367.812) achieves a direct assay of ssDNA at nanomolar level, which is a further step in label-free ultrasensitive sensing technique. Considerable improvement is recorded in the detection limit of ssDNA as 1.2 × 10-18 m based on the coupling effect between nanotriangles and gold nanoparticles. This work combines high bulk- and surface-sensitivities, providing a simple way toward label-free ultralow-concentration biomolecular detection.
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Affiliation(s)
- Shimeng Chen
- School of Optoelectronic Engineering and Instrumentation ScienceDalian University of TechnologyDalian116024China
| | - Chuan Liu
- State Key Laboratory of Structural Analysis for Industrial EquipmentDalian University of TechnologyDalian116024China
| | - Yun Liu
- School of PhysicsDalian University of TechnologyDalian116024China
| | - Qiang Liu
- School of PhysicsDalian University of TechnologyDalian116024China
| | - Mengdi Lu
- School of PhysicsDalian University of TechnologyDalian116024China
| | - Sheng Bi
- Key Laboratory for Precision and Non‐traditional MachiningTechnology of the Ministry of EducationDalian University of TechnologyDalian116024China
| | - Zhenguo Jing
- School of PhysicsDalian University of TechnologyDalian116024China
| | - Qingxu Yu
- School of Optoelectronic Engineering and Instrumentation ScienceDalian University of TechnologyDalian116024China
| | - Wei Peng
- School of PhysicsDalian University of TechnologyDalian116024China
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7
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Uddin MKM, Rahman A, Ather MF, Ahmed T, Rahman SMM, Ahmed S, Banu S. Distribution and Frequency of rpoB Mutations Detected by Xpert MTB/RIF Assay Among Beijing and Non-Beijing Rifampicin Resistant Mycobacterium tuberculosis Isolates in Bangladesh. Infect Drug Resist 2020; 13:789-797. [PMID: 32210593 PMCID: PMC7073589 DOI: 10.2147/idr.s240408] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
Background Rifampicin resistance (RR) is a key indicator of multidrug-resistant tuberculosis (MDR-TB) and 95% of the RR is associated with the mutation in the 81-bp rifampicin resistance determining region (RRDR) of the rpoB gene of Mycobacterium tuberculosis complex (MTBC). The Xpert MTB/RIF (Xpert) assay uses five overlapping molecular beacon probes (A-E) complementary to RRDR region that detect MTBC and mutations associated with RR. The objective of the study was to investigate the distribution and frequency of mutations detected by Xpert assay among Beijing and non-Beijing RR-TB isolates. Methods A total of 205 randomly selected RR-TB specimens detected by Xpert assay were included in this study. A portion of specimens was further subjected to culture, MTBDRplus test and the positive culture isolates were genotyped by spoligotyping. Results We found that the most frequent mutation occurred at probe E (S531L) binding region in both Beijing and non-Beijing isolates (61.9% and 66.9%, respectively). The Beijing family had higher mutation rates than non-Beijing (19.0% vs 12.4%) at probe B (D516V) while the non-Beijing family had higher mutations at probe D (H526D or H526Y) than the Beijing (13.2% vs 10.7%) family. Mutations at probes Aand C were less common in both Beijing and non-Beijing isolates. There was no significant difference (P=0.36) in the occurrence of mutations at different probes between Beijing and non-Beijing isolates. Conclusions The study results revealed that the most frequent mutation occurs in the region of probe E and the least common mutations at probe A and C among both Beijing and non-Beijing RR-TB cases. This first insight into the probe mutation variation and frequencies among the RR-TB cases in Bangladesh forms the baseline information for further investigation.
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Affiliation(s)
| | - Arfatur Rahman
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), Parkville VIC 3052, Australia
| | - Md Fahim Ather
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - Tanvir Ahmed
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | | | - Shahriar Ahmed
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - Sayera Banu
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
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Hu P, Zhang H, Fleming J, Zhu G, Zhang S, Wang Y, Liu F, Yi S, Chen Z, Chen Z, Liu B, Gong D, Wan L, Wang X, Tan Y, Bai L, Bi L. Retrospective Analysis of False-Positive and Disputed Rifampin Resistance Xpert MTB/RIF Assay Results in Clinical Samples from a Referral Hospital in Hunan, China. J Clin Microbiol 2019; 57:e01707-18. [PMID: 30674578 PMCID: PMC6440781 DOI: 10.1128/jcm.01707-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/16/2019] [Indexed: 11/20/2022] Open
Abstract
Concerns about the specificity of the Xpert MTB/RIF (Xpert) assay have arisen, as false-positive errors in the determination of Mycobacterium tuberculosis complex (MTBC) infection and rifampin (RIF) resistance in clinical practice have been reported. Here, we investigated 33 cases where patients were determined to be RIF susceptible using the Bactec MGIT 960 (MGIT) culture system but RIF resistant using the Xpert assay. Isolates from two of these patients were found not to have any mutations in the rifampin resistance determining region (RRDR) region of rpoB and had good treatment outcomes with first-line antituberculosis (anti-TB) drugs. The remaining 31 patients included 5 new cases and 26 previously treated patients. A large number of well-documented disputed mutations, including Leu511Pro, Asp516Tyr, His526Asn, His526Leu, His526Cys, and Leu533Pro, were detected, and mutations, including a 508 to 509 deletion and His526Gly, were described here as disputed mutations for the first time. Twenty-one (81%) of the 26 previously treated patients had poor treatment outcomes, and isolates from 19 (90%) of these 21 patients were resistant to isoniazid (INH) as determined using the MGIT culture system. Twenty-seven of the 31 isolates with disputed rpoB mutations were phenotypically resistant to INH, 21 (78%) being predicted by GenoType MTBDRplus to have a high level of INH resistance. Most (77.4%) of the isolates with disputed mutations were of the Beijing lineage. These findings have implications for the interpretation of false-positive and disputed rifampin resistance Xpert MTB/RIF results in clinical samples and provide guidance on how clinicians should manage patients carrying isolates with disputed rpoB mutations.
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Affiliation(s)
- Peilei Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Clinical Laboratory, Hunan Chest Hospital, Changsha, China
| | - Hongtai Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Joy Fleming
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guofeng Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shuai Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yaguo Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fengping Liu
- Clinical Laboratory, Hunan Chest Hospital, Changsha, China
| | - Songlin Yi
- Clinical Laboratory, Hunan Chest Hospital, Changsha, China
| | - Zhongnan Chen
- Clinical Laboratory, Hunan Chest Hospital, Changsha, China
| | - Zhenhua Chen
- Clinical Laboratory, Hunan Chest Hospital, Changsha, China
| | - Binbin Liu
- Clinical Laboratory, Hunan Chest Hospital, Changsha, China
| | - Daofang Gong
- Clinical Laboratory, Hunan Chest Hospital, Changsha, China
| | - Li Wan
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xingyun Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yunhong Tan
- Clinical Laboratory, Hunan Chest Hospital, Changsha, China
| | - Liqiong Bai
- Clinical Laboratory, Hunan Chest Hospital, Changsha, China
| | - Lijun Bi
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Stomatology and Medicine, Foshan University, Foshan, Guangdong, China
- Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan, Guangdong, China
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9
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DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb) 2018; 113:139-152. [PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
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Govindaswamy A, Sakthi D, Pai R, Jeyaseelan L, Michael JS. Pyrosequencing: a rapid and effective sequencing method to diagnose drug-resistant tuberculosis. J Med Microbiol 2018; 67:1212-1216. [PMID: 30028665 DOI: 10.1099/jmm.0.000669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE This study was undertaken to evaluate the efficiency of the pyrosequencing (PSQ) assay for the rapid detection of resistance to rifampicin (RIF), fluoroquinolones (FQs) and second-line injectables (SLIs) such as capreomycin (CAP) and kanamycin (KAN) in Mycobacterium tuberculosis (Mtb) clinical isolates. METHODOLOGY Pyrosequencing is a simple and accurate short read DNA sequencing method for genome analysis. DNA extraction from Mtb clinical isolates was performed using Tris-HCl buffer and chloroform. The rpoB (RIF), gyrA (FQs) and rrs (aminoglycosides) genes were amplified, followed by sequencing using the PyroMark Q24 ID system. The PSQ results were compared with the results from the conventional drug susceptibility testing performed in the laboratory. RESULTS The sensitivity of the PSQ assay for the detection of resistance to RIF, FQ, CAP and KAN was 100 %, 100 %, 40 % and 50 %, respectively. The specificity of the PSQ assay was 100 %. CONCLUSION The PSQ assay is a rapid and effective method for detecting drug resistance mutations from Mtb clinical isolates in a short period of time.
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Affiliation(s)
- Aishwarya Govindaswamy
- 1Department of Clinical Microbiology, Christian Medical College, Vellore 632 004, India
| | - Dhananjayan Sakthi
- 2Department of General Pathology, Christian Medical College, Vellore 632 004, India
| | - Rekha Pai
- 2Department of General Pathology, Christian Medical College, Vellore 632 004, India
| | | | - Joy Sarojini Michael
- 1Department of Clinical Microbiology, Christian Medical College, Vellore 632 004, India
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11
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Lu M, Hong L, Liang Y, Charron B, Zhu H, Peng W, Masson JF. Enhancement of Gold Nanoparticle Coupling with a 2D Plasmonic Crystal at High Incidence Angles. Anal Chem 2018; 90:6683-6692. [PMID: 29738232 DOI: 10.1021/acs.analchem.8b00496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
2D nanoplasmonic substrates excited in transmission spectroscopy are ideal for several biosensing, metamaterial, and optical applications. We show that their excellent properties can be further improved with plasmonic coupling of Au nanoparticles (AuNPs) on gold-coated nanodisk arrays excited at large incidence angles of up to 50°. The Bragg modes (BM) thereby strongly couple to AuNP immobilized on the plasmonic substrate due to shorter decay length of the plasmon at higher incidence angles, leading to a further enhanced field between the AuNP and the plasmonic substrate. The field was highest and two hotspots were created at orthogonal positions for AuNP located close to the corner of the Au film and Au nanodisk, which was also observed for AuNP dimers. Hybridization between single-stranded DNA (ssDNA) immobilized on the surface of the AuNPs and the capture ssDNA on the gold-coated nanodisk arrays led to at least a 5-fold signal improvement and a 7-fold lower limit of detection at 7 pM for ssDNA-functionalized AuNPs at large incident angles. Thus, we demonstrate that higher field strength can be accessed and the significant advantages of working with high incidence angles with AuNP on a 2D plasmonic crystal in plasmonic sensing.
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Affiliation(s)
- Mengdi Lu
- College of Physics and Optoelectronics Engineering , Dalian University of Technology , Dalian 116024 , China.,Département de chimie and Centre Québécois sur les Matériaux Fonctionnels (CQMF) , Université de Montréal , CP. 6128 Succ. Centre-Ville , Montreal , QC H3C 3J7 , Canada
| | - Long Hong
- School of Life Sciences , Peking University , Beijing 100871 , China
| | - Yuzhang Liang
- National Laboratory of Solid State Microstructures , Nanjing University , Nanjing 210093 , China
| | - Benjamin Charron
- Département de chimie and Centre Québécois sur les Matériaux Fonctionnels (CQMF) , Université de Montréal , CP. 6128 Succ. Centre-Ville , Montreal , QC H3C 3J7 , Canada
| | - Hu Zhu
- Département de chimie and Centre Québécois sur les Matériaux Fonctionnels (CQMF) , Université de Montréal , CP. 6128 Succ. Centre-Ville , Montreal , QC H3C 3J7 , Canada
| | - Wei Peng
- College of Physics and Optoelectronics Engineering , Dalian University of Technology , Dalian 116024 , China
| | - Jean-Francois Masson
- Département de chimie and Centre Québécois sur les Matériaux Fonctionnels (CQMF) , Université de Montréal , CP. 6128 Succ. Centre-Ville , Montreal , QC H3C 3J7 , Canada
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12
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Prakash R, Gupta R, Katoch VM, Tiwari PK. Molecular modelling and docking analysis of katG and rpoB gene in MDR-TB isolates from North Central Indian population. J Infect Public Health 2017; 10:593-599. [DOI: 10.1016/j.jiph.2017.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/10/2016] [Accepted: 01/07/2017] [Indexed: 10/20/2022] Open
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Rapid Molecular Detection of Multidrug-Resistant Tuberculosis by PCR-Nucleic Acid Lateral Flow Immunoassay. PLoS One 2015; 10:e0137791. [PMID: 26355296 PMCID: PMC4565584 DOI: 10.1371/journal.pone.0137791] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/21/2015] [Indexed: 01/18/2023] Open
Abstract
Several existing molecular tests for multidrug-resistant tuberculosis (MDR-TB) are limited by complexity and cost, hindering their widespread application. The objective of this proof of concept study was to develop a simple Nucleic Acid Lateral Flow (NALF) immunoassay as a potential diagnostic alternative, to complement conventional PCR, for the rapid molecular detection of MDR-TB. The NALF device was designed using antibodies for the indirect detection of labeled PCR amplification products. Multiplex PCR was optimized to permit the simultaneous detection of the drug resistant determining mutations in the 81-bp hot spot region of the rpoB gene (rifampicin resistance), while semi-nested PCR was optimized for the S315T mutation detection in the katG gene (isoniazid resistance). The amplification process additionally targeted a conserved region of the genes as Mycobacterium tuberculosis (Mtb) DNA control. The optimized conditions were validated with the H37Rv wild-type (WT) Mtb isolate and Mtb isolates with known mutations (MT) within the rpoB and katG genes. Results indicate the correct identification of WT (drug susceptible) and MT (drug resistant) Mtb isolates, with the least limit of detection (LOD) being 104 genomic copies per PCR reaction. NALF is a simple, rapid and low-cost device suitable for low resource settings where conventional PCR is already employed on a regular basis. Moreover, the use of antibody-based NALF to target primer-labels, without the requirement for DNA hybridization, renders the device generic, which could easily be adapted for the molecular diagnosis of other infectious and non-infectious diseases requiring nucleic acid detection.
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