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INTRODUCTION: The study of Candida glabrata genes associated with fluconazole resistance, from a molecular perspective, increases the understanding of the phenomenon with a view to its clinical applicability. OBJECTIVE: We sought to establish the predictive molecular profile of fluconazole resistance in Candida glabrata by analyzing the ERG11, ERG3, CgCDR1, and CgSNQ2 genes. METHOD: Expression was quantified using RT-qPCR. Metrics were obtained through molecular docking and Fisher discriminant functions. Additionally, a predictive classification was made against the susceptibility of C. glabrata to fluconazole. RESULTS: The relative expression of the ERG3, CgCDR1, and CgSNQ2 genes was higher in the fluconazole-resistant strains than in the fluconazole-susceptible, dose-dependent strains. The gene with the highest relative expression in the fluconazole-exposed strains was CgCDR1, and in both the resistant and susceptible, dose-dependent strains exposed to fluconazole, this was also the case. The molecular docking model generated a median number of contacts between fluconazole and ERG11 that was lower than the median number of contacts between fluconazole and ERG3, -CgCDR1, and -CgSNQ2. The predicted classification through the multivariate model for fluconazole susceptibility achieved an accuracy of 73.5%. CONCLUSION: The resistant strains had significant expression levels of genes encoding efflux pumps and the ERG3 gene. Molecular analysis makes the identification of a low affinity between fluconazole and its pharmacological target possible, which may explain the lower intrinsic susceptibility of the fungus to fluconazole.
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ABSTRACT Purpose: This study aimed to evaluate the pre-sence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in the ocular surface of individuals clinically suspected of coronavirus disease 2019 (COVID-19) and determine the accuracy of different approaches of molecular testing on the ocular surface based on the nasopharyngeal positivity status for COVID-19. Methods: A total of 152 individuals with suspected COVID-19 symptoms who simultaneously underwent nasopharyngeal and two different tear film collection techniques for quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) were included. Tears were collected and randomized: one eye had the filter strip for the Schirmer test and the contralateral eye had conjunctival swab/cytology in the inferior fornix. All patients underwent slit lamp biomicroscopy. The accuracy of various ocular surface collection techniques used for the detection of SARS-CoV-2 RNA was determined. Results: Of the 152 patients enrolled in the study, 86 (56.6%) had COVID-19 confirmed by nasopharyngeal PCR. Both tear film collection techniques detected viral particles: the Schirmer test was positive in 16.3% (14/86) and the conjunctival swab/cytology in 17.4% (15/86), with no statistically significant differences. No positive ocular tests were found among those with negative nasopharyngeal PCR tests. The overall agreement of the ocular tests was 92.7%, and in combination, the sensitivity would increase to 23.2%. The mean cycle threshold values in the nasopharyngeal, Schirmer, and conjunctival swab/cytology tests were 18.2 ± 5.3, 35.6 ± 1.4, and 36.4 ± 3.9, respectively. Compared with the nasopharyngeal test, the Schirmer (p=0.001) and conjunctival swab/cytology (p<0.001) tests had significantly different Ct values. Conclusion: The Schirmer (16.3%) and conjunctival swab (17.4%) tests were comparably capable of detecting SARS-CoV-2 RNA in the ocular surface by RT-PCR accurately based on nasopharyngeal status and demonstrated indistinct sensitivity and specificity. Simultaneous specimen sampling and processing from the nasopharyngeal, Schirmer, and conjunctival swab/cytology tests demonstrated significantly lower viral load in both ocular surface approaches than in the nasopharyngeal test. Ocular manifestations detected by slit lamp biomicroscopy were not associated with ocular RT-PCR positivity.
RESUMO Objetivo: Avaliar a presença de RNA de coronavírus 2 causador de síndrome respiratória aguda grave (SARS-CoV-2) na superfície ocular de indivíduos clinicamente suspeitos com COVID-19 e determinar a precisão de diferentes abordagens de testes moleculares na superfície ocular com base no status de positividade do RT-qPCR de nasofaringe para COVID-19. Métodos: 152 indivíduos com sintomas suspeitos para a COVID-19 foram submetidos a coleta de reação em cadeia da polimerase de nasofaringe simultaneamente a duas técnicas diferentes de coleta de filme lacrimal para RT-qPCR: aleatoriamente, um olho com a tira filtro do teste de Schirmer e, o olho contralateral, com citologia (swab) conjuntival no fórnice inferior. Todos os indivíduos foram submetidos à biomicroscopia com lâmpada de fenda. Resultados: Dos 152 pacientes, 86 (56,6%) tiveram a COVID-19 confirmada por PCR de nasofaringe. Ambas as técnicas de coleta detectaram partículas virais: o teste de Schirmer foi positivo em 16,3% (14/86) e a citologia conjuntival em 17,4% (15/86), sem diferenças estatisticamente significativas. Não houve testes oculares positivos entre aqueles com reação em cadeia da polimerase de nasofaringe negativo. A concordância geral dos testes oculares foi de 92,7% e, em combinação, a sensibilidade aumentaria para 23,2%. Os valores médios do limiar de ciclo nos testes de nasofaringe, Schirmer e citologia conjuntival foram 18,2 ± 5,3, 35,6 ± 1,4 e 36,4 ± 3,9, respectivamente. Conclusão: Os testes de Schirmer (16,3%) e swab conjuntival (17,4%) foram igualmente capazes de detectar RNA de SARS-CoV-2 na superfície ocular por RT-PCR e demonstraram sensibilidade e especificidade indistintas. A coleta simultânea de amostras ao processamento dos testes de RT-PCR de nasofaringe, Schirmer e citologia (swab) conjuntival demonstraram carga viral significativamente menor em ambas as abordagens da superfície ocular em comparação com o teste de nasofaringe. As manifestações oculares detectadas pela biomicroscopia com lâmpada de fenda não foram claramente associadas à positividade do RT-PCR ocular.
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Introduction. Brazil was one of the most affected countries by the COVID-19 pandemic. Instituto Adolfo Lutz (IAL) is the reference laboratory for COVID-19 in São Paulo, the most populous state in Brazil. In April 2020, a secondary diagnostic pole named IAL-2 was created to enhance IAL's capacity for COVID-19 diagnosis.Hypothesis/Gap Statement. Public health laboratories must be prepared to rapidly respond to emerging epidemics or pandemics.Aim. To describe the design of IAL-2 and correlate the results of RT-qPCR tests for COVID-19 with secondary data on suspected cases of SARS-CoV-2 infection in the São Paulo state.Methodology. This is a retrospective study based on the analysis of secondary data from patients suspected of infection by SARS-CoV-2 whose clinical samples were submitted to real-time PCR after reverse transcription (RT-qPCR) at IAL-2, between 1 April 2020 and 8 March 2022. RT-qPCR Ct results of the different kits used were also analysed.Results. IAL-2 was implemented in April 2020, just over a month after the detection of the first COVID-19 case in Brazil. The laboratory performed 304,250 RT-qPCR tests during the study period, of which 98 319 (32.3â%) were positive, 205827 (67.7â%) negative, and 104 (0.03â%) inconclusive for SARS-CoV-2. RT-qPCR Ct values≤30 for E/N genes of SARS-CoV-2 were presented by 79.7â% of all the samples included in the study.Conclusion. IAL was able to rapidly implement a new laboratory structure to support the processing of an enormous number of samples for diagnosis of COVID-19, outlining strategies to carry out work with quality, using different RT-qPCR protocols.
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COVID-19 , Humanos , COVID-19/diagnóstico , SARS-CoV-2/genética , Teste para COVID-19 , Pandemias , Estudos Retrospectivos , Saúde Pública , Técnicas de Laboratório Clínico/métodos , Sensibilidade e Especificidade , Brasil/epidemiologia , RNA Viral/genéticaRESUMO
Introducción: La COVID-19 es una preocupación mundial, requiere enfoque integral para reducir la transmisión, comenzando por la detección de casos, atención hospitalaria y seguimiento posterior. Objetivo: Caracterizar a pacientes positivos persistentes a COVID-19 en cuanto a epidemiología, clínica y datos de laboratorio. Métodos: Se realizó un estudio descriptivo transversal en 16 pacientes positivos persistentes a SARS-CoV-2 diagnosticados por RCP-TR en hisopado nasofaríngeo, en el Hospital Comandante Manuel Fajardo Rivero de Santa Clara en el período de septiembre 2020 a noviembre 2020. Resultados: Predominó el sexo femenino en un 75 %, el grupo de edad más representativo fue de 40-59 años de edad (68,75 %), el 37,50 % de los casos fueron asintomáticos y el síntoma más frecuente fue la fiebre menor de siete días 31,25 %. Existió linfopenia en el hemograma inicial con media en 27,49, índice neutrófilo leucocitario por encima de tres en cuatro pacientes con una media inicial 3,42. Estadía hospitalaria de 20,75 días de promedio. La mitad no tenía historia de enfermedad conocida, la comorbilidad más frecuente fue la hipertensión arterial 43,75 %. El índice neutrófilo leucocitario por encima de tres en pacientes con comorbilidades, evolutivo para todos menor de tres. Conclusiones: Predominó el sexo femenino, el grupo de edad más representativo fue de 40-59 años, es frecuente que se presenten asintomáticos y la fiebre fue el síntoma más usual. Existió linfopenia en el hemograma inicial. La mitad de los contagiados sin comorbilidades. El índice neutrófilo leucocitario evolutivo fue menor de tres para todos los pacientes.
Introduction: COVID-19 is a global concern, it requires a comprehensive approach to reduce transmission, starting with case detection, hospital care and subsequent follow-up. Objective: To characterize persistent COVID-19 positive patients in terms of epidemiology, clinical and laboratory data. Methods: A cross-sectional descriptive study was carried out in 16 persistent SARS-CoV-2 positive patients diagnosed by RT-CPR in nasopharyngeal swab, at Comandante Manuel Fajardo Rivero Hospital of Santa Clara in the period from September 2020 to November 2020. Results: The female sex predominated in 75%, the most representative age group was 40-59 years of age (68.75%), 37.50% of the cases were asymptomatic and the most frequent symptom was fever less than seven days 31.25%. There was lymphopenia in the initial hemogram with an average of 27.49, and a leukocyte neutrophil index above three in 4 patients with an initial average of 3.42. Hospital stay of 20.75 days on average. Half had no history of known disease, the most frequent comorbidity was arterial hypertension 43.75 %. The neutrophil leukocyte index above 3 in patients with comorbidities, evolutionary for all pariente was less than 3. Conclusions: The female sex predominates, the most representative age group is 40-59 years, it is frequent that they present asymptomatic and fever is the most usual symptom. There is lymphopenia on the initial blood count. Half of those infected without comorbidities. The evolutionary leukocyte neutrophil index was less than 3 for all patients.
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ABSTRACT BACKGROUND: Hematological recurrence is the second most frequent cause of failure in the treatment of gastric cancer. The detection of circulating tumor markers in peripheral blood by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) method may be a useful tool to predict recurrence and determine the patient's prognosis. However, no consensus has been reached regarding the association between the tumor markers level in peripheral blood and its impact on patient survival. AIMS: To evaluate the expression of the circulating tumor markers CK20 and MUC1 in peripheral blood samples from patients with gastric cancer by qRT-PCR, and to verify the association of their expression levels with clinicopathological characteristics and survival. METHODS: A total of 31 patients with gastric adenocarcinoma were prospectively included in this study. CK20 and MUC1 expression levels were analyzed from peripheral blood by the qRT-PCR technique. RESULTS: There was no statistically significant (p>0.05) association between CK20 expression levels and clinical, pathological, and surgical features. Higher MUC1 expression levels were associated with female patients (p=0.01). There was a correlation between both gene levels (R=0.81, p<0.001), and CK20 level and tumor size (R=0.39, p=0.034). CONCLUSIONS: CK20 and MUC1 expression levels could be assessed by qRT-PCR from total peripheral blood samples of patients with gastric cancer. CK20 levels were correlated to MUC1 levels as well as to tumor size. There was no difference in disease-free survival and overall survival regarding both genetic markers expression in this series.
RESUMO RACIONAL: A recorrência hematológica é a segunda causa mais frequente de falha no tratamento do câncer gástrico. A detecção de marcadores tumorais circulantes no sangue periférico, pelo método de reação em cadeia da polimerase de transcrição reversa quantitativa (qRT-PCR) pode ser uma ferramenta útil para prever a recorrência e determinar o prognóstico do paciente. No entanto, ainda não foi alcançado consenso em relação à associação entre o nível de marcadores tumorais circulantes no sangue periférico e seu impacto na sobrevida do paciente. OBJETIVOS: Avaliar a expressão de CK20 e MUC1 em amostras de sangue periférico de pacientes com câncer gástrico por meio de qRT-PCR e verificar a associação dos níveis de expressão com características clinicopatológicas e sobrevida. MÉTODOS: Trinta e um pacientes com adenocarcinoma gástrico foram incluídos, prospectivamente. Os níveis de expressão de CK20 e MUC1 foram analisados a partir de sangue periférico por meio de qRT-PCR. RESULTADOS: Não houve associação estatisticamente significativa (p>0,05) entre os níveis de expressão de CK20 com características clínicas, patológicas e cirúrgicas. Níveis mais elevados de expressão de MUC1 estavam associados a pacientes do sexo feminino (p=0,01). Houve correlação entre os níveis de ambos os genes (R=0,81, p<0,001), nível de CK20 e tamanho do tumor (R=0,39, p=0,034). CONCLUSÕES: Os níveis de CK20 e MUC1 podem ser avaliados por qRT-PCR a partir de amostras de sangue periférico total de pacientes com câncer gástrico, os níveis de CK20 estavam correlacionados com os de MUC1, assim como tamanho do tumor. Não houve diferença de sobrevida global ou livre de doença em relação à expressão de ambos marcadores genéticos nesta série.
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ABSTRACT Cycle threshold (Ct) values in COVID-19 reverse-transcription polymerase chain reaction (RT-PCR) tests estimate the viral load in biological samples. Studies have investigated variables associated with SARS-CoV-2 viral load, aiming to identify factors associated with higher transmissibility. Using the results from tests performed between May/2020-July/2022 obtained from the database of a referent hospital in Sao Paulo, Brazil, we investigated associations between Ct values and patient's age, gender, sample collection setting and pandemic period according to the predominant SARS-CoV-2 variant locally. We also examined variations in Ct values, COVID-19 incidence, mortality, and vaccination coverage over time. The study sample included 42,741 tests. Gender was not significantly associated with Ct values. Age, sample collection setting and the pandemic period were significantly associated with Ct values even after adjustment to the multivariable model. Results showed lower Ct values in older groups, during the Gamma and Delta periods, and in samples collected in emergency units; and higher Ct values in children under 10 years old, home-based tests, during the Omicron period. We found evidence of a linear trend in the association between age and Ct values, with Ct values decreasing as age increases. We found no clear temporal associations between Ct values and local indicators of COVID-19 incidence, mortality, or vaccination between February/2020-November/2022. Our findings suggest that SARS-CoV-2 Ct values, a proxy for viral load and transmissibility, can be influenced by demographic and epidemiological variables.
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ABSTRACT This study proposes a strategy for large-scale testing among a large number of people for the early diagnosis of COVID-19 to elucidate the epidemiological situation. Pool testing involves the analysis of pooled samples. This study aimed to discuss a reverse transcription technique followed by quantitative real-time polymerase chain reaction using pool testing to detect SARS-CoV-2 in nasopharyngeal swab samples. The study proposes an innovative diagnostic strategy that contributes to resource optimization, cost reduction, and improved agility of feedback from results.
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Objective: To compare the isothermal molecular screening techniques CPA and RT-LAMP, against the gold standard test, reverse transcription quantitative polymerase chain reaction (RT-qPCR), and to determine its agreement. Materials and Methods: Paired comparative case-control study. For the evaluation of the CPA method, 70 cases and 130 controls were used, while for RT-LAMP, 30 cases and 70 controls were used. The sensitivity and specificity of both tests were calculated. Subsequently, the bias-corrected Kappa index was calculated by resampling. Results: Both techniques have adequate and equivalent values of sensitivity (RT-LAMP: 82.8%, CPA: 83%) and specificity (RT-LAMP and CPA: 91.5%), as well as a high concordance (88%), and Kappa-index (0.72). Conclusion: Both isothermal molecular screening techniques are suitable for SARS-CoV-2 screening, with a similar sensitivity and specificity.
Objetivo : Comparar las técnicas de cribado molecular isotérmico CPA y RT-LAMP, frente a la prueba de referencia, la reacción en cadena de la polimerasa cuantitativa de transcripción inversa (RT-qPCR), y determinar su concordancia. Materiales y métodos : Estudio comparativo de casos y controles emparejados. Para la evaluación del método CPA se utilizaron 70 casos y 130 controles, mientras que para la RT-LAMP se utilizaron 30 casos y 70 controles. Se calcularon la sensibilidad y la especificidad de ambas pruebas. Posteriormente, se calculó el índice Kappa corregido por sesgo mediante un nuevo muestreo. Resultados: Ambas técnicas presentan valores adecuados y equivalentes de sensibilidad (RT-LAMP: 82,8 %, CPA: 83 %) y especificidad (RT-LAMP y CPA: 91,5 %), así como una alta concordancia (88 %), y un índice Kappa (0,72). Conclusiones: Ambas técnicas de cribado molecular isotérmico son adecuadas para el cribado del SARS-CoV-2, con una sensibilidad y especificidad similares.
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Rabies is an encephalitis caused by rabies virus, whose transmission occurs upon contact with infected animals' saliva. The diagnosis is usually performed post-mortem through a direct fluorescent antibody test (DFAT). If the DFAT results are negative, they must be confirmed with an isolation test, usually the mouse inoculation test (MIT), which implies the suffering and death of the animals, high costs and most importantly, up to 28 days to confirm a negative result. Another issue related to rabies diagnosis is the sample collection and storage, which is critical for the rabies virus' RNA genome. Thus, this study aimed to evaluate (i) reverse transcriptase polymerase chain reaction (RT-PCR) and Rabies Tissue Culture Infection Tests (RTCIT) in comparison to DFAT and MIT and (ii) FTA® cards as an alternative sample collection and preservation method. Eighty animal samples were evaluated through DFAT, RTCIT and RT-PCR; MIT was performed only in DFAT-negative samples. FTA® cards were evaluated with a subset of 64 samples, with sufficient material for imprinting. Sensitivity, specificity, positive (PPV) and negative predictive values (NPV), agreement and Cohen's kappa were calculated for each test combination. RTCIT had higher sensitivity (92.5%) and RT-PCR had higher specificity (92.3%) compared to DFAT. The combination of tests enhanced sensitivity, NPV and Cohen's kappa (considering positive results by RTCIT or RT-PCR), and specificity and PPV (when both tests were concordant). The PCR based on FTA® cards as sample source was specific (84.6%-96.2%) but presented lower sensitivity (29.7%-73.0%), although it could detect as positive four DFAT-negative samples. RTCIT and RT-PCR may be used as confirmatory tests in DFAT-negative samples. Moreover, FTA® cards may be helpful for sample collection in field situations where a long time is needed until the sample undergoes laboratory testing.
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Vírus da Raiva , Raiva , Doenças dos Roedores , Animais , Camundongos , Raiva/diagnóstico , Raiva/veterinária , Reação em Cadeia da Polimerase/veterinária , Manejo de Espécimes/veterinária , RNA Viral/análise , Sensibilidade e Especificidade , Reação em Cadeia da Polimerase Via Transcriptase Reversa/veterináriaRESUMO
RESUMO Objetivo: O presente estudo avaliou a prevalência da elevação da troponina e sua capacidade de prever a mortalidade em 60 dias em pacientes com COVID-19 internados em unidade de terapia intensiva. Metódos: Um estudo longitudinal prospectivo e unicêntrico foi realizado em uma coorte de pacientes em terapia intensiva devido a diagnóstico de COVID-19 confirmado, usando teste de reação em cadeia da polimerase em tempo real de maio a dezembro de 2020. Uma curva Característica de Operação do Receptor foi construída para predizer o óbito de acordo com o nível de troponina, calculando a área sob a curva e seus intervalos de confiança. Um modelo de risco proporcional de Cox foi gerado para relatar as razões de risco com intervalo de confiança de 95% e o valor de p para sua associação com mortalidade em 60 dias. Resultados: Foram incluídos 296 pacientes com taxa de mortalidade em 60 dias de 51%. A troponina foi positiva em 39,9% (29,6% versus 49,7% em sobreviventes e não sobreviventes, respectivamente). Foi encontrada área sob a curva de 0,65 (IC95% 0,59 - 0,71) para prever a mortalidade. O modelo univariado de Cox demonstrou razão de risco de 1,94 (IC95% 1,41 - 2,67) e p < 0,001, mas essa relação não se manteve no modelo de análise multivariado, no qual a razão de risco foi de 1,387 (IC95% 0,21 - 1,56) e o valor de p foi de 0,12. Conclusão: A elevação da troponina é frequentemente encontrada em pacientes em terapia intensiva para COVID-19. Embora seus níveis sejam maiores em pacientes que vão a óbito, nenhuma relação foi encontrada em um modelo de análise multivariado, o que indica que a troponina não deve ser utilizada como único marcador prognóstico de mortalidade nessa população.
ABSTRACT Objective: The current study assessed the prevalence of troponin elevation and its capacity to predict 60day mortality in COVID-19 patients in intensive care. Methods: A longitudinal prospective single-center study was performed on a cohort of patients in intensive care due to a COVID-19 diagnosis confirmed using real-time test polymerase chain reaction from May to December 2020. A Receiver Operating Characteristic curve was constructed to predict death according to troponin level by calculating the area under the curve and its confidence intervals. A Cox proportional hazards model was generated to report the hazard ratios with confidence intervals of 95% and the p value for its association with 60day mortality. Results: A total of 296 patients were included with a 51% 60-day mortality rate. Troponin was positive in 39.9% (29.6% versus 49.7% in survivors and non-survivors, respectively). An area under the curve of 0.65 was found (95%CI: 0.59 - 0.71) to predict mortality. The Cox univariate model demonstrated a hazard ratio of 1.94 (95%CI: 1.41 - 2.67) and p < 0.001, but this relationship did not remain in the multivariate model, in which the hazard ratio was 1.387 (95%CI: 0.21 - 1.56) and the p value was 0.12. Conclusion: Troponin elevation is frequently found in patients in intensive care for COVID-19. Although its levels are higher in patients who die, no relationship was found in a multivariate model, which indicates that troponin should not be used as an only prognostic marker for mortality in this population.
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SUMMARY OBJECTIVE: This study aimed to evaluate the SARS-CoV-2 immunoglobulin G (IgG) levels after 6 months of polymerase chain reaction (PCR) negative but assumed to be COVID-19 positive cases to investigate the relationship between IgG levels and thoracic computed tomography (CT) findings. METHODS: This was a single-center study that included patients whose PCR test results were negative at least three times using nasopharyngeal swabs but had clinical findings of COVID-19 and thoracic CT findings compatible with viral pneumonia. Six months after discharge, the IgG antibodies were analyzed. The cutoff value for negative and positive serology was defined as <1.4 (index S/C) and ≥1.4 (index S/C), respectively. In addition, the patients were categorized according to their thoracic CT findings as high (typical) and low (atypical). Also, the patients were grouped into classes as <5% lung involvement versus ≥5% lung involvement. RESULTS: The patients' mean age was 49.78±12.96 years. PCR was negative, but patients with COVID-19 symptoms who had SARS-CoV-2 IgG positive were 81.9% (n=95). The antibody titer and lung involvement ≥5% were statistically significantly higher in SARS-CoV-2 IgG positive cases (p<0.001 and p=0.021). Age and chest CT findings were the risk factors for lung involvement (OR=1.08, p<0.001 and OR=2.19, p=0.010, respectively). CONCLUSION: This study is valuable because increasing severity (≥5%) of lung involvement appears to be associated with high and persistent IgG antibody titers. In probable cases of COVID-19, even if the PCR test is negative, high IgG titers 6 months after discharge can predict the rate of lung parenchymal involvement.
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ABSTRACT Objective To compare inter-rater reliability, diagnostic accuracy, and extension of pulmonary involvement in children with suspected COVID-19 submitted to supine or supine and lateral decubitus computed tomography imaging. Methods Retrospective study carried out between March 2020 and March 2021 with patients submitted to reverse transcription-polymerase chain reaction testing and chest computed tomography. Patients were divided into two groups: supine or supine and lateral decubitus imaging. Standardized reporting systems of computed tomographic findings in COVID-19 and chest computed tomography score were used. Results One hundred and seventeen patients were enrolled. Moderate to substantial inter-rater reliability was observed for standardized reporting systems (weighted kappa, 0.553-0.764; p<0.001). Inter-rater reliability for the chest computed tomography score was substantial (weighted kappa, 0.620-0.670; p<0.001). Standardized reporting systems failed to predict COVID-19 in children, regardless of additional lateral decubitus imaging (area under the receiver operating characteristic curve, 0.491-0.608). Chest computed tomography scores assigned to lateral decubitus images were significantly lower. Conclusion Additional lateral decubitus imaging does not improve the accuracy of standardized reporting systems of computed tomographic findings in COVID-19 but may provide a more accurate estimation of lung involvement in uncooperative patients.
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RESUMEN Objetivo Determinar la prevalencia de Chlamydia trachomatis (CT), virus herpes simple-2 (VHS-2) y N. gonorrhoeae (NG) y los factores de riesgo relacionados con la infección, en un grupo de estudiantes universitarios de la ciudad de Medellín. Metodología Se realizó un estudio descriptivo en un grupo de 323 estudiantes universitarios. A través de un formulario en línea, se realizó el reporte de los factores de riesgo y síntomas relacionados con infecciones de transmisión sexual (ITS) y luego se determinó la presencia de anticuerpos IgG y IgM para CT y VHS-2 y se realizó una prueba de PCR-RT para detectar NG y CT. Resultados La frecuencia de IgG para CT fue del 13% y la positividad para IgM fue del 11,9%. La frecuencia de IgG para VHS-2 fue del 11,8% y la frecuencia de CT y NG por la prueba PCR-RT fue del 1,5% y del 0%, respectivamente. Los factores de riesgo más frecuentes fueron: vida sexual activa en el 96,9%, uso algunas veces o nunca del condón en un 75,2%. Reportaron que tenían secreción genital el 13,6% de los estudiantes; úlceras, el 2,8%; verrugas, el 5,3%; ardor al orinar, el 15,5%; ampollas, el 4,6%, y diagnóstico previo de una ITS, el 18,9% de los estudiantes. Conclusión Se encontró CT y VHS-2 entre los jóvenes estudiados y además una alta frecuencia de factores de riesgo para la adquisición de ITS. Se recomienda mejorar las campañas de prevención y diagnóstico de las ITS en los jóvenes universitarios.
ABSTRACT Objective The aim of this study was to determine the prevalence of Chlamydia trachomatis (CT), Herpes Simple-2 virus (HSV-2) and N. gonorrhoeae (NG), and the risk factors related to the infection in a group of college students in the city of Medellín, Colombia. Methods A descriptive study was carried out in a group of 323 university students. Through an online form, the risk factors and symptoms related to sexually transmitted infection (STI) were reported, and then the presence of IgG and IgM antibodies for CT and HSV-2 was determined, and RT-PCR testing was performed to detect NG and CT. Results 13% was the IgG frequency for CT while 11.9% was for IgM. The frequency for IgG for VHS-2 was 11.8 while the frequencies determined by RT-PCR for CT and NG were 1.5% and 0.0% respectively. The risk factors most commonly associated were active sex life, 96.9%, and random use of condom, 75.2%. It was also found that 13.6% of the students had genital secretions, 2.8% had ulcers, 5.3% had genital warts, 4.6% had blisters, 15.5% had dysuria, and 18.9% had a previous STI diagnosis. Conclusions CT and HVS-2 were found among college students, besides a series of risk factors associated with STI. It is recomended to improve prevention and diagnosis campaigns among young college students.
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OBJECTIVES: The objective of this study was to evaluate the survival experience of suspicion COVID-19 hospitalized patients with pneumonia and negative baseline reverse-transcription quantitative polymerase chain reaction (RT-qPCR) test results. STUDY DESIGN: We conducted a nationwide retrospective cohort study in Mexico. METHODS: Adult pneumonia inpatients fulfilling suspected COVID-19 criteria, and hospital entry from March to August 2020, were enrolled. The Kaplan-Meier method was to use to compare survival estimates among patients with negative RT-qPCR nasopharyngeal or oropharyngeal swabs and those with a baseline positive test. RESULTS: Data from 64,624 individuals fulfilling suspected COVID-19 criteria were analyzed and 1.6% of them had negative RT-qPCR tests. The overall mortality rate was higher among laboratory-positive patients (48.5% vs. 34.2%, P < 0.001) and, at any given threshold, the survival estimates were higher among RT-qPCR-negative pneumonia inpatients. CONCLUSIONS: The pathogenic mechanism of COVID-19 remains poorly understood and suspected cases with pneumonia and negative laboratory results represent a major challenge for healthcare systems. Our findings suggest that RT-qPCR-negative inpatients may have an improved disease prognosis, but the in-hospital mortality was still high among them. However, further research is needed to clarify the clinical and epidemiological implications of our results.
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COVID-19/mortalidade , Pneumonia/mortalidade , SARS-CoV-2/isolamento & purificação , Adulto , Idoso , COVID-19/diagnóstico , Teste para COVID-19 , Feminino , Humanos , Pacientes Internados , Masculino , México/epidemiologia , Pessoa de Meia-Idade , Pneumonia/diagnóstico , Estudos Retrospectivos , Reação em Cadeia da Polimerase Via Transcriptase ReversaRESUMO
OBJECTIVE: To identify factors associated with the risk of death in adolescent and adult inpatients with laboratory-positive (reverse-transcription polymerase chain reaction) influenza in Mexico during consecutive influenza seasons (2018-2020). METHODS: A retrospective cohort study used national surveillance system data, enrolling 3.422 individuals. The association between various risk factors and 30-day in-hospital lethality were evaluated through risk ratios (RRs) and 95% confidence intervals (CIs). RESULTS: The lethality rate was 18.1%. Flu vaccination history (RR=0.56, 95% CI 0.42-0.78), early antiviral drug administration (≤2 days from symptom onset [reference ≥5 days], RR=0.68, 95% CI 0.58-0.81), and a history of asthma (RR=0.66, 95% CI 0.47-0.95) showed protective effects against influenza-attributable death. Mechanical ventilator support produced the highest increase in death risk (RR=3.31, 95% CI 2.89-3.79). Male sex, older age, AH1N1 subtype, and other chronic diseases were also associated with fatal in-hospital influenza-related outcomes. CONCLUSIONS: Our findings highlight the major relevance of promoting immunization in high-risk individuals, together with ensuring early and effective antiviral management in suspected influenza cases.
Assuntos
Influenza Humana , Adolescente , Adulto , Idoso , Hospitais , Humanos , Influenza Humana/epidemiologia , Laboratórios , Masculino , Estudos Retrospectivos , Fatores de RiscoRESUMO
BACKGROUND Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target genes by molecular methods has been chosen as the main approach to identify individuals with Coronavirus disease 2019 (COVID-19) infection. OBJECTIVES In this study, we developed an open-source RNA standard-based real-time quantitative RT-PCR (RT-qPCR) assay for quantitative diagnostics of SARS-CoV-2 from nasopharynx, oropharynx, saliva and plasma samples. METHODS AND FINDINGS We evaluated three SARS-CoV-2 target genes and selected the RNA-dependent RNA polymerase (RdRp) gene, given its better performance. To improve the efficiency of the assay, a primer gradient containing 25 primers forward and reverse concentration combinations was performed. The forward and reverse primer pairs with 400 nM and 500 nM concentrations, respectively, showed the highest sensitivity. The LOD95% was ~60 copies per reaction. From the four biological matrices tested, none of them interfered with the viral load measurement. Comparison with the AllplexTM 2019-nCoV assay (Seegene) demonstrated that our test presents 90% sensitivity and 100% specificity. MAIN CONCLUSIONS We developed an efficient molecular method able to measure absolute SARS-CoV-2 viral load with high replicability, sensitivity and specificity in different clinical samples.
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ABSTRACT Objective To evaluate the role of chest computed tomography in patients with COVID-19 who presented initial negative result in reverse transcriptase-polymerase chain reaction (RT-PCR). Methods A single-center, retrospective study that evaluated 39 patients with negative RT-PCR for COVID-19, who underwent chest computed tomography and had a final clinical or serological diagnosis of COVID-19. The visual tomographic classification was evaluated according to the Consensus of the Radiological Society of North America and software developed with artificial intelligence for automatic detection of findings and chance estimation of COVID-19. Results In the visual tomographic analysis, only one of them (3%) presented computed tomography classified as negative, 69% were classified as typical and 28% as indeterminate. In the evaluation using the software, only four (about 10%) had a probability of COVID-19 <25%. Conclusion Computed tomography can play an important role in management of suspected cases of COVID-19 with initial negative results in RT-PCR, especially considering those patients outside the ideal window for sample collection for RT-PCR.
RESUMO Objetivo Avaliar o papel da tomografia computadorizada de tórax em pacientes com COVID-19 que apresentaram reação em cadeia da polimerase via transcriptase reversa (RT-PCR) inicial falsamente negativa. Métodos Estudo retrospectivo de centro único que avaliou 39 pacientes com RT-PCR negativa para COVID-19, submetidos à tomografia computadorizada de tórax e que tiveram diagnóstico final clínico ou serológico de COVID-19. A classificação tomográfica visual foi avaliada de acordo com o Consenso da Radiological Society of North America e o software desenvolvido com inteligência artificial para detecção automática de achados e estimativa de probabilidade de COVID-19. Resultados Na análise tomográfica visual, somente um deles (3%) apresentou tomografia computadorizada classificada como tendo resultado negativo, 69% foram classificados como típicos e 28% como indeterminados. Na avaliação com uso de software, somente quatro (cerca de 10%) tiveram probabilidade de COVID-19 <25%. Conclusão A tomografia computadorizada pode desempenhar papel importante no manejo de casos suspeitos de COVID-19 com RT-PCR inicialmente negativa, principalmente levando-se em consideração os pacientes que estão fora da janela ideal para coleta de amostra para RT-PCR.
Assuntos
Humanos , COVID-19 , Inteligência Artificial , Tomografia Computadorizada por Raios X , Estudos Retrospectivos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , SARS-CoV-2 , PulmãoRESUMO
COVID-19 is the viral infection caused by SARS-CoV-2 declared by the World Health Organization (WHO) as a pandemic. Patients with cancer have a higher risk to acquire the infection and worse prognosis as they have to attend more medical visits in healthcare institutions, receive medical and surgical treatments, and be subjected to diagnostic studies such as PET/CT in nuclear medicine services where the infection may be an incidental finding. We present here F18-FDG PET/CT (Positron Emission Tomography and Computed Tomography with 2-deoxy-2-[fluorine-18]fluoro-D-glucose), images with findings of COVID-19 from patients with different oncological conditions but no respiratory symptoms.
La COVID-19 es la infección viral causada por el SARS-CoV-2 y declarada por la Organización Mundial de la Salud (OMS) como pandemia. Los pacientes con cáncer tienen un mayor riesgo de adquirir la infección y un peor pronóstico, ya que deben asistir a visitas médicas en diferentes centros hospitalarios, reciben tratamientos médicos y quirúrgicos y deben someterse a estudios diagnósticos como la PET/CT en servicios de medicina nuclear, lo que es ocasión para el hallazgo incidental de la infección. Se presentan las imágenes de tomografías computarizadas por emisión de positrones con 18-fluorodesoxiglucosa (F18) (Positron Emission Tomography and Computed Tomography with 2-deoxy-2-[fluorine-18]fluoro-D-glucose, PET/CT F18-FDG) en las que se evidenció la COVID-19 en pacientes con diversas enfermedades oncológicas, pero sin sintomatología respiratoria.
Assuntos
Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico por imagem , Achados Incidentais , Neoplasias/complicações , Pneumonia Viral/diagnóstico por imagem , Tomografia por Emissão de Pósitrons combinada à Tomografia Computadorizada , Adulto , Idoso , Doenças Assintomáticas , COVID-19 , Teste para COVID-19 , Carcinoma de Células em Anel de Sinete/complicações , Carcinoma de Células em Anel de Sinete/diagnóstico por imagem , Carcinoma de Células em Anel de Sinete/secundário , Técnicas de Laboratório Clínico , Infecções por Coronavirus/complicações , Infecções por Coronavirus/diagnóstico , Feminino , Radioisótopos de Flúor , Fluordesoxiglucose F18 , Humanos , Metástase Linfática/diagnóstico por imagem , Linfoma não Hodgkin/complicações , Linfoma não Hodgkin/diagnóstico por imagem , Masculino , Pessoa de Meia-Idade , Neoplasias/diagnóstico por imagem , Pandemias , Derrame Pleural/diagnóstico por imagem , Derrame Pleural/etiologia , Pneumonia Viral/complicações , Compostos Radiofarmacêuticos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , SARS-CoV-2 , Seminoma/complicações , Seminoma/diagnóstico por imagem , Seminoma/secundário , Neoplasias GástricasRESUMO
Introduction: The 2019 coronavirus pandemic (COVID-19) has caused around 25 million cases worldwide. Asymptomatic patients have been described as potential sources of transmission. However, there are difficulties to detect them and to establish their role in the dynamics of virus transmission, which hinders the implementation of prevention strategies. Objective: To describe the behavior of asymptomatic SARS-CoV-2 virus infection in a cohort of workers at the El Dorado "Luis Carlos Galán Sarmiento" International Airport in Bogotá, Colombia. Materials and methods: A prospective cohort of 212 workers from the El Dorado airport was designed. The follow-up began in June, 2020. A survey was used to characterize health and work conditions. Every 21 day, a nasopharyngeal swab was taken to identify the presence of SARS-CoV-2 using RT-PCR. We analyzed the behavior of the cycle threshold (ORF1ab and N genes) according to the day of follow-up. Results: In the first three follow-ups of the cohort, we found an incidence of SARS-CoV-2 infection of 16.51%. The proportion of positive contacts was 14.08%. The median threshold for cycle threshold was 33.53. Conclusion: We characterized the asymptomatic SARS-CoV-2 infection in a cohort of workers. The identification of asymptomatic infected persons continues to be a challenge for epidemiological surveillance systems.
Introducción. La pandemia de COVID-19 ha ocasionado cerca de 25 millones de casos en el mundo. Se ha descrito que los pacientes asintomáticos pueden ser fuentes de transmisión. Sin embargo, es difícil detectarlos y no es claro su papel en la dinámica de transmisión del virus, lo que obstaculiza la implementación de estrategias para la prevención. Objetivo. Describir el comportamiento de la infección asintomática por SARS-CoV-2 en una cohorte de trabajadores del Aeropuerto Internacional El Dorado "Luis Carlos Galán Sarmiento" de Bogotá, Colombia. Materiales y métodos. Se diseñó una cohorte prospectiva de trabajadores del Aeropuerto El Dorado. El seguimiento se inició en junio de 2020 con una encuesta a cada trabajador para caracterizar sus condiciones de salud y trabajo. Cada 21 días se tomó una muestra de hisopado nasofaríngeo para detectar la presencia del SARS-CoV-2 mediante reacción en cadena de la polimerasa con transcriptasa inversa (RT-PCR). Se analizó el comportamiento del umbral del ciclo (cycle threshold) de los genes ORF1ab y N según el día de seguimiento. Resultados. En los primeros tres seguimientos de la cohorte se encontró una incidencia de la infección por SARS-CoV-2 del 16,51 %. La proporción de contactos positivos fue del 14,08 %. La mediana del umbral del ciclo fue de 33,53. Conclusión. Se determinaron las características de la infección asintomática por el SARSCoV-2 en una cohorte de trabajadores. La detección de infectados asintomáticos sigue siendo un reto para los sistemas de vigilancia epidemiológica.
Assuntos
Aeroportos , Infecções Assintomáticas , Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Nasofaringe/virologia , Pandemias , Pneumonia Viral/diagnóstico , Adulto , Infecções Assintomáticas/epidemiologia , Betacoronavirus/genética , Betacoronavirus/fisiologia , COVID-19 , Teste para COVID-19 , Colômbia , Busca de Comunicante , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Proteínas do Nucleocapsídeo de Coronavírus , Feminino , Seguimentos , Humanos , Masculino , Pessoa de Meia-Idade , Proteínas do Nucleocapsídeo/genética , Fosfoproteínas , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Poliproteínas , Estudos Prospectivos , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , SARS-CoV-2 , Inquéritos e Questionários , Proteínas Virais/genética , Replicação Viral/genética , Local de TrabalhoRESUMO
PURPOSE: To investigate the diagnostic performance of an Artificial Intelligence (AI) system for detection of COVID-19 in chest radiographs (CXR), and compare results to those of physicians working alone, or with AI support. MATERIALS AND METHODS: An AI system was fine-tuned to discriminate confirmed COVID-19 pneumonia, from other viral and bacterial pneumonia and non-pneumonia patients and used to review 302 CXR images from adult patients retrospectively sourced from nine different databases. Fifty-four physicians blind to diagnosis, were invited to interpret images under identical conditions in a test set, and randomly assigned either to receive or not receive support from the AI system. Comparisons were then made between diagnostic performance of physicians working with and without AI support. AI system performance was evaluated using the area under the receiver operating characteristic (AUROC), and sensitivity and specificity of physician performance compared to that of the AI system. RESULTS: Discrimination by the AI system of COVID-19 pneumonia showed an AUROC curve of 0.96 in the validation and 0.83 in the external test set, respectively. The AI system outperformed physicians in the AUROC overall (70% increase in sensitivity and 1% increase in specificity, pâ¯<â¯0.0001). When working with AI support, physicians increased their diagnostic sensitivity from 47% to 61% (pâ¯<â¯0.001), although specificity decreased from 79% to 75% (pâ¯=â¯0.007). CONCLUSIONS: Our results suggest interpreting chest radiographs (CXR) supported by AI, increases physician diagnostic sensitivity for COVID-19 detection. This approach involving a human-machine partnership may help expedite triaging efforts and improve resource allocation in the current crisis.