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Leung KSS, Tam KKG, Ng TTL, Lao HY, Shek RCM, Ma OCK, Yu SH, Chen JX, Han Q, Siu GKH, Yam WC. Clinical utility of target amplicon sequencing test for rapid diagnosis of drug-resistant Mycobacterium tuberculosis from respiratory specimens. Front Microbiol 2022; 13:974428. [PMID: 36160212 PMCID: PMC9505518 DOI: 10.3389/fmicb.2022.974428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
An in-house-developed target amplicon sequencing by next-generation sequencing technology (TB-NGS) enables simultaneous detection of resistance-related mutations in Mycobacterium tuberculosis (MTB) against 8 anti-tuberculosis drug classes. In this multi-center study, we investigated the clinical utility of incorporating TB-NGS for rapid drug-resistant MTB detection in high endemic regions in southeast China. From January 2018 to November 2019, 4,047 respiratory specimens were available from patients suffering lower respiratory tract infections in Hong Kong and Guangzhou, among which 501 were TB-positive as detected by in-house IS6110-qPCR assay with diagnostic sensitivity and specificity of 97.9 and 99.2%, respectively. Preliminary resistance screening by GenoType MTBDRplus and MTBDRsl identified 25 drug-resistant specimens including 10 multidrug-resistant TB. TB-NGS was performed using MiSeq on all drug-resistant specimens alongside 67 pan-susceptible specimens, and demonstrated 100% concordance to phenotypic drug susceptibility test. All phenotypically resistant specimens with dominating resistance-related mutations exhibited a mutation frequency of over 60%. Three quasispecies were identified with mutation frequency of less than 35% among phenotypically susceptible specimens. They were well distinguished from phenotypically resistant cases and thus would not complicate TB-NGS results interpretations. This is the first large-scale study that explored the use of laboratory-developed NGS platforms for rapid TB diagnosis. By incorporating TB-NGS with our proposed diagnostic algorithm, the workflow would provide a user-friendly, cost-effective routine diagnostic solution for complicated TB cases with an average turnaround time of 6 working days. This is critical for timely management of drug resistant TB patients and expediting public health control on the emergence of drug-resistant TB.
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Affiliation(s)
- Kenneth Siu-Sing Leung
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kingsley King-Gee Tam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Raymond Chiu-Man Shek
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | | | - Shi-Hui Yu
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou, China
| | | | - Qi Han
- Guangzhou KingMed Diagnostics Group, Guangzhou, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- *Correspondence: Wing-Cheong Yam,
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Campelo TA, Lima LNC, Lima KVB, Silva CS, da Conceição ML, Barreto JAP, Mota APP, Sancho SDO, Frota CC. Molecular characterization of pre-extensive drug resistant Mycobacterium tuberculosis in Northeast Brazil. Rev Inst Med Trop Sao Paulo 2020; 62:e4. [PMID: 32049255 PMCID: PMC7014566 DOI: 10.1590/s1678-9946202062004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022] Open
Abstract
In Fortaleza, the capital of Ceara State, Brazil, the detection rate of tuberculosis (TB) in 2018 was 65.5/100,000 inhabitants with a cure rate of 59.1%, which is higher than the country average. This study investigated the risk factors associated with drug-resistant tuberculosis (DR-TB) and identified the drug-resistance phenotype and resistance-conferring mutations. The geographic distribution of DR-TB in Fortaleza, Brazil, was also determined. From March 2017 to February 2018, 41 DR-TB isolates and 69 drug-susceptible pulmonary TB isolates were obtained from patients seen at a referral hospital in Fortaleza, Brazil. Samples were subjected to phenotypic and genetic analysis of resistance; the spatial distribution of the participants was also analyzed. Primary resistance was high (50.9%) among participants. The following risk factors for DR were identified: being female ( p = 0.03), having diabetes ( p < 0.01), history of previous TB disease ( p < 0.01), and the number of intra-domiciliary contacts ( p < 0.01). Analysis by multiplex allele-specific polymerase chain reaction detected mutations in the genes katG (65.8%) , rpoB (43.9%), inhA promoter (14.6%), and gyrA (9.8%). Sequencing identified mutations in the the genes katG (75.6%), inhA promoter (19.5%), rpoB (85.4%), and gyrA (100%). There was no mutation in the rrs gene. Spatial analysis showed DR-TB isolates distributed in areas of low socioeconomic status in the city of Fortaleza. Our results emphasized the importance of detecting resistance to TB drugs. The resistance found in the gene gyrA is of concern due to the high number of pre-extensive DR-TB cases in Fortaleza.
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Affiliation(s)
- Thales Alves Campelo
- Universidade Federal do Ceará , Faculdade de Medicina, Departamento de Patologia e Medicina Legal , Fortaleza , Ceará , Brazil
| | - Luana Nepomuceno Costa Lima
- Instituto Evandro Chagas , Seção de Bacteriologia e Micologia, Ananindeua , Pará , Brazil
- Universidade do Estado do Pará , Programa de Pós-Graduação em Biologia Parasitária na Amazônia , Belém , Pará , Brazil
| | - Karla Valéria Batista Lima
- Instituto Evandro Chagas , Seção de Bacteriologia e Micologia, Ananindeua , Pará , Brazil
- Universidade do Estado do Pará , Programa de Pós-Graduação em Biologia Parasitária na Amazônia , Belém , Pará , Brazil
| | - Caroliny Soares Silva
- Universidade Federal do Ceará , Faculdade de Medicina, Departamento de Patologia e Medicina Legal , Fortaleza , Ceará , Brazil
| | - Marília Lima da Conceição
- Universidade do Estado do Pará , Programa de Pós-Graduação em Biologia Parasitária na Amazônia , Belém , Pará , Brazil
| | | | - Aquiles Paulino Peres Mota
- Universidade Federal do Ceará , Faculdade de Medicina, Departamento de Patologia e Medicina Legal , Fortaleza , Ceará , Brazil
| | - Soraya de Oliveira Sancho
- Universidade Federal do Ceará , Faculdade de Medicina, Departamento de Patologia e Medicina Legal , Fortaleza , Ceará , Brazil
| | - Cristiane Cunha Frota
- Universidade Federal do Ceará , Faculdade de Medicina, Departamento de Patologia e Medicina Legal , Fortaleza , Ceará , Brazil
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Rajwani R, Yam WC, Zhang Y, Kang Y, Wong BKC, Leung KSS, Tam KKG, Tulu KT, Zhu L, Siu GKH. Comparative Whole-Genomic Analysis of an Ancient L2 Lineage Mycobacterium tuberculosis Reveals a Novel Phylogenetic Clade and Common Genetic Determinants of Hypervirulent Strains. Front Cell Infect Microbiol 2018; 7:539. [PMID: 29376038 PMCID: PMC5770396 DOI: 10.3389/fcimb.2017.00539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/26/2017] [Indexed: 12/25/2022] Open
Abstract
Background: Development of improved therapeutics against tuberculosis (TB) is hindered by an inadequate understanding of the relationship between disease severity and genetic diversity of its causative agent, Mycobacterium tuberculosis. We previously isolated a hypervirulent M. tuberculosis strain H112 from an HIV-negative patient with an aggressive disease progression from pulmonary TB to tuberculous meningitis—the most severe manifestation of tuberculosis. Human macrophage challenge experiment demonstrated that the strain H112 exhibited significantly better intracellular survivability and induced lower level of TNF-α than the reference virulent strain H37Rv and other 123 clinical isolates. Aim: The present study aimed to identify the potential genetic determinants of mycobacterial virulence that were common to strain H112 and hypervirulent M. tuberculosis strains of the same phylogenetic clade isolated in other global regions. Methods: A low-virulent M. tuberculosis strain H54 which belonged to the same phylogenetic lineage (L2) as strain H112 was selected from a collection of 115 clinical isolates. Both H112 and H54 were whole-genome-sequenced using PacBio sequencing technology. A comparative genomics approach was adopted to identify mutations present in strain H112 but absent in strain H54. Subsequently, an extensive phylogenetic analysis was conducted by including all publically available M. tuberculosis genomes. Single-nucleotide-polymorphisms (SNPs) and structural variations (SVs) common to hypervirulent strains in the global collection of genomes were considered as potential genetic determinants of hypervirulence. Results:Sequencing data revealed that both H112 and H54 were identified as members of the same sub-lineage L2.2.1. After excluding the lineage-related mutations shared between H112 and H54, we analyzed the phylogenetic relatedness of H112 with global collection of M. tuberculosis genomes (n = 4,338), and identified a novel phylogenetic clade in which four hypervirulent strains isolated from geographically diverse regions were clustered together. All hypervirulent strains in the clade shared 12 SNPs and 5 SVs with H112, including those affecting key virulence-associated loci, notably, a deleterious SNP (rv0178 p. D150E) within mce1 operon and an intergenic deletion (854259_ 854261delCC) in close-proximity to phoP. Conclusion: The present study identified common genetic factors in a novel phylogenetic clade of hypervirulent M. tuberculosis. The causative role of these mutations in mycobacterial virulence should be validated in future study.
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Affiliation(s)
- Rahim Rajwani
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong
| | - Wing Cheong Yam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | | | - Kenneth Siu Sing Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Kingsley King Gee Tam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ketema Tafess Tulu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong
| | - Li Zhu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong
| | - Gilman Kit Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, Hong Kong
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Yin F, Chan JFW, Zhu Q, Fu R, Chen JHK, Choi GKY, Tee KM, Li L, Qian S, Yam WC, Lu G, Yuen KY. Development and in-use evaluation of a novel Luminex MicroPlex microsphere-based (TRIOL) assay for simultaneous identification of Mycobacterium tuberculosis and detection of first-line and second-line anti-tuberculous drug resistance in China. J Clin Pathol 2016; 70:342-349. [PMID: 27646524 DOI: 10.1136/jclinpath-2016-203952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/23/2016] [Accepted: 08/28/2016] [Indexed: 11/03/2022]
Abstract
AIMS Rapid and accurate diagnostic assays with simultaneous microbial identification and drug resistance detection are essential for optimising treatment and control of tuberculosis. METHODS We developed a novel multiplex (TRIOL, Tuberculosis-Rifampicin-Isoniazid-Ofloxacin-Luminex) assay using the Luminex xMAP system that simultaneously identifies Mycobacterium tuberculosis and detects resistance to first-line and second-line anti-tuberculous drugs, and compared its performance with that by PCR sequencing, using phenotypic drug susceptibility testing as the gold standard. RESULTS Identification of M. tuberculosis by the TRIOL assay was highly sensitive (100%) and specific (100%). The overall drug-specific specificities were excellent (100%). The overall sensitivity of the TRIOL assay was lower than that of the PCR-sequencing assays (72.4% vs 82.8%) because of a lower sensitivity of detecting rifampicin resistance (71.4% vs 92.9%). The sensitivity of detecting isoniazid and ofloxacin resistance was as good as the PCR-sequencing assays. Importantly, the TRIOL assay did not miss any mutations that were included in the assay. All of the resistant isolates that were missed had uncommon mutations or unknown resistance mechanisms that were not included in the assay. CONCLUSIONS The TRIOL assay has higher throughput, lower cost and is less labour intensive than the PCR-sequencing assays. The TRIOL assay is advantageous in having the capability to detect resistance to multiple drugs and an open-architecture system that allows addition of more specific primers to detect uncommon mutations. Inclusion of additional primers for the identification of non-tuberculous mycobacteria, spoligotyping and improvement of rifampicin resistance detection would enhance the use of the TRIOL assay in future clinical and epidemiological studies.
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Affiliation(s)
- Feifei Yin
- Key Laboratory of Translation Medicine Tropical Diseases, Department of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.,Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Qixuan Zhu
- Key Laboratory of Translation Medicine Tropical Diseases, Department of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, China
| | - Ruijia Fu
- Key Laboratory of Translation Medicine Tropical Diseases, Department of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, China
| | - Jonathan Hon-Kwan Chen
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Garnet Kwan-Yue Choi
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Kah-Meng Tee
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Lihua Li
- Key Laboratory of Translation Medicine Tropical Diseases, Department of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, China
| | - Shiuyun Qian
- Key Laboratory of Translation Medicine Tropical Diseases, Department of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, China
| | - Wing-Cheong Yam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.,Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Gang Lu
- Key Laboratory of Translation Medicine Tropical Diseases, Department of Ministry of Education, Hainan Medical University, Haikou, Hainan, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.,Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
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Drobniewski F, Cooke M, Jordan J, Casali N, Mugwagwa T, Broda A, Townsend C, Sivaramakrishnan A, Green N, Jit M, Lipman M, Lord J, White PJ, Abubakar I. Systematic review, meta-analysis and economic modelling of molecular diagnostic tests for antibiotic resistance in tuberculosis. Health Technol Assess 2016; 19:1-188, vii-viii. [PMID: 25952553 DOI: 10.3310/hta19340] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Drug-resistant tuberculosis (TB), especially multidrug-resistant (MDR, resistance to rifampicin and isoniazid) disease, is associated with a worse patient outcome. Drug resistance diagnosed using microbiological culture takes days to weeks, as TB bacteria grow slowly. Rapid molecular tests for drug resistance detection (1 day) are commercially available and may promote faster initiation of appropriate treatment. OBJECTIVES To (1) conduct a systematic review of evidence regarding diagnostic accuracy of molecular genetic tests for drug resistance, (2) conduct a health-economic evaluation of screening and diagnostic strategies, including comparison of alternative models of service provision and assessment of the value of targeting rapid testing at high-risk subgroups, and (3) construct a transmission-dynamic mathematical model that translates the estimates of diagnostic accuracy into estimates of clinical impact. REVIEW METHODS AND DATA SOURCES A standardised search strategy identified relevant studies from EMBASE, PubMed, MEDLINE, Bioscience Information Service (BIOSIS), System for Information on Grey Literature in Europe Social Policy & Practice (SIGLE) and Web of Science, published between 1 January 2000 and 15 August 2013. Additional 'grey' sources were included. Quality was assessed using quality assessment of diagnostic accuracy studies version 2 (QUADAS-2). For each diagnostic strategy and population subgroup, a care pathway was constructed to specify which medical treatments and health services that individuals would receive from presentation to the point where they either did or did not complete TB treatment successfully. A total cost was estimated from a health service perspective for each care pathway, and the health impact was estimated in terms of the mean discounted quality-adjusted life-years (QALYs) lost as a result of disease and treatment. Costs and QALYs were both discounted at 3.5% per year. An integrated transmission-dynamic and economic model was used to evaluate the cost-effectiveness of introducing rapid molecular testing (in addition to culture and drug sensitivity testing). Probabilistic sensitivity analysis was performed to evaluate the impact on cost-effectiveness of diagnostic and treatment time delays, diagnosis and treatment costs, and associated QALYs. RESULTS A total of 8922 titles and abstracts were identified, with 557 papers being potentially eligible. Of these, 56 studies contained sufficient test information for analysis. All three commercial tests performed well when detecting drug resistance in clinical samples, although with evidence of heterogeneity between studies. Pooled sensitivity for GenoType® MTBDRplus (Hain Lifescience, Nehren, Germany) (isoniazid and rifampicin resistance), INNO-LiPA Rif.TB® (Fujirebio Europe, Ghent, Belgium) (rifampicin resistance) and Xpert® MTB/RIF (Cepheid Inc., Sunnyvale, CA, USA) (rifampicin resistance) was 83.4%, 94.6%, 95.4% and 96.8%, respectively; equivalent pooled specificity was 99.6%, 98.2%, 99.7% and 98.4%, respectively. Results of the transmission model suggest that all of the rapid assays considered here, if added to the current diagnostic pathway, would be cost-saving and achieve a reduction in expected QALY loss compared with current practice. GenoType MTBDRplus appeared to be the most cost-effective of the rapid tests in the South Asian population, although results were similar for GeneXpert. In all other scenarios GeneXpert appeared to be the most cost-effective strategy. CONCLUSIONS Rapid molecular tests for rifampicin and isoniazid resistance were sensitive and specific. They may also be cost-effective when added to culture drug susceptibility testing in the UK. There is global interest in point-of-care testing and further work is needed to review the performance of emerging tests and the wider health-economic impact of decentralised testing in clinics and primary care, as well as non-health-care settings, such as shelters and prisons. STUDY REGISTRATION This study is registered as PROSPERO CRD42011001537. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Francis Drobniewski
- Public Health England National Mycobacterium Reference Laboratory, London, UK
| | - Mary Cooke
- Centre for Infectious Disease Epidemiology, Research Department of Infection and Population Health, University College London, London, UK
| | - Jake Jordan
- Health Economics Research Group, Brunel University, Uxbridge, UK
| | - Nicola Casali
- Department of Infectious Diseases and Immunity, Imperial College London, London, UK
| | - Tendai Mugwagwa
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Agnieszka Broda
- Department of Infectious Diseases and Immunity, Imperial College London, London, UK
| | | | | | - Nathan Green
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Mark Jit
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Marc Lipman
- Division of Medicine, University College London, London, UK
| | - Joanne Lord
- Health Economics Research Group, Brunel University, Uxbridge, UK
| | - Peter J White
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, UK
| | - Ibrahim Abubakar
- Centre for Infectious Disease Epidemiology, Research Department of Infection and Population Health, University College London, London, UK
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de Freitas FAD, Bernardo V, Gomgnimbou MK, Sola C, Siqueira HR, Pereira MAS, Fandinho FCO, Gomes HM, Araújo MEI, Suffys PN, Marques EA, Albano RM. Multidrug resistant Mycobacterium tuberculosis: a retrospective katG and rpoB mutation profile analysis in isolates from a reference center in Brazil. PLoS One 2014; 9:e104100. [PMID: 25093512 PMCID: PMC4122415 DOI: 10.1371/journal.pone.0104100] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/07/2014] [Indexed: 01/27/2023] Open
Abstract
Background Multidrug resistance is a critical factor in tuberculosis control. To gain better understanding of multidrug resistant tuberculosis in Brazil, a retrospective study was performed to compare genotypic diversity and drug resistance associated mutations in Mycobacterium tuberculosis isolates from a national reference center. Methods and Findings Ninety-nine multidrug resistant isolates from 12 Brazilian states were studied. Drug-resistance patterns were determined and the rpoB and katG genes were screened for mutations. Genotypic diversity was investigated by IS6110-RFLP and Luminex 47 spoligotyping. Mutations in rpoB and katG were seen in 91% and 93% of the isolates, respectively. Codon 315 katG mutations occurred in 82.8% of the isolates with a predominance of the Ser315Thr substitution. Twenty-five isolates were clustered in 11 groups with identical IS6110-RFLP patterns while 74 showed unique patterns with no association between mutation frequencies or susceptibility profiles. The most prevalent spoligotyping lineages were LAM (47%), T (17%) and Haarlen (12%). The Haarlen lineage showed a higher frequency of codon 516 rpoB mutations while codon 531 mutations prevailed in the other isolates. Conclusions Our data suggest that there were no major multidrug resistant M. tuberculosis strains transmitted among patients referred to the reference center, indicating an independent acquisition of resistance. In addition, drug resistance associated mutation profiles were well established among the main spoligotyping lineages found in these Brazilian multidrug resistant isolates, providing useful data for patient management and treatment.
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Affiliation(s)
- Flávia A. D. de Freitas
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vagner Bernardo
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michel K. Gomgnimbou
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie– Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - Christophe Sola
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie– Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - Hélio R. Siqueira
- Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Márcia A. S. Pereira
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fátima C. O. Fandinho
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Harrison M. Gomes
- Laboratório de Biologia Molecular Aplicada a Micobacteria, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcelo E. I. Araújo
- Laboratório de Biologia Molecular Aplicada a Micobacteria, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Philip N. Suffys
- Laboratório de Biologia Molecular Aplicada a Micobacteria, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Elizabeth A. Marques
- Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodolpho M. Albano
- Departamento de Bioquímica, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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An upstream truncation of the furA-katG operon confers high-level isoniazid resistance in a Mycobacterium tuberculosis clinical isolate with no known resistance-associated mutations. Antimicrob Agents Chemother 2014; 58:6093-100. [PMID: 25092698 DOI: 10.1128/aac.03277-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the major causes of isoniazid (INH) resistance in Mycobacterium tuberculosis are confined to structural mutations in katG and promoter mutations in the mabA-inhA operon, a significant proportion of INH-resistant strains have unknown resistance mechanisms. Recently, we identified a high-level INH-resistant M. tuberculosis clinical isolate, GB005, with no known resistance-associated mutations. A comprehensive study was performed to investigate the molecular basis of drug resistance in this strain. Although no mutations were found throughout the katG and furA-katG intergenic region, the katG expression and the catalase activity were greatly diminished compared to those in H37Rv (P < 0.01). Northern blotting revealed that the katG transcript from the isolate was smaller than that of H37Rv. Sequencing analysis of furA and upstream genes discovered a 7.2-kb truncation extended from the 96th base preceding the initiation codon of katG. Complementation of the M. tuberculosis Δ(furA-katG) strain with katG and different portions of the truncated region identified a 134-bp upstream fragment of furA that was essential for full catalase activity and INH susceptibility in M. tuberculosis. The promoter activity of this fragment was also shown to be stronger than that of the furA-katG intergenic region (P < 0.01). Collectively, these findings demonstrate that deletion of the 134-bp furA upstream fragment is responsible for the reduction in katG expression, resulting in INH resistance in GB005. To our knowledge, this is the first report showing that deletion of the upstream region preceding the furA-katG operon causes high-level INH resistance in a clinical isolate of M. tuberculosis.
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Yam WC, Siu KHG. Rapid identification of mycobacteria and rapid detection of drug resistance in Mycobacterium tuberculosis in cultured isolates and in respiratory specimens. Methods Mol Biol 2013; 943:171-99. [PMID: 23104290 DOI: 10.1007/978-1-60327-353-4_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Recent advances in molecular biology and better understanding of the genetic basis of drug resistance have allowed rapid identification of mycobacteria and rapid detection of drug resistance of Mycobacterium tuberculosis present in cultured isolates or in respiratory specimens. In this chapter, several simple nucleic acid amplification-based techniques are introduced as molecular approach for clinical diagnosis of tuberculosis. A one-tube nested IS6110-based polymerase chain reaction (PCR) is used for M. tuberculosis complex identification; the use of a multiplex allele-specific PCR is demonstrated to detect the isoniazid resistance; PCR-sequencing assays are applied for rifampicin and ofloxacin resistance detection and 16S rDNA sequencing is utilized for identification of mycobacterial species from cultures of acid fast bacilli (AFB). Despite the high specificity and sensitivity of the molecular techniques, mycobacterial culture remains the "Gold Standard" for tuberculosis diagnosis. Negative results of molecular tests never preclude the infection or the presence of drug resistance. These technological advancements are, therefore, not intended to replace the conventional tests, but rather have major complementary roles in tuberculosis diagnosis.
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Affiliation(s)
- Wing-Cheong Yam
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.
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Singh A, Arutyunov D, Szymanski CM, Evoy S. Bacteriophage based probes for pathogen detection. Analyst 2012; 137:3405-21. [PMID: 22724121 DOI: 10.1039/c2an35371g] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapid and specific detection of pathogenic bacteria is important for the proper treatment, containment and prevention of human, animal and plant diseases. Identifying unique biological probes to achieve a high degree of specificity and minimize false positives has therefore garnered much interest in recent years. Bacteriophages are obligate intracellular parasites that subvert bacterial cell resources for their own multiplication and production of disseminative new virions, which repeat the cycle by binding specifically to the host surface receptors and injecting genetic material into the bacterial cells. The precision of host recognition in phages is imparted by the receptor binding proteins (RBPs) that are often located in the tail-spike or tail fiber protein assemblies of the virions. Phage host recognition specificity has been traditionally exploited for bacterial typing using laborious and time consuming bacterial growth assays. At the same time this feature makes phage virions or RBPs an excellent choice for the development of probes capable of selectively capturing bacteria on solid surfaces with subsequent quick and automatic detection of the binding event. This review focuses on the description of pathogen detection approaches based on immobilized phage virions as well as pure recombinant RBPs. Specific advantages of RBP-based molecular probes are also discussed.
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Affiliation(s)
- Amit Singh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4, Canada.
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Vadwai V, Shetty A, Rodrigues C. Multiplex allele specific PCR for rapid detection of extensively drug resistant tuberculosis. Tuberculosis (Edinb) 2012; 92:236-42. [DOI: 10.1016/j.tube.2012.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/18/2012] [Accepted: 01/22/2012] [Indexed: 10/28/2022]
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