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1.
An. bras. dermatol ; 96(1): 82-84, Jan.-Feb. 2021. graf
Article in English | LILACS | ID: biblio-1152789

ABSTRACT

Abstract Cutaneous tuberculosis is a rare infection that is difficult to diagnose, because it shows less sensitivity and specificity in classic complementary exams when compared with the pulmonary form. The Xpert MTB/RIF® method offers an early diagnosis that identifies the DNA of Mycobacterium tuberculosis and the main mutations that give the bacterium resistance to rifampicin. The authors present a case of scrofuloderma whose diagnosis was quickly obtained through the secretion of a cervical lesion, allowing an early diagnosis and the initiation of appropriate treatment.


Subject(s)
Humans , Tuberculosis, Cutaneous/diagnosis , Tuberculosis, Cutaneous/drug therapy , Antibiotics, Antitubercular/therapeutic use , Antibiotics, Antitubercular/pharmacology , Mycobacterium tuberculosis/genetics , Rifampin/therapeutic use , Sensitivity and Specificity , Drug Resistance, Bacterial , Lymph Nodes
2.
Braz. j. infect. dis ; 25(1): 101544, jan., 2021. tab
Article in English | LILACS | ID: biblio-1249299

ABSTRACT

ABSTRACT Multidrug-resistant tuberculosis (MDR-TB) represents a significant impact in transmission, outcome, and health costs. The World Health Organization recommends implementation of rapid diagnostic methods for multidrug-resistance detection. This study was performed to evaluate the frequency of pre- and extensively drug resistant tuberculosis (pre-XDR-TB and XDR-TB) among MDR-TB patients, the pattern of resistance mutations for fluoroquinolones and the clinical outcome. Adult patients followed at a Brazilian regional reference center for TB, from January 2013 to June 2019 were included. Stored Mycobacterium tuberculosis (Mtb) cultures were recovered, the DNA was extracted, and the susceptibility test was performed using the line probe assay for second line antimycobacterial drugs, Genotype MTBDRsl version 2.0 (Hain Lifescience, CmbH, Germany). Among 33 MDR-TB included patients, we diagnosed XDR-TB or pre-XDR in five (15%) cases. Of these, mutations related to fluoroquinolones resistance were observed in four Mtb isolates, including one who had no phenotypic resistance profile. In two other patients with phenotypic resistance to ofloxacin, genotypic resistance was not found. Case fatality rate was 60% in pre/XDR-TB group, compared to 3.6% in the remaining of patients. This study observed few cases of pre-XDR and XDR-TB among a MDR-TB cohort. Phenotypic and genotypic assays presented good agreement. Clinical outcome was more favorable for patients with susceptibility to fluoroquinolones and injectable drugs.


Subject(s)
Humans , Adult , Pharmaceutical Preparations , Mycobacterium tuberculosis/genetics , Brazil , Microbial Sensitivity Tests , Tuberculosis, Multidrug-Resistant , Drug Resistance, Multiple, Bacterial/genetics , Antitubercular Agents/therapeutic use , Antitubercular Agents/pharmacology
3.
Mem. Inst. Oswaldo Cruz ; 116: e200517, 2021. tab, graf
Article in English | LILACS | ID: biblio-1154877

ABSTRACT

Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial interspersed repetitive units - variable tandem repeats (MIRU-VNTR) of 1,613 isolates were: 73%, 33% and 28% based on 12, 15 and 24-loci, respectively; while for RFLP-IS6110 were: 84% among prison population in Rio de Janeiro, 69% among multidrug-resistant isolates in Rio Grande do Sul, and 56.2% in general population in São Paulo. These findings could improve tuberculosis (TB) surveillance and set up a solid basis to build a database of Mycobacterium genomes.


Subject(s)
Humans , Polymorphism, Restriction Fragment Length/genetics , Minisatellite Repeats/genetics , Mycobacterium tuberculosis/genetics , Brazil/epidemiology , Bacterial Typing Techniques , Molecular Epidemiology , Whole Genome Sequencing , Genotype , Mycobacterium tuberculosis/isolation & purification
4.
Braz. j. infect. dis ; 25(3): 101593, 2021. graf
Article in English | LILACS | ID: biblio-1339428

ABSTRACT

ABSTRACT Tuberculosis verrucosa cutis is a rare medical condition that is caused by the inoculation of Mycobacterium tuberculosis into the skin of a previously sensitized individual. This clinical form of tuberculosis corresponds to 1-2% of all cases of tuberculosis and due to the paucibacillary characteristic of the lesions, patients can be misdiagnosed, accounting for the chronification of the skin infection. Herein, we report the case of a 26-year-old male farmer, presenting plaques with verrucosa and hyperkeratosis features in the left thigh and buttocks during 15 years. M. tuberculosis was identified by PCR and the patient was treated with standard anti-tuberculosis drugs, with subsequent improvement of the skin lesions.


Subject(s)
Humans , Male , Adult , Tuberculosis, Cutaneous/diagnosis , Tuberculosis, Cutaneous/drug therapy , Mycobacterium tuberculosis/genetics , Skin , Brazil , Antitubercular Agents/therapeutic use
5.
Rev. Soc. Bras. Med. Trop ; 54: e07552020, 2021. tab
Article in English | LILACS | ID: biblio-1155600

ABSTRACT

Abstract INTRODUCTION: The intensification of research and innovation with the creation of networks of rapid and effective molecular tests as strategies for the end of tuberculosis are essential to avoid late diagnosis and for the eradication of the disease. We aimed to evaluate the cost-effectiveness of Xpert®MTB/RIF (Xpert) in the diagnosis of drug-resistant tuberculosis in reference units, in scenarios with and without subsidies, and the respective cost adjustment for today. METHODS: The analyses were performed considering as criterion of effectiveness, negative culture or clinical improvement in the sixth month of follow-up. The comparison was performed using two diagnostic strategies for the drug susceptibility test (DST), BactecTMMGITTM960 System, versus Xpert. The cost effectiveness and incremental cost-effectiveness ratio (ICER) were calculated and dollar-corrected for American inflation (US$ 1.00 = R$ 5,29). RESULTS: Subsidized Xpert had the lowest cost of US$ 33.48 (R$67,52) and the highest incremental average efficiency (13.57), thus being a dominated analysis. After the inflation was calculated, the mean cost was DST-MGIT=US$ 74.85 (R$ 396,73) and Xpert = US$ 37.33 (R$197,86) with subsidies. CONCLUSIONS: The Xpert in the diagnosis of TB-DR in these reference units was cost-effective with subsidies. In the absence of a subsidy, Xpert in TB-DR is not characterized as cost effective. This factor reveals the vulnerability of countries dependent on international organizations' subsidy policies.


Subject(s)
Humans , Tuberculosis/diagnosis , Tuberculosis, Multidrug-Resistant/diagnosis , Mycobacterium tuberculosis/genetics , Sensitivity and Specificity , Cost-Benefit Analysis
6.
Rev. Soc. Bras. Med. Trop ; 54: e0728-2020, 2021. tab, graf
Article in English | LILACS | ID: biblio-1155535

ABSTRACT

Abstract INTRODUCTION: Mycobacterium tuberculosis (MTB) is a causative agent of tuberculosis (TB) that causes death worldwide. METHODS: MTB was subjected to phenotypic drug-susceptibility tests (DST), and drug-resistant genes were sequenced. RESULTS: Previously treated patients were more likely to have positive smear results and exhibit drug resistance. New patients were more likely to be mono SM-resistant and less likely to be INH- and RIF-resistant. The most common mutations were katG (S315T), rpoB (S450L), rpsL (K43R), and embB (M306V). CONCLUSIONS: The proportion of mono-SM-resistant TB among new patients was higher.


Subject(s)
Humans , Pharmaceutical Preparations , Tuberculosis, Multidrug-Resistant , Mycobacterium tuberculosis/genetics , Bacterial Proteins/genetics , Microbial Sensitivity Tests , China , Mutation , Antitubercular Agents/pharmacology
7.
Chinese Journal of Biotechnology ; (12): 2503-2512, 2021.
Article in Chinese | WPRIM | ID: wpr-887816

ABSTRACT

The purpose of this study is to provide a simple and reliable genetic typing approach for molecular drug susceptibility test of Mycobacterium tuberculosis, through the developing of fluorescence molecular marker of rifampicin resistance gene rpoB. Eleven fluorescent molecular markers of the rpoB gene were established by using the sequence difference between the amino acid positions 531, 526, 516, 511 and 513 of rpoB gene of rifampicin-resistant strains and the alleles of rifampicin-sensitive strains, combined with the PARMS technique (Penta-primer amplification refractory mutation system). We used 104 clinical isolates of Mycobacterium tuberculosis to validate this marker and it was verified by sequencing as 100% correct. These samples were also tested with proportional drug sensitivity test. The coincidence rate was 94.23%. The molecular markers had high reliability for genotyping of rpoB gene. It can also detect low-concentration drug-resistant samples (511/533 unit point mutations) whose phenotypic susceptibility cannot be detected. The eleven sets of fluorescent molecular markers could cover 92%-96% of rpoB gene mutation types of rifampicin-resistant strains, and provide new idea for rapid detection of rifampin-resistant Mycobacterium tuberculosis.


Subject(s)
Bacterial Proteins/genetics , DNA-Directed RNA Polymerases/genetics , Drug Resistance, Bacterial/genetics , Microbial Sensitivity Tests , Mutation , Mycobacterium tuberculosis/genetics , Reproducibility of Results , Rifampin/pharmacology , Technology
8.
Arq. neuropsiquiatr ; 78(11): 700-707, Nov. 2020. tab, graf
Article in English | LILACS | ID: biblio-1142365

ABSTRACT

ABSTRACT Background: The timely diagnosis of tuberculous meningitis (TBM) is challenging. Molecular diagnostic tools are necessary for TBM, particularly in low- and middle-income countries. Objectives: We aimed to calculate the diagnostics characteristics of Xpert MTB/RIF for the detection of Mycobacterium tuberculosis in the cerebrospinal fluid (CSF) and the frequency of rifampicin (RIF)-resistance in the CSF samples. Methods: A total of 313 consecutive CSF samples were studied and categorized into TBM definite, probable, possible, or not TBM cases based on the clinical, laboratory, and imaging data. Results: For the definite TBM cases (n=7), the sensitivity, specificity, efficiency, and positive likelihood ratio were 100, 97, 97, and 38%, respectively. However, for the TBM definite associated with the probable cases (n=24), the sensitivity decreased to 46%. All CSF samples that were Xpert MTB/RIF-positive were RIF susceptible. Conclusion: Xpert MTB/RIF showed high discriminating value among the microbiology-proven TBM cases, although the values for the probable and possible TBM cases were reduced. Xpert MTB/RIF contributes significantly to the diagnosis of TBM, mainly when coupled with the conventional microbiological tests and clinical algorithms.


RESUMO Introdução: O diagnóstico da meningite tuberculosa (TBM) é desafiador. Ferramentas de diagnóstico molecular são necessárias para esse diagnóstico, particularmente em países de baixa e média renda. Objetivos: Calcular as características diagnósticas do Xpert MTB/RIF para a detecção de Mycobacterium tuberculosis no líquido cefalorraquidiano (LCR) e a frequência de resistência à rifampicina (RIF) nas amostras do LCR. Métodos: Um total de 313 amostras consecutivas de LCR foram estudadas e categorizadas em casos de TBM definida, provável, possível ou não TBM, com base nos dados clínicos, laboratoriais e de imagem. Resultados: Para os casos definidos de TBM (n=7), sensibilidade, especificidade, eficiência e razão de verossimilhança positiva foram de 100, 97, 97 e 38%, respectivamente. No entanto, para os casos de TBM definidos associados aos prováveis (n=24), a sensibilidade diminuiu para 46%. Todas as amostras de LCR que foram positivas para Xpert MTB/RIF foram suscetíveis a RIF. Conclusão: O Xpert MTB/RIF mostrou alto valor discriminante entre os casos TBM comprovados por microbiologia, porém o valor nos casos prováveis e possíveis de TBM foram reduzidos. O Xpert MTB/RIF contribui significativamente para o diagnóstico de TBM, principalmente quando associado aos testes microbiológicos convencionais e algoritmos clínicos.


Subject(s)
Humans , Tuberculosis, Meningeal/diagnosis , Tuberculosis, Meningeal/drug therapy , Mycobacterium tuberculosis/genetics , Rifampin/pharmacology , Brazil , Sensitivity and Specificity
9.
Mem. Inst. Oswaldo Cruz ; 115: e190407, 2020. tab
Article in English | LILACS | ID: biblio-1101275

ABSTRACT

BACKGROUND Early diagnosis of tuberculosis (TB) and identification of strains of Mycobacterium tuberculosis resistant to anti-TB drugs are considered the main factors for disease control. OBJECTIVES To standardise a real-time polymerase chain reaction (qPCR) assay technique and apply it to identify mutations involved in M. tuberculosis resistance to Isoniazid (INH) directly in Ziehl-Neelsen (ZN) stained slides. METHODS Were analysed 55 independent DNA samples extracted from clinical isolates of M. tuberculosis by sequencing. For application in TB diagnosis resistance, 59 ZN-stained slides were used. The sensitivity, specificity and Kappa index, with a 95% confidence interval (CI95%), were determined. FINDINGS The agreement between the tests was, for the katG target, the Kappa index of 0.89 (CI95%: 0.7-1.0). The sensitivity and specificity were 97.6% (CI95%: 87.7-99.9) and 91.7% (CI95%: 61.5-99.5), respectively. For inhA, the Kappa index was 0.92 (CI95%: 0.8-1.0), the sensitivity and specificity were 94.4% (CI95%: 72.7-99.8) and 97.3% (CI95%: 85.8-99.9), respectively. The use of ZN-stained slides for drug-resistant TB detection showed significant results when compared to other standard tests for drug resistance. MAIN CONCLUSIONS qPCR genotyping proved to be an efficient method to detect genes that confer M. tuberculosis resistance to INH. Thus, qPCR genotyping may be an alternative instead of sequencing.


Subject(s)
Humans , Genetic Markers/genetics , Drug Resistance, Bacterial/genetics , Isoniazid/pharmacology , Mutation/genetics , Mycobacterium tuberculosis/genetics , Antitubercular Agents/pharmacology , DNA, Bacterial/genetics , Microbial Sensitivity Tests , Sensitivity and Specificity , Real-Time Polymerase Chain Reaction , Genotype , Mycobacterium tuberculosis/drug effects
10.
Mem. Inst. Oswaldo Cruz ; 115: e200520, 2020. tab, graf
Article in English | LILACS | ID: biblio-1154871

ABSTRACT

BACKGROUND The evaluation of procedures for drug susceptibility prediction of Mycobacterium tuberculosis based on genomic data against the conventional reference method test based on culture is realistic considering the scenario of growing number of tools proposals based on whole-genome sequences (WGS). OBJECTIVES This study aimed to evaluate drug susceptibility testing (DST) outcome based on WGS tools and the phenotypic methods performed on isolates of M. tuberculosis Lineage 1 from the state of Pará, Brazil, generally associated with low levels of drug resistance. METHODOLOGY Culture based DST was performed using the Proportion Method in Löwenstein-Jensen medium on 71 isolates that had been submitted to WGS. We analysed the seven main genome sequence-based tools for resistance and lineage prediction applied to M. tuberculosis and for comparison evaluation we have used the Kappa concordance test. FINDINGS When comparing the WGS-based tools against the DST, we observed the highest level of agreement using TB-profiler. Among the tools, TB-profiler, KvarQ and Mykrobe were those which identified the largest number of TB-MDR cases. Comparing the four most sensitive tools regarding resistance prediction, agreement was observed for 43 genomes. MAIN CONCLUSIONS Drug resistance profiling using next-generation sequencing offers rapid assessment of resistance-associated mutations, therefore facilitating rapid access to effective treatment.


Subject(s)
Humans , Tuberculosis, Multidrug-Resistant/genetics , Drug Resistance, Multiple, Bacterial/genetics , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/genetics , Antitubercular Agents/pharmacology , Brazil , Pharmaceutical Preparations , Microbial Sensitivity Tests , Tuberculosis, Multidrug-Resistant/drug therapy , Drug Resistance, Multiple, Bacterial/drug effects , Whole Genome Sequencing , Mycobacterium tuberculosis/isolation & purification , Antitubercular Agents/therapeutic use
11.
Rev. Soc. Bras. Med. Trop ; 53: e20190175, 2020. tab
Article in English | LILACS | ID: biblio-1057267

ABSTRACT

Abstract INTRODUCTION: The present study sought to assess the mean and activity based cost (ABC) of the laboratory diagnosis for tuberculosis through the application of conventional and molecular techniques-Xpert®MTB/RIF and Genotype®MTBDRplus-in a tertiary referral hospital in Brazil. METHODS: The mean cost and ABC formed the basis for the cost analysis of the TB laboratory diagnosis. RESULTS: The mean cost and ABC were US$ 4.00 and US$ 3.24, respectively, for a bacilloscopy; US$ 6.73 and US$ 5.27 for a Lowenstein-Jensen (LJ) culture; US$ 105.42 and US$ 76.56 for a drug sensitivity test (DST)-proportions method (PM) in LJ; US$ 148.45 and US$ 136.80 for a DST-BACTECTM MGITTM 960 system; US$ 11.53 and US$ 9.89 for an Xpert®MTB/RIF; and US$ 84.21 and US$ 48.38 for a Genotype®MTBDRplus. CONCLUSIONS: The mean cost and ABC proved to be good decision-making parameters in the diagnosis of TB and MDR-TB. The effective implementation of algorithms will depend on the conditions at each location.


Subject(s)
Humans , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/economics , Tuberculosis, Multidrug-Resistant/diagnosis , Tuberculosis, Multidrug-Resistant/economics , Costs and Cost Analysis/statistics & numerical data , Mycobacterium tuberculosis/genetics , Brazil , Sensitivity and Specificity , Tertiary Care Centers , Genotype , Mycobacterium tuberculosis/isolation & purification
12.
Rev. Soc. Bras. Med. Trop ; 53: e20190404, 2020. tab, graf
Article in English | LILACS, ColecionaSUS, SES-SP | ID: biblio-1136910

ABSTRACT

Abstract INTRODUCTION: We aimed to estimate the prevalence and transmission of drug-resistant tuberculosis in a high-burden Brazilian setting under directly observed therapy short-course strategy. METHODS: Isolates of culture-confirmed pulmonary tuberculosis patients from Guarulhos, Brazil, diagnosed in October 2007-2011 were subjected to drug susceptibility and IS6110-restriction fragment length polymorphism testing. RESULTS: The overall resistance prevalence was 11.5% and the multi-drug resistance rate was 4.2%. Twenty-six (43.3%) of 60 drug-resistant isolates were clustered. Epidemiological relationships were identified in 11 (42.3%) patients; 30.8% of the cases were transmitted in households. CONCLUSIONS: Drug-resistant tuberculosis was relatively low and transmitted in households and the community.


Subject(s)
Humans , Male , Female , Adolescent , Adult , Young Adult , Tuberculosis, Multidrug-Resistant/epidemiology , Directly Observed Therapy/methods , Mycobacterium tuberculosis/drug effects , Polymorphism, Restriction Fragment Length , Brazil/epidemiology , Prevalence , Cross-Sectional Studies , Tuberculosis, Multidrug-Resistant , Tuberculosis, Multidrug-Resistant/drug therapy , Mycobacterium tuberculosis/genetics
13.
Rev. Soc. Bras. Med. Trop ; 53: e20200205, 2020. tab, graf
Article in English | LILACS, ColecionaSUS, SES-SP | ID: biblio-1136899

ABSTRACT

Abstract INTRODUCTION: The diagnostic accuracy of Xpert MTB/RIF (Xpert) in pulmonary tuberculosis (PTB) in children is lower than in adults. In Brazil, the diagnosis of PTB is based on a diagnostic score system (DSS). This study aims to study the role of Xpert in children and adolescents with PTB symptoms. METHODS: A cross-sectional study was conducted in 3 referral centers to TB. Children and adolescents (0-19 years old) whose respiratory samples were submitted to Xpert were included. Statistical analysis (bivariate and logistic regression) to assess the simultaneous influence of TB-related variables on the occurrence of Xpert detectable in TB cases was done. To evaluate the agreement or disagreement between Xpert results with acid-fast bacillus (AFB) and cultures, κ method was used (significancy level of 5%). RESULTS: Eighty-eight patients were included in the study and PTB occurred in 43 patients (49%) and Xpert was detectable in 21 patients (24%). Adolescents and positive culture results were independent predictive variables of Xpert positivity. DSS sensitivity compared with the final diagnosis of TB was 100% (95% CI, 88.1-100%), specificity was 97.2% (95% CI, 85.5-99.9%). The accuracy of the method was 98.5% (95% CI, 91.7-99.9%). CONCLUSIONS: Xpert contributed to diagnosis in 9% of patients with AFB and in culture negative cases. DSS indicated relevance for this diagnostic approach of intrathoracic TB (ITB) in reference centers for presenting data both with high sensitivity and specificity.


Subject(s)
Humans , Infant, Newborn , Infant , Child, Preschool , Child , Adolescent , Adult , Young Adult , Sputum/microbiology , Tuberculosis, Pulmonary/diagnosis , Mycobacterium tuberculosis/isolation & purification , Referral and Consultation , Tuberculosis, Pulmonary/epidemiology , Brazil/epidemiology , Cross-Sectional Studies , Mycobacterium tuberculosis/genetics
14.
Rev. Soc. Bras. Med. Trop ; 53: e20200211, 2020. tab, graf
Article in English | LILACS, ColecionaSUS, SES-SP | ID: biblio-1136883

ABSTRACT

Abstract INTRODUCTION: Nontuberculous mycobacteria (NTM) species, as human pathogens, are increasing in the world, as is the difficulty of accurately identifying them. Differential diagnosis, especially between the M. tuberculosis complex and NTM species, and the characterization of NTM species is important. This study aimed to evaluate the performance of a molecular system based on multiplex real-time PCR with high-resolution melting (HRM) for the identification and differentiation of NTM species of clinical importance of an endemic area for tuberculosis in northeastern Brazil. METHODS: The technical protocol of the molecular system was based on multiplex real-time PCR-HRM, and evaluated the sensitivity and specificity of the detection of NTM species in mycobacterial clinical isolates from the studied region. The gold standard method was specific gene sequencing. RESULTS: The sensitivity and specificity of multiplex real-time PCR-HRM modified for differentiation between NTM and M. tuberculosis were 90% and 100%, respectively. The PCR-HRM sensitivities for the characterization of NTM species (M. kansasii, M. abscesses, M. avium, and M. fortuitum) were 94.59%, 80%, 57.14%, and 54%, respectively. CONCLUSIONS The multiplex real-time PCR-HRM modified assay has the potential to rapidly and efficiently identify nontuberculous mycobacteria of clinical importance, which is crucial for immediate implementation of the appropriate therapy and thus avoiding complications and sequelae in patients.


Subject(s)
Humans , Tuberculosis , Mycobacterium Infections, Nontuberculous/diagnosis , Mycobacterium tuberculosis/genetics , Brazil , Real-Time Polymerase Chain Reaction , Nontuberculous Mycobacteria/genetics
15.
Rev. Soc. Bras. Med. Trop ; 53: e20190470, 2020. tab, graf
Article in English | LILACS, ColecionaSUS, SES-SP | ID: biblio-1136864

ABSTRACT

Abstract INTRODUCTION: Tuberculosis is listed among the top 10 causes of deaths worldwide. The resistant strains causing this disease have been considered to be responsible for public health emergencies and health security threats. As stated by the World Health Organization (WHO), around 558,000 different cases coupled with resistance to rifampicin (the most operative first-line drug) have been estimated to date. Therefore, in order to detect the resistant strains using the genomes of Mycobacterium tuberculosis (MTB), we propose a new methodology for the analysis of genomic similarities that associate the different levels of decomposition of the genome (discrete non-decimated wavelet transform) and the Hurst exponent. METHODS: The signals corresponding to the ten analyzed sequences were obtained by assessing GC content, and then these signals were decomposed using the discrete non-decimated wavelet transform along with the Daubechies wavelet with four null moments at five levels of decomposition. The Hurst exponent was calculated at each decomposition level using five different methods. The cluster analysis was performed using the results obtained for the Hurst exponent. RESULTS: The aggregated variance, differenced aggregated variance, and aggregated absolute value methods presented the formation of three groups, whereas the Peng and R/S methods presented the formation of two groups. The aggregated variance method exhibited the best results with respect to the group formation between similar strains. CONCLUSION: The evaluation of Hurst exponent associated with discrete non-decimated wavelet transform can be used as a measure of similarity between genome sequences, thus leading to a refinement in the analysis.


Subject(s)
Humans , Genome, Bacterial/genetics , Wavelet Analysis , Models, Genetic , Mycobacterium tuberculosis/genetics
16.
Rev. Soc. Bras. Med. Trop ; 53: e20200051, 2020. tab
Article in English | LILACS, ColecionaSUS, SES-SP | ID: biblio-1136823

ABSTRACT

Abstract INTRODUCTION: Laboratory and clinical features of childhood tuberculosis (TB) are non-specific and establishing an accurate diagnosis remains a challenge. This study evaluated a Single tube nested-PCR (STNPCR) to detect genomic DNA of Mycobacterium tuberculosis complex in blood and urine. METHODS: Biological samples were obtained from children (<15 years old) with clinical suspicion of pulmonary and extrapulmonary TB at public hospitals in Recife-Pernambuco, Brazil. Cultures yielded negative results in a majority of childhood TB cases, which are generally paucibacillary. A set of clinical, epidemiological, radiological, and laboratory criteria with evident clinical improvement after anti-TB treatment were frequently used to define childhood TB cases. RESULTS: Ninety children with clinical suspicion were enrolled in this study (44 with TB and 46 without TB). The pulmonary TB group had 20 confirmed cases and 46 negative controls, while the extrapulmonary TB group had 24 confirmed cases. The STNPCR showed sensitivities to pulmonary and extrapulmonary TB of 47.4% and 52.2% (blood) and 38.8% and 20% (urine), respectively. Considering the low performance of STNPCR on separate samples, we decided to perform a combined analysis (parallel sensitivity analysis) of the results from blood and urine samples. The parallel sensitivity increased to 65% in blood and 62.5% in urine. The specificity in both samples ranged from 93.5-97.8%. CONCLUSIONS: Although STNPCR showed moderate sensitivity, the specificity is high; therefore, the test can be used as an auxiliary tool to diagnose TB in children. It is a rapid test that demonstrated better performance than other diagnostic tests in paucibacillary samples as it does in childhood tuberculosis.


Subject(s)
Humans , Male , Female , Infant, Newborn , Infant , Child, Preschool , Child , Adolescent , Tuberculosis, Pulmonary/diagnosis , Mycobacterium tuberculosis/isolation & purification , Tuberculosis, Pulmonary/urine , Tuberculosis, Pulmonary/blood , Brazil , Case-Control Studies , Polymerase Chain Reaction , Prospective Studies , Diagnostic Tests, Routine , Mycobacterium tuberculosis/genetics
17.
Mem. Inst. Oswaldo Cruz ; 115: e200055, 2020. tab, graf
Article in English | LILACS, SES-SP | ID: biblio-1135234

ABSTRACT

BACKGROUND Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis, and the number of new cases of multidrug resistant TB (MDR-TB), pre extensively drug-resistant TB (pre-XDR-TB) and extensively drug-resistant TB (XDR-TB) has increased considerably worldwide. OBJECTIVES Herein, using 156 M. tuberculosis isolates from 106 patients previously classified as MDR or pre-XDR or XDR isolates, we investigated the genetic mutation profiles associated with phenotypic resistances in patients with MDR-TB, pre-XDR-TB and XDR-TB, treatment outcomes and resistance evolution. METHODS Molecular analyses were performed by partial sequencing of the rpoB, katG, gyrA, gyrB, rrs genes and analysis of the fabG-inhA promoter region. Clinical, epidemiologic and demographic data were obtained from the TB Notification database system of São Paulo (TB-WEB) and the Information System for Special Tuberculosis Treatments (SITE-TB). FINDINGS Drug resistance was attributed to previously known mutations and a novel Asp449Val mutation in gyrB was observed in four isolates from the same patient. Ten patients had more than one isolate evaluated and eight of these patients displayed resistance progression. MAIN CONCLUSIONS The present study is the first to report the frequency of mutations related to second-line drug resistance in MDR-TB, pre-XDR-TB and XDR-TB isolates. The results could lead to the improvement of available technologies for the rapid detection of drug resistant TB.


Subject(s)
Humans , Male , Female , Adolescent , Adult , Young Adult , Tuberculosis, Multidrug-Resistant/microbiology , Drug Resistance, Multiple, Bacterial/genetics , Mutation/genetics , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/genetics , Antitubercular Agents/pharmacology , Socioeconomic Factors , Brazil , Microbial Sensitivity Tests , Extensively Drug-Resistant Tuberculosis/microbiology , Middle Aged , Mycobacterium tuberculosis/isolation & purification
18.
Mem. Inst. Oswaldo Cruz ; 115: e200215, 2020. tab, graf
Article in English | LILACS, SES-SP | ID: biblio-1135232

ABSTRACT

The human-adapted strains of the Mycobacterium tuberculosis complex (MTBC) comprise seven phylogenetic lineages originally associated with their geographical distribution. Here, we report the genomes of three drug-resistant clinical isolates of the Latin American-Mediterranean (LAM) family collected in Kazakhstan. We utilised whole-genome sequencing to study the distribution and drug resistance of these isolates. Phylogenetic analysis grouped the genomes described in this study with the sequences from Russia, Uzbekistan, and Kazakhstan belonging to the LAM family. One isolate has acquired extensive drug resistance to seven antituberculosis drugs. Our results suggest at least two multi-drug resistant (MDR)/extensively drug-resistant (XDR)-associated genotypes of the LAM family circulate in Kazakhstan.


Subject(s)
Humans , Tuberculosis, Multidrug-Resistant/drug therapy , Drug Resistance, Multiple, Bacterial/drug effects , Mycobacterium tuberculosis/genetics , Antitubercular Agents/pharmacology , Phylogeny , Kazakhstan , Tuberculosis, Multidrug-Resistant/genetics , Genomics , Genotype , Latin America
19.
Biomédica (Bogotá) ; 39(supl.2): 78-92, ago. 2019. tab, graf
Article in English | LILACS | ID: biblio-1038830

ABSTRACT

ABSTRACT Introduction: Tuberculosis continues to be a public health priority. Indigenous peoples are vulnerable groups with cultural determinants that increase the risk of the disease. Objective: To determine molecular epidemiology and phenotypical features and of Mycobacterium tuberculosis isolates from indigenous people in Colombia during the period from 2009 to 2014. Materials and methods: We conducted an analytical observational study; we analyzed 234 isolates to determine their patterns of sensitivity to antituberculosis drugs and their molecular structures by spoligotyping. Results: The isolates came from 41 indigenous groups, predominantly the Wayúu (13.10%) and Emberá Chamí (11.35%). We found 102 spoligotypes distributed among seven genetic families (37.2% LAM, 15.8% Haarlem, 8.1% T, 3.4% U, 2.6% S, 2.1% X, and 0.9%, Beijing). The association analysis showed that the non-clustered isolates were related to prior treatment, relapse, orphan spoligotypes, and the Beijing family. The H family presented an association with the Arhuaco and Camëntŝá indigenous groups, the U family was associated with the Wounaan group, and the T family was associated with the Motilón Barí group. Conclusions: This is the first national study on M. tuberculosis characterization in indigenous groups. The study evidenced that diagnosis in indigenous people is late. We described 53% of orphan patterns that could be typical of the Colombian indigenous population. The high percentage of grouping by spoligotyping (62%) could indicate cases of active transmission, a situation that should be corroborated using a second genotyping marker. A new Beijing spoligotype (Beijing-like SIT 406) was identified in Colombia.


RESUMEN Introducción. La tuberculosis es prioridad de salud pública. Los pueblos indígenas son vulnerables debido a los factores culturales determinantes que aumentan el riesgo de tuberculosis. Objetivo. Determinar la epidemiologia molecular y las características fenotípicas de los aislamientos de Mycobacterium tuberculosis de pueblos indígenas de Colombia entre 2009 y 2014. Materiales y métodos. Se hizo un estudio observacional analítico; se analizaron 234 aislamientos para determinar la sensibilidad a los fármacos antituberculosos y la estructura molecular usando spoligotyping. La información epidemiológica se recolectó utilizando el formato único de vigilancia de micobacterias. Resultados. Los aislamientos provenían de 41 grupos indígenas, principalmente los wayúu (13,10 %) y emberá chamí (11,35 %). Se encontraron 102 genotipos distribuidos en siete familias genéticas (37,2 %, LAM; 15,8 %, Haarlem; 8,1 %, T; 3,4 %, U; 2,6 %, S; 2,1 %, X, y 0,9%, Beijing). El análisis de asociación mostró que los aislamientos no agrupados se asociaron con el tratamiento previo, las recaídas, los genotipos huérfanos y la familia Beijing. La familia H presentó una asociación con los grupos indígenas arhuaco y camëntŝá, la familia U se asoció con el grupo wounaan y la familia T con el grupo motilón barí. Conclusiones. Este es el primer estudio nacional de caracterización de M. tuberculosis en grupos indígenas. Se evidenció que el diagnóstico en indígenas es tardío, y que 53 % de los patrones huérfanos podrían ser típicos de la población indígena colombiana. El alto porcentaje de agrupamiento por spoligotyping (62%) podría indicar casos de transmisión activa, una situación que debe ser corroborada usando un segundo marcador de genotipificación. Se identificó un nuevo genotipo (Beijing-like SIT 406) en Colombia.


Subject(s)
Adolescent , Adult , Aged , Aged, 80 and over , Child , Child, Preschool , Female , Humans , Infant , Male , Middle Aged , Pregnancy , Young Adult , Tuberculosis/microbiology , Indians, South American , Mycobacterium tuberculosis/isolation & purification , Phenotype , Pregnancy Complications, Infectious/epidemiology , Tuberculosis/ethnology , Tuberculosis/epidemiology , Repetitive Sequences, Nucleic Acid , Polymerase Chain Reaction , Colombia/epidemiology , Culture , Delayed Diagnosis , Genotype , Mycobacterium tuberculosis/classification , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/genetics , Antitubercular Agents/pharmacology
20.
Biomédica (Bogotá) ; 39(supl.1): 71-85, mayo 2019. tab, graf
Article in Spanish | LILACS | ID: biblio-1011456

ABSTRACT

Resumen Introducción. La tuberculosis continúa siendo uno de los problemas de salud más importantes a nivel mundial y, con la infección por el virus de la inmunodeficiencia humana (HIV), constituye la principal causa de muerte por infecciones. En el 2016, se notificaron 6,3 millones de casos nuevos de la enfermedad. Objetivo. Describir los patrones genéticos determinados mediante la genotipificación del número variable de repeticiones en tándem de unidades repetitivas interespaciadas de micobacterias (Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats, MIRU-VNTR) en la población de estudio y compararlos con los hallados en otros estudios locales e internacionales. Materiales y métodos. Mediante MIRU-VNTR, entre el 2013 y el 2015 se hizo la genotipificación de 105 muestras de ADN extraídas del esputo o de aislamientos en cultivo de M. tuberculosis provenientes de pacientes residentes en Cali con diagnóstico de tuberculosis pulmonar. La amplificación de 24 loci MIRU-VNTR se hizo por medio de la reacción en cadena de la polimerasa (PCR). Los amplicones resultantes se visualizaron por electroforesis en geles de agarosa (2 %) teñidos con SYBR Safe™. La asignación de los alelos se hizo con un análisis gráfico con el programa GelAnalyzer 2010. Los resultados obtenidos se analizaron con el algoritmo UPGMA y se compararon con las bases de datos internacionales MIRU-VNTRplus y SITVITWEB. Resultados. Se genotipificaron por completo 62 de las muestras y se obtuvieron 58 perfiles diferentes de MIRU-VNTR. Al comparar con las bases de datos internacionales, su distribución por linajes fue la siguiente: 54,8 % para el LAM, 25,8 % para el Haarlem, 14,5 % para el S, 3,2 % para el Beijing y 1,6 % para el Cameroon. Los patrones MIRU-VNTR correspondieron a 20 tipos internacionales de MIRU (MIRU International Types, MIT) diferentes, y los más frecuentes fueron el MIT 190 y el MIT 110, con 22,6 y 6,5 %, respectivamente. Conclusión. Estos resultados confirmaron hallazgos previos sobre el predominio de los linajes LAM y Haarlem en la ciudad y la presencia de los MIT encontrados en otra ciudad de Colombia.


Abstract Introduction: Tuberculosis continues to be one of the main public health problems in the world. Together with the HIV infection, it is one of the main causes of death due to infections worldwide. In 2016, 6.3 million new cases of the disease were reported. Objective: To describe the genetic patterns determined by genotyping using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) in the study population and compare them with other studies carried out in Cali, Colombia, and the world. Materials and methods: We genotyped a total of 105 DNA samples extracted from sputum or culture isolates of the Mycobacterium tuberculosis complex, which were obtained from pulmonary tuberculosis diagnosed patients over the period 2013-2015, in Cali. We performed PCR amplification of 24 loci by MIRU-VNTR on the DNA extracted from the samples. The amplicons were visualized in agarose gel electrophoresis (2%) with SYBR Safe™ staining. Then, the alleles were designated by graphical analysis using the GelAnalyzer 2010 software. These results were analyzed using the UPGMA logarithm and compared with the registers from the MIRU-VNTR plus and SITVITWEB databases. Results: We genotyped 62 of the samples completely and we obtained 58 different MIRU-VNTR profiles. By comparing with the international databases, we determined the following distributions per lineage: LAM, 54.8%; Haarlem,25.8%; S, 14.5%; Beijing, 3.2%, and Cameroon, 1.6%. The MIRU-VNTR patterns corresponded to 17 different MITs; the most frequent were MIT 190 and MIT 110, with 22.6% and 6.5%, respectively. Conclusions: These results demonstrated previous observations about the predominance of the LAM and Haarlem lineages in the city, and the presence of the MITs found in another city of Colombia.


Subject(s)
Adolescent , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Young Adult , Tuberculosis, Pulmonary/microbiology , DNA, Bacterial/genetics , Minisatellite Repeats , Interspersed Repetitive Sequences , Mycobacterium tuberculosis/genetics , Phylogeny , Socioeconomic Factors , Sputum/microbiology , Tuberculosis, Pulmonary/epidemiology , Algorithms , Drug Resistance, Microbial , Global Health , Risk Factors , Databases, Factual , Colombia/epidemiology , Electrophoresis, Agar Gel , Genotyping Techniques , Genotype , Mycobacterium tuberculosis/isolation & purification , Mycobacterium tuberculosis/drug effects
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