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Xie L, Zhu XY, Xu L, Xu XX, Ruan ZF, Huang MX, Chen L, Jiang XW. Accurate and affordable detection of rifampicin and isoniazid resistance in Tuberculosis sputum specimens by multiplex PCR-multiple probes melting analysis. Infection 2024:10.1007/s15010-024-02295-w. [PMID: 38884858 DOI: 10.1007/s15010-024-02295-w] [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: 10/26/2023] [Accepted: 05/10/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Escalating cases of multidrug-resistant tuberculosis (MDR-TB) pose a major challenge to global TB control efforts, necessitating innovative diagnostics to empower decentralized detection of gene mutations associated with resistance to rifampicin (RIF) and isoniazid (INH) in Mycobacterium tuberculosis (M. tuberculosis) in resource-constrained settings. METHODS Combining multiplex fluorescent PCR and Multiple Probes Melting Analysis, we identified mutations in the rpoB, katG, ahpC and inhA genes from sputum specimens. We first constructed a reference plasmid library comprising 40 prevalent mutations in the target genes' resistance determining regions and promoters, serving as positive controls. Our assay utilizes a four-tube asymmetric PCR method with specifically designed molecular beacon probes, enabling simultaneous detection of all 40 mutations. We evaluated the assay's effectiveness using DNA isolated from 50 clinically confirmed M. tuberculosis sputum specimens, comparing our results with those obtained from Sanger sequencing and retrospective validation involving bacteriological culture and phenotypic drug susceptibility testing (pDST). We also included the commercial Xpert MTB/RIF assay for accuracy comparison. RESULTS Our data demonstrated remarkable sensitivity in detecting resistance to RIF and INH, achieving values of 93.33% and 95.24%, respectively, with a specificity of 100%. The concordance between our assay and pDST was 98.00%. Furthermore, the accuracy of our assay was comparable to both Sanger sequencing and the Xpert assay. Importantly, our assay boasts a 4.2-h turnaround time and costs only $10 per test, making it an optimal choice for peripheral healthcare settings. CONCLUSION These findings highlight our assay's potential as a promising tool for rapidly, accurately, and affordably detecting MDR-TB.
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Affiliation(s)
- Long Xie
- Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Xiao-Ya Zhu
- State Key Laboratory of Virology, School of Life Sciences, Wuhan University, Wuhan, China
| | - Li Xu
- Research Institute, DAAN Gene Co., Ltd., Guangzhou, China
- The Medicine and Biological Engineering Technology Research Centre of the Ministry of Health, Guangzhou, China
| | - Xiao-Xie Xu
- Research Institute, DAAN Gene Co., Ltd., Guangzhou, China
- The Medicine and Biological Engineering Technology Research Centre of the Ministry of Health, Guangzhou, China
| | - Ze-Fan Ruan
- Research Institute, DAAN Gene Co., Ltd., Guangzhou, China
- The Medicine and Biological Engineering Technology Research Centre of the Ministry of Health, Guangzhou, China
| | - Ming-Xiang Huang
- Fuzhou Pulmonary Hospital and Fujian Medical University Clinical Teaching Hospital, Fuzhou, China.
| | - Li Chen
- Chaoshan Hospital, The First Affiliated Hospital of Jinan University, Chaozhou, China.
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Xi-Wen Jiang
- Research Institute, DAAN Gene Co., Ltd., Guangzhou, China.
- The Medicine and Biological Engineering Technology Research Centre of the Ministry of Health, Guangzhou, China.
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China.
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Chand AB, Basnet A, Maharjan B, Rai G, Joshi YP, Bhatt LR, Sen B, Rai SK. Drug-resistant Mycobacterium tuberculosis among Nepalese patients at a tuberculosis referral center. PLoS One 2024; 19:e0301210. [PMID: 38709710 PMCID: PMC11073693 DOI: 10.1371/journal.pone.0301210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/12/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Multidrug-resistant tuberculosis (MDR-TB), characterized by isoniazid and rifampicin resistance, is caused by chromosomal mutations that restrict treatment options and complicate tuberculosis management. This study sought to investigate the prevalence of pre-extensively drug-resistant (pre-XDR) and extensively drug-resistant (XDR) tuberculosis, as well as mutation pattern, in Nepalese patients with MDR/rifampicin-resistant (RR)-TB strains. METHODS A cross-sectional study was conducted on MDR/RR-TB patients at the German Nepal Tuberculosis Project from June 2017 to June 2018. The MTBDRsl line probe assay identified pre-XDR-TB and XDR-TB. Pre-XDR-TB included MDR/RR-TB with resistance to any fluoroquinolone (FLQ), while XDR-TB included MDR/RR-TB with resistance to any FLQ and at least one additional group A drug. Mutation status was determined by comparing bands on reaction zones [gyrA and gyrB for FLQ resistance, rrs for SILD resistance, and eis for low-level kanamycin resistance, according to the GenoType MTBDRsl VER 2.0, Hain Lifescience GmbH, Nehren, Germany definition of pre-XDR and XDR] to the evaluation sheet. SPSS version 17.0 was used for data analysis. RESULTS Out of a total of 171 patients with MDR/RR-TB, 160 had (93.57%) had MTBC, of whom 57 (35.63%) had pre-XDR-TB and 10 (6.25%) had XDR-TB. Among the pre-XDR-TB strains, 56 (98.25%) were FLQ resistant, while 1 (1.75%) was SLID resistant. The most frequent mutations were found at codons MUT3C (57.14%, 32/56) and MUT1 (23.21%, 13/56) of the gyrA gene. One patient had SLID resistant genotype at the MUT1 codon of the rrs gene (100%, 1/1). XDR-TB mutation bands were mostly detected on MUT1 (30%, 3/10) of the gyrA and rrs, MUT3C (30%, 3/10) of the gyrA, and MUT1 (30%, 3/10) of the rrs. CONCLUSIONS Pre-XDR-TB had a significantly higher likelihood than XDR-TB, with different specific mutation bands present in gyrA and rrs genes.
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Affiliation(s)
- Arun Bahadur Chand
- Department of Microbiology, KIST Medical College and Teaching Hospital, Lalitpur, Nepal
- Department of Medical Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
- German Nepal Tuberculosis Project, Kathmandu, Nepal
| | - Ajaya Basnet
- Department of Medical Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
| | | | - Ganesh Rai
- Department of Medical Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
| | - Yadav Prasad Joshi
- Department of Public Health, Manmohan Memorial Institute of Health Sciences, Kathmandu, Nepal
| | - Lok Raj Bhatt
- Department of Microbiology, KIST Medical College and Teaching Hospital, Lalitpur, Nepal
| | - Bindu Sen
- Department of Dentistry, KIST Medical College and Teaching Hospital, Lalitpur, Nepal
| | - Shiba Kumar Rai
- Department of Medical Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
- Department of Microbiology, Nepal Medical College Teaching Hospital, Kathmandu, Nepal
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Li Y, Li Y, Wang T, Li Y, Tao N, Kong X, Zhang Y, Han Q, Liu Y, Li H. Multidrug-resistant Mycobacterium tuberculosis transmission in Shandong, China. Medicine (Baltimore) 2024; 103:e37617. [PMID: 38518003 PMCID: PMC10956945 DOI: 10.1097/md.0000000000037617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/23/2024] [Indexed: 03/24/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) has imposed a significant economic and health burden worldwide, notably in China. Using whole genome sequence, we sought to understand the mutation and transmission of MDR-TB in Shandong. A retrospective study of patients diagnosed with pulmonary tuberculosis in Shandong from 2009 to 2018 was conducted. To explore transmission patterns, we performed whole genome sequencing on MDR-TB isolates, identified genomic clusters, and assessed the drug resistance of TB isolates. Our study analyzed 167 isolates of MDR-TB, finding that 100 were clustered. The predominant lineage among MDR-TB isolates was lineage 2, specifically with a notable 88.6% belonging to lineage 2.2.1. Lineage 4 constituted a smaller proportion, accounting for 4.2% of the isolates. We discovered that Shandong has a significant clustering percentage for MDR-TB, with Jining having the highest percentage among all Shandong cities. The clustering percentages of MDR-TB, pre-extensively drug-resistant tuberculosis, and extensively drug-resistant tuberculosis were 59.9%, 66.0%, and 71.4%, respectively, and the clustering percentages increased with the expansion of the anti-TB spectrum. Isolates from genomic clusters 1 and 3 belonged to lineage 2.2.1 and showed signs of cross-regional transmission. The distribution of rrs A1401G and katG S315T mutations in lineage 2.2.1 and 2.2.2 strains differed significantly (P < .05). MDR-TB isolates with rpoB I480V, embA-12C > T, and rrs A1401G mutations showed a higher likelihood of clustering (P < .05). Our findings indicate a significant problem of local transmission of MDR-TB in Shandong, China. Beijing lineage isolates and some drug-resistant mutations account for the MDR-TB transmission in Shandong.
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Affiliation(s)
- Yingying Li
- Department of Chinese Medicine Integrated with Western Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yifan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Tingting Wang
- Department of Chinese Medicine Integrated with Western Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yameng Li
- Department of Chinese Medicine Integrated with Western Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ningning Tao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xianglong Kong
- Shandong Artificial Intelligence Institute Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Yuzhen Zhang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qilin Han
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Huaichen Li
- Department of Chinese Medicine Integrated with Western Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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Nwachukwu NO, Ulasi AE, Okoronkwo CU, Unegbu VN. Pre-extensively drug-resistant tuberculosis among pulmonary multidrug-resistant tuberculosis patients in Eastern Nigeria. Lung India 2023; 40:492-495. [PMID: 37961955 PMCID: PMC10723212 DOI: 10.4103/lungindia.lungindia_337_23] [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: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/20/2023] [Indexed: 11/15/2023] Open
Abstract
Background Pre-extensively drug-resistant tuberculosis (Pre-XDR-TB), an emerging form of drug-resistant tuberculosis, is challenging efforts at tuberculosis control, leading to treatment failure among multidrug-resistant tuberculosis (MDR-TB) patients and progression to extensively drug-resistant tuberculosis (XDR-TB). We determined the rate of Pre-XDR-TB among multidrug-resistant patients in Southeast, Nigeria. Methods A prospective laboratory-based study was carried out at the South East Zonal Tuberculosis Reference Laboratory from January 2021 to December 2021. Second-line drug (SLD) resistance was performed on 225 sputum samples of multidrug-resistant patients prior to treatment initiation using GenoType MTBDRsl genotypic drug susceptibility testing (DST) method. Results The rate of Pre-XDR-TB among 225 MDR-TB cases was 3.1%. Fluoroquinolone-resistant Pre-XDR-TB was observed (100%) in previously treated tuberculosis cases. Only one (0.4%) case showed resistance to both fluoroquinolone (FQ) and one second-line injectable drug (XDR-TB). The extensively drug-resistant case observed was a de-novo resistance. Exactly 0.9% of the multidrug-resistant cases showed resistance to second-line injectables. Conclusion The prevalence of Pre-XDR-TB among MDR-TB cases was high. There is need for rapid detection of Pre-XDR-TB among MDR-TB cases before treatment initiation.
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Affiliation(s)
- Ndubuisi O. Nwachukwu
- Department of Medical Laboratory Science, Abia State University Uturu, P.M.B 2000, Uturu, Abia State, Nigeria
- Department of Microbiology, Abia State University Uturu, P.M.B 2000, Uturu, Nigeria
| | - Amara E. Ulasi
- Department of Animal and Environmental Biology, Abia State University Uturu, P.M.B 200b0, Uturu, Abia State, Nigeria
| | | | - Valentine N. Unegbu
- Department of Biology Science, University of Agriculture and Environmental Sciences, Umuagwo, Imo State, Nigeria
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5
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Wang J, Yu C, Xu Y, Chen Z, Qiu W, Chen S, Pei H, Zhong Y. Analysis of Drug-Resistance Characteristics and Genetic Diversity of Multidrug-Resistant Tuberculosis Based on Whole-Genome Sequencing on the Hainan Island, China. Infect Drug Resist 2023; 16:5783-5798. [PMID: 37692467 PMCID: PMC10487742 DOI: 10.2147/idr.s423955] [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: 06/22/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Purpose Given the high burden of Tuberculosis (TB) in China, the prevalence of multidrug-resistant tuberculosis (MDR-TB) is significant. Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) enables the identification of lineages, drug-resistant mutations, and transmission patterns, offering valuable insights for TB control, clinical diagnosis, and treatment. Methods We collected 202 MDR-MTB strains from 3519 suspected pulmonary TB patients treated at The Second Affiliated Hospital of Hainan Medical University between July 2019 and June 2021. Proportional drug-susceptibility testing was performed using 8 common anti-tuberculosis drugs. Subsequently, the genotypic drug resistance and genetic characteristics were analyzed by the WGS. Results Lineages are identified by TB-profiler revealed 202 MDR-MTB strains, showcasing three predominant lineages, with lineage 2 being the most prevalent. Close genomic relatedness analysis and evidence of MTB transmission led to the formation of 15 clusters comprising 42 isolates, resulting in a clustering rate of 20.8%. Novelty, lineage 2.1 (non-Beijing) accounted for 27.2% of the MDR-MTB strains, which is rare in China and Neighboring countries. Regarding first-line anti-TB drugs, genes associated with rifampicin resistance, primarily the rpoB gene, were detected in 200 strains (99.0%). Genes conferring resistance to isoniazid, ethambutol, and streptomycin were identified in 191 (94.5%), 125 (61.9%), and 100 (49.5%) strains, respectively. Among the second-line drugs, 97 (48.0%) strains exhibited genes encoding resistance to fluoroquinolones. Comparing the results to phenotypic drug susceptibility-based testing, the sensitivity of WGS for detecting resistance to each of the six drugs (rifampicin, isoniazid, ethambutol, ofloxacin, kanamycin, capreomycin) was 90% or higher. With the exception of ethambutol, the specificity of WGS prediction for the remaining drugs exceeded 88%. Conclusion Our study provides crucial insights into genetic mutation types, genetic diversity, and transmission of MDR-MTB on Hainan Island, serving as a significant reference for MDR-MTB surveillance and clinical decision-making.
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Affiliation(s)
- Jieying Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Chunchun Yu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Yuni Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Zhuolin Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Wenhua Qiu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Shaowen Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Hua Pei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
| | - Yeteng Zhong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, People’s Republic of China
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Diriba G, Alemu A, Tola HH, Yenew B, Amare M, Eshetu K, Sinshaw W, Abebaw Y, Meaza A, Seid G, Moga S, Zerihun B, Getu M, Dagne B, Mollalign H, Tadesse M, Buta B, Wordofa N, Alemu E, Erresso A, Hailu M, Tefera Z, Wondimu A, Belhu T, Gamtesa DF, Getahun M, Kebede A, Abdela S. Pre-extensively drug-resistant tuberculosis among multidrug-resistant tuberculosis patients in Ethiopia: a laboratory-based surveillance study. IJID REGIONS 2022; 5:39-43. [PMID: 36176268 PMCID: PMC9513164 DOI: 10.1016/j.ijregi.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 11/23/2022]
Abstract
Background The rise of drug-resistant tuberculosis (DR-TB) has presented a substantial challenge to the national tuberculosis (TB) control program. Understanding the epidemiology of pre-extensively drug-resistant tuberculosis (pre-XDR-TB) could help clinicians to adapt MDR-TB treatment regimens at an earlier stage. This study aimed to assess second-line anti-TB drug resistance among MDR-TB patients in Ethiopia using routine laboratory-based data. Methods Laboratory-based cross-sectional data were collected from the national TB reference laboratory and seven regional tuberculosis culture laboratories in Ethiopia from July 2019 to March 2022. The required data, such as drug-susceptibility testing (DST) results and sociodemographics, were collected on a structured checklist from laboratory registration books and electronic databases. Data were entered into a Microsoft Excel spreadsheet and analyzed using SPSS version 23. Descriptive statistics were performed to show the distribution and magnitude of drug resistance. Results Second-line drugs (SLDs) susceptibility testing was performed for 644 MDR isolates, of which 19 (3%) were found to be pre-XDR-TB cases. Of the total MDR-TB isolates, 19 (3%) were resistant to at least one fluoroquinolone drug, while 11 (1.7%) were resistant to at least one injectable second-line drug. Of the 644 MDR-TB isolates, 1.9% (5/261) pre-XDR were from new MDR-TB cases, while 3.7% (14/383) were from previously treated MDR-TB patients. The most frequently identified mutations, based on MTBDRsl results, were in codon A90V of the gyrA gene (77.3%) and A1401G of the rrs gene (45.5%). Conclusion The overall prevalence of pre-XDR-TB in Ethiopia is considerable. The majority of SLD resistance mutations were in the gyrA gene at position A90V. Modern, rapid DST is necessary to enable identification of pre-XDR-TB and XDR-TB in supporting proper regimen administration for patients.
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Affiliation(s)
- Getu Diriba
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ayinalem Alemu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Bazezew Yenew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Misikir Amare
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Kirubel Eshetu
- USAID Eliminate TB Project, Management Sciences for Health, Addis Ababa, Ethiopia
| | | | | | - Abyot Meaza
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Getachew Seid
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Shewki Moga
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Melak Getu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Biniyam Dagne
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | - Bedo Buta
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Niguse Wordofa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ephrem Alemu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Michael Hailu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Zigba Tefera
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Tegegn Belhu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | - Abebaw Kebede
- Africa Centers for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Saro Abdela
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
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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.
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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
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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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Sarwer MI, Khan MT, Khurshid S. Novel rrs mutations in second-line injectable drug-resistant clinical isolates of Mycobacterium tuberculosis from the Punjab province of Pakistan. J Infect Chemother 2022; 28:1119-1124. [DOI: 10.1016/j.jiac.2022.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022]
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Bai W, Liu L, Wu L, Chen S, Wu S, Wang Z, Xu K, Chi Q, Pan Y, Xu X. Assessing the utility of the Xpert Mycobacterium tuberculosis/rifampin assay for analysis of bronchoalveolar lavage fluid in patients with suspected pulmonary tuberculosis. J Clin Lab Anal 2021; 36:e24154. [PMID: 34850984 PMCID: PMC8761447 DOI: 10.1002/jcla.24154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/09/2021] [Accepted: 11/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background There is limited research assessing the utility of the Xpert Mycobacterium tuberculosis/rifampin (MTB/RIF) assay for the analysis of bronchoalveolar lavage fluid (BALF) in Chinese patients with suspected pulmonary tuberculosis (PTB). Thus, our objective was to determine the diagnostic accuracy of the Xpert MTB/RIF assay and evaluate its utility for the determination of rifampicin resistance. Methods We retrospectively analyzed BALF from 214 patients with suspected PTB between January 2018 and March 2019. Using mycobacterial culture or final clinical diagnosis as the reference standard, the diagnostic accuracy of the smear microscopy (SM), tuberculosis bacillus DNA (TB‐DNA), Xpert MTB/RIF assay, and the determination of rifampicin resistance based on the Xpert MTB/RIF assay were compared. Results As compared to mycobacterial culture, the sensitivity of the Xpert MTB/RIF assay, SM, and TB‐DNA were 85.5% (74.2%–93.1%), 38.7% (26.6%–51.9%), and 67.7% (54.7%–79.1%), respectively. As compared to the final diagnosis, the specificity of the Xpert MTB/RIF assay, SM, and TB‐DNA were 100.0% (95.9%–100.0%), 94.3% (87.1%–98.1%), and 98.9% (93.8%–100.0%), respectively. The sensitivity and specificity of the rifampicin resistance detection using the Xpert MTB/RIF assay were 100% and 98.0%, respectively, with liquid culture as the reference. Conclusions This study demonstrates that the analysis of BALF with the Xpert MTB/RIF assay provides a rapid and accurate tool for the early diagnosis of PTB. The accuracy of diagnosis was superior compared with the SM and TB‐DNA. Moreover, Xpert is a quick and accurate method for the diagnosis of rifampicin‐resistant tuberculosis and can also provide more effective guidance for the treatment of PTB or multidrug‐resistant tuberculosis (MDR‐TB).
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Affiliation(s)
- Wenjing Bai
- Department of Clinical Laboratory Medicine, Wenzhou Central Hospital, Wenzhou, China
| | - Lingling Liu
- Department of Clinical Laboratory Medicine, Wenzhou Longwan First People's Hospital, Wenzhou, China
| | - Lianpeng Wu
- Department of Clinical Laboratory Medicine, Wenzhou Central Hospital, Wenzhou, China
| | - Shanshan Chen
- Department of Blood Transfusion, People's Hospital of Pingyang County, Wenzhou, China
| | - Shuangliao Wu
- Department of Clinical Laboratory Medicine, Wenzhou Central Hospital, Wenzhou, China
| | - Zhihui Wang
- Department of Obstetrics and Gynecology, Wenzhou Central Hospital, Wenzhou, China
| | - Ke Xu
- Department of Clinical Laboratory Medicine, Wenzhou Central Hospital, Wenzhou, China
| | - Qiong Chi
- Department of Respiratory and Critical Care Medicine, Key Laboratory of precision medicine of Wenzhou, Wenzhou Central Hospital, Wenzhou, China
| | - Yong Pan
- Department of Clinical Laboratory Medicine, Key Laboratory of precision medicine of Wenzhou, Wenzhou Central Hospital, Wenzhou, China
| | - Xueqin Xu
- Department of Clinical Laboratory Medicine, Key Laboratory of precision medicine of Wenzhou, Wenzhou Central Hospital, Wenzhou, China
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Li T, Shi T, Sun Y, Chen F, Jiang W, Chen Y. Molecular characteristics of drug-resistance Mycobacterium tuberculosis strains isolated from extra pulmonary tuberculosis sites. Enferm Infecc Microbiol Clin 2021; 39:168-173. [PMID: 32605840 DOI: 10.1016/j.eimc.2020.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/08/2020] [Accepted: 04/01/2020] [Indexed: 12/25/2022]
Abstract
OBJECTIVES China is the second high tuberculosis (TB) burden country in the world. This article was to determinate the molecular characteristic of drug resistance Mycobacterium tuberculosis (DRTB) strains from extra pulmonary tuberculosis (EPTB). METHODS The medical records of patients with EPTB were reviewed and collected from 2006 to 2016. The drug sensitivity of all samples was studied. All multiple drug resistance (MDR) and extensive drug resistance (XDR) strains were included. The detection of the deletion of region of difference 105 (RD105) and mycobacterial interspersed repetitive-unit variable-number tandem-repeat (MIRU-VNTR) were used to discriminate the molecular type of EPTB strains. RESULTS 162 DRTB isolates were from patients with EPTB including 104 male and 58 female. Beijing genotype had a significant correlation with the patterns of DR (P<0.05), re-treatment patients (P<0.05) and gender (P<0.05). The history of treatment had a statistically significant correlation with patterns of DR (P<0.05) and gender (P<0.05). Patterns of DR had no correlation with gender (P>0.05). Of 162 strains Beijing family strains represented 91.4%. The cluster rate was 17.9% and clustering ratio was 11.1%. Beijing family genotype is predominant in the patients with EPTB. The cluster rate and clustering ratio was low. CONCLUSIONS Beijing family genotype is predominant and highly epidemic in the patients with drug resistance extra pulmonary tuberculosis (DR-EPTB). The cluster rate and clustering ratio was low. Genotype of re-treatment male patient with DR-EPTB is more likely Beijing family genotype.
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Affiliation(s)
- Tongxin Li
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Tao Shi
- Department of Orthopedics, Tianjin First Center Hospital, Tianjin, China.
| | - Ying Sun
- Department of Respiratory, Tianjin Hexi Hospital, Tianjin, China
| | - Fei Chen
- Department of Orthopedics, Bozhou District People's Hospital, Zunyi City, Guizhou Province, China
| | - Wenxue Jiang
- Department of Orthopedics, Tianjin First Center Hospital, Tianjin, China
| | - Yaokai Chen
- Central Laboratory, Chongqing Public Health Medical Center, Chongqing, China
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Yang J, Zhang T, Xian X, Li Y, Wang R, Wang P, Zhang M, Wang J. Molecular Characteristics and Drug Resistance of Mycobacterium tuberculosis Isolate Circulating in Shaanxi Province, Northwestern China. Microb Drug Resist 2021; 27:1207-1217. [PMID: 33794134 DOI: 10.1089/mdr.2020.0496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Objective: Shaanxi is the most highly populated province with high burdens of tuberculosis in northwestern China. The aim of this study was to investigate the molecular characteristics and drug resistance of Mycobacterium tuberculosis isolates from Shaanxi province of China in 2018. Methods: Phenotypic drug susceptibility testing and spoligotyping methods were performed on 518 M. tuberculosis isolates; drug-resistant isolates were sequenced in 11 drug loci, including katG, inhA, oxyR-ahpC, rpoB, embB, rpsL, rrs1 (nucleotides 388-1084), gyrA, gyrB, rrs2 (nucleotides 1158-1674), and eis. Results: The prevalences of isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin, and kanamycin resistance were 22.0%, 19.3%, 7.9%, 23.8%, 10.4%, and 3.3%, respectively. The Beijing family (82.8%) was the predominant genotype, followed by the T (9.3%), H (0.6%), CAS (0.4%), LAM (0.4%), and U (0.4%) families. The percentage of Beijing genotype in a central area (88.1%) was higher than in the south (77.3%) and the north area (80.1%) (p < 0.05), while the sex, age, and treatment history between Beijing and non-Beijing family were not statistically different. Mutation analysis found that the most prevalent mutations were katG315, rpoB531, embB306, rpsL43, gyrA94, and rrs1401; the Beijing family exhibited a high rate of isoniazid-resistant isolates carrying katG315 mutations (p < 0.05). Furthermore, compared with the phenotypic data, the sensitivities of isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin, and kanamycin resistance by sequencing base on 11 loci were 85.1%, 94.0%, 53.7%, 74.8%, 77.8%, and 64.7%, respectively. Conclusions: Shaanxi has a serious epidemic of drug-resistant tuberculosis, Beijing family is the predominant genotype, and the distribution showed geographic diversity. The prevalence of Beijing genotypes has a tendency to promote the transmission of high-level isoniazid-resistant M. tuberculosis. Besides, the hot spot regions localized in the embB, rrs2, and eis gene appear not to serve as excellent biomarkers for predicting ethambutol and kanamycin resistance in Shaanxi.
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Affiliation(s)
- Jian Yang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Clinical Laboratory and Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Tianhua Zhang
- Administration Office, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Xiaoping Xian
- Administration Office, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Yan Li
- Clinical Laboratory and Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Rui Wang
- Clinical Laboratory and Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Panting Wang
- Clinical Laboratory and Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Meng Zhang
- Clinical Laboratory and Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, China
| | - Junyang Wang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
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Evaluation of the frequency of mutation genes in multidrug-resistant tuberculosis (MDR-TB) strains in Beijing, China. Epidemiol Infect 2021; 149:e21. [PMID: 33397543 PMCID: PMC8057498 DOI: 10.1017/s0950268820003131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The aim of this study was to explore the frequency and distribution of gene mutations that are related to isoniazid (INH) and rifampin (RIF)-resistance in the strains of the multidrug-resistant tuberculosis (MDR-TB) Mycobacterium tuberculosis (M.tb) in Beijing, China. In this retrospective study, the genotypes of 173 MDR-TB strains were analysed by spoligotyping. The katG, inhA genes and the promoter region of inhA, in which genetic mutations confer INH resistance; and the rpoB gene, in which genetic mutations confer RIF resistance, were sequenced. The percentage of resistance-associated nucleotide alterations among the strains of different genotypes was also analysed. In total, 90.8% (157/173) of the MDR strains belonged to the Beijing genotype. Population characteristics were not significantly different among the strains of different genotypes. In total, 50.3% (87/173) strains had mutations at codon S315T of katG; 16.8% (29/173) of strains had mutations in the inhA promoter region; of them, 5.5% (15/173) had point mutations at -15 base (C→T) of the inhA promoter region. In total, 86.7% (150/173) strains had mutations at rpoB gene; of them, 40% (69/173) strains had mutations at codon S531L of rpoB. The frequency of mutations was not significantly higher in Beijing genotypic MDR strains than in non-Beijing genotypes. Beijing genotypic MDR-TB strains were spreading in Beijing and present a major challenge to TB control in this region. A high prevalence of katG Ser315Thr, inhA promoter region (-15C→T) and rpoB (S531L) mutations was observed. Molecular diagnostics based on gene mutations was a useful method for rapid detection of MDR-TB in Beijing, China.
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Hu Y, Liu J, Shen J, Feng X, Liu W, Zhu D, Zheng H, Hu D. Genotyping and Molecular Characterization of Fluoroquinolone's Resistance Among Multidrug-Resistant Mycobacterium tuberculosis in Southwest of China. Microb Drug Resist 2020; 27:865-870. [PMID: 33305990 DOI: 10.1089/mdr.2019.0339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although fluoroquinolones (FQs) are the backbone drugs for the treatment of multidrug-resistant tuberculosis (MDR-TB), the knowledge about the resistance pattern and molecular characterization of new-generation FQs in Chongqing is limited. This study aimed to investigate the resistance rate and mutation types of later-generation FQs against MDR-TB in Chongqing, and further to explore the relationship between different genotypes and phenotypes. A total of 967 clinical strains were characterized using multilocus sequence typing and drug susceptibility testing, followed by analysis of genotype/phenotype association. The 229 (23.7%, 229/967) isolates were identified as MDR-TB. The most effective agent against MDR-TB was gatifloxacin (GFX) (20.1%, 46/229), and the highest resistant rate was observed in ofloxacin (OFX) (41.0%, 94/229). Of the 190 strains (83.0%) identified as Beijing genotype, 111 isolates were modern Beijing genotype (58.4%) and 79 isolates were ancient Beijing genotype (41.6%). By analyzing 94 OFX-resistant isolates, 13 isolates were clustered with the cumulative clustering rate of 13.8% (13/94). Of the 91 isolates (39.7%, 91/229) with a mutation in gyrA gene, mutation in codon 94 was the most prevalent. Only 15 isolates (6.6%, 15/229) harbored a mutation in gyrB gene. There was no significant difference in the mutation rate of gyrA gene between Beijing and non-Beijing genotype, clustered isolates, and nonclustered isolates (p > 0.05).
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Affiliation(s)
- Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Jie Liu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Jing Shen
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Xin Feng
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Wenguo Liu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Damian Zhu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Huiwen Zheng
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Daiyu Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
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Catanzaro DG, Colman RE, Linger Y, Georghiou SB, Kukhtin AV, Seifert M, Holmberg RC, Mshaiel H, Chiles P, Hillery N, Cooney CG, Rodwell TC. Laboratory Evaluation of a Lateral-Flow Cell for Molecular Detection of First-Line and Second-Line Antituberculosis Drug Resistance. J Clin Microbiol 2020; 58:e01417-20. [PMID: 32817085 PMCID: PMC7587100 DOI: 10.1128/jcm.01417-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/12/2020] [Indexed: 01/05/2023] Open
Abstract
Despite the WHO's call for universal drug susceptibility testing for all patients being evaluated for tuberculosis (TB), a lack of rapid diagnostic tests which can fully describe TB resistance patterns is a major challenge in ensuring that all persons diagnosed with drug-resistant TB are started on an appropriate treatment regime. We evaluated the accuracy of the Akonni Biosystems XDR-TB TruArray and lateral-flow cell (XDR-LFC), a novel multiplex assay to simultaneously detect mutations across seven genes that confer resistance to both first- and second-line anti-TB drugs. The XDR-LFC includes 271 discrete three-dimensional gel elements with target-specific probes for identifying mutations in katG, inhA promoter, and ahpC promoter (isoniazid), rpoB (rifampin), gyrA (fluoroquinolones), rrs and eis promoter (kanamycin), and rrs (capreomycin and amikacin). We evaluated XDR-LFC performance with 87 phenotypically and genotypically characterized clinical Mycobacterium tuberculosis isolates. The overall assay levels of accuracy for mutation detection in specific genes were 98.6% for eis promoter and 100.0% for the genes katG, inhA promoter, ahpC promoter, rpoB, gyrA, and rrs The sensitivity and specificity against phenotypic reference were 100% and 100% for isoniazid, 98.4% and 50% for rifampin (specificity increased to 100% once the strains with documented low-level resistance mutations in rpoB were excluded), 96.2% and 100% for fluoroquinolones, 92.6% and 100% for kanamycin, 93.9% and 97.4% for capreomycin, and 80% and 100% for amikacin. The XDR-LFC solution appears to be a promising new tool for accurate detection of resistance to both first- and second-line anti-TB drugs.
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Affiliation(s)
- Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Rebecca E Colman
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | | | | | | | - Marva Seifert
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | | | - Haifa Mshaiel
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Peter Chiles
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Naomi Hillery
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, California, USA
| | | | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
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Islam MM, Tan Y, Hameed HMA, Liu Y, Chhotaray C, Cai X, Liu Z, Lu Z, Wang S, Cai X, Su B, Li X, Tan S, Liu J, Zhang T. Prevalence and molecular characterization of amikacin resistance among Mycobacterium tuberculosis clinical isolates from southern China. J Glob Antimicrob Resist 2020; 22:290-295. [PMID: 32142951 DOI: 10.1016/j.jgar.2020.02.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 01/22/2020] [Accepted: 02/21/2020] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVES Amikacin is the only second-line injectable antituberculosis (anti-TB) drug still recommended for multidrug-resistant tuberculosis (MDR-TB) treatment when a short MDR-TB regimen is designed. Mutations in rrs and eis are reported to be associated with resistance to amikacin. In this study, we investigated the incidence of rrs, eis, tap and whiB7 mutations in amikacin-resistant Mycobacterium tuberculosis clinical isolates to find the proportion of different mutations related to amikacin resistance. METHODS A total of 395 clinical isolates of M. tuberculosis were used for phenotypic drug susceptibility testing (DST) to 10 drugs with the Löwenstein-Jensen (L-J) method. We sequenced rrs, eis, tap and whiB7 genes in 178 M. tuberculosis clinical isolates (89 amikacin-resistant isolates and 89 of 306 amikacin-susceptible isolates). RESULTS Our data showed that 22.53% (89/395) M. tuberculosis clinical isolates were resistant to amikacin. Of the 89 amikacin-resistant isolates, 89.89% (80/89) were MDR-TB, of which 12.36% (11/89) were pre-extensively drug-resistant TB (pre-XDR-TB) and 77.53% (69/89) were XDR-TB. The rrs mutations were found in 82% (73/89) in amikacin-resistant M. tuberculosis clinical isolates. The A1401G alteration in the rrs gene was the most dominant mutation (80.90%; 72/89). Five mutations were detected as new in rrs, tap and whiB7. Notably, 13.48% (12/89) amikacin-resistant isolates had no known mutation in these genes. CONCLUSIONS Our data reveal that the rrs mutation is a predominant molecular marker of amikacin resistance in southern China. Analysis of the rrs gene mutations will significantly reduce the time and cost to diagnose amikacin resistance in TB patients. Other unknown amikacin resistance mechanism(s) exist.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Yang Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Xiaoyin Cai
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China
| | - Xingshan Cai
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Biyi Su
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, China; Guangdong Hong Kong Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China.
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Shibabaw A, Gelaw B, Gebreyes W, Robinson R, Wang SH, Tessema B. The burden of pre-extensively and extensively drug-resistant tuberculosis among MDR-TB patients in the Amhara region, Ethiopia. PLoS One 2020; 15:e0229040. [PMID: 32053661 PMCID: PMC7018133 DOI: 10.1371/journal.pone.0229040] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/28/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The emergence of pre-extensively and extensively drug-resistant tuberculosis (Pre-XDR/XDR-TB) is the major hurdle for TB prevention and care programs especially in developing countries like Ethiopia. The less emphasis on universal access to laboratory techniques for the rapid diagnosis of TB and drug susceptibility testing (DST) makes the management of MDR-TB a challenge. Early detection of second line anti-TB drugs resistance is essential to reduce transmission of Pre-XDR/XDR-TB strains and adjusting the treatment regimen in MDR-TB. OBJECTIVE To determine the prevalence and resistance pattern of Pre-XDR- and XDR-TB among MDR-TB patients in the Amhara region, Ethiopia. METHODS A cross sectional study was carried out in nine MDR-TB treatment centers in the Amhara region. Sputum samples were collected from all pulmonary rifampicin resistant (RR) or MDR-TB patients prior to anti-TB treatment. Lӧwenstein-Jensen (LJ) culture, Ziehl Neelsen (ZN) smear, MTBDRplus and MTBDRsl assays were performed according to the standard procedures. Data were analyzed using SPSS 20 software. Chi-square and/or Fishers exact test was employed. RESULTS Overall, 6.3% of MDR-TB isolates were resistant to at least one second line drugs. Pre-XDR-TB and XDR-TB isolates accounted 5.7% and 0.6% respectively. Moreover, 3.4% were resistant to FQs and 3.4% were resistant to second line injectable drugs. All isolates were susceptible for low level kanamycin. Almost all pre-XDR-TB strains (90%) were previously treated with anti-TB drugs. Drug resistant Mycobacterium tuberculosis isolates were disproportionately distributed in districts of the Amhara region and the majorities were concentrated in urban areas. CONCLUSIONS The high proportion of MDR-TB patients resistant to at least one second line drug is alarming. Strengthening the laboratory facilities to monitor pre-XDR and XDR-TB patients is crucial. The TB programs need to give emphasis on the effective and rational use of second line drugs for newly diagnosed MDR-TB patients to prevent the emergence of pre-XDR/XDR-TB strains.
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Affiliation(s)
- Agumas Shibabaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, Ohio, United States of America
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
| | - Baye Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Wondwossen Gebreyes
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, Ohio, United States of America
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Richard Robinson
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Shu-Hua Wang
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, Ohio, United States of America
- Department of Internal Medicine, Division of infectious diseases, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Belay Tessema
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Li Q, Wang Y, Li Y, Gao H, Zhang Z, Feng F, Dai E. Characterisation of drug resistance-associated mutations among clinical multidrug-resistant Mycobacterium tuberculosis isolates from Hebei Province, China. J Glob Antimicrob Resist 2019; 18:168-176. [DOI: 10.1016/j.jgar.2019.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/09/2019] [Accepted: 03/14/2019] [Indexed: 10/27/2022] Open
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Zhao LL, Huang MX, Xiao TY, Liu HC, Li MC, Zhao XQ, Liu ZG, Jiang Y, Wan KL. Prevalence, risk and genetic characteristics of drug-resistant tuberculosis in a tertiary care tuberculosis hospital in China. Infect Drug Resist 2019; 12:2457-2465. [PMID: 31496759 PMCID: PMC6689547 DOI: 10.2147/idr.s209971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/04/2019] [Indexed: 01/07/2023] Open
Abstract
Objectives To explore the prevalence, risk and genetic characteristics of drug-resistant tuberculosis (TB) from a tertiary care TB hospital in China. Patients and methods We carried out a retrospective study including isolates from 189 patients with pulmonary TB at Fuzhou Pulmonary Hospital. All isolates from these patients were subjected to drug susceptibility testing and genotyping. For drug-resistant isolates, DNA sequencing was used to investigate mutations in 12 loci, including katG, inhA, oxyR–ahpC, rpoB, rpsL, rrs1 (nucleotides 388–1084 of rrs), embB, tlyA, eis, rrs2 (nucleotides 1158–1674 of rrs), gyrA and gyrB. Results Among 189 isolates, 28.6% were resistant to at least one of the seven anti-TB drugs, including isoniazid (INH), rifampin (RIF), streptomycin (STR), ethambutol (EMB), capreomycin (CAP), kanzmycin (KAN) and ofloxacin (OFX). The proportion of multidrug-resistant TB and extensively drug-resistant TB isolates was 9.5% and 1.1%, respectively. Patients in rural areas as well as previously treated patients showed a significantly increased risk of developing drug resistance. In addition, among these isolates, 111 (58.7%) were Beijing genotype strains, 84 (75.7%) of which belonged to modern Beijing sublineage. There was no association between genotype and drug resistance. The most common mutations were katG315, rpoB531 rpsL43, embB306, rrs1401 and gyrA94. Conclusion These findings provided additional information of drug-resistant TB in China. Previously treated patients and patients in rural areas should receive greater attention owing to their higher risk of developing drug resistance.
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Affiliation(s)
- Li-Li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Ming-Xiang Huang
- Clinical Laboratory, Fuzhou Pulmonary Hospital, Fuzhou, 350008, People's Republic of China
| | - Tong-Yang Xiao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Hai-Can Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Ma-Chao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Xiu-Qin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Zhi-Guang Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
| | - Kang-Lin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China
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Adam MAM, Ali HMH, Khalil EAG. Diagnostic predictive values of the Hain genotype MTBDRsl assay in mycobacterial strains isolated from Sudan. Pan Afr Med J 2019; 32:124. [PMID: 31236189 PMCID: PMC6573780 DOI: 10.11604/pamj.2019.32.124.12762] [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: 05/15/2017] [Accepted: 02/02/2019] [Indexed: 11/29/2022] Open
Abstract
Introduction hain GenoType MTBDRsl is nucleic acid amplification assay based on reverse hybridization with specific oligonucleotide probes on nitrocellulose strips. MTBDRsl identifies M. tuberculosis complex and detects resistance to fluoroquinolone, second line injectable drugs and ethambutol evident as mutations of gyrA, rrs and embB genes respectively. This study aimed to evaluate the diagnostic performance of the Hain GenoType MTBDRsl Assay using 1% proportion method on LJ medium as gold standard. Methods a total of 52 rifampicin resistant (RR) isolates were tested for second line drug sensitivity by 1% proportion method and by MTBDRsl assay. Results two strains were identified as mycobacteria other than tuberculosis MOTT and the rest were Mycobacterium tuberculosis complex MTBC. Five of the MTBC isolates (5/50; 10%) showed resistance to at least one second line drug and one isolate (1/50; 2%) was XDR. XDR strain was concordantly detected by the two methods. One of two Kanamycin-resistant isolates showed discordant results. Ofloxacin showed one false positive and one false negative result. Most discrepancies were detected with Ethambutol. The sensitivity, specificity, positive and negative predictive values were respectively as follows: Ethambutol (63.3.4%, 85.7%, 94.4% and 62%), for Kanamycin (67%, 100%, 100% and 97.9%), for Amikacin and Capreomycin (100%, 100%, 100% and 100%), for Ofloxacin (75%, 97.5%, 75% and 97.8%). For XDR isolate the values were 100%, 100%, 100% and 100% respectively. Conclusion MTBDRsl showed high specificity and negative predictive values making it acceptable and time-saving for early presumptive detection of resistance to second-line drugs in Sudan.
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Affiliation(s)
- Muatsim Ahmed Mohammed Adam
- National Public Health Laboratory, National Tuberculosis Reference Laboratory, Federal Ministry of Health, Khartoum, Sudan
| | | | - Eltahir Awad Gasim Khalil
- Department of Clinical Pathology & Immunology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
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Luo D, Chen Q, Xiong G, Peng Y, Liu T, Chen X, Zeng L, Chen K. Prevalence and molecular characterization of multidrug-resistant M. tuberculosis in Jiangxi province, China. Sci Rep 2019; 9:7315. [PMID: 31086215 PMCID: PMC6513856 DOI: 10.1038/s41598-019-43547-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/24/2019] [Indexed: 11/17/2022] Open
Abstract
Multidrug-resistant Mycobacterium tuberculosis (MDR-TB) is a severe health threat to human beings; however, the epidemic and molecular characteristics exist along with the change in the geographic environment and genealogy. Jiangxi province is located in southeast China, which is a high-MDR-TB burden area. Rifampin (RIF) and isoniazid (INH) are the most important first-line anti-tuberculosis drugs. The major drug target genes include rpoB for RIF and katG, inhA, and ahpC for INH. To determine the frequency and distribution of mycobacterial mutations in these genes, we sequenced specific genes of M. tuberculosis that are associated with resistance to RIF and INH in 157 phenotypic MDR isolates. At the same time, RD105 DTM-PCR and 15 loci MIRU-VNTR were performed to demonstrate the genetic lineage. It was shown that the Beijing genotype was predominant (84.1%) among these strains. The results also showed mutations within the 81 bp core region of rpoB in 93.6% of strains and mutations in a structural gene (katG) and two regulatory regions (the promoter of inhA and intergenic region of oxyR-ahpC) were shown in 88.5% of phenotypic MDR isolates. There were no significant differences in codon mutations between the Beijing and non-Beijing genotypes, as well as the clustered and no-clustered strains. The most prevalent mutations involved in RIF and INH were Ser531Leu in rpoB (55.4%) and Ser315Thr in KatG (56.1%), respectively. There was no significant difference in RIF and INH resistance between MDR-TB and other drug-resistant tuberculosis (DR-TB). The results demonstrated that some MDR-TB patients are predicted to have recent transmission.
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Affiliation(s)
- Dong Luo
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Qiang Chen
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Guangchu Xiong
- Department of Clinical Laboratory, Jiangxi Provincial Chest Hospital, Nanchang, 330006, China
| | - Yiping Peng
- Department of Clinical Laboratory, Jiangxi Provincial Chest Hospital, Nanchang, 330006, China
| | - Tao Liu
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Xiaowen Chen
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Lingbing Zeng
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Kaisen Chen
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
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22
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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.
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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
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23
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Anupurba S, Sinha P, Banerjee T, Srivastava GN. Rapid detection of drug-resistant Mycobacterium tuberculosis directly from clinical specimens using allele-specific polymerase chain reaction assay. Indian J Med Res 2019; 150:33-42. [PMID: 31571627 PMCID: PMC6798613 DOI: 10.4103/ijmr.ijmr_374_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background & objectives: Rapid detection of drug resistance in Mycobacterium tuberculosis (MTB) is essential for the efficient control of tuberculosis. Hence, in this study a nested-allele-specific (NAS) PCR, nested multiple allele-specific PCR (NMAS-PCR) and multiple allele-specific (MAS) PCR assays were evaluated that enabled detection of the most common mutations responsible for isoniazid (INH) and rifampicin (RIF) resistance in MTB isolates directly from clinical specimens. Methods: Six pairs of primers, mutated and wild type, were used for the six targets such as codon 516, 526 and 531 of rpoB, codon 315 of katG and C15-T substitution in the promoter region of mabA-inhA using allele-specific (AS) PCR assays (NAS-PCR, NMAS-PCR and MAS-PCR). The performance of AS PCR method was compared with phenotypic drug susceptibility testing (DST). Results: The usefulness of AS PCR assays was evaluated with 391 clinical specimens (251 Acid fast bacilli smear positive and MTB culture positive; 93 smear negative and MTB culture positive; 47 smear positive and MTB culture negative) and 344 MTB culture positive isolates. With culture-based phenotypic DST as a reference standard, the sensitivity and specificity of the NAS-PCR, NMAS-PCR and MAS-PCR assay for drug resistance-related genetic mutation detection were 98.6 and 97.8 per cent for INH, 97.5 and 97.9 per cent for RIF and 98.9 and 100 per cent for multidrug resistance (MDR). Interpretation & conclusions: The performance of AS PCR assays showed that those could be less expensive and technically executable methods for rapid detection of MDR-TB directly from clinical specimens.
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24
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Huang Z, Du J, Deng Z, Luo Q, Xiong G, Wang Y, Zhang X, Li J. Multicentre laboratory validation of the nitrate reductase assay using liquid medium for the rapid detection of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis. Tuberculosis (Edinb) 2018; 113:242-248. [PMID: 30514509 DOI: 10.1016/j.tube.2018.11.001] [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: 05/30/2016] [Revised: 09/22/2018] [Accepted: 11/01/2018] [Indexed: 11/27/2022]
Abstract
To perform a multicentre study evaluating the performance of the nitrate reductase assay (NRA) using liquid medium for the detection of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis and to establish the MICs and critical concentrations of rifampicin, isoniazid, ofloxacin, amikacin, kanamycin and capreomycin. The study was carried out in three phases. Phase I determined the MIC of each drug. Phase II established the critical concentration of each drug. Phase III validated critical concentrations for the six drugs tested by the NRA using liquid medium compared with the agar proportion method or MGIT 960 system at each site. The critical concentrations for the six drugs used in the NRA are as follows: rifampicin, 1 mg/L; isoniazid, 0.2 mg/L; ofloxacin, 2 mg/L; amikacin, 2 mg/L; kanamycin, 5 mg/L; capreomycin, 2.5 mg/L. Phase III: Excellent agreement was obtained for all drugs tested at the majority of sites. The accuracy was 97%-100% for rifampicin, 96.8%-99.2% for isoniazid, 98%-100% for ofloxacin, 96.8%-98.5% for amikacin, 96.4%-99.5% for kanamycin and 96.8%-100% for capreomycin. Results for NRA using liquid medium were obtained in a median time of 7 days. NRA performed in liquid medium offers a rapid, economical and feasible method for detection of M. tuberculosis resistance to first- and second-line drugs in resource-limited settings.
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Affiliation(s)
- Zikun Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jinghui Du
- Department of Clinical Laboratory, First Teaching Hospital of Tianjin University of TCM, Tianjin, China
| | - Zhen Deng
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qing Luo
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Guoliang Xiong
- Province Tuberculosis Reference Laboratory, Jiangxi Chest Hospital, Nanchang, Jiangxi, China
| | - Yaoxing Wang
- Clinical Microbiology Laboratory, Baoshan Branch, Shanghai First People's Hospital, Shanghai, China
| | - Xi Zhang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Junming Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
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25
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Genetics and roadblocks of drug resistant tuberculosis. INFECTION GENETICS AND EVOLUTION 2018; 72:113-130. [PMID: 30261266 DOI: 10.1016/j.meegid.2018.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 11/22/2022]
Abstract
Considering the extensive evolutionary history of Mycobacterium tuberculosis, anti-Tuberculosis (TB) drug therapy exerts a recent selective pressure. However, in a microorganism devoid of horizontal gene transfer and with a strictly clonal populational structure such as M. tuberculosis the usual, but not sole, path to overcome drug susceptibility is through de novo mutations on a relatively strict set of genes. The possible allelic diversity that can be associated with drug resistance through several mechanisms such as target alteration or target overexpression, will dictate how these genes can become associated with drug resistance. The success demonstrated by this pathogenic microbe in this latter process and its ability to spread is currently one of the major obstacles to an effective TB elimination. This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms that enable one strain to reacquire the original fitness levels, it will be theoretically possible to make more informed decisions and develop novel strategies that can force M. tuberculosis microevolutionary trajectory down through a path of decreasing fitness levels.
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Characterization of Mutations Conferring Resistance to Rifampin in Mycobacterium tuberculosis Clinical Strains. Antimicrob Agents Chemother 2018; 62:AAC.01093-18. [PMID: 30061294 DOI: 10.1128/aac.01093-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/26/2018] [Indexed: 11/20/2022] Open
Abstract
Resistance of Mycobacterium tuberculosis to rifampin (RMP), mediated by mutations in the rpoB gene coding for the beta-subunit of RNA polymerase, poses a serious threat to the efficacy of clinical management and, thus, control programs for tuberculosis (TB). The contribution of many individual rpoB mutations to the development and level of RMP resistance remains elusive. In this study, the incidence of mutations throughout the rpoB gene among 115 Mycobacterium tuberculosis clinical isolates, both resistant and susceptible to RMP, was determined. Of the newly discovered rpoB mutations, the role of three substitutions in the causation of RMP resistance was empirically tested. The results from in vitro mutagenesis experiments were combined with the assessment of the prevalence of rpoB mutations, and their reciprocal co-occurrences, across global M. tuberculosis populations. Twenty-two different types of mutations in the rpoB gene were identified and distributed among 58 (89.2%) RMP-resistant strains. The MICs of RMP were within the range of 40 to 800 mg/liter, with MIC50 and MIC90 values of 400 and 800 mg/liter, respectively. None of the mutations (Gln429His, Met434Ile, and Arg827Cys) inspected for their role in the development of RMP resistance produced an RMP-resistant phenotype in isogenic M. tuberculosis H37Rv strain-derived mutants. These mutations are supposed to compensate for fitness impairment incurred by other mutations directly associated with drug resistance.
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Wang Y, Xu H, Li Y, Gao H, Zhang Z, Liu Y, Lu J, Dai E. Genotypicdiversity of drug-resistant Mycobacterium tuberculosis isolates from Hebei, China. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3744-3752. [PMID: 31949758 PMCID: PMC6962832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/08/2018] [Indexed: 06/10/2023]
Abstract
Drug-resistant tuberculosis (DR-TB), particularly multidrug-resistant tuberculosis (MDR-TB), has been identified as a major challenge for effective TB control. For rapid detection and proper treatment, molecular assays based on the identification of mutations in genes associated with drug resistance have been established to determine drug resistance. However, there is as yet little information about drug resistance-associated mutations of clinical Mycobacterium tuberculosis isolates from Hebei. In this study, four genetic loci katG, inhA, oxyR-ahpC intergenic region and rpoB were sequenced among 276 DR-TB isolates from Hebei to understand the association between specific mutations, drug resistance phenotypes and spoligotyping genotypes. Altogether, 83.8% of INH resistant isolates harbored at least one mutation of katG, inhA, and oxyR-ahpC intergenic region and 78.4% of RIF resistant isolates harbored one or more mutations in rpoB. The predominant mutation patterns of rpoB and katG in Hebei was Ser531Leu and Ser315Thr, respectively. Additionally, 91.2% of MDR isolates harbored at least one mutation in these four targeted fragments. Compared with the phenotypic data, the sensitivity and specificity of co-testing of katG, inhA promoter and oxyR-ahpC intergenic region for INH resistance were 83.8% and 96.8%, respectively and the rpoB exhibited a sensitivity of 78.4% and a specificity of 95.3% for RIF resistance. Furthermore, there was no association between drug resistance-conferring mutations and spoligotypes. This finding will be useful for the establishment of rapid molecular diagnostic methods in Hebei province, China.
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Affiliation(s)
- Yuling Wang
- Department of Tuberculosis, The Fifth Hospital of Shijiazhuang, Hebei Medical UniversityShijiazhuang, Hebei, China
| | - Hong Xu
- Department of Laboratory Medicine, The Fourth Hospital of Shijiazhuang, Shijiazhuang Obstetrics and Gynecology HospitalShijiazhuang, Hebei, China
| | - Yanan Li
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical UniversityShijiazhuang, Hebei, China
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical UniversityShijiazhuang, Hebei, China
| | - Zhi Zhang
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical UniversityShijiazhuang, Hebei, China
| | - Yuzhen Liu
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical UniversityShijiazhuang, Hebei, China
| | - Jianhua Lu
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical UniversityShijiazhuang, Hebei, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical UniversityShijiazhuang, Hebei, China
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Hameed HMA, Islam MM, Chhotaray C, Wang C, Liu Y, Tan Y, Li X, Tan S, Delorme V, Yew WW, Liu J, Zhang T. Molecular Targets Related Drug Resistance Mechanisms in MDR-, XDR-, and TDR- Mycobacterium tuberculosis Strains. Front Cell Infect Microbiol 2018; 8:114. [PMID: 29755957 PMCID: PMC5932416 DOI: 10.3389/fcimb.2018.00114] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 03/23/2018] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB) is a formidable infectious disease that remains a major cause of death worldwide today. Escalating application of genomic techniques has expedited the identification of increasing number of mutations associated with drug resistance in Mycobacterium tuberculosis. Unfortunately the prevalence of bacillary resistance becomes alarming in many parts of the world, with the daunting scenarios of multidrug-resistant tuberculosis (MDR-TB), extensively drug-resistant tuberculosis (XDR-TB) and total drug-resistant tuberculosis (TDR-TB), due to number of resistance pathways, alongside some apparently obscure ones. Recent advances in the understanding of the molecular/ genetic basis of drug targets and drug resistance mechanisms have been steadily made. Intriguing findings through whole genome sequencing and other molecular approaches facilitate the further understanding of biology and pathology of M. tuberculosis for the development of new therapeutics to meet the immense challenge of global health.
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Affiliation(s)
- H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Institute of Health Sciences, Anhui University, Hefei, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Vincent Delorme
- Tuberculosis Research Laboratory, Institut Pasteur Korea, Seongnam-si, South Korea
| | - Wing W Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
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Xu G, Mao X, Wang J, Pan H. Clustering and recent transmission of Mycobacterium tuberculosis in a Chinese population. Infect Drug Resist 2018; 11:323-330. [PMID: 29563813 PMCID: PMC5846054 DOI: 10.2147/idr.s156534] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose The objectives of the present study were to characterize the clinical isolates prevailing in the northeast of Jiangsu and to investigate the mode of transmission. The study also aimed to explore the extent to which Mycobacterium tuberculosis strains contributed to drug resistance and the possible factors related to the recent transmission. Patients and methods We consecutively enrolled 912 culture-confirmed pulmonary tuberculosis (TB) cases from 1 January 2013 to 31 December 2014 in Lianyungang City, which is located in the center of China’s vast ocean area and the northeast of Jiangsu province. Isolates were genotyped using 15-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing. The Hunter–Gaston discrimination index (HGDI) was used to estimate the discriminatory power and diversity of molecular markers. Results Among 741 successfully genotyped isolates, 144 (19.43%) strains formed 46 clusters, while 597 (80.57%) isolates had the unique MIRU pattern. The total HGDI for all 15 loci was 0.999. The average cluster size was 3 (2–13) patients. The estimated proportion of recent transmission was 13.34%. Patients with unfavorable treatment outcomes were infected with clustered strains at a higher proportion than were those with favorable treatment outcomes (adjusted OR: 1.78, 95% CI: 1.14–2.85, P=0.012). Conclusion The probability of recent TB transmission was relatively low in the study site, while the cases mainly arose from the activation of previous infection. Spatial analysis showed that strains forming larger clusters had the characteristics of regional aggregation.
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Affiliation(s)
- Guisheng Xu
- Department of Epidemiology, Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi, China
| | - Jianming Wang
- Department of Epidemiology, Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongqiu Pan
- Department of Tuberculosis, The Third Hospital of Zhenjiang, Zhenjiang, China
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Oudghiri A, Karimi H, Chetioui F, Zakham F, Bourkadi JE, Elmessaoudi MD, Laglaoui A, Chaoui I, El Mzibri M. Molecular characterization of mutations associated with resistance to second-line tuberculosis drug among multidrug-resistant tuberculosis patients from high prevalence tuberculosis city in Morocco. BMC Infect Dis 2018; 18:98. [PMID: 29486710 PMCID: PMC5830342 DOI: 10.1186/s12879-018-3009-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 02/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The emergence of extensively drug-resistant tuberculosis (XDR-TB) has raised public health concern for global TB control. Although multi drug-resistant tuberculosis (MDR- TB) prevalence and associated genetic mutations in Morocco are well documented, scarce information on XDR TB is available. Hence, the evaluation of pre-XDR and XDR prevalence, as well as the mutation status of gyrA, gyrB, rrs, tlyA genes and eis promoter region, associated with resistance to second line drugs, is of great value for better management of M/XDR TB in Morocco. OBJECTIVES To evaluate pre-XDR and XDR prevalence, as well as the mutation status of gyrA, gyrB, rrs, tlyA genes and eis promoter region, associated with resistance to second line drug resistance, in 703 clinical isolates from TB patients recruited in Casablanca, and to assess the usefulness of molecular tools in clinical laboratories for better management of M/XDR TB in Morocco. METHODS Drug susceptibility testing (DST) was performed by the proportional method for first line drugs, and then the selected MDR isolates were tested for second line drugs (Ofloxacin, Kanamycin, Amikacin and Capreomycin). Along with DST, all samples were subjected to rpoB, katG and p-inhA mutation analysis by PCR and DNA sequencing. MDR isolates as well as 30 pan-susceptible strains were subjected to PCR and DNA sequencing of gyrA, gyrB, rrs, tlyA genes and eis promoter, associated with resistance to fluoroquinolones and injectable drugs. RESULTS Among the 703 analysed strains, 12.8% were MDR; Ser531Leu and Ser315Thr being the most common recorded mutations within rpoB and katG genes associated with RIF and INH resistance respectively. Drug susceptibility testing for second line drugs showed that among the 90 MDR strains, 22.2% (20/90) were resistant to OFX, 2.22% (2/90) to KAN, 3.33% (3/90) to AMK and 1.11% (1/90) to CAP. Genotypic analysis revealed that 19 MDR strains harbored mutations in the gyrA gene; the most recorded mutation being Asp91Ala accounting for 47.6% (10/21), and 2 isolates harbored mutations in the promoter region of eis gene. No mutation was found in gyrB, rrs and tlyA genes. Moreover, none of the pan-susceptible isolates displayed mutations in targeted genes. CONCLUSION Most of mutations associated with SLD resistance occurred in gyrA gene (codons 90-94) and eis promoter region. These findings highlight the impact of mutations in gyrA on the development of fluroquinolones resistance and provide the first estimates of the proportion of pre-XDR-TB among MDR-TB cases in Morocco.
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Affiliation(s)
- Amal Oudghiri
- Unité de Biologie et Recherches Médicales, Centre National de l'Energie, des Sciences et Techniques Nucléaires, BP 1382 RP, 10001, Rabat, Morocco
- Equipe de Recherche en Biotechnologies et Génie des Biomolécules, Faculté des Sciences et Techniques de Tanger, Ancienne Route de l'Aéroport, Km 10, Ziaten, BP 416, Tanger, Morocco
| | - Hind Karimi
- Equipe de Recherche en Biotechnologies et Génie des Biomolécules, Faculté des Sciences et Techniques de Tanger, Ancienne Route de l'Aéroport, Km 10, Ziaten, BP 416, Tanger, Morocco
| | - Fouad Chetioui
- Laboratoire de la Tuberculose, Institut Pasteur du Maroc, Casablanca, 1 Place Louis Pasteur, Boulevard Abdelmoumen, 20250, Casablanca, Morocco
| | - Fathiah Zakham
- Unité de Biologie et Recherches Médicales, Centre National de l'Energie, des Sciences et Techniques Nucléaires, BP 1382 RP, 10001, Rabat, Morocco
| | - Jamal Eddine Bourkadi
- Service de Pneumo-Phtisiologie, Hôpital Moulay Youssef, CHU Rabat, Avenue Sidi Mohamed Ben Abdallah, Al Akkari, Rabat, Morocco
| | - My Driss Elmessaoudi
- Laboratoire de la Tuberculose, Institut Pasteur du Maroc, Casablanca, 1 Place Louis Pasteur, Boulevard Abdelmoumen, 20250, Casablanca, Morocco
| | - Amin Laglaoui
- Equipe de Recherche en Biotechnologies et Génie des Biomolécules, Faculté des Sciences et Techniques de Tanger, Ancienne Route de l'Aéroport, Km 10, Ziaten, BP 416, Tanger, Morocco
| | - Imane Chaoui
- Unité de Biologie et Recherches Médicales, Centre National de l'Energie, des Sciences et Techniques Nucléaires, BP 1382 RP, 10001, Rabat, Morocco.
| | - Mohammed El Mzibri
- Unité de Biologie et Recherches Médicales, Centre National de l'Energie, des Sciences et Techniques Nucléaires, BP 1382 RP, 10001, Rabat, Morocco
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Osei-Wusu S, Amo Omari M, Asante-Poku A, Darko Otchere I, Asare P, Forson A, Otu J, Antonio M, Yeboah-Manu D. Second-line anti-tuberculosis drug resistance testing in Ghana identifies the first extensively drug-resistant tuberculosis case. Infect Drug Resist 2018; 11:239-246. [PMID: 29503573 PMCID: PMC5825993 DOI: 10.2147/idr.s152720] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Drug resistance surveillance is crucial for tuberculosis (TB) control. Therefore, our goal was to determine the prevalence of second-line anti-TB drug resistance among diverse primary drug-resistant Mycobacterium tuberculosis complex (MTBC) isolates in Ghana. MATERIALS AND METHODS One hundred and seventeen MTBC isolates with varying first-line drug resistance were analyzed. Additional resistance to second-line anti-TB drugs (streptomycin [STR], amikacin [AMK] and moxifloxacin [MOX]) was profiled using the Etest and GenoType MTBDRsl version 2.0. Genes associated with resistance to AMK and MOX (gyrA, gyrB, eis, rrs, tap, whiB7 and tlyA) were then analyzed for mutation. RESULTS Thirty-seven (31.9%) isolates had minimum inhibitory concentration (MIC) values ≥2 µg/mL against STR while 12 (10.3%) isolates had MIC values ≥1 µg/mL for AMK. Only one multidrug-resistant (MDR) isolate (Isolate ID: TB/Nm 919) had an MIC value of ≥0.125 µg/mL for MOX (MIC = 3 µg/mL). This isolate also had the highest MIC value for AMK (MIC = 16 µg/mL) and was confirmed as resistant to AMK and MOX by the line probe assay GenoType MTBDRsl version 2.0. Mutations associated with the resistance were: gyrA (G88C) and rrs (A514C and A1401G). CONCLUSION Our findings suggest the need to include routine second-line anti-TB drug susceptibility testing of MDR/rifampicin-resistant isolates in our diagnostic algorithm.
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Affiliation(s)
- Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West Africa Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Michael Amo Omari
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Audrey Forson
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Jacob Otu
- Medical Research Council Unit, Fajara, The Gambia
| | | | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
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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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Evaluation of antituberculosis activity and DFT study on dipyrromethane-derived hydrazone derivatives. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Initial second-line drug resistance of Mycobacterium tuberculosis isolates from Sudanese retreatment-patients. J Clin Tuberc Other Mycobact Dis 2017; 9:21-23. [PMID: 31723713 PMCID: PMC6850260 DOI: 10.1016/j.jctube.2017.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 10/08/2017] [Accepted: 10/24/2017] [Indexed: 11/21/2022] Open
Abstract
Setting Multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) are a major public health threat. Objective This study aimed to determine resistance patterns to second line anti-TB drugs (SLDs), and to determine the frequency of extensively drug resistant Mycobacterium tuberculosis (XDR-TB). Design During the period from July 2009 to July 2010; sputum specimens were collected from TB retreatment patients; isolates were tested for sensitivity to first line anti-TB drugs by the 1% proportion method; MDR strains were tested for second line anti-TB drugs sensitivity by 1% proportion method and by version 1. Hain GenoType MTBDRsl Assay. Results One hundred and forty three mycobacterial isolates were successfully recovered from a total of 239 specimens (143/239; 59.8%). Fifty six strains were rifampicin resistant (RR); of these 54 were multi-drug resistant (MDR); two were RIF/INH-resistant mycobacterium other than tuberculosis (MOTT). Five of MDR (5/50; 10%) showed resistance to at least one second line drug and one isolate (1/50; 2%) was XDR. The XDR strain was concordantly detected by the two methods. Conclusion Initial resistance to second line anti-TB drugs among MDR-TB patients is at 10% levels and XDR-TB is prevalent at low levels (2%). Nevertheless; without great efforts from national tuberculosis control program (NTP) this figure can fuel the TB epidemics in Sudan.
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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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Li D, Song Y, Zhang CL, Li X, Xia X, Zhang AM. Screening mutations in drug-resistant Mycobacterium tuberculosis strains in Yunnan, China. J Infect Public Health 2017. [DOI: 10.1016/j.jiph.2017.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Jaiswal I, Jain A, Singh P, Verma S, Prakash S, Dixit P, Suryakant, Singh M. Mutations in katG and inhA genes of isoniazid-resistant and -sensitive clinical isolates of Mycobacterium tuberculosis from cases of pulmonary tuberculosis and their association with minimum inhibitory concentration of isoniazid. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2017. [DOI: 10.1016/j.cegh.2016.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Prevalence and Molecular Characterization of Second-Line Drugs Resistance among Multidrug-Resistant Mycobacterium tuberculosis Isolates in Southwest of China. BIOMED RESEARCH INTERNATIONAL 2017; 2017:4563826. [PMID: 28798931 PMCID: PMC5536135 DOI: 10.1155/2017/4563826] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/28/2017] [Accepted: 06/18/2017] [Indexed: 01/13/2023]
Abstract
This study aimed to investigate the prevalence of multidrug-resistant tuberculosis (MDR-TB) isolates resistant to the second-line antituberculosis drugs (SLDs) and its association with resistant-related gene mutations in Mycobacterium tuberculosis (M.tb) isolates from Southwest of China. There were 81 isolates resistant to at least one of the SLDs among 156 MDR-TB isolates (81/156, 51.9%). The rates of general resistance to each of the drugs were as follows: OFX (66/156, 42.3%), KAN (26/156, 16.7%), CAP (13/156, 8.3%), PTO (11/156, 7.1%), PAS (22/156, 14.1%), and AMK (20/156, 12.8%). Therefore, the most predominant pattern was resistant to OFX compared with other SLDs (P < 0.001). The results of sequencing showed that 80.2% OFX-resistant MDR-TB isolates contained gyrA mutation and 88.5% KAN-resistant isolates had rrs mutations with the most frequent mutation being A1401G. These results suggest that improper use of SLDs especially OFX is a real threat to effective MDR-TB treatment not only in China but also in the whole world. Furthermore the tuberculosis control agencies should carry out SLDs susceptibility testing and rapid screening in a broader population of TB patients immediately and the SLDs should be strictly regulated by the administration in order to maintain their efficacy to treat MDR-TB.
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Zarei Z, Emami A, Moghadami M, Kashkooli GS, Pirbonyeh N. Molecular characterization of Isoniazid and Rifampicin target genes in multi-drug resistant Mycobacterium tuberculosis isolates from southwest of Iran. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2016.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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A First Insight into the Genetic Diversity and Drug Susceptibility Pattern of Mycobacterium tuberculosis Complex in Zhejiang, China. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8937539. [PMID: 27995145 PMCID: PMC5138472 DOI: 10.1155/2016/8937539] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/09/2016] [Accepted: 10/24/2016] [Indexed: 11/18/2022]
Abstract
In this study, our aim was to determine the predominant genotypes among the Mycobacterium tuberculosis (MTB) strains circulating in Zhejiang Province. In addition, we also sought to determine the potential associations between MTB genotypes and susceptibility to first-line drugs. Out of these isolates, 673 (71.6%) were classified into the Beijing genotype, while the other 267 (28.4%) were from non-Beijing families. The highest proportion of Beijing genotype was found in Huzhou (80.0%) and the lowest in Lishui (48.3%). Statistical analysis revealed that there was a significant difference in the prevalence of Beijing genotype among different regions (χ2 = 17.57, P = 0.04). In addition, the overall proportions of drug resistance to INH, RIF, SM, and EMB were 13.2% (124/940), 21.8% (75/940), 3.4% (32/940), and 5.9% (55/940) in Zhejiang, respectively. Further comparison revealed that there was no significant difference in drug susceptibility profiles between Beijing and non-Beijing strains (P > 0.05). In conclusion, we describe the genetic diversity and drug susceptibility pattern of MTB in Zhejiang for the first time. Our data demonstrate that Beijing genotype is the predominant lineage in Zhejiang, while the distribution of Beijing-genotype strains shows geographic diversity. In addition, no correlation is observed between Beijing genotype and anti-TB drug resistance.
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Islam MM, Hameed HMA, Mugweru J, Chhotaray C, Wang C, Tan Y, Liu J, Li X, Tan S, Ojima I, Yew WW, Nuermberger E, Lamichhane G, Zhang T. Drug resistance mechanisms and novel drug targets for tuberculosis therapy. J Genet Genomics 2016; 44:21-37. [PMID: 28117224 DOI: 10.1016/j.jgg.2016.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Drug-resistant tuberculosis (TB) poses a significant challenge to the successful treatment and control of TB worldwide. Resistance to anti-TB drugs has existed since the beginning of the chemotherapy era. New insights into the resistant mechanisms of anti-TB drugs have been provided. Better understanding of drug resistance mechanisms helps in the development of new tools for the rapid diagnosis of drug-resistant TB. There is also a pressing need in the development of new drugs with novel targets to improve the current treatment of TB and to prevent the emergence of drug resistance in Mycobacterium tuberculosis. This review summarizes the anti-TB drug resistance mechanisms, furnishes some possible novel drug targets in the development of new agents for TB therapy and discusses the usefulness using known targets to develop new anti-TB drugs. Whole genome sequencing is currently an advanced technology to uncover drug resistance mechanisms in M. tuberculosis. However, further research is required to unravel the significance of some newly discovered gene mutations in their contribution to drug resistance.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Iwao Ojima
- Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Wing Wai Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric Nuermberger
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Yin QQ, Jiao WW, Li QJ, Xu F, Li JQ, Sun L, Li YJ, Huang HR, Shen AD. Prevalence and molecular characteristics of drug-resistant Mycobacterium tuberculosis in Beijing, China: 2006 versus 2012. BMC Microbiol 2016; 16:85. [PMID: 27176471 PMCID: PMC4866484 DOI: 10.1186/s12866-016-0699-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/29/2016] [Indexed: 11/29/2022] Open
Abstract
Background As the epidemic of MDR-TB and XDR-TB becomes increasingly severe, it is important to determine the clinical characteristics and molecular epidemiology of MDR-TB and XDR-TB. Recently, many studies have shown that clinical features and molecular characteristics of drug-resistant strains vary in different geographical areas, however, further information is needed to assess the dynamic evolution of drug-resistant TB. Comparative studies between different time periods are necessary to elucidate the development of drug-resistant TB. Results A total of 255 and 537 strains were collected from Beijing Chest Hospital in 2006 and in 2012, respectively. Drug-resistance rates and mutations associated with resistance to first-line anti-tuberculosis (TB) drugs were compared. The overall rate of drug resistance among strains of TB in 2012 was 54.4 %, significantly higher than that in 2006 (34.9 %, P < 0.001). Rates of resistance to each first-line drug (isoniazid, rifampicin, streptomycin and ethambutol) and to second-line drug ofloxacin increased significantly from 2006 to 2012. The overall MDR rate also increased significantly from 2006 (14.9 %) to 2012 (27.0 %). The rate of MDR increased significantly between these two time periods in previously treated cases (P = 0.023) but not in new cases (P = 0.073), and the rate of XDR was similar in new cases at the two time periods, but was marginally higher in 2012 in previously treated cases (P = 0.056). Previous treatment was found to be a risk factor for drug-resistant TB, especially for MDR-TB. In addition, the proportion of drug resistant isolates in which katG, the mabA-inhA promoter, oxyR-ahpC intergenic region, rpoB, rpsL, and embB were mutated was similar in 2006 and 2012, however patterns of mutation in these loci were more diverse in 2012 compared to 2006. Conclusions Our data suggests that the prevalence of drug resistant TB remains high in Beijing, China, and that increasing rates of resistance in M. tuberculosis to all anti-TB drugs should be considered when choosing an optimal anti-TB regimen. Moreover, acquired multi-drug resistance may play a primary role in the MDR-TB epidemic in Beijing, China. Consequently, this highlights the importance of an earlier start to effective and supervised treatment in order to reduce the burden of retreatment.
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Affiliation(s)
- Qing-Qin Yin
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Wei-Wei Jiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Qin-Jing Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Fang Xu
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jie-Qiong Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lin Sun
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Ying-Jia Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hai-Rong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China.
| | - A-Dong Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.
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Rahman A, Sahrin M, Afrin S, Earley K, Ahmed S, Rahman SMM, Banu S. Comparison of Xpert MTB/RIF Assay and GenoType MTBDRplus DNA Probes for Detection of Mutations Associated with Rifampicin Resistance in Mycobacterium tuberculosis. PLoS One 2016; 11:e0152694. [PMID: 27054344 PMCID: PMC4824420 DOI: 10.1371/journal.pone.0152694] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/17/2016] [Indexed: 01/31/2023] Open
Abstract
Background GeneXpert MTB/RIF (Xpert) and Genotype MTBDRplus (DRplus) are two World Health Organization (WHO) endorsed probe based molecular drug susceptibility testing (DST) methods for rapid diagnosis of drug resistant tuberculosis. Both methods target the same 81 bp Rifampicin Resistance Determining Region (RRDR) of bacterial RNA polymerase β subunit (rpoB) for detection of Rifampicin (RIF) resistance associated mutations using DNA probes. So there is a correspondence of the probes of each other and expected similarity of probe binding. Methods We analyzed 92 sputum specimens by Xpert, DRplus and LJ proportion method (LJ-DST). We compared molecular DSTs with gold standard LJ-DST. We wanted to see the agreement level of two molecular methods for detection of RIF resistance associated mutations. The 81bp RRDR region of rpoB gene of discrepant cases between the two molecular methods was sequenced by Sanger sequencing. Results The agreement of Xpert and DRplus with LJ-DST for detection of RIF susceptibility was found to be 93.5% and 92.4%, respectively. We also found 92.4% overall agreement of two molecular methods for the detection of RIF susceptibility. A total of 84 out of 92 samples (91.3%) had agreement on the molecular locus of RRDR mutation by DRplus and Xpert. Sanger sequencing of 81bp RRDR revealed that Xpert probes detected seven of eight discrepant cases correctly and DRplus was erroneous in all the eight cases. Conclusion Although the overall concordance with LJ-DST was similar for both Xpert and DRplus assay, Xpert demonstrated more accuracy in the detection of RIF susceptibility for discrepant isolates compared with DRplus. This observation would be helpful for the improvement of probe based detection of drug resistance associated mutations especially rpoB mutation in M. tuberculosis.
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Affiliation(s)
- Arfatur Rahman
- International Center for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Mahfuza Sahrin
- International Center for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Sadia Afrin
- International Center for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Keith Earley
- Oregon Health and Science University, Portland, United States of America
| | - Shahriar Ahmed
- International Center for Diarrheal Disease Research, Dhaka, Bangladesh
| | | | - Sayera Banu
- International Center for Diarrheal Disease Research, Dhaka, Bangladesh
- * E-mail:
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44
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Haarlem 3 is the predominant genotype family in multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis in the capital of Iran: A 5-year survey. J Glob Antimicrob Resist 2016; 5:7-10. [PMID: 27436458 DOI: 10.1016/j.jgar.2016.01.007] [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: 11/13/2015] [Revised: 12/16/2015] [Accepted: 01/20/2016] [Indexed: 11/23/2022] Open
Abstract
The objective of this study was to further understand the genetic diversity of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis isolates prevalent in Tehran, the capital city of Iran. From January 2010 to March 2015, a total of 723 M. tuberculosis strains were isolated from patients with pulmonary tuberculosis (TB). A total of 23 MDR, pre-XDR and XDR M. tuberculosis isolates were genotyped by spoligotyping and 24-loci mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing. The results showed that the MDR, pre-XDR and XDR M. tuberculosis strains mainly belonged to the Haarlem 3 genotype (11/23; 47.8%), followed by the Beijing family (9/23; 39.1%). In addition, the 23 strains were clustered into 21 genotypes using a 24-loci MIRU-VNTR. In conclusion, Haarlem 3 genotype was the predominant genotype among the isolates from MDR-TB cases in this study, which could be of special concern.
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Resistance to Isoniazid and Ethionamide in Mycobacterium tuberculosis: Genes, Mutations, and Causalities. Microbiol Spectr 2016; 2:MGM2-0014-2013. [PMID: 26104204 DOI: 10.1128/microbiolspec.mgm2-0014-2013] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Isoniazid (INH) is the cornerstone of tuberculosis (TB) chemotherapy, used for both treatment and prophylaxis of TB. The antimycobacterial activity of INH was discovered in 1952, and almost as soon as its activity was published, the first INH-resistant Mycobacterium tuberculosis strains were reported. INH and its structural analog and second-line anti-TB drug ethionamide (ETH) are pro-drugs. INH is activated by the catalase-peroxidase KatG, while ETH is activated by the monooxygenase EthA. The resulting active species reacts with NAD+ to form an INH-NAD or ETH-NAD adduct, which inhibits the enoyl ACP reductase InhA, leading to mycolic acid biosynthesis inhibition and mycobacterial cell death. The major mechanism of INH resistance is mutation in katG, encoding the activator of INH. One specific KatG variant, S315T, is found in 94% of INH-resistant clinical isolates. The second mechanism of INH resistance is a mutation in the promoter region of inhA (c-15t), which results in inhA overexpression and leads to titration of the drug. Mutations in the inhA open reading frame and promoter region are also the major mechanism of resistance to ETH, found more often in ETH-resistant clinical isolates than mutations in the activator of ETH. Other mechanisms of resistance to INH and ETH include expression changes of the drugs' activators, redox alteration, drug inactivation, and efflux pump activation. In this article, we describe each known mechanism of resistance to INH and ETH and its importance in M. tuberculosis clinical isolates.
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Chen Y, Zhao B, Liu HC, Sun Q, Zhao XQ, Liu ZG, Wan KL, Zhao LL. Prevalence of mutations conferring resistance among multi- and extensively drug-resistant Mycobacterium tuberculosis isolates in China. J Antibiot (Tokyo) 2015; 69:149-52. [PMID: 26486879 DOI: 10.1038/ja.2015.106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 11/09/2022]
Abstract
To identify the mutations in multi- and extensively drug-resistant tuberculosis isolates and to evaluate the use of molecular markers of resistance, we analyzed 257 multi- and extensively drug-resistant isolates and 64 pan-sensitive isolates from 23 provinces in China. Seven loci associated with drug resistance, including rpoB for rifampin (RIF), katG, inhA and oxyR-ahpC for isoniazid (INH), gyrA and gyrB for ofloxacin (OFX), and rrs for kanmycin (KAN), were examined by DNA sequencing. Compared with the phenotypic data, the sensitivity and specificity for DNA sequencing were 91.1% and 98.4% for RIF, 80.2% and 98.4% for INH, 72.2% and 98.3% for OFX and 40% and 98.2% for KAN, respectively. The most common mutations found in RIF, INH, OFX and KAN resistance were Ser531Leu (48.2%) in rpoB, Ser315Thr (49.8%) in katG, C(-15)T (10.5%) in inhA, Asp94Gly (20.3%), Asp94Ala (12.7%) and Ala90Val (21.5%) in gyrA, and A1401G (40%) in rrs. This molecular information will be helpful to establish new molecular biology-based methods for diagnosing multi- and extensively drug-resistant tuberculosis in China.
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Affiliation(s)
- Yan Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hai-can Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qing Sun
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Pathogenic Biology Institute, University of South China, Hunan Province, China
| | - Xiu-qin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhi-guang Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kang-lin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li-li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Hu Y, Mathema B, Zhao Q, Chen L, Lu W, Wang W, Kreiswirth B, Xu B. Acquisition of second-line drug resistance and extensive drug resistance during recent transmission of Mycobacterium tuberculosis in rural China. Clin Microbiol Infect 2015; 21:1093.e9-1093.e18. [PMID: 26348262 DOI: 10.1016/j.cmi.2015.08.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 08/10/2015] [Accepted: 08/27/2015] [Indexed: 11/17/2022]
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is prevalent in countries with a high TB burden, like China. As little is known about the emergence and spread of second-line drug (SLD) -resistant TB, we investigate the emergence and transmission of SLD-resistant Mycobacterium tuberculosis in rural China. In a multi-centre population-based study, we described the bacterial population structure and the transmission characteristics of SLD-resistant TB using Spoligotyping in combination with genotyping based on 24-locus MIRU-VNTR (mycobacterial interspersed repetitive unit-variable-number tandem repeat) plus four highly variable loci for the Beijing family, in four rural Chinese regions with diverse geographic and socio-demographic characteristics. Transmission networks among genotypically clustered patients were constructed using social network analysis. Of 1332 M. tuberculosis patient isolates recovered, the Beijing family represented 74.8% of all isolates and an association with MDR and simultaneous resistance between first-line drugs and SLDs. The genotyping analysis revealed that 189 isolates shared MIRU-VNTR patterns in 78 clusters with clustering rate and recent transmission rate of 14.2% and 8.3%, respectively. Fifty-three SLD-resistant isolates were observed in 31 clusters, 30 of which contained the strains with different drug susceptibility profiles and genetic mutations. In conjunction with molecular data, socio-network analysis indicated a key role of Central Township in the transmission across a highly interconnected network where SLD resistance accumulation occurred during transmission. SLD-resistant M. tuberculosis has been spreading in rural China with Beijing family being the dominant strains. Primary transmission of SLD-resistant strains in the population highlights the importance of routine drug susceptibility testing and effective anti-tuberculosis regimens for drug-resistant TB.
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Affiliation(s)
- Y Hu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China
| | - B Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA; Tuberculosis Center, Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Q Zhao
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China
| | - L Chen
- Tuberculosis Center, Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - W Lu
- Department of Chronic Infectious Diseases, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - W Wang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China
| | - B Kreiswirth
- Tuberculosis Center, Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - B Xu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, China.
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Jagielski T, Bakuła Z, Roeske K, Kamiński M, Napiórkowska A, Augustynowicz-Kopeć E, Zwolska Z, Bielecki J. Mutation profiling for detection of isoniazid resistance in Mycobacterium tuberculosis clinical isolates. J Antimicrob Chemother 2015; 70:3214-21. [PMID: 26311839 DOI: 10.1093/jac/dkv253] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/21/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Progress in the detection of drug-resistant TB has been underpinned by the development and implementation of new, reliable and rapid diagnostic tools. These rely mostly on the detection of specific mutations conferring resistance to anti-TB drugs. The aim of this study was to search for mutations associated with isoniazid resistance among Mycobacterium tuberculosis clinical isolates. METHODS A collection of 150 M. tuberculosis strains, including 50 MDR, 50 isoniazid-monoresistant and 50 pan-susceptible strains, was used. For all the strains, seven structural genes (katG, inhA, ahpC, kasA, ndh, nat and mshA) and two regulatory regions (mabA-inhA promoter and oxyR-ahpC intergenic region) were PCR amplified and sequenced in their entirety. RESULTS Sixty-six distinct mutations were detected at all nine loci investigated, accounting for 109 (72.7%) of the strains tested. The number of strains with any mutation among the MDR, isoniazid-monoresistant and pan-susceptible groups was 49 (98%), 37 (74%) and 23 (46%), respectively. Mutations in the katG gene predominated, with 29 different types distributed among 46 (92%) MDR, 31 (62%) isoniazid-monoresistant and 2 (4%) pan-susceptible strains. Twenty-nine and 19 mutations were found exclusively in MDR and isoniazid-monoresistant strains, respectively. CONCLUSIONS This study revealed 17 mutations, previously unreported, that might be of potential use as new surrogate markers of isoniazid resistance. Their diagnostic accuracy needs to be confirmed on larger strain samples and from different geographical settings. For isoniazid resistance detection, molecular approaches should still be a complement to rather than a replacement for conventional drug susceptibility testing. This is supported by the lack of mutations in any of the nine genetic loci investigated in 18 isoniazid-resistant strains from this study.
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Affiliation(s)
- Tomasz Jagielski
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Zofia Bakuła
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Katarzyna Roeske
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Michał Kamiński
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agnieszka Napiórkowska
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Płocka 26, 01-138 Warsaw, Poland
| | - Zofia Zwolska
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Płocka 26, 01-138 Warsaw, Poland
| | - Jacek Bielecki
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
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Zhang Z, Lu J, Liu M, Wang Y, Qu G, Li H, Wang J, Pang Y, Liu C, Zhao Y. Genotyping and molecular characteristics of multidrug-resistant Mycobacterium tuberculosis isolates from China. J Infect 2015; 70:335-45. [DOI: 10.1016/j.jinf.2014.11.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/23/2014] [Accepted: 11/25/2014] [Indexed: 01/02/2023]
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50
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Frequency and geographic distribution of gyrA and gyrB mutations associated with fluoroquinolone resistance in clinical Mycobacterium tuberculosis isolates: a systematic review. PLoS One 2015; 10:e0120470. [PMID: 25816236 PMCID: PMC4376704 DOI: 10.1371/journal.pone.0120470] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/23/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The detection of mutations in the gyrA and gyrB genes in the Mycobacterium tuberculosis genome that have been demonstrated to confer phenotypic resistance to fluoroquinolones is the most promising technology for rapid diagnosis of fluoroquinolone resistance. METHODS In order to characterize the diversity and frequency of gyrA and gyrB mutations and to describe the global distribution of these mutations, we conducted a systematic review, from May 1996 to April 2013, of all published studies evaluating Mycobacterium tuberculosis mutations associated with resistance to fluoroquinolones. The overall goal of the study was to determine the potential utility and reliability of these mutations as diagnostic markers to detect phenotypic fluoroquinolone resistance in Mycobacterium tuberculosis and to describe their geographic distribution. RESULTS Forty-six studies, covering four continents and 18 countries, provided mutation data for 3,846 unique clinical isolates with phenotypic resistance profiles to fluoroquinolones. The gyrA mutations occurring most frequently in fluoroquinolone-resistant isolates, ranged from 21-32% for D94G and 13-20% for A90V, by drug. Eighty seven percent of all strains that were phenotypically resistant to moxifloxacin and 83% of ofloxacin resistant isolates contained mutations in gyrA. Additionally we found that 83% and 80% of moxifloxacin and ofloxacin resistant strains respectively, were observed to have mutations in the gyrA codons interrogated by the existing MTBDRsl line probe assay. In China and Russia, 83% and 84% of fluoroquinolone resistant strains respectively, were observed to have gyrA mutations in the gene regions covered by the MTBDRsl assay. CONCLUSIONS Molecular diagnostics, specifically the Genotype MTBDRsl assay, focusing on codons 88-94 should have moderate to high sensitivity in most countries. While we did observe geographic differences in the frequencies of single gyrA mutations across countries, molecular diagnostics based on detection of all gyrA mutations demonstrated to confer resistance should have broad and global utility.
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