RESUMO
Within-host Mycobacterium tuberculosis (Mtb) diversity may detect antibiotic resistance or predict tuberculosis treatment failure and is best captured through sequencing directly from sputum. Here, we compared three sample pre-processing steps for DNA decontamination and studied the yield of a new target enrichment protocol for optimal whole-genome sequencing (WGS) from direct patient samples. Mtb-positive NALC-NaOH-treated patient sputum sediments were pooled, and heat inactivated, split in replicates, and treated by either a wash, DNase I, or benzonase digestion. Levels of contaminating host DNA and target Mtb DNA were assessed by quantitative PCR (qPCR), followed by WGS with and without custom dsDNA target enrichment. The pre-treatment sample has a high host-to-target ratio of DNA (6,168 ± 1,638 host copies/ng to 212.3 ± 59.4 Mtb copies/ng) that significantly decreased with all three treatments. Benzonase treatment resulted in the highest enrichment of Mtb DNA at 100-fold compared with control (3,422 ± 2,162 host copies/ng to 11,721 ± 7,096 Mtb copies/ng). The custom dsDNA probe panel successfully enriched libraries from as little as 0.45 pg of Mtb DNA (100 genome copies). Applied to direct sputum the dsDNA target enrichment panel increased the percent of sequencing reads mapping to the Mtb target for all three pre-processing methods. Comparing the results of the benzonase sample sequenced both with and without enrichment, the percent of sequencing reads mapping to the Mtb increased to 90.95% from 1.18%. We demonstrate a low limit of detection for a new custom dsDNA Mtb target enrichment panel that has a favorable cost profile. The results also demonstrate that pre-processing to remove contaminating extracellular DNA prior to cell lysis and DNA extraction improves the host-to-Mtb DNA ratio but is not adequate to support average coverage WGS without target capture.
Assuntos
Mycobacterium tuberculosis , Tuberculose , Humanos , Mycobacterium tuberculosis/genética , Tuberculose/diagnóstico , Tuberculose/tratamento farmacológico , Sequenciamento Completo do Genoma , Sequência de Bases , DNA , Escarro/microbiologiaRESUMO
Assuntos
Consumo de Bebidas Alcoólicas , Antituberculosos , Infecções por HIV , Isoniazida , Tuberculose Latente , Humanos , Isoniazida/administração & dosagem , Antituberculosos/administração & dosagem , Antituberculosos/efeitos adversos , Uganda/epidemiologia , Tuberculose Latente/tratamento farmacológico , Masculino , Infecções por HIV/tratamento farmacológico , Feminino , Consumo de Bebidas Alcoólicas/efeitos adversos , Consumo de Bebidas Alcoólicas/epidemiologia , Adulto , Cadeias de Markov , Teste Tuberculínico , Tuberculose/prevenção & controle , Tuberculose/epidemiologia , Doença Hepática Induzida por Substâncias e Drogas/prevenção & controle , Doença Hepática Induzida por Substâncias e Drogas/etiologia , Doença Hepática Induzida por Substâncias e Drogas/epidemiologia , Adulto Jovem , Pessoa de Meia-IdadeRESUMO
BACKGROUND: Smoking of illicit drugs may lead to more rapid TB disease progression or late treatment presentation, yet research on this topic is scant. We examined the association between smoked drug use and bacterial burden among patients newly initiated on drug-susceptible TB (DS-TB) therapy.METHODS: Data from 303 participants initiating DS-TB treatment in the Western Cape Province, South Africa, were analyzed. Smoked drug use was defined as self-reported or biologically verified methamphetamine, methaqualone and/or cannabis use. Proportional hazard and logistic regression models (adjusted for age, sex, HIV status and tobacco use) examined associations between smoked drug use and mycobacterial time to culture positivity (TTP), acid-fast bacilli sputum smear positivity and lung cavitation.RESULTS: People who smoked drugs (PWSD) comprised 54.8% (n = 166) of the cohort. TTP was faster for PWSD (hazard ratio 1.48, 95% CI 1.10-1.97; P = 0.008). Smear positivity was higher among PWSD (OR 2.28, 95% CI 1.22-4.34; P = 0.011). Smoked drug use (OR 1.08, 95% CI 0.62-1.87; P = 0.799) was not associated with increased cavitation.CONCLUSIONS: PWSD had a higher bacterial burden at diagnosis than those who do not smoke drugs. Screening for TB among PWSD in the community may facilitate earlier linkage to TB treatment and reduce community transmission.
Assuntos
Infecções por HIV , Mycobacterium , Tuberculose Pulmonar , Humanos , Tuberculose Pulmonar/diagnóstico , Fumaça , Fumar/epidemiologia , Uso de Tabaco , Escarro/microbiologiaRESUMO
Alcohol use is associated with increased risk of developing tuberculosis (TB) disease, yet the impact of alcohol use on TB treatment outcomes has not been summarized. We aimed to quantitatively review evidence of the relationship between alcohol use and poor TB treatment outcomes. We conducted a systematic review of PubMed, EMBASE, and Web of Science (January 1980-May 2018). We categorized studies as having a high- or low-quality alcohol use definition and examined poor treatment outcomes individually and as two aggregated definitions (i.e., including or excluding loss to follow-up [LTFU]). We analyzed drug-susceptible (DS-) and multidrug-resistant (MDR-) TB studies separately. Our systematic review yielded 111 studies reporting alcohol use as a predictor of DS- and MDR-TB treatment outcomes. Alcohol use was associated with increased odds of poor treatment outcomes (i.e., death, treatment failure, and LTFU) in DS (OR 1.99, 95% CI 1.57-2.51) and MDR-TB studies (OR 2.00, 95% CI 1.73-2.32). This association persisted for aggregated poor treatment outcomes excluding LTFU, each individual poor outcome, and across sub-group and sensitivity analyses. Only 19% of studies used high-quality alcohol definitions. Alcohol use significantly increased the risk of poor treatment outcomes in both DS- and MDR-TB patients. This study highlights the need for improved assessment of alcohol use in TB outcomes research and potentially modified treatment guidelines for TB patients who consume alcohol.
Assuntos
Antituberculosos , Tuberculose Resistente a Múltiplos Medicamentos , Consumo de Bebidas Alcoólicas/efeitos adversos , Consumo de Bebidas Alcoólicas/epidemiologia , Antituberculosos/efeitos adversos , Humanos , Falha de Tratamento , Resultado do Tratamento , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológicoRESUMO
SETTING: Xpert® MTB/RIF is the first-line diagnostic test for Mycobacterium tuberculosis and rifampicin (RIF) resistance in South Africa. OBJECTIVE: To describe the rates of Xpert RIF resistance not confirmed on follow-up testing, as well as the patient and test characteristics associated with discordant results. DESIGN: Retrospective review of patients with isolates showing Xpert RIF resistance. Line-probe assay, phenotypic drug susceptibility testing or repeat Xpert were all considered confirmatory tests of RIF resistance. 'Discordance' was defined as a patient with RIF resistance identified on initial Xpert testing, with a subsequent confirmatory test indicating RIF susceptibility. Associations were analysed using Pearson χ² difference of proportions and modified Poisson regression. RESULTS: RIF discordance occurred in 22/263 subjects and was associated with Xpert probe B, probe binding delay, as opposed to probe dropout, and probe binding delays (ΔCt) of between 4 and 4.9. CONCLUSION: Discordant RIF resistance was common in our cohort and was associated with Xpert probe delay and use of probe B.
Assuntos
Antibióticos Antituberculose/farmacologia , Mycobacterium tuberculosis/efeitos dos fármacos , Rifampina/farmacologia , Tuberculose/epidemiologia , Adulto , Feminino , Humanos , Masculino , Testes de Sensibilidade Microbiana , Mycobacterium tuberculosis/isolamento & purificação , Técnicas de Amplificação de Ácido Nucleico/métodos , Estudos Retrospectivos , África do Sul , Tuberculose/tratamento farmacológico , Tuberculose/microbiologia , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Tuberculose Resistente a Múltiplos Medicamentos/microbiologiaRESUMO
SETTING: Tuberculosis (TB) diagnosis and treatment requires patients to have multiple encounters with health care systems and the different stakeholders who play a role in curing them to coordinate their efforts. To optimize this process, high-quality, readily available data are required. Data systems to facilitate these linkages are a neglected priority which, if weak, fundamentally undermine TB control interventions. OBJECTIVE: To describe lessons learnt from the use of programmatic data for TB patient care and research. DESIGN: We did a survey of researcher and clinical provider experiences with information systems and developed a tiered approach to addressing frequently reported barriers to high-quality care. RESULTS: Unreliable linkages, incomplete data, lack of a reliable unique patient identifier, and lack of data management expertise were the most important data-related barriers to high-quality patient care and research. We propose the creation of health service delivery environments that facilitate, prioritize, and evaluate high-quality data entry during patient or specimen registration. CONCLUSION: An integrated approach, focused on high-quality data, and centered on unique patient identification will form the foundation for linkages across health systems that reduce patient management errors, bolster surveillance, and enhance the quality of research based on programmatic data.
RESUMO
SETTING: Ethiopia has a high prevalence of tuberculosis (TB) and is one of the countries with the highest burden of multidrug-resistant TB (MDR-TB). OBJECTIVE: To understand the costs that patients incur in obtaining diagnosis and treatment for MDR-TB. DESIGN: In March 2013, interviews were conducted with 169 MDR-TB patients at three hospitals in Ethiopia to identify the cost to patients and the impact on employment and family income. RESULTS: The average MDR-TB patient incurred a total cost of US$1378, which represented 25 months of a mid-treatment household income of US$54. The impact on the patient's employment and on overall patient and family income was generally catastrophic: 74% of all respondents reported losing their jobs, 66% of patients lost household income, and household income was reduced by 38%. To help cover the costs, 38% of patients sold some type of property, while 7% leased out property and 41% took out loans, any of which could jeopardize their future financial situation even further. CONCLUSION: Despite services being officially free of charge, most patients incurred catastrophic costs and suffered significant income loss as a result of obtaining diagnosis and treatment for MDR-TB.
Assuntos
Efeitos Psicossociais da Doença , Custos de Cuidados de Saúde/estatística & dados numéricos , Renda/estatística & dados numéricos , Tuberculose Resistente a Múltiplos Medicamentos/economia , Adolescente , Adulto , Países em Desenvolvimento , Emprego/estatística & dados numéricos , Etiópia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Tuberculose Resistente a Múltiplos Medicamentos/terapia , Adulto JovemRESUMO
Fluoroquinolone (FQ) drug susceptibility testing (DST) is an important step in the design of effective treatment regimens for multidrug-resistant tuberculosis. Here we compare ciprofloxacin, ofloxacin and moxifloxacin (MFX) resistance results from 226 multidrug-resistant samples. The low level of concordance observed suggests that DST should be performed for the specific FQ planned for clinical use. The results also support the new World Health Organization recommendation for testing MFX at a critical concentration of 2.0 µg/ml.
Assuntos
Fluoroquinolonas/farmacologia , Mycobacterium tuberculosis/efeitos dos fármacos , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Ciprofloxacina/farmacologia , Relação Dose-Resposta a Droga , Humanos , Testes de Sensibilidade Microbiana , Moxifloxacina , Ofloxacino/farmacologia , Resultado do TratamentoRESUMO
BACKGROUND: Attention has recently been focused on central nervous system neuropeptides as potential mediators of the symptom profile of obsessive-compulsive disorder (OCD). Increased CSF levels of the anxiolytic neuropeptide oxytocin have been reported in OCD. CSF levels of NPY, another anxiolytic neuropeptide, have not been studied. METHODS: We measured CSF oxytocin and NPY in 14 OCD patients and 26 healthy normal volunteers. RESULTS: There were no significant differences between the OCD patients and control subjects in CSF oxytocin or NPY levels. In both the OCD and control groups, women had significantly higher CSF oxytocin levels than men. CONCLUSIONS: These results do not support a prior finding of elevated CSF oxytocin in OCD patients and do not provide any evidence for an abnormality of NPY regulation in OCD.
Assuntos
Neuropeptídeo Y/líquido cefalorraquidiano , Transtorno Obsessivo-Compulsivo/líquido cefalorraquidiano , Ocitocina/líquido cefalorraquidiano , Adulto , Estudos de Casos e Controles , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Fatores SexuaisRESUMO
BACKGROUND: Several lines of evidence suggest that gonadal steroid hormones play a role in the onset and exacerbation of obsessive-compulsive disorder (OCD). In this study, we examined the effects of treatment with flutamide, a synthetic, nonsteroidal, competitive antagonist of the androgen receptor, on OCD symptoms. METHOD: Eight outpatients meeting DSM-III-R criteria for OCD participated in an 8-week open trial of flutamide. The dose was increased from 250 mg/day to 750 mg/day over the first 4 weeks and maintained at 750 mg/day for the final 4 weeks. The primary outcome measures for OCD symptoms were the Yale-Brown Obsessive Compulsive Scale and the Maudsley Inventory and for anxiety symptoms, the Beck Anxiety Inventory and the Hamilton Rating Scale for Anxiety. Subjects also provided self-ratings of aggression and sexual interest and activity. RESULTS: There were no reductions in measures of obsession and compulsions or measures of anxiety over the 8-week trial. However, self-ratings of feelings of aggression did fall significantly over the 8-week trial (p < .001). CONCLUSION: The lack of response to treatment with flutamide, an androgen receptor antagonist, suggests that any effects of gonadal steroids to exacerbate OCD symptoms are more likely to be mediated through estrogen receptors or through mechanisms that do not involve classical intracellular androgen receptors. Future treatment trials should examine agents that antagonize estrogen receptors or otherwise inhibit estrogen activity.
Assuntos
Antagonistas de Androgênios/uso terapêutico , Flutamida/uso terapêutico , Transtorno Obsessivo-Compulsivo/tratamento farmacológico , Adulto , Agressão/efeitos dos fármacos , Assistência Ambulatorial , Antagonistas de Receptores de Andrógenos , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Transtorno Obsessivo-Compulsivo/psicologia , Inventário de Personalidade , Escalas de Graduação Psiquiátrica , Inibidores Seletivos de Recaptação de Serotonina/uso terapêutico , Índice de Gravidade de Doença , Resultado do TratamentoRESUMO
SETTING: Brewelskloof Hospital, Western Cape, South Africa. OBJECTIVES: To verify the perceived increase in rifampicin monoresistant tuberculosis (RMR-TB) in the Cape Winelands-Overberg region and to identify potential risk factors. DESIGN: A retrospective descriptive study of trends in RMR-TB over a 5-year period (2004-2008), followed by a case-control study of RMR and isoniazid (INH) monoresistant TB cases, diagnosed from April 2007 to March 2009, to assess for risk factors. RESULTS: The total number of RMR-TB cases more than tripled, from 31 in 2004 to 98 in 2008. The calculated doubling time was 1.63 years (95%CI 1.18-2.66). For the assessment of risk factors, 95 RMR-TB cases were objectively verified on genotypic and phenotypic analysis. Of 108 specimens genotypically identified as RMR cases, 13 (12%) were misidentified, multidrug-resistant TB. On multivariate analysis, previous use of antiretroviral therapy (OR 6.4, 95%CI 1.3-31.8), alcohol use (OR 4.8, 95%CI 2.0-11.3) and age ≥ 40 years (OR 5.8, 95%CI 2.4-13.6) were significantly associated with RMR-TB. CONCLUSION: RMR-TB is rapidly increasing in the study setting, particularly among patients with advanced human immunodeficiency virus (HIV) disease. Routine drug susceptibility testing should be considered in all TB-HIV co-infected patients, and absence of INH resistance should be confirmed phenotypically if genotypic RMR-TB is detected.