Independent clinic-based evaluation of point-of-care testing for the screening of Chlamydia trachomatis, Neisseria gonorrhoea and Trichomonas vaginalis in women-at-risk in Australia, Guatemala, Morocco, and South Africa.

BACKGROUND: In 2018, the World Health Organization commenced a multi-country validation study of the Cepheid GeneXpert for a range of molecular-based point-of-care (POC) tests in primary care settings. One study arm focused on the evaluation of POC tests for screening 'women at risk' for chlamydia (CT), gonorrhoea (NG) and trichomonas (TV) in four countries - Australia, Guatemala, Morocco and South Africa. METHODS: Study participants completed a pre-test questionnaire which included demographics, clinical information and general questions on POC testing (POCT). Two vaginal swab samples (either self-collected or clinician collected) from each patient were tested on the GeneXpert at the POC and at a reference laboratory using quality-assured nucleic acid amplification tests (NAATs). RESULTS: One thousand three hundred and eighty-three women were enrolled: 58.6% from South Africa, 29.2% from Morocco, 6.2% from Guatemala, and 6.0% from Australia. 1296 samples for CT/NG and 1380 samples for TV were tested by the GeneXpert and the reference NAAT. The rate of unsuccessful tests on the GeneXpert was 1.9% for CT, 1.5% for NG and 0.96% for TV. The prevalence of CT, NG and TV was 31%, 13% and 23%, respectively. 1.5% of samples were positive for all three infections; 7.8% were positive for CT and NG; 2.4% were positive for NG and TV; and 7.3% were positive for CT and TV. Compared to reference NAATs, pooled estimates of sensitivity for the GeneXpert tests were 83.7% (95% confidence intervals 69.2-92.1) for CT, 90.5% (85.1-94.1) for NG and 64.7% (58.1-70.7) for TV (although estimates varied considerably between countries). Estimates for specificity were ≥96% for all three tests both within- and between-countries. Pooled positive and negative likelihood ratios were: 32.7 ([CI] 21.2-50.5) and 0.17 (0.08-0.33) for CT; 95.3 (36.9-245.7) and 0.10 (0.06-0.15) for NG; and 56.5 (31.6-101.1) and 0.35 (0.27-0.47) for TV. CONCLUSION: This multi-country evaluation is the first of its kind world-wide. Positive likelihood ratios, as well as specificity estimates, indicate the GeneXpert POC test results for CT, NG and TV were clinically acceptable for ruling in the presence of disease. However, negative likelihood ratios and variable sensitivity estimates from this study were poorer than expected for ruling out these infections, particularly for TV. TRIAL REGISTRATION: Ethics approval to conduct the ProSPeRo study was granted by the WHO Ethics Review Committee, as well as local ethics committees from all participating countries.

How has the municipal availability of the GeneXpert®MTB/RIF system affected the detection of drug-resistant tuberculosis in Brazil?

OBJECTIVE: To evaluate the association between the availability of GeneXpert®MTB/RIF in municipalities and the proportion of people who have access to this diagnostic technology for tuberculosis (TB), as well as the resistance detected by the surveillance system in Brazil. METHODS: We analysed 4998 Brazilian municipalities that reported 432,937 new TB cases between 2015 and 2020. We compared municipalities with and without the availability of GeneXpert®MTB/RIF regarding the effective access to GeneXpert®MTB/RIF diagnosis and the prevalence of detected resistance. RESULTS: Municipalities with at least one GeneXpert®MTB/RIF system had three times (95% CI 2.9-3.0) the access to diagnostic tests and 80.4% (95% CI 70.6%-90.2%) higher detection of resistance, compared with municipalities without this technology. We estimated that there have been 1890 cases of undetected resistance during this period in the country. CONCLUSIONS: The availability of GeneXpert®MTB/RIF system in the municipality increased the sensitivity of the surveillance for detecting TB resistance. PUBLIC HEALTH IMPLICATIONS: It is a priority to strengthen laboratory networks and narrow the gap in access to rapid diagnosis in remote areas to improve the detection and control of drug-resistant tuberculosis.

Parinaud syndrome due to cofirmed neurotuberculosis in a lupus eritematosis systemic patient.

INTRODUCTION: This article aims to describe a patient with Parinaud syndrome due to neurotuberculosis confirmed by cerebrospinal fluid analysis. CASE REPORT: Initially, patient sought medical care, performed a chest x-ray and later a chest CT scan, with a probable diagnosis of miliary tuberculosis. In addition, she presented binocular diplopia worse at right lateral gaze, paresis of vertical gaze, light near-dissociation and convergent retraction nystagmus and presence of mycobacterium tuberculosis on PCR Xpert MTB/RIF. The treatment of miliary tuberculosis was interrupted due to pharmacodermia, but after diagnosis of neurotuberculosis, it was restarted with isoniazid, pyrazinamide and ethambutol with partial visual symptoms improvement. DISCUSSION: This case demonstrates the importance of pursuing diagnosis through more accurate techniques, especially in a patient with previous treatment pharmacoderma, whose absence of proper diagnosis and treatment would be extremely deleterious.

Investigação da presença do bacilo Mycobacterium tuberculosis em amostras sugestivas de tuberculose oral / Investigation of the presence of Mycobacterium tuberculosis bacillus in samples suggestive of oral tuberculosis

A Tuberculose (TB) é um considerável problema de saúde pública mundial. Em 2021, de acordo com a Organização Mundial de Saúde (OMS) estimou-se que, no mundo, cerca de 10,6 milhões de pessoas desenvolveram TB e 1,4 milhão morreu devido à doença. Com isso, tornou-se a principal causa de morte por infecção em todo o mundo e uma das dez principais causas de morte em geral. A TB tem o pulmão como o principal sítio de acometimento, sendo denominada de TB Pulmonar (TBP). Porém pode ser diagnosticada em muitos órgãos do corpo de maneira Extrapulmonar (TBEP), sendo o linfonodo o local mais comum. Porém, o envolvimento pleural, neurológico, sinovial, pericárdico, abdominal, geniturinário e oral tem sido descrito, o que mostra a potencial capacidade de disseminação do Mycobacterium tuberculosis (MTB). A detecção do Bacilos Álcool-Ácido Resistentes (BAAR), geralmente ocorre pela observação das características microscópicas da morfologia dos tecidos, presença de granulomas com necrose caseosa, histiócitos epitelióides e células gigantes do tipo Langhans, associada à coloração para BAAR, pela técnica de Ziehl Neelsen (ZN). Ademais, investigação por imuno-histoquímica (IHQ), testes de amplificação de ácido nucleico pela Reação em Cadeia da Polimerase Hemianinhada (nested-PCR) e pelo sistema de detecção automatizado GeneXpert® MTB/RIF são métodos aplicados para o diagnóstico da infecção. Com isso, este estudo teve como objetivo investigar a presença do bacilo Mycobacterium tuberculosis em amostras orais em parafina que continham granulomas com necrose caseosa. Ao todo, como critério de inclusão, foram selecionadas biópsias que apresentaram granulomas com necrose caseosa, sugerindo o diagnóstico de TB. Foram excluídas aquelas que após a revisão das fichas e histológicas, não apresentavam os granulomas exibindo necrose caseosa e aquelas que foram de biópsias intraósseas. O M. tuberculosis foi procurado por meio da coloração de ZN, IHC, nested-PCR e ensaios GeneXpert® MTB/RIF. Foram então selecionadas nove amostras com granulomas com necrose caseosa. Houve predominância de indivíduos do sexo masculino (2,5:1), com idade média de 50 anos (±23,08; 19-89), sendo a língua o local anatômico mais afetado (n=4). O bacilo não foi identificado pela técnica de ZN em nenhuma amostra, e a coloração por IHC mostrou um padrão granular grosseiro, sugerindo M. tuberculosis, em três delas. Nested-PCR e os ensaios GeneXpert® MTB/RIF foram positivos em duas e três das amostras, respectivamente. Conclui-se que testes moleculares e IHC podem ser métodos auxiliares úteis para casos suspeitos de tuberculose.

Tuberculosis (TB) is a significant global public health issue. In 2021, according to the World Health Organization (WHO), it was estimated that approximately 10.6 million people developed TB worldwide, and 1.4 million died from the disease. Consequently, it became the leading cause of death due to infection worldwide and one of the top ten overall causes of death. TB primarily affects the lungs and is referred to as Pulmonary TB (PTB). However, it can be diagnosed in various organs of the body as Extrapulmonary TB (EPTB), with lymph nodes being the most common site of involvement. Moreover, pleural, neurological, synovial, pericardial, abdominal, genitourinary, and oral involvement have been described, demonstrating the potential for Mycobacterium tuberculosis (MTB) dissemination. The detection of Acid-Fast Bacilli (AFB) typically involves the observation of microscopic tissue characteristics, the presence of granulomas with caseous necrosis, epithelioid histiocytes, and Langhans giant cells, along with AFB staining using the Ziehl-Neelsen (ZN) technique. Furthermore, immunohistochemistry (IHC), nucleic acid amplification tests by Nested Polymerase Chain Reaction (nested-PCR), and the automated detection system GeneXpert® MTB/RIF are methods employed for diagnosing the infection. Therefore, the aim of this study was to investigate the presence of Mycobacterium tuberculosis in paraffin-embedded oral samples containing granulomas with caseous necrosis. Inclusion criteria were based on the selection of biopsies displaying granulomas with caseous necrosis, suggesting a diagnosis of TB. Biopsies without these features upon review of records and histological findings, as well as intraosseous biopsies, were excluded. M. tuberculosis was sought using ZN staining, IHC, nested-PCR, and GeneXpert® MTB/RIF assays. Nine samples with granulomas and caseous necrosis were selected. The majority of individuals were male (2.5:1 ratio), with an average age of 50 years (±23.08; range 19-89), and the tongue was the most affected anatomical site (n=4). AFB was not identified by the ZN technique in any of the samples, and IHC staining exhibited a coarse granular pattern, suggestive of M. tuberculosis, in three of them. Nested-PCR and GeneXpert® MTB/RIF assays yielded positive results in two and three of the samples, respectively. In conclusion, molecular tests and IHC can be valuable auxiliary methods for suspected cases of tuberculosis.

GeneXpert como método de diagnóstico de la tuberculosis en Santiago de Cuba / GeneXpert as diagnostic method of tuberculosis in Santiago de Cuba

Introducción: La tuberculosis es un problema de salud en el mundo, por lo que se necesitan métodos como el GeneXpert para realizar un diagnóstico rápido y seguro. Objetivo: Determinar la precisión del GeneXpert como método para el diagnóstico de la tuberculosis en Santiago de Cuba en relación con los estudios tradicionales. Métodos: Se efectuó un estudio descriptivo y transversal desde diciembre de 2018 hasta igual mes de 2019 de 31 pacientes a quienes se les realizaron los 3 métodos para el diagnóstico de la tuberculosis. Se utilizaron variables, tales como edad, sexo, muestras estudiadas, positividad de los métodos utilizados, así como concordancia entre el GeneXpert y el cultivo mediante el índice de Kappa. Resultados: En la serie predominaron los pacientes mayores de 50 años (48,4 %), el sexo masculino (66,7 %) y el esputo como muestra más representativa (80,6 %); asimismo, el cultivo resultó positivo en 32,3 % y el GeneXpert en 22,6 %. En tanto, se diagnosticó tuberculosis en 11 pacientes y el índice de Kappa fue de 0,58. Conclusiones: La determinación de GeneXpert en el diagnóstico de la tuberculosis es precisa, dada su sensibilidad y especificidad altas en relación con los estudios tradicionales de esputo y cultivo, lo cual se confirmó por la elevada concordancia del índice de Kappa.

Introduction: Tuberculosis is a health problem worldwide, reason why methods as the GeneXpert are needed to carry out a quick and safe diagnosis. Objective: To determine the accuracy of GeneXpert as a method for the diagnosis of tuberculosis in Santiago de Cuba in connection with the traditional studies. Methods: A descriptive and cross-sectional study was carried out from December, 2018 to the same month in 2019 of 31 patients to whom the 3 methods for the diagnosis of tuberculosis were carried out. Some variables were used, such as age, sex, studied samples, positivity of the used methods, as well as consistency between the GeneXpert and the culture by means of the Kappa index. Results: In the series there was a prevalence of the patients over 50 years (48.4 %), male sex (66.7 %) and sputum as more representative sample (80.6 %); also, the culture was positive in 32.3 % and GeneXpert in 22.6 %. As long as, tuberculosis was diagnosed in 11 patients and the Kappa index was 0.58. Conclusions: The determination of GeneXpert in the diagnosis of tuberculosis is necessary, given its high sensibility and specificity in connection with the traditional studies of sputum and culture, which was confirmed due to the high consistency of the Kappa index.

O impacto do GeneXpert® MTB/Rif na detecção da tuberculose e seu padrão espacial em Ribeirão Preto-SP / The impact of GeneXpert® MTB/Rif in the detection of tuberculosis and its spatial pattern in Ribeirão Preto-SP

INTRODUÇÃO: Em 2010 a OMS autorizou o uso do sistema GeneXpert® MTB/RIF para a realização do Teste Rápido Molecular para TB (TRM-TB). Objetivou-se-se analisar o impacto do GeneXpert® MTB/RIF na detecção da TB e da TB multidroga-resistente e seu padrão de distribuição espacial em Ribeirão Preto-SP. MÉTODOS: Estudo ecológico realizado em Ribeirão Preto-SP. A população do estudo foi composta de casos de TB notificados no Sistema de Controle de Pacientes com Tuberculose (TBWeb) no período de 2006 a 2017. A análise descritiva dos casos foi realizada por meio de estatística descritiva dos parâmetros quantitativos através do software IBM SPS Statistics versão 25. Para classificar a tendência temporal e observar o impacto da implementação do TRM-TB, foram utilizadas as metodologias Prais-Winsten e Série Temporal Interrompida (STI) através do software StataSE versão 14 e também a modelagem ARIMA com a finalidade de obter uma previsão da taxa de TB para os próximos anos através do software RStudio. Para identificar os padrões espaciais da doença no município foram empregadas as técnicas de estimador de densidade de Kernel, G e G* e varredura (puramente espacial, variação nas tendências temporais e espaço-temporal). RESULTADOS: A tendência temporal da TB apresentou decréscimo de 18,1%/ano e de 6,9%/ano para em crianças. O Distrito Norte apresentou decréscimo de 6,67%/ano e o distrito Leste crescimento de 17,5%/ano na incidência de TB. A TB resistente, após a implementação do TRM-TB, apresentou aumento de 0,6% por ano. Na maioria dos anos analisados, a cultura é solicitada para menos da metade dos casos de TB. Foi identificado um aumento no número de solicitações de TMR e estacionariedade nas solicitações de baciloscopia. A maior parte dos casos foi diagnóstica por meio de demanda ambulatorial. Com as análises espaciais utilizadas foi observado que os casos e os aglomerados não se formam de maneira aleatória no espaço, verificando-se que a TB é distribuída desigualmente no município. CONCLUSÃO: Apesar da TB resistente não ser um problema no cenário, o estudo evidenciou um crescimento na sua incidência, o que o coloca em estado de alerta. O uso da análise espacial possibilitou a identificação das áreas prioritárias, colocando-as em evidência para ações de vigilância em saúde. Ressalta-se a importância do uso de ferramentas de análise espacial na identificação de áreas que devem ser priorizadas para o controle da TB, sendo necessária maior atenção aos indivíduos que se enquadram no perfil indicado como "de risco" para a doença

INTRODUCTION: In 2010, the WHO authorized the use of the GeneXpert® MTB/RIF system to perform the Molecular Rapid Test for TB (TRM-TB). The objective was to analyze the impact of GeneXpert® MTB/RIF in the detection of TB and multidrug-resistant TB and its spatial distribution pattern in Ribeirão Preto-SP. METHODS: Ecological study carried out in Ribeirão Preto-SP. The study population consisted of TB cases reported in the Tuberculosis Patient Control System (TBWeb) from 2006 to 2017. Descriptive analysis of cases was performed using descriptive statistics of quantitative parameters through the IBM SPS Statistics software version 25. To classify the temporal trend and observe the impact of the TRM-TB implementation, the Prais-Winsten and Interrupted Time Series (STI) methodologies were used through the StataSE software version 14 and also the ARIMA modeling in order to obtain a prediction of the TB rate for the coming years through RStudio software. To identify the spatial patterns of the disease in the city, the techniques of Kernel density estimator, G and G* and scanning (purely spatial, variation in temporal and spatio-temporal trends) were used. RESULTS: The temporal trend of TB showed a decrease of 18.1%/year and of 6.9%/year for children. The Northern District showed a decrease of 6.67%/year and the East District a growth of 17.5%/year in the incidence of TB. Resistant TB, after the implementation of the TRM-TB, increased by 0.6% per year. In most of the years analyzed, culture is requested for less than half of TB cases. An increase in the number of RMT requests and stationarity in smear microscopy requests was identified. Most cases were diagnosed through outpatient demand. With the spatial analysis used, it was observed that cases and clusters do not form randomly in space, verifying that TB is unevenly distributed in the municipality. CONCLUSION: Although resistant TB is not a problem in the scenario, the study showed an increase in its incidence, which puts it on alert. The use of spatial analysis made it possible to identify priority areas, putting them in evidence for health surveillance actions. We emphasize the importance of using spatial analysis tools to identify areas that should be prioritized for TB control, requiring greater attention to individuals who fit the profile indicated as "at risk" for the disease

O impacto do GeneXpert® MTB/Rif na detecção da tuberculose e seu padrão espacial em Ribeirão Preto-SP / The impact of GeneXpert® MTB/Rif in the detection of tuberculosis and its spatial pattern in Ribeirão Preto-SP

INTRODUÇÃO: Em 2010 a OMS autorizou o uso do sistema GeneXpert® MTB/RIF para a realização do Teste Rápido Molecular para TB (TRM-TB). Objetivou-se-se analisar o impacto do GeneXpert® MTB/RIF na detecção da TB e da TB multidroga-resistente e seu padrão de distribuição espacial em Ribeirão Preto-SP. MÉTODOS: Estudo ecológico realizado em Ribeirão Preto-SP. A população do estudo foi composta de casos de TB notificados no Sistema de Controle de Pacientes com Tuberculose (TBWeb) no período de 2006 a 2017. A análise descritiva dos casos foi realizada por meio de estatística descritiva dos parâmetros quantitativos através do software IBM SPS Statistics versão 25. Para classificar a tendência temporal e observar o impacto da implementação do TRM-TB, foram utilizadas as metodologias Prais-Winsten e Série Temporal Interrompida (STI) através do software StataSE versão 14 e também a modelagem ARIMA com a finalidade de obter uma previsão da taxa de TB para os próximos anos através do software RStudio. Para identificar os padrões espaciais da doença no município foram empregadas as técnicas de estimador de densidade de Kernel, G e G* e varredura (puramente espacial, variação nas tendências temporais e espaço-temporal). RESULTADOS: A tendência temporal da TB apresentou decréscimo de 18,1%/ano e de 6,9%/ano para em crianças. O Distrito Norte apresentou decréscimo de 6,67%/ano e o distrito Leste crescimento de 17,5%/ano na incidência de TB. A TB resistente, após a implementação do TRM-TB, apresentou aumento de 0,6% por ano. Na maioria dos anos analisados, a cultura é solicitada para menos da metade dos casos de TB. Foi identificado um aumento no número de solicitações de TMR e estacionariedade nas solicitações de baciloscopia. A maior parte dos casos foi diagnóstica por meio de demanda ambulatorial. Com as análises espaciais utilizadas foi observado que os casos e os aglomerados não se formam de maneira aleatória no espaço, verificando-se que a TB é distribuída desigualmente no município. CONCLUSÃO: Apesar da TB resistente não ser um problema no cenário, o estudo evidenciou um crescimento na sua incidência, o que o coloca em estado de alerta. O uso da análise espacial possibilitou a identificação das áreas prioritárias, colocando-as em evidência para ações de vigilância em saúde. Ressalta-se a importância do uso de ferramentas de análise espacial na identificação de áreas que devem ser priorizadas para o controle da TB, sendo necessária maior atenção aos indivíduos que se enquadram no perfil indicado como "de risco" para a doença.

INTRODUCTION: In 2010, the WHO authorized the use of the GeneXpert® MTB/RIF system to perform the Molecular Rapid Test for TB (TRM-TB). The objective was to analyze the impact of GeneXpert® MTB/RIF in the detection of TB and multidrug-resistant TB and its spatial distribution pattern in Ribeirão Preto-SP. METHODS: Ecological study carried out in Ribeirão Preto-SP. The study population consisted of TB cases reported in the Tuberculosis Patient Control System (TBWeb) from 2006 to 2017. Descriptive analysis of cases was performed using descriptive statistics of quantitative parameters through the IBM SPS Statistics software version 25. To classify the temporal trend and observe the impact of the TRM-TB implementation, the Prais-Winsten and Interrupted Time Series (STI) methodologies were used through the StataSE software version 14 and also the ARIMA modeling in order to obtain a prediction of the TB rate for the coming years through RStudio software. To identify the spatial patterns of the disease in the city, the techniques of Kernel density estimator, G and G* and scanning (purely spatial, variation in temporal and spatio-temporal trends) were used. RESULTS: The temporal trend of TB showed a decrease of 18.1%/year and of 6.9%/year for children. The Northern District showed a decrease of 6.67%/year and the East District a growth of 17.5%/year in the incidence of TB. Resistant TB, after the implementation of the TRM-TB, increased by 0.6% per year. In most of the years analyzed, culture is requested for less than half of TB cases. An increase in the number of RMT requests and stationarity in smear microscopy requests was identified. Most cases were diagnosed through outpatient demand. With the spatial analysis used, it was observed that cases and clusters do not form randomly in space, verifying that TB is unevenly distributed in the municipality. CONCLUSION: Although resistant TB is not a problem in the scenario, the study showed an increase in its incidence, which puts it on alert. The use of spatial analysis made it possible to identify priority areas, putting them in evidence for health surveillance actions. We emphasize the importance of using spatial analysis tools to identify areas that should be prioritized for TB control, requiring greater attention to individuals who fit the profile indicated as "at risk" for the disease.

Validation of the GeneXpert Xpress SARS-CoV-2 PCR assay using saliva as biological specimen.

In the pandemic, rapid and accurate detection of SARS-CoV-2 is crucial in controlling the outbreak. Recent studies have shown a high detection rate using saliva/oral fluids as specimens for laboratory detection of the virus. We intended to evaluate the test performance of the Xpert Xpress SARS-CoV-2 cartridge assay in comparison to a conventional qRT-PCR testing, using saliva as biological specimen. Forty saliva samples from symptomatic participants were collected. Conventional qRT-PCR was performed for amplification of E and RdRp genes and the Xpert Xpress SARS-CoV-2 assay amplified E and N2 genes. In the conventional assay, the median cycle threshold value of the E gene was 34.9, and of the RdRp gene was 38.3. In the Xpert Xpress assay, the median cycle threshold value of the E gene was 29.7, and of the N2 gene was 31.6. These results can allow a broaden use of molecular tests for management of COVID-19 pandemic, especially in resources-limited settings.

Diagnosis of Tuberculosis Using Gastric Aspirates in Pediatric Patients in Haiti.

BACKGROUND: We aimed to determine whether the Xpert MTB/RIF (Xpert) assay is a useful adjunct to culture for the rapid diagnosis of tuberculosis (TB) using gastric lavage aspirates (GLAs) in children aged < 5 years. METHODS: We reviewed the yield from diagnostic modalities in children suspected of having TB followed at an infectious disease research and treatment center in Port-au-Prince, Haiti, from 2011 to 2016. RESULTS: In 187 children clinically diagnosed with TB, a microbiologic diagnosis could be established in 40 (21%). Cultures, Xpert, and smears were positive in 30 (19%), 28 (17%), and 3 (1.6%) children, respectively. Ten cases that would not have been diagnosed by culture alone were found by the use of the Xpert assay. Collecting 2 GLA samples optimized microbiologic yield. CONCLUSIONS: In GLAs, Xpert increased the yield of microbiologically documented cases by 33%. Additionally, the rapidity of diagnosis potentially makes Xpert a valuable adjunct in initiating treatment for TB in children. Smear microscopy has low sensitivity in GLA and did not add to the documented cases. Our findings also highlight the low rate of microbiologic confirmation of clinically diagnosed TB.

Validation of the GeneXpert Xpress SARS-CoV-2 PCR assay using saliva as biological specimen

ABSTRACT In the pandemic, rapid and accurate detection of SARS-CoV-2 is crucial in controlling the outbreak. Recent studies have shown a high detection rate using saliva/oral fluids as specimens for laboratory detection of the virus. We intended to evaluate the test performance of the Xpert Xpress SARS-CoV-2 cartridge assay in comparison to a conventional qRT-PCR testing, using saliva as biological specimen. Forty saliva samples from symptomatic participants were collected. Conventional qRT-PCR was performed for amplification of E and RdRp genes and the Xpert Xpress SARS-CoV-2 assay amplified E and N2 genes. In the conventional assay, the median cycle threshold value of the E gene was 34.9, and of the RdRp gene was 38.3. In the Xpert Xpress assay, the median cycle threshold value of the E gene was 29.7, and of the N2 gene was 31.6. These results can allow a broaden use of molecular tests for management of COVID-19 pandemic, especially in resources-limited settings.

Streptococcus agalactiae colonization and screening approach in high-risk pregnant women in southern Brazil.

INTRODUCTION: Considering that Group B Streptococcus (GBS) persists as an important cause of neonatal morbidity and mortality, the objective of this study was to evaluate the frequency of maternal colonization by GBS, comparing the culture by the Granada broth with the GeneXpert real-time PCR diagnostic methods and the impact of chemoprophylaxis in high-risk pregnant women. METHODOLOGY: A prospective cohort of 110 pregnant women hospitalized for gestational complications was formed and recruited following interview and collection of rectovaginal swabs. RESULTS: The frequency of maternal colonization was 28.2% and statistically associated with Capurro> 37 weeks (p = 0.030) and neonatal infection (p = 0.008). Chemoprophylaxis was offered to 80% of those colonized. Among the pregnant women treated, a fivefold reduction in the rate of prematurity and rate of neonatal infection was observed. The sensitivity was 76.6% and 86.6% in culture and PCR, respectively, with an optimal index of agreement between the methods (K = 0.877). Grenade culture was considered an easy and low-cost method, while GeneXpert presented higher cost and error rate of 10%. However, 23.3% of the pregnant women were diagnosed exclusively by GeneXpert and the results were obtained in two hours. CONCLUSIONS: This study showed a significant prevalence of maternal colonization for GBS and that both culture and molecular methods had peculiarities that allow different applicability, with the culture being feasible for antenatal screening and in the hospital for high-risk pregnant women with no sign of imminent delivery and GeneXpert being prioritized for situations of preterm birth.

GeneXpert® MTB/RIF assay with transbronchial lung cryobiopsy for Mycobacterium tuberculosis diagnosis.

BACKGROUND: Early tuberculosis (TB) diagnostic is one of the critical steps to TB control. GeneXpert MTB/RIF has been widely proven for a prompt TB diagnosis. The use of GeneXpert MTB/RIF assay with transbronchial lung cryobiopsy samples may increase diagnostic accuracy. We aim to assess the diagnostic of TB with GeneXpert MTB/RIF assay with transbronchial lung cryobiopsy. METHODS: Patients with suspected diagnosis of TB and negative smear microscopies, with TB culture and GeneXpert MTB/RIF assay with transbronchial lung cryobiopsy were included in this cross-sectional study. Participants were enrolled from 2016 to 2018 at National Institute of Respiratory Diseases, Mexico. RESULTS: We included 54 patients (77.8% males) aged 30 to 65 years. The sensitivity of the GeneXpert MTB/RIF assay with transbronchial lung cryobiopsy was 81.3% (95% CI, 62.1-100%), with a specificity of 100% (95% CI, 100-100%) and a negative predictive value of 92.7% (95% CI, 84.7-100%). Twenty-two patients of the total population have HIV, the sensitivity of the test in these patients was 87.5% (95% CI, 64.6-100%). Also, 28 patients with a peripheral localized lesion which had a solid pattern were identified (51.9%). The sensitivity in patients with peripheral localized lesions was 88.9% (68.4-100%). CONCLUSIONS: The GeneXpert MTB/RIF assay with transbronchial lung cryobiopsy test is as efficient as broncho alveolar lavage for TB diagnosis. Transbronchial lung cryobiopsy increases a major diagnostic opportunity when the nature of illness is malignant. Transbronchial lung cryobiopsy is efficient in HIV patients, especially in patients with peripheral localized lesion.

Comparison of GeneXpert MTB/RIF assay and LED-FM microscopy for the diagnosis of extra pulmonary tuberculosis in Khyber Pakhtunkhwa, Pakistan

GeneXpert is one of the recent technological instruments used to diagnose tuberculosis in a short span of time. In this study, the performance of GeneXpert MTB/RIF assay for the diagnosis of extrapulmonary tuberculosis (EPTB) was compared with light-emitting diode Fluorescent Microscopy (LED-FM) in Khyber Pakhtunkhwa, Pakistan. A total of 737 EPTB samples were collected from tuberculosis (TB) suspected patients. Out of these samples, male to female ratio was 53% (n = 390) to 47% (n = 347) respectively. The sensitivity and specificity was 73% and 100% for GeneXpert, while 40% and 100% for LED-FM microscopy. This shows that the sensitivity of GeneXpert is 4050%, higher than LED-FM microscopy. GeneXpert also detected low number of bacilli as compared to LED-FM microscopy.(AU)

Comparison of GeneXpert MTB/RIF assay and LED-FM microscopy for the diagnosis of extra pulmonary tuberculosis in Khyber Pakhtunkhwa, Pakistan

ABSTRACT GeneXpert is one of the recent technological instruments used to diagnose tuberculosis in a short span of time. In this study, the performance of GeneXpert MTB/RIF assay for the diagnosis of extrapulmonary tuberculosis (EPTB) was compared with light-emitting diode Fluorescent Microscopy (LED-FM) in Khyber Pakhtunkhwa, Pakistan. A total of 737 EPTB samples were collected from tuberculosis (TB) suspected patients. Out of these samples, male to female ratio was 53% (n = 390) to 47% (n = 347) respectively. The sensitivity and specificity was 73% and 100% for GeneXpert, while 40% and 100% for LED-FM microscopy. This shows that the sensitivity of GeneXpert is 40-50%, higher than LED-FM microscopy. GeneXpert also detected low number of bacilli as compared to LED-FM microscopy.

Comparison of GeneXpert MTB/RIF assay and LED-FM microscopy for the diagnosis of extra pulmonary tuberculosis in Khyber Pakhtunkhwa, Pakistan.

GeneXpert is one of the recent technological instruments used to diagnose tuberculosis in a short span of time. In this study, the performance of GeneXpert MTB/RIF assay for the diagnosis of extrapulmonary tuberculosis (EPTB) was compared with light-emitting diode Fluorescent Microscopy (LED-FM) in Khyber Pakhtunkhwa, Pakistan. A total of 737 EPTB samples were collected from tuberculosis (TB) suspected patients. Out of these samples, male to female ratio was 53% (n=390) to 47% (n=347) respectively. The sensitivity and specificity was 73% and 100% for GeneXpert, while 40% and 100% for LED-FM microscopy. This shows that the sensitivity of GeneXpert is 40-50%, higher than LED-FM microscopy. GeneXpert also detected low number of bacilli as compared to LED-FM microscopy.

Prevalencia y factores relacionados con la infección por Clostridium difficile en un centro hospitalario de alta complejidad en Cali (Colombia) / Prevalence and factors related to Clostridium difficile infection in a high complexity hospital in Cali, Colombia

Objetivos: Estimar la prevalencia y los factores relacionados con la infección por Clostridium difficile en un hospital de alta complejidad en Cali (Colombia). Métodos: Se realizó un estudio de casos y controles en pacientes que consultaron por diarrea o la desarrollaron durante la hospitalización y que tuvieron un resultado positivo en la prueba de PCR para Clostridium difficile. Durante el 2012 a 2014, se incluyeron 29 casos y 58 controles. Resultados: La prevalencia de Clostridium difficile hospitalaria en la institución fue de 10 por 10.000 pacientes hospitalizados; en 3 casos se identificó la cepa NAP1-027. Los factores relacionados a Clostridium difficile fueron la diabetes mellitus (OR = 7,4; IC 95%: 1,1-47,6; p = 0,035), la leucemia (OR: 4,1; IC 95%: 1,0-16,5; p =0,043) y el consumo de antibióticos por más de 7 días (OR = 7,0; IC 95%: 2,3-21,1; p = 0,001). Conclusión: Se confirmó la asociación entre el uso previo de antibióticos y la infección por Clostridium difficile, de acuerdo con lo reportado en la literatura mundial. Este estudio describe por primera vez en nuestro país la cepa hipervirulenta NAP1/O27 en pacientes hospitalizados.

Objectives: To estimate the prevalence and factors related to infection by Clostridium difficile in a high complexity hospital in Cali, Colombia. Methods: A case and control study was conducted in patients consulting for diarrhea or diarrhea developed during hospitalisation with a positive CRP test result for Clostridium difficile. During 2012-2014, 29 cases and 58 controls were included. Results: The prevalence of Clostridium difficile in the hospital was 10 per 10.000 hospitalised patients, in 3 cases the NAP1/O27 strain was identified. Factors associatedwith Clostridium difficile were diabetes mellitus (OR = 7.4, IC95%: 1.1-47.6, P=.035), leukaemia (OR: 4.1, IC95%: 1,0-16.5, P=.043) and consumption of antibiotics for more than 7 days (OR = 7.0, IC95%: 2,3-21.1, P=.001). Conclusions: This study confirmed the association of Clostridium difficile infection with the use of previous antibiotics, in accordance with that reported in literature. This study describes for the first time in our country the hypervirulent NAP1/O27 in hospitalised patients.

Tuberculose / Tuberculosis

O diagnóstico laboratorial da tuberculose é de fundamental importância para o correto tratamento e controle da disseminação da doença. Dentre os principais métodos diagnósticos, os testes baseados em biologia molecular vêm ocupando cada vez mais um papel de destaque; entretanto, ainda não substituem por completo os métodos tradicionais, como a cultura e a pesquisa direta. A dosagem da adenosina deaminase (ADA) tem utilidade no diagnóstico de doença extrapulmonar e o teste de liberação de interferon gama linfocitário (IGRA) é de utilidade no diagnóstico de tuberculose latente. A utilização conjunta dos diferentes métodos disponíveis tem trazido grandes vantagens clínicas

The laboratory diagnosis of tuberculosis is of fundamental importance for the correct treatment and control the spread of the disease. Among the main diagnostic methods, the tests based on molecular biology are occupying an increasingly prominent role, however, has not yet completely replace traditional methods such as culture and direct search. The determination of adenosine deaminase (ADA) has useful in diagnosis of extrapulmonary disease and the interferon gamma release assay (IGRA) is useful in the diagnosis of latent tuberculosis. The combination use of different methods available has brought great clinical advantages