1
|
Parwati I, Chaidir L, Yunus M, Montain MM, Budhiarko D, Selasih SF, Ristandi RB, Rachman RW, Nurhayati RD, Pambudi I, Budiyati AD. Evaluation of a real-time PCR assay performance to detect Mycobacterium tuberculosis, rifampicin, and isoniazid resistance in sputum specimens: a multicenter study in two major cities of Indonesia. Front Microbiol 2024; 15:1372647. [PMID: 38800757 PMCID: PMC11123600 DOI: 10.3389/fmicb.2024.1372647] [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: 01/18/2024] [Accepted: 04/11/2024] [Indexed: 05/29/2024] Open
Abstract
Background Tuberculosis (TB) is one of the major global health issues due to its high mortality rate, especially in low- and middle-income countries. One of the key success points of the TB eradication program is early TB diagnosis, which requires rapid and accurate diagnostic testing. This study aimed to evaluate the performance of a newly developed RT-PCR kit (Indigen MTB/DR-TB RT-PCR) in a routine TB clinical setting. Method A multi-fluorescence RT-PCR assay was designed and developed to detect regions within IS6110, rpoB, katG, and inhA of the Mycobacterium tuberculosis (MTB) genes. Sputum specimens were obtained from suspected TB patients who visited TB healthcare facilities in two major cities of Indonesia from September 2022 to May 2023. Specimens were assessed using Indigen MTB/DR-TB RT-PCR, acid-fast bacillus (AFB) smear microscopy, MTB culture, and drug susceptibility testing (DST) methods. Fisher's exact test (χ2) was used to analyze the Indigen performance relative to culture methods. Result The performance of Indigen MTB/DR-TB RT-PCR to detect MTB was assessed using 610 sputum specimens obtained from suspected patients. The overall sensitivity and specificity were 94.12% (95% CI: 90.86-96.48%) and 98.32% (95% CI: 96.20-99.46%), respectively. When the analysis was performed on AFB smear-negative TB subjects (386 subjects), a lower sensitivity level was found at 78.57% (95% CI: 68.26-86.78%), while the specificity level remained similar at 98.34% (95% CI: 96.18-99.46%). The overall performance of Indigen MTB/DR-TB RT-PCR to detect MTB showed substantial agreement with the MTB culture method (kappa value 0.93). In comparison to DST, the sensitivity and specificity levels of Indigen to detect RIF resistance or INH resistance were 78.2% (95% CI: 61.8-90.2%) and 82.8% (95% CI: 64.2-94.2%), respectively, while the specificity level for both groups was at 100% (95% CI, 87.7-100%). Conclusion Indigen MTB/DR-TB RT-PCR demonstrated reliable performance for TB molecular diagnostic testing and can be implemented in routine TB diagnostic settings.
Collapse
Affiliation(s)
- Ida Parwati
- Department of Clinical Pathology, Faculty of Medicine, Universitas Padjadjaran/Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - Lidya Chaidir
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Muhammad Yunus
- Stem Cell and Cancer Institute, PT. Kalbe Farma, Jakarta, Indonesia
| | - Maya Marinda Montain
- Unit Pelayanan Fungsional Balai Besar Kesehatan Paru Masyarakat Bandung (UPF BBKPM), Bandung, Indonesia
| | - Dini Budhiarko
- Stem Cell and Cancer Institute, PT. Kalbe Farma, Jakarta, Indonesia
| | | | | | | | | | - Imran Pambudi
- Directorate General of Diseases Prevention and Control, Ministry of Health of the Republic of Indonesia, Jakarta, Indonesia
| | | |
Collapse
|
2
|
Xiong XS, Zhang XD, Yan JW, Huang TT, Liu ZZ, Li ZK, Wang L, Li F. Identification of Mycobacterium tuberculosis Resistance to Common Antibiotics: An Overview of Current Methods and Techniques. Infect Drug Resist 2024; 17:1491-1506. [PMID: 38628245 PMCID: PMC11020249 DOI: 10.2147/idr.s457308] [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: 01/14/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is an essential cause of tuberculosis treatment failure and death of tuberculosis patients. The rapid and reliable profiling of Mycobacterium tuberculosis (MTB) drug resistance in the early stage is a critical research area for public health. Then, most traditional approaches for detecting MTB are time-consuming and costly, leading to the inappropriate therapeutic schedule resting on the ambiguous information of MTB drug resistance, increasing patient economic burden, morbidity, and mortality. Therefore, novel diagnosis methods are frequently required to meet the emerging challenges of MTB drug resistance distinguish. Considering the difficulty in treating MDR-TB, it is urgently required for the development of rapid and accurate methods in the identification of drug resistance profiles of MTB in clinical diagnosis. This review discussed recent advances in MTB drug resistance detection, focusing on developing emerging approaches and their applications in tangled clinical situations. In particular, a brief overview of antibiotic resistance to MTB was present, referred to as intrinsic bacterial resistance, consisting of cell wall barriers and efflux pumping action and acquired resistance caused by genetic mutations. Then, different drug susceptibility test (DST) methods were described, including phenotype DST, genotype DST and novel DST methods. The phenotype DST includes nitrate reductase assay, RocheTM solid ratio method, and liquid culture method and genotype DST includes fluorescent PCR, GeneXpert, PCR reverse dot hybridization, ddPCR, next-generation sequencing and gene chips. Then, novel DST methods were described, including metabolism testing, cell-free DNA probe, CRISPR assay, and spectral analysis technique. The limitations, challenges, and perspectives of different techniques for drug resistance are also discussed. These methods significantly improve the detection sensitivity and accuracy of multidrug-resistant tuberculosis (MRT) and can effectively curb the incidence of drug-resistant tuberculosis and accelerate the process of tuberculosis eradication.
Collapse
Affiliation(s)
- Xue-Song Xiong
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| | - Xue-Di Zhang
- Department of Laboratory Medicine, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Jia-Wei Yan
- Department of Laboratory Medicine, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Ting-Ting Huang
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| | - Zhan-Zhong Liu
- Department of Pharmacy, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Zheng-Kang Li
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Liang Wang
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Fen Li
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| |
Collapse
|
3
|
Cao G, Yang N, Xiong Y, Shi M, Wang L, Nie F, Huo D, Hou C. Completely Free from PAM Limitations: Asymmetric RPA with CRISPR/Cas12a for Nucleic Acid Assays. ACS Sens 2023; 8:4655-4663. [PMID: 38010352 DOI: 10.1021/acssensors.3c01686] [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] [Indexed: 11/29/2023]
Abstract
Experimentally, Cas12a can recognize multiple protospacer adjacent motif (PAM) sequences and is not restricted to the "TTTN". However, the application of the CRISPR/Cas12a system is still limited by the PAM for double-stranded DNA (dsDNA). Here, we developed asymmetric RPA (Asy-RPA) to completely break the limitations of PAM. Asy-RPA not only achieved efficient amplification but also converted dsDNA to single-stranded DNA (ssDNA) without complicated steps. The ssDNA products activated the trans-cleavage activity of Cas12a, outputting signals. The application of Asy-RPA completely freed Cas12a from the PAM, which can be more widely used in nucleic acid detection, such as lumpy skin disease virus, with an actual detection limit as low as 1.21 × 101 copies·μL-1. More importantly, Cas12a was intolerant to mutations on ssDNA. This provided technical support for the detection and identification of wild-type Mycobacterium tuberculosis (WT-TB) and rifampin-resistant mutant-type M. tuberculosis (MT-TB). The detection limit was as low as 1 fM for 1% mixed samples. The detection and availability of different treatment options for treatment-resistant and WT-TB were significant for the elimination of TB. In summary, the platform consisting of Asy-RPA and CRISPR/Cas12a was suitable for the detection of various viruses and bacteria and was a boon for the detection of dsDNA without recognizable PAM.
Collapse
Affiliation(s)
- Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs. Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Nannan Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs. Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Yifan Xiong
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs. Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Meimei Shi
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs. Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Lin Wang
- Science and Technology Research Center of China Customs, Beijing 100730, PR China
| | - Fuping Nie
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs. Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, PR China
| |
Collapse
|
4
|
Nguyen TBN, Nguyen TKD, Trương VH, Tran TTN, Phan VBT, Nguyen TT, Nguyen HB, Ngo VQT, Mai VT, Molicotti P. Drug resistance and the genotypic characteristics of rpoB and katG in rifampicin- and/or isoniazid-resistant Mycobacterium tuberculosis isolates in central Vietnam. Osong Public Health Res Perspect 2023; 14:347-355. [PMID: 37920892 PMCID: PMC10626318 DOI: 10.24171/j.phrp.2023.0124] [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: 05/09/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) and drug-resistant TB (DR-TB) are national health burdens in Vietnam. In this study, we investigated the prevalence of rifampicin (RIF) and/or isoniazid (isonicotinic acid hydrazide, INH) resistance in patients with suspected TB, and applied appropriate techniques to help rapidly target DR-TB. METHODS In total, 1,547 clinical specimens were collected and cultured using the BACTEC MGIT system (Becton Dickinson and Co.). A resazurin microtiter assay (REMA) was used to determine the proportions of RIF and/or INH resistance. A real-time polymerase chain reaction panel with TaqMan probes was employed to identify the mutations of rpoB and katG associated with DR-TB in clinical isolates. Genotyping of the identified mutations was also performed. RESULTS A total of 468 Mycobacterium tuberculosis isolates were identified using the REMA. Of these isolates, 106 (22.6%) were found to be resistant to 1 or both antibiotics. Of the resistant isolates, 74 isolates (69.8%) were resistant to isoniazid (INH) only, while 1 isolate (0.94%) was resistant to RIF only. Notably, 31 isolates (29.24%) were resistant to both antibiotics. Of the 41 phenotypically INH-resistant isolates, 19 (46.3%) had the Ser315Thr mutation. There were 8 different rpoB mutations in 22 (68.8%) of the RIF-resistant isolates. The most frequently detected mutations were at codons 531 (37.5%), 526 (18.8%), and 516 (6.3%). CONCLUSION To help prevent new cases of DR-TB in Vietnam, it is crucial to gain a comprehensive understanding of the genotypic DR-TB isolates.
Collapse
Affiliation(s)
- Thi Binh Nguyen Nguyen
- Department of Infectious Diseases and Tuberculosis, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | | | | | - Thi Tuyet Ngoc Tran
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - van Bao Thang Phan
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Thi Tuyen Nguyen
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Hoang Bach Nguyen
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Viet Quynh Tram Ngo
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Van Tuan Mai
- Department of Microbiology, Hue Central Hospital, Hue, Vietnam
| | - Paola Molicotti
- Department of Biomedical Science, Microbiology and Clinical Microbiology, University of Sassari, Sassari, Italy
| |
Collapse
|
5
|
Zhang R, Ou X, Sun X, Fan G, Zhao B, Tian F, Li F, Shen X, Zhao Y, Ma X. Multiplex LNA probe-based RAP assay for rapid and highly sensitive detection of rifampicin-resistant Mycobacterium tuberculosis. Front Microbiol 2023; 14:1141424. [PMID: 37180280 PMCID: PMC10172479 DOI: 10.3389/fmicb.2023.1141424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Objectives The World Health Organization (WHO) Global tuberculosis Report 2021 stated that rifampicin-resistant tuberculosis (RR-TB) remains a major public health threat. However, the in-practice diagnostic techniques for RR-TB have a variety of limitations including longer time, lack of sensitivity, and undetectable low proportion of heterogeneous drug resistance. Methods Here we developed a multiplex LNA probe-based RAP method (MLP-RAP) for more sensitive detection of multiple point mutations of the RR-TB and its heteroresistance. A total of 126 clinical isolates and 78 sputum samples collected from the National Tuberculosis Reference Laboratory, China CDC, were tested by MLP-RAP assay. In parallel, qPCR and Sanger sequencing of nested PCR product assay were also performed for comparison. Results The sensitivity of the MLP-RAP assay could reach 5 copies/μl using recombinant plasmids, which is 20 times more sensitive than qPCR (100 copies/μl). In addition, the detection ability of rifampicin heteroresistance was 5%. The MLP-RAP assay had low requirements (boiling method) for nucleic acid extraction and the reaction could be completed within 1 h when placed in a fluorescent qPCR instrument. The result of the clinical evaluation showed that the MLP-RAP method could cover codons 516, 526, 531, and 533 with good specificity. 41 out of 78 boiled sputum samples were detected positive by MLP-RAP assay, which was further confirmed by Sanger sequencing of nested PCR product assay, on the contrary, qPCR was able to detect 32 samples only. Compared with Sanger sequencing of nested PCR product assay, both the specificity and sensitivity of the MLP-RAP assay were 100%. Conclusion MLP-RAP assay can detect RR-TB infection with high sensitivity and specificity, indicating that this assay has the prospect of being applied for rapid and sensitive RR-TB detection in general laboratories where fluorescent qPCR instrument is available.
Collapse
Affiliation(s)
- Ruiqing Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuli Sun
- Clinical Laboratory, North China University of Science and Technology, Tangshan, China
| | - Guohao Fan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fengyu Tian
- Hebei Key Laboratory of Molecular Medicine, Hebei Medical University, Shijiazhuang, China
| | - Fengyu Li
- Hebei Key Laboratory of Molecular Medicine, Hebei Medical University, Shijiazhuang, China
| | - Xinxin Shen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
6
|
Jain B, Kulkarni S. Development of DNA Bio-chip for Detection of Mutations of rpoB, embB and inhA Genes in Drug-Resistant Mycobacterium Tuberculosis. Indian J Clin Biochem 2023; 38:242-250. [PMID: 37025431 PMCID: PMC10070561 DOI: 10.1007/s12291-022-01044-w] [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: 02/23/2022] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
Abstract
Drug-resistant (DR) tuberculosis (TB) is a global threat to health security and TB control programs. Since conventional drug susceptibility testing (DST) takes several weeks, we have developed a molecular method for the rapid identification of DR strains of Mycobacterium Tuberculosis (M.tb) utilizing DNA bio-chips. DNA bio-chips were prepared by immobilizing oligonucleotides (probes) on highly microporous polycarbonate track-etched membranes (PC-TEM) as novel support. Bio-chip was designed to contain 15 specific probes to detect mutations in three genes (rpoB, embB, and inhA). A sensitive and specific chemiluminescence based bio-chip assay was developed based on multiplex PCR followed by hybridization on bio-chip. Fifty culture isolates were used to evaluate the ability of in-house developed bio-chip to detect the mutations. Bio-chip analysis shows that 37.7% of samples show wild type sequences, 53.3% of samples were monoresistance showing resistance to either rifampicin (RMP), isoniazid (INH), or ethambutol (EMB). 4.4% of samples were polydrug resistant showing mutations in both the rpoB gene and embB gene while 4.4% of samples were multidrug-resistant (MDR), harboring mutations in the rpoB and inhA genes. The results were compared with DST and sequencing. Compared to sequencing, bio-chip assay shows a sensitivity of 96.5% and specificity of 100% for RMP resistance. For EMB and INH, the results were in complete agreement with sequencing. This study demonstrates the first-time use of PC-TEMs for developing DNA bio-chip for the detection of mutations associated with drug resistance in M.tb. Developed DNA bio-chip accurately detected different mutations present in culture isolates and thus provides detailed and reliable data for clinical diagnosis.
Collapse
Affiliation(s)
- Bharti Jain
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Savita Kulkarni
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Parel, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| |
Collapse
|
7
|
Cao G, Qiu Y, Long K, Ma Y, Luo H, Yang M, Hou J, Huo D, Hou C. Rapid and Ultrasensitive Approach for the Simultaneous Detection of Multilocus Mutations to Distinguish Rifampicin-Resistant Mycobacterium tuberculosis. Anal Chem 2022; 94:17653-17661. [PMID: 36473113 DOI: 10.1021/acs.analchem.2c04399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The untested empirical medications exacerbated the development of multidrug-resistant Mycobacterium tuberculosis (MDR-TB). Here, we develop a rapid and specific method based on loop-mediated isothermal amplification and duplex-specific nuclease for distinguishing rifampicin-resistant M. tuberculosis. Three probes were designed for the codons 516, 526, and 531 on the RNA polymerase β-subunit (rpoB) gene. These three sites accounted for more than 90% of the total mutations of the ropB gene in the rifampicin-resistant strain. The approach can perform simultaneous and sensitive detection of three mutant sites with the actual detection limit as 10 aM of DNA and 62.5 cfu·mL-1 of bacteria in 67 min under isothermal conditions. Moreover, the positive mode of the approach for MDR-TB can not only deal with the randomness and diversity of mutations but also provide an easier way for medical staff to read the results. Therefore, it is a particularly valuable method to handle major and urgent MDR-TB diagnostics.
Collapse
Affiliation(s)
- Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Yue Qiu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Keyi Long
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Yi Ma
- Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, P. R. China
| | - Huibo Luo
- Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, P. R. China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Jingzhou Hou
- Postdoctoral Research Station, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China.,Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, P. R. China.,Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, Zigong 643000, P. R. China
| |
Collapse
|
8
|
Gaballah A, Ghazal A, Almiry R, Hussein S, Emad R, El-Sherbini E. Fingerprinting of Mycobacterium tuberculosis isolates by MIRU-VNTR genotyping and detection of isoniazid resistance by real-time PCR. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Tuberculosis (TB) is a great public health problem in developing countries such as Egypt. Genotyping of
Mycobacterium tuberculosis
isolates has a prominent role in the field of TB prevention.
Aim. This study aimed to evaluate real-time PCR using Minor Groove Binder (MGB) probes and to identify circulating lineages/sub-lineages of
M. tuberculosis
and their transmission patterns.
Hypothesis. We hypothesize that MIRU-VNTR technique is efficient in identifying circulating
M. tuberculosis
lineages in Egypt.
Methodology. Fifty sputum specimens positive for acid-fast bacilli were included. Isoniazid (INH) resistance was detected using the 1 % proportion method. Real-time PCR using MGB-probes was used for simultaneous detection of TB infection and INH resistance. Partial sequencing of the katG gene was used to confirm INH resistance results. A standard 15 Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (15-MIRU-VNTR) approach was used for genotyping through the MIRU-VNTRplus online platform.
Results. Only seven specimens showed phenotypic resistance to INH.
M. tuberculosis
was detected in all samples, while a mutation in the katG gene codon 315 was detected only in five samples, which were also phenotypically INH-resistant. Sequencing of the katG gene showed codon 315 mutation genotypically and phenotypically in the five INH-resistant isolates. Molecular genotyping of
M. tuberculosis
isolates revealed that the majority of isolates (26/50, 52 %) belonged to the S family of lineage_4. A low clustering rate (2 %) was observed among our isolates. According to the Hunter-Gaston Discriminatory Index (HGDI), 11 MIRU-VNTR loci were highly or moderately discriminative, while four loci were less polymorphic.
Conclusion. MIRU-VNTR genotyping revealed a low clustering rate with a low recent transmission rate of
M. tuberculosis
strains in Alexandria, Egypt.
Collapse
Affiliation(s)
- Ahmed Gaballah
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Abeer Ghazal
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Reda Almiry
- Department of Clinical Pathology, Alexandria Armed Forces Hospital, Alexandria, Egypt
| | - Somaya Hussein
- Elmamoura Chest Hospital, Egyptian Ministry of Health, Alexandria, Egypt
| | - Rasha Emad
- Alexandria Main University Hospital, Alexandria University, Alexandria, Egypt
| | - Eglal El-Sherbini
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| |
Collapse
|
9
|
Wu XM, Zhang JH, Feng ZS, Chen WX, Zhang F, Li Y. An ultra-sensitive "turn-off" fluorescent sensor for the trace detection of rifampicin based on glutathione-stabilized copper nanoclusters. Analyst 2020; 145:1227-1235. [PMID: 31898707 DOI: 10.1039/c9an01994d] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Rifampicin is a common antibiotic used in human and veterinary medicine to treat tuberculosis and other diseases caused by numerous pathogenic bacteria. However, the excessive or improper use of rifampicin usually leads to a series of problems, including bacterial resistance, excessive drug-resistance and water pollution. Thus, it is of great importance to develop selective and sensitive assays for monitoring rifampicin in biological systems. In this study, we designed a fluorescence "turn-off" strategy for the trace detection of rifampicin based on a glutathione-stabilized copper nanoclusters (GSH-Cu NC) sensor. In an aqueous solution, the fluorescence of the GSH-Cu NCs at 632 nm can be quenched effectively and selectively by rifampicin due to the inner-filter effect (IFE) of fluorescence mechanism. Distinctively, this GSH-Cu NC sensor exhibited excellent fluorescence sensing capability for the trace detection of rifampicin with a very low limit of detection (LOD) of 16 pM in a wide linear range from 50 to 10 000 pM. It is not only more sensitive than the other methods previously reported for the detection of rifampicin, but also has an outstanding selectivity and strong anti-interference in complex samples. Furthermore, the as-developed GSH-Cu NCs were also successfully applied to determine rifampicin in different real samples with quantitative spike recoveries ranging from 97% to 105%.
Collapse
Affiliation(s)
- Xiao-Man Wu
- Tianjin Key laboratory of Structure and Performance for Functional Molecules, MOE Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, College of Chemistry, Tianjin Normal University, 393 Binshui West Road, Tianjin 300387, PR China.
| | | | | | | | | | | |
Collapse
|
10
|
Anukool U, Phunpae P, Tharinjaroen CS, Butr-Indr B, Saikaew S, Netirat N, Intorasoot S, Suthachai V, Tragoolpua K, Chaiprasert A. Genotypic Distribution and a Potential Diagnostic Assay of Multidrug-Resistant Tuberculosis in Northern Thailand. Infect Drug Resist 2020; 13:3375-3382. [PMID: 33061484 PMCID: PMC7533241 DOI: 10.2147/idr.s263082] [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: 05/28/2020] [Accepted: 08/04/2020] [Indexed: 01/21/2023] Open
Abstract
Introduction Knowledge of the prevalence and distribution of multidrug-resistant tuberculosis (MDR-TB) genotypes in northern Thailand is still limited. An accurate, rapid, and cost-effective diagnostic of MDR-TB is crucial to improve treatment and control of increased MDR-TB. Materials and Methods The molecular diagnostic assays named “RIF-RD” and “INH-RD” were designed to detect rifampicin (RIF) and isoniazid (INH) resistance based on real-time PCR and high-resolution melting curve analysis. Applying the ∆Tm cutoff values, the RIF-RD and INH-RD were evaluated against the standard drug susceptibility testing (DST) using 107 and 103 clinical Mycobacterium tuberculosis (Mtb) isolates from northern Thailand. DNA sequence analysis of partial rpoB, katG, and inhA promoter of 73 Mtb isolates, which included 30 MDR-TB, was performed to elucidate the mutations involved with RIF and INH resistance. Results When compared with the phenotypic DST, RIF-RD targeting rpoB showed sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 83.9, 98.6, 96.9, and 92.0%, respectively. The multiplex reaction of the INH-RD targeted both katG and inhA promoter showed high sensitivity, specificity, PPV, and NPV of 97.1, 94.2, 89.2, and 98.5%, respectively. Six patterns of rpoB mutation, predominately at codons 531 (50%) and 526 (40%) along with a rare S522L (3.33%) and D516V (3.33%), were detected. A single pattern of katG mutation (S315T) (63.3%) and four patterns of inhA promoter mutation, predominately −15 (C>T), were found. Approximately, 17% of MDR-TB strains possessed double mutations within the katG and inhA promoter. Conclusion Up to 86.7% and 96.7% of MDR-TB could be accurately detected by RIF-RD and INH-RD, emphasizing its usefulness as a low unit price assay for rapid screening of MDR-TB, with confirmation of INH resistance in low and middle-income countries. The MDR-TB genotypes provided will be beneficial for TB control and the development of drug-resistant TB diagnostic technology in the future.
Collapse
Affiliation(s)
- Usanee Anukool
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand.,Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand
| | - Ponrut Phunpae
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand.,Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand
| | - Chayada Sitthidet Tharinjaroen
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand.,Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand
| | - Bordin Butr-Indr
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand.,Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand
| | - Sukanya Saikaew
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand.,Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand.,Faculty of Public Health Chiang Mai University, Muang District, Chiang Mai 50200, Thailand
| | - Nathiprada Netirat
- Office of Disease Prevention and Control, 1 (ODPC 1) Chiang Mai, Department of Disease Control, Ministry of Public Health Thailand, Muang District, Chiang Mai 50000, Thailand
| | - Sorasak Intorasoot
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand.,Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand
| | - Vorasak Suthachai
- Office of Disease Prevention and Control, 1 (ODPC 1) Chiang Mai, Department of Disease Control, Ministry of Public Health Thailand, Muang District, Chiang Mai 50000, Thailand
| | - Khajornsak Tragoolpua
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand.,Infectious Diseases Research Unit (IDRU), Faculty of Associated Medical Sciences, Chiang Mai University, Muang District, Chiang Mai 50200, Thailand
| | - Angkana Chaiprasert
- Office for Research and Development Affairs, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| |
Collapse
|
11
|
AlMatar M, Var I, Kayar B, Köksal F. Differential Expression of Resistant and Efflux Pump Genes in MDR-TB Isolates. Endocr Metab Immune Disord Drug Targets 2020; 20:271-287. [DOI: 10.2174/1871530319666191009153834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/21/2019] [Accepted: 07/22/2019] [Indexed: 12/20/2022]
Abstract
Background:Numerous investigations demonstrate efflux as a worldwide bacterial mode of action which contributes to the resistance of drugs. The activity of antibiotics, which subjects to efflux, can be improved by the combined usage of efflux inhibitors. However, the efflux role to the overall levels of antibiotic resistance of clinical M. tuberculosis isolates is inadequately comprehended and is still disregarded by many.Method:Here, we assessed the contribution of resistant genes associated with isoniazid (INH) and rifampin (R) resistance to the levels of drug resistance in the (27) clinical isolates of MDR-TB. Additionally, the role of the resistance for six putative drug efflux pump genes to the antibiotics was investigated. The level of katG expression was down-regulated in 24/27 (88.88%) of MDR-TB isolates. Of the 27 MDR-TB isolates, inhA, oxyR-ahpC, and rpoB showed either overexpression or up-regulation in 8 (29.62%), 4 (14.81 %), and 24 (88.88%), respectively. Moreover, the efflux pump genes drrA, drrB, efpA, Rv2459, Rv1634, and Rv1250 were overexpressed under INH/RIF plus fresh pomegranate juice (FPJ) stress signifying the efflux pumps contribution to the overall levels of the resistance of MDR-TB isolates.Conclusion:These results displayed that the levels of drug resistance of MDR-TB clinical isolates are due to combination among drug efflux pump and the presence of mutations in target genes, a truth which is often ignored by the specialists of tuberculosis in favour of the almost undoubted significance of drug target- gene mutations for the resistance in M. tuberculosis.
Collapse
Affiliation(s)
- Manaf AlMatar
- Department of Biotechnology, Institute of Natural and Applied Sciences (Fen Bilimleri Enstitusu), Cukurova University, Adana, Turkey
| | - Işıl Var
- Department of Food Engineering, Agricultural Faculty, Cukurova University, Adana, Turkey
| | - Begüm Kayar
- Department of Medical Microbiology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Fatih Köksal
- Department of Medical Microbiology, Faculty of Medicine, Cukurova University, Adana, Turkey
| |
Collapse
|
12
|
Yang P, Song Y, Xia X, Zhang AM. Rapid screening mutations of first-line-drug-resistant genes in Mycobacterium tuberculosis strains by allele-specific real-time quantitative PCR. PeerJ 2019; 7:e6696. [PMID: 30972260 PMCID: PMC6448557 DOI: 10.7717/peerj.6696] [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: 10/29/2018] [Accepted: 02/27/2019] [Indexed: 12/27/2022] Open
Abstract
Tuberculosis (TB) is a worldwide health, economic, and social burden, especially in developing countries. Drug-resistant TB is the most serious type of this burden. Thus, it is necessary to screen drug-resistant mutations by using a simple and rapid detection method. A total of 32 pairs of allele-specific PCR (AS-PCR) primers were designed to screen mutation and/or wild-type alleles of 16 variations in four first-line drug-resistant genes (katG, rpoB, rpsL, and embB) of TB strains. A pair of primers was designed to amplify 16S rRNA gene and to verify successful amplification. Subsequently, we tested the specificity and sensitivity of these AS-PCR primers. The optimized condition of these AS-PCR primers was first confirmed. All mutations could be screened in general AS-PCR, but only 13 of 16 variations were intuitively investigated by using real-time quantitative PCR (qPCR) and AS-PCR primers. The results of specificity assay suggested that the AS-PCR primers with mutation and/or wildtype alleles could successfully amplify the corresponding allele under optimized PCR conditions. The sensitivity of nine pairs of primers was 500 copy numbers, and the other seven pairs of primers could successfully amplify correct fragments with a template comprising 103 or 104 copy numbers template. An optimized AS-qPCR was established to screen drug-resistant mutations in TB strains with high specificity and sensitivity.
Collapse
Affiliation(s)
- Pengpeng Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yuzhu Song
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| |
Collapse
|
13
|
Highly Sensitive Detection of Isoniazid Heteroresistance in Mycobacterium tuberculosis by DeepMelt Assay. J Clin Microbiol 2018; 56:JCM.01239-17. [PMID: 29118176 DOI: 10.1128/jcm.01239-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022] Open
Abstract
Detection of heteroresistance of Mycobacterium tuberculosis remains challenging using current genotypic drug susceptibility testing methods. Here, we described a melting curve analysis-based approach, termed DeepMelt, that can detect less-abundant mutants through selective clamping of the wild type in mixed populations. The singleplex DeepMelt assay detected 0.01% katG S315T in 105M. tuberculosis genomes/μl. The multiplex DeepMelt TB/INH detected 1% of mutant species in the four loci associated with isoniazid resistance in 104M. tuberculosis genomes/μl. The DeepMelt TB/INH assay was tested on a panel of DNA extracted from 602 precharacterized clinical isolates. Using the 1% proportion method as the gold standard, the sensitivity was found to be increased from 93.6% (176/188, 95% confidence interval [CI] = 89.2 to 96.3%) to 95.7% (180/188, 95% CI = 91.8 to 97.8%) compared to the MeltPro TB/INH assay. Further evaluation of 109 smear-positive sputum specimens increased the sensitivity from 83.3% (20/24, 95% CI = 64.2 to 93.3%) to 91.7% (22/24, 95% CI = 74.2 to 97.7%). In both cases, the specificity remained nearly unchanged. All heteroresistant samples newly identified by the DeepMelt TB/INH assay were confirmed by DNA sequencing and even partially by digital PCR. The DeepMelt assay may fill the gap between current genotypic and phenotypic drug susceptibility testing for detecting drug-resistant tuberculosis patients.
Collapse
|