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Abstract Newcastle disease (ND) is an infectious, highly contagious and lethal disease of avian species. It is considered that ducks are natural reservoir or carrier for Newcastle disease virus (NDV) and are resistant against different strains of NDV. Current study was designed to evaluate the pathogenesis of Newcastle disease in domestic ducks through histopathology, immunohistochemistry (IHC) and serum biochemical changes. For this purpose, eighty ducks were reared for 42 days and divided in two groups A and B. Ducks in group A were challenged with (NDV) at rate of 0.1 ml of ELD50 (virus titer 107.32/100µl) on second week of age, whereas Group B was control negative. Splenomegaly, atrophy of thymus and necrotic lesion in kidney were observed on 9th day of post infection. Hepatic degeneration and mononuclear cell infiltration were noticed in proventriculus and intestine in challenged ducks. Viral antigen detected in lungs, intestine, proventriculus and lymphoid organs of infected ducks through IHC. Albumin and total protein values were significantly low in infected groups A as compared to control group B. ALT, AST, and ALP values were significantly high in infected group A. On 5th and 7th day of post infection oropharyngeal swabs were negative for NDV and cloacal swabs were positive for NDV through Reverse transcriptase polymerase chain reaction. It is concluded that ducks are susceptible to NDV and virulent strain of NDV caused disease in ducks.
Resumo A doença de Newcastle (DN) é uma doença infecciosa, altamente contagiosa e letal de espécies aviárias. Considera-se que os patos são reservatórios ou portadores naturais do vírus da doença de Newcastle (VDN) e são resistentes a diferentes cepas de VDN. O presente estudo foi desenvolvido para avaliar a patogênese da DN em patos domésticos por meio de histopatologia, imuno-histoquímica (IHQ) e alterações bioquímicas séricas. Para este propósito, 80 patos foram criados por 42 dias e divididos em dois grupos A e B. Os patos do grupo A foram submetidos ao VDN a uma taxa de 0,1 ml de ELD50 (título viral de 107,32 / 100 µl) na segunda semana de idade, enquanto o Grupo B foi controle negativo. Esplenomegalia, atrofia do timo e lesão necrótica no rim foram observadas no 9º dia pós-infecção. Degeneração hepática e infiltração de células mononucleares foram observadas no proventrículo e intestino em patos infectados. Antígeno viral foi detectado em pulmões, intestino, proventrículo e órgãos linfoides de patos infectados por IHQ. Os valores de albumina e proteína total foram significativamente baixos no grupo A infectado em comparação com o grupo B. Os valores de ALT, AST e ALP foram significativamente altos no grupo A. No 5º e no 7º dia após a infecção, os esfregaços orofaríngeos foram negativos para VDN, enquanto os esfregaços cloacais foram positivos para VDN por meio da reação em cadeia da polimerase via transcriptase reversa. Conclui-se que os patos são suscetíveis ao VDN e à cepa virulenta de VDN que causou doenças em patos.
Subject(s)
Animals , Newcastle disease virus , Ducks , Newcastle Disease/diagnosisABSTRACT
ABSTRACT Background: Sporotrichosis, a cosmopolitan mycosis caused by dimorphic fungi of the Sporothrix complex, affects humans and animals. This study aimed to develop new molecular markers for Sporothrix genome detection in biological samples using PCR. Methods: A specific region of DNA sequences from the Sporothrix genus, publicly available in GenBank, was chosen for primer design. After testing the in silico specificity of these primers, in vitro specificity was evaluated using the PCR technique. Results: Three specific primers with 100% specificity for the Sporothrix genus were generated. Conclusions: PCR using the designed primers can be used to develop molecular diagnostics for sporotrichosis.
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ABSTRACT BACKGROUND: Occult hepatitis B virus infection (OBI) is defined as the presence of hepatitis B virus (HBV) deoxyribonucleic acid (DNA) in the liver of individuals with undetectable hepatitis B virus surface antigen (HBsAg) in the serum. The actual prevalence of OBI and its clinical relevance are not yet fully understood. OBJECTIVE: To evaluate the prevalence of HBV DNA in liver biopsies of HBsAg-negative patients with chronic liver disease of different etiologies in a referral center in Brazil and compare two different HBV DNA amplification protocols to detect HBV. DESIGN AND SETTING: This cross-sectional observational study was conducted at the Liver Outpatient Clinic, Hospital das Clínicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil, between January 2016 and December 2019. METHODS: HBV DNA was investigated in 104 liver biopsy samples from individuals with chronic liver disease of different etiologies, in whom HBsAg was undetectable in serum by nested-polymerase chain reaction (nested-PCR), using two different protocols. RESULTS: OBI, diagnosed by detecting HBV DNA using both protocols, was detected in 6.7% of the 104 individuals investigated. Both protocols showed a good reliability. CONCLUSION: In addition to the differences in the prevalence of HBV infection in different regions, variations in the polymerase chain reaction technique used for HBV DNA amplification may be responsible for the large variations in the prevalence of OBI identified in different studies. There is a need for better standardization of the diagnostic methods used to diagnose this entity.
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Acinetobacter baumannii is widely recognized in clinical environments due to its infectious capacity, antimicrobial adaptability, and lethality. Analyzing the prevalence of this agent in intra- and extra-hospital environments may reveal target indicators for appropriate management interventions. In this observational cross-sectional study, we evaluated the prevalence of A. baumannii within hospitals with intensive care units and in their external surroundings in a macro-health region of Brazil. Samples of Columba livia (pigeon) droppings from the external environment of four hospitals (n = 40), from floor surfaces (n = 20), and door handles (n = 20) of different hospital wards were collected based on random sampling, all of which were evaluated for the presence of A. baumannii using polymerase chain reactions (PCR). The sensitivity and specificity of the technique was verified after the collected samples were contaminated with clinical samples positive for A. baumannii. We detected a significantly higher A. baumannii prevalence (87.50%, CI = 71.29100.00) in samples collected within the hospital environment compared with those obtained from the external environment (12.50%, CI = 0.0028. 71) (p = 0.003). In addition, samples collected from floor surfaces contained bacterial densities (181.3 ± 11.58) that exceeded those in environmental (93.32 ± 1.56) and door handle (142.70 ± 17.14) samples by 94% and 78.71%, respectively. The findings of this study will enhance our understanding of the spatial distribution of A. baumannii and additionally, validate the efficiency of PCR for diagnosis of this infectious agent.
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Aim: To assess oral microbial status in patients with acute lymphoblastic leukemia (ALL) undergoing high-dose chemotherapy and to unravel possible associations between nosocomial pathogens and the establishment of chemotherapy-induced oral mucositis (CIOM). Methods: Oral mucosa, saliva, and peripheral blood samples were collected from 46 ALL subjects one day prior to chemotherapy (D0) and 2 weeks after treatment initiation (D14). Clinical intraoral inspection was performed by a single practitioner, with mucositis classification performed according to the WHO oral toxicity scale. Blood components were quantified by automatic flow cytometry, while oral Staphylococcus aureus and Pseudomonas aeruginosa were detected by Polymerase Chain Reaction with species-specific primers. Associations among bacteria and clinical findings were determined by Fisher's Exact test, longitudinal bacterial changes by paired Macnemar, and correlations among blood parameters and mucositis status or bacteria via Mann-Whitney. Results: S. aureus displayed higher detection rates at D14 (p < 0.05) and was positively associated with mucositis, adoption of a non-solid diet (all p < 0.001), nausea and fever (all p < 0.05). Conversely, P. aeruginosa did not correlate to CIOM clinical parameters. At the systemic standpoint, lower hemoglobin levels associated with CIOM and fever events (all p < 0.01). Conclusion: The study evidences S. aureus as a potential pathogen in ALL-CIOM, reaffirming microbial control as an important preventive measure during high-dose immunosuppressive therapy. The weight of non-white-blood-cell parameters should be validated as novel CIOM biomarkers in prospective research
Subject(s)
Humans , Male , Female , Middle Aged , Stomatitis , Bacteria , Polymerase Chain Reaction , Precursor Cell Lymphoblastic Leukemia-Lymphoma , Antineoplastic Agents , Drug TherapyABSTRACT
ObjectiveIn recent years， with the sharp decline of wild resources in Arisaematis Rhizoma and Pinelliae Rhizoma and the immaturity of medicinal cultivation technology， their adulterants have appeared frequently in the market， and the main identifying characteristics have mostly disappeared in the circulation of medicinal materials. Therefore， there is an urgent need to establish a molecular identification method that can quickly and effectively identify the specificity of Arisaematis Rhizoma and Pinelliae Rhizoma. MethodAfter comparison of the rbcL sequences of Arisaematis Rhizoma，Pinelliae Rhizoma， and their adulterants， the specific enzyme cleavage sites Hae Ⅲ and Dra Ⅰ of Arisaematis Rhizoma and Pinelliae Rhizoma， respectively， were selected and identified by polymerase chain reaction-restriction fragment length polymorphism（PCR-RFLP）. The main system conditions of PCR-RFLP reaction were established and optimized， and their durability and the ability to detect genuine， adulterants， and mixed counterfeits were investigated. ResultThe PCR-RFLP identification method of Arisaematis Rhizoma and Pinelliae Rhizoma was established. After specific primer amplification， Arisaematis Rhizoma and Pinelliae Rhizoma could be digested by Hae Ⅲ and Dra Ⅰ-restricted endonucleases respectively， at annealing temperature of 54 ℃， the number of cycles of 35， and the amount of DNA template of 3-30 ng， producing two fragments or small cut fragments with a single band between 100-250 bp， whereas the mixed counterfeits were not cleaved and both showed a band at 250 bp. The method is highly accurate in identifying adulterants and mixed counterfeits of Arisaematis Rhizoma or Pinelliae Rhizoma. ConclusionThe PCR-RFLP method developed in this study allows for the rapid identification of Arisaematis Rhizoma and Pinelliae Rhizoma.
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Abstract This study aimed to evaluate the association of the variables age, gender, arch position, tooth length, root canal amplitude, and periapical lesion size with the occurrence of postoperative signs and symptoms (pain, tenderness, and edema) and the use of postoperative analgesics following root canal treatment with foraminal enlargement in single-rooted teeth with apical periodontitis. This prospective longitudinal study included 105 patients requiring root canal treatment of maxillary or mandibular single-rooted teeth with periapical lesion. After root canal treatment in a single session, pain intensity and tenderness were recorded daily for 7 days and on days 14 and 30. Edema was evaluated by two independent evaluators within 48 h, 72 h, and 7 days after treatment. Ordinal and logistic regressions were performed (p < 0.05). Female gender (beta = 1.02; p < 0.01), mandibular teeth (beta = 25.50; p < 0.01), medium root canal amplitude (beta = 0.93; p = 0.03), and edema (beta = 1.88; p < 0.01) were associated with increased postoperative pain and tenderness, while the use of analgesics (beta = -1.82; p < 0.01) and time in days (beta = -0.23; p < 0.01) were associated with a decrease in these signs and symptoms. Edema was considered a risk factor for analgesic requirement (Odds Ratio [OR] = 61.46; p < 0.01). Factors such as gender, arch position, and root canal amplitude were associated with postoperative signs and symptoms. The use of analgesics was more required in edema and was associated with decreased pain.
Resumo Este estudo teve como objetivo avaliar a associação das variáveis idade, sexo, posição no arco, comprimento do dente, amplitude do canal radicular e tamanho da lesão periapical com a ocorrência de sinais e sintomas pós-operatórios (dor, dor ao toque e edema) e o uso de analgésicos após o tratamento endodôntico com alargamento foraminal em dentes uniradiculares com lesão periapical. Este estudo longitudinal prospectivo incluiu 105 pacientes que necessitavam de tratamento endodôntico em dentes uniradiculares superiores ou inferiores com lesão periapical. Após o tratamento do canal radicular em uma sessão, a intensidade da dor e a dor ao toque foram registradas diariamente por 7 dias e nos dias 14 e 30. O edema foi avaliado por dois avaliadores independentes dentro de 48 h, 72 h e 7 dias após o tratamento. Foram realizadas regressões ordinal e logística, e a significância estatística foi fixada em um valor de p < 0,05. Gênero feminino (beta = 1,02; p < 0.01), dentes inferiores (beta = 25,50; p < 0.01), amplitude média do canal radicular (beta = 0,93; p = 0,03) e edema (beta = 1,88; p < 0.01) foram associados ao aumento da dor e dor ao toque pós-operatória, enquanto o uso de analgésicos (beta = -1,82; p < 0.01) e o tempo em dias (beta = -0,23; p < 0.01) foram associados à diminuição desses sinais e sintomas. O edema foi considerado fator de risco para necessidade de analgésico (Odds Ratio [OR] = 61,46; p < 0.01). Fatores como sexo, posição do arco e amplitude do canal radicular foram associados aos sinais e sintomas pós-operatórios. O uso de analgésicos foi mais necessário no edema e foi associado à diminuição da dor.
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Objective: The study aimed to evaluate molecular and immunological methods and to propose a workflow using them for tuberculosis (TB) diagnosis routine. Methods: A cross-sectional retrospective study was performed, including 121 liquid cultures from a TB laboratory located in the extreme south of Brazil. All cultures were positive for Mycobacterium tuberculosis complex (MTBC) by in-house Polymerase Chain Reaction (PCR) using DNA extracted by the CTAB method (PCR-CTAB) for IS6110 detection. These cultures were subjected to faster tests than this one, the immunological MPT64 assay and the PCR using DNA extracted by thermal lysis method (PCR-TL), and these were evaluated for MTBC identification using PCR-CTAB as a reference method. Results: The sensitivity of MPT64 assay and PCR-TL to identify MTBC in positive cultures by PCR-CTAB were 73.6% (89/121) and 98.3% (119/121), respectively. We proposed a workflow based on the use of MPT64 assay in liquid cultures suggestive of MTBC, and in case of a negative result, we suggest the performance of PCR-TL. The PCR-CTAB is suggested only if faster tests are negative. Conclusions: Methods capable of confirming MTBC in cultures should continue to be standardized, tested, and optimized to meet the ideal requirements of simplicity, quickness, and effectiveness. The molecular and immunological methods evaluated have differences in the execution and detection of MTBC in cultures, but they are rapid tools for laboratory TB diagnosi
Objetivos: O estudo objetivou avaliar métodos molecular e imunológico e propor um fluxo de trabalho utilizando-os para a rotina de diagnóstico da tuberculose (TB). Métodos: Foi realizado um estudo transversal retrospectivo, incluindo 121 culturas líquidas de um laboratório de TB localizado no extremo sul do Brasil. Todas as culturas foram positivas para o complexo Mycobacterium tuberculosis (CMTB) por Reação em Cadeia da Polimerase (PCR) in-house para detecção do IS6110, usando DNA extraído pelo método CTAB (PCR-CTAB). Essas culturas foram submetidas a testes mais rápidos que este, o ensaio imunológico MPT64 e a PCR com DNA extraído pelo método de lise térmica (PCR-LT), e estas foram avaliadas para identificação de CMTB usando PCR-CTAB como método de referência. Resultados: A sensibilidade do ensaio MPT64 e da PCR-LT para identificar o CMTB em culturas positivas pela PCRCTAB foi de 73,6% (89/121) e 98,3% (119/121), respectivamente. Propusemos um fluxo de trabalho baseado no uso do ensaio MPT64 em culturas líquidas sugestivas de CMTB e, em caso de resultado negativo, sugerimos a realização de PCR-LT. Sugere-se a PCR-CTAB apenas se os testes mais rápidos forem negativos. Conclusões: Os métodos capazes de confirmar o CMTB em culturas devem continuar sendo padronizados, testados e otimizados para atender aos requisitos ideais de simplicidade, rapidez e eficácia. Os métodos molecular e imunológico avaliados apresentam diferenças na execução e detecção do CMTB em culturas, mas são ferramentas rápidas para o diagnóstico laboratorial da TB.
Subject(s)
Mycobacterium tuberculosis , Tuberculosis , DNA , Polymerase Chain Reaction , Diagnostic Tests, Routine , Cetrimonium , MycobacteriumABSTRACT
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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Abstract Periodontitis and arterial hypertension are two of the pathologies with the highest global prevalence; evidence reported so far has been favorable to an association between them. This cross-sectional study aimed to evaluate and compare the microbiological counts of hypertensive and normotensive patients with periodontitis. Sociodemographic, behavioral, systemic health data and periodontal clinical parameters were assessed. Counts of A. actinomycetemcomitans, P. intermedia, P. gingivalis and F. nucleatum were performed by real-time polymerase chain reaction using subgingival biofilm samples. Thirty-eight patients were included in this preliminary analysis, divided into two groups: Normotensive Group (NG) (n = 14) and Hypertensive Group (HG) (n = 24). Patients diagnosed with periodontitis composed both groups. Data analysis was performed with significance level of 5%. There was no significant difference between groups for clinical periodontitis diagnosis. In addition, hypertensive individuals had higher P. intermedia, P. gingivalis, and F. nucleatum counts when compared to normotensive individuals. The parameters probing pocket depth, bleeding on probing, and A. actinomycetemcomitans count did not presented statistical differences between groups. With these preliminary results, it can be concluded that the presence of arterial hypertension may be associated with a greater quantity of periodontopathogenic bacterial of some species in individuals with periodontitis.
Resumo A periodontite e a hipertensão arterial são duas das patologias com maior prevalência global, as evidências relatadas até o momento têm sido favoráveis a uma associação entre elas. Este estudo transversal teve como objetivo avaliar e comparar contagem microbiológicas de pacientes hipertensos e normotensos com periodontite. Dados sociodemográficos, comportamentais, de saúde sistêmica e parâmetros clínicos periodontais foram avaliados. Contagens de A. actinomycetemcomitans, P. intermedia, P. gingivalis e F. nucleatum foram realizadas por reação em cadeia da polimerase em tempo real utilizando amostras de biofilme subgengival. Trinta e oito pacientes foram incluídos nesta análise preliminar, divididos em dois grupos: Grupo Normotenso (GN) (n = 14) e Grupo Hipertenso (GH) (n = 24). Pacientes diagnosticados com periodontite compuseram os dois grupos. A análise dos dados foi realizada com nível de significância de 5%. Não houve diferença significativa entre os grupos para o diagnóstico clínico de periodontite. Além disso, os hipertensos apresentaram maior contagem de P. intermedia, P. gingivalis e F. nucleatum quando comparados aos normotensos. Os parâmetros profundidade de sondagem, sangramento à sondagem e contagem de A. actinomycetemcomitans não apresentaram diferenças estatísticas entre os grupos. Com esses resultados preliminares, pode-se concluir que a presença de hipertensão arterial pode estar associada a uma maior quantidade de bactérias periodontopatogênicas de algumas espécies em indivíduos com periodontite.
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ABSTRACT Background: Prognostic factors in previously healthy young patients with COVID-19 remained understudied. Objective: The objective of the study was to identify factors associated with in-hospital death or need for invasive mechanical ventilation (IMV) in young (aged ≤ 65 years) and previously healthy patients with COVID-19. Methods: We conducted a prospective cohort study that included patients admitted with COVID-19. The primary outcome was in-hospital death/need for IMV. Secondary outcomes included need for IMV during follow-up, days on IMV, length of stay (LOS), hospital-acquired pneumonia/ventilator-associated pneumonia (HAP/VAP), and pulmonary embolism (PE). Bivariate and multivariate analyses were performed. Results: Among 92 patients, primary outcome occurred in 16 (17%), death in 12 (13%), need for IMV in 16 (17%), HAP/VAP in 7 (8%), and PE in 2 (2%). Median LOS and IMV duration were 7 and 12 days, respectively. Independent associations were found between the primary outcome and male sex (Adjusted odds ratio [aOR] 7.1, 95%CI 1.1-46.0, p < 0.05), D-dimer levels > 1000ng/mL (aOR 9.0, 95%CI 1.6-49.1, p < 0.05), and RT-PCR Ct-value ≤ 24 on initial swab samples (aOR 14.3, 95%CI 2.0-101.5, p < 0.01). Conclusions: In young and non-comorbid COVID-19 patients, male sex, higher levels of D-dimer, and low SARS-CoV-2 RT-PCR Ct-value on an initial nasopharyngeal swab were independently associated with increased in-hospital mortality or need for IMV.
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ABSTRACT Introduction: The Zika Virus (ZIKV) is a single-stranded RNA genome virus, belonging to the family Flaviviridae, genus Flavivirus. Outbreaks around the world have demonstrated that the presence of asymptomatic viremic blood donors provides an increase in the risk of transfusion transmission (TT) and nucleic acid test (NAT) screening has been proposed to ensure the blood safety. This study implemented an "in-house" method to detect ZIKV RNA in blood sample donations. Methods: Primary plasma tubes are submitted to nucleic acid extraction on an automated platform. After extraction, the NAT set-up is performed in the robotic pipettor, in which an amplification mixture containing primers and probes for ZIKV and Polio vaccine virus (PV) are added in duplex as an internal control. The real-time polymerase chain reaction is then performed in a thermocycler, using the protocol established by the supplier. Results: From May 2016 to May 2018, 3,369 samples were collected from 3,221 blood donors (confidence coefficient 95%), of which 31 were considered false positive (0.92%), as they did not confirm initial reactivity when repeated in duplicates and 14 (0.42%) had their results invalid due to repeat failure in the internal control, 4 (0.12%), due to insufficient sample volume and 2 (0.05%), due to automatic pipettor failures. No Zika RNA reactive sample was identified. Conclusion: The test showed feasible to be incorporated into the blood screening routine. Our data do not indicate the need to screen for ZIKV RNA in São Paulo during the evaluated period. However, a generic NAT system covering a group of flaviviruses which are circulating in the region, such as DENV and YFV, among others, could be a useful tool.
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El diagnóstico molecular, mediante la aplicación de técnicas molecu- lares, ha permitido estudiar microorganismos presentes en el inicio y progresión de la caries dental, enfermedad periodontal, y en los fracasos endodónticos. Las técnicas moleculares permiten la detección y cuan- tificación del material genético del ácido desoxirribonucleico (DNA), ácido ribonucleico (RNA) o proteínas, lo que posibilita el estudio del genoma completo o secuencias de DNA específicas. Estas técnicas surgen como una necesidad de detectar microorganismos de difícil o lento crecimiento en cultivos; la técnica más utilizada es la reacción en cadena de la polimerasa (PCR) que permite la amplificación de peque- ños segmentos de material genético al utilizar cebadores, por lo que es un método económico, preciso, sensible y rápido para la detección de microorganismos. El presente artículo de revisión bibliográfica servirá para informar sobre los avances de las técnicas moleculares utilizadas para el diagnóstico en la práctica odontológica (AU)
Molecular diagnosis, through the application of molecular techniques, has made it possible to study microorganisms present in the onset and progression of dental caries, periodontal disease, and endodontic failures. Molecular techniques allow the detection and quantification of the genetic material of deoxyribonucleic acid (DNA), ribonucleic acid (RNA) or proteins, allowing the study of the complete genome or specific DNA sequences, they arise as a need to detect difficult or slow growing microorganisms in cultures. The most widely used technique is the polymerase chain reaction (PCR) that allows the amplification of small segments of genetic material using primers, it is an economical, precise, sensitive and fast method for the detection of microorganisms. This bibliographic review article will serve to report on the advances in molecular techniques used for diagnosis in dental practice (AU)
Subject(s)
Polymerase Chain Reaction , Molecular Biology/methods , Periodontitis/diagnosis , Dental Caries/diagnosis , Dental Pulp Diseases/diagnosisABSTRACT
Abstract Introduction: Acute respiratory infection in children has a high burden of disease. Detection of multiple micro -organisms through molecular testing of nasopharyngeal swab samples could change the paradigm of a single pathogen being the cause of respiratory disease in children and prove its usefulness in clinical practice. Objective: To characterize the pathogens identified in nasopharyngeal swab samples by means of multiplex realtime polymerase chain reaction (RT-PCR), as well as clinical variables and laboratory findings in children <5 years diagnosed with acute lower respiratory tract infection (ALRTI) and hospitalized in Bogotá D.C., Colombia. Materials and methods: Cross-sectional study conducted in 81 children hospitalized between September 2019 and March 2020 at the Clínica Cafam and in whom nasopharyngeal swab samples were collected for microbiological identification using the Allplex™ multiplex RT-PCR assay. Correlations between the number of pathogens and blood cells and C-reactive protein levels were determined by Spearman's rank correlation coefficient. Results: Patients' mean age was 17.23 months (±14.44), 54.32% were males, and 51.85% were young infants. A total of 149 microorganisms (60.40% viruses) were identified in 63 children (77.78%). Mixed infection and coinfection were reported in 48.15% and 11.11% of children, respectively. Regarding clinical findings, shortness of breath, upper airway obstruction, cough, fever and pharyngitis were the most common clinical signs and/or symptoms in patients with mixed infection (32.97%), coinfection (64.40%), mixed infection (29.78%), and absence of microorganism (22.00%), respectively. A negative correlation was observed between the number of leukocytes and the number of neutrophils and the number of microorganisms detected in the preschoolers group (r=-0.46; p =0.058 and r=-0.51; p =0.033, respectively). Furthermore, a positive correlation was found between monocyte count and the number of microorganisms detected (r=0.53; p =0.0096). Conclusion: Multiplex RT-PCR assay allowed the identification of microorganisms in most children, as well as cases of mixed infection and coinfection in more than half of the sample. In addition, clinical findings in these children were highly heterogeneous as per the assay result..
Resumen Introducción. La infección respiratoria aguda en niños tiene una alta carga de enfermedad. La detección de múltiples microorganismos a través de pruebas moleculares en hisopados nasales podría cambiar el paradigma de patógeno único causal de enfermedad respiratoria en niños y ser de utilidad en la práctica clínica. Objetivo. Caracterizar los patógenos identificados mediante la técnica de reacción en cadena de polimerasa multiplex en tiempo real (RT-PCR) en hisopado nasal, así como las variables clínicas y los resultados de laboratorio en niños <5 años diagnosticados con infección respiratoria aguda baja (IRAB) y hospitalizados en Bogotá D.C., Colombia. Materiales y métodos. Estudio transversal realizado en 81 niños hospitalizados entre septiembre de 2019 y marzo de 2020 en la clínica Cafam y en quienes se hizo hisopado nasal para realizar la identificación microbiològica mediante la prueba RT-PCR multiplex Allplex. Las correlaciones entre el número de patógenos y los niveles de células del hemograma y el nivel de proteína C reactiva se determinaron mediante el coeficiente de correlación de Spearman. Resultados. La edad promedio fue 17.23 meses (±14.44), 54.32% fueron varones y 51.85%, lactantes menores. Se identificaron 149 microorganismos (60.40% virus) en 63 niños (77.78%). Hubo infección mixta en el 48.15% y coinfección en 11.11% de los niños. Respecto a los hallazgos clínicos, la dificultad respiratoria, la obstrucción de la vía respiratoria alta, la tos, la fiebre y la faringitis fueron más comunes en los casos de infección mixta (32.97%), ausencia de microorganismo (16.00%), coinfección (64.40%), infección mixta (29.78%) y ausencia de microorganismo (22.00%), respectivamente. Se observó una correlación negativa entre el número de leucocitos y neutrófilos y el número de microorganismos detectados en preescolares (r=-0.46; p=0.058 y r=-0.51; p=0.033) y una positiva entre el recuento de monocitos y el número de microorganismos detectados (r=0.53; p =0.0096). Conclusión. La prueba RT-PCR multiplex permitió identificar microorganismos en la mayoría de niños, así como casos de infección mixta y coinfección en más de la mitad de la muestra. Además, los hallazgos clínicos fueron altamente heterogéneos entre los niños según el resultado de la prueba.
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RESUMEN Objetivo. Desarrollar y evaluar un método de bajo costo basado en celulosa para la purificación rápida y amplificación directa de ADN de Bordetella pertussis de hisopados nasofaríngeos. Materiales y métodos. Se prepararon discos de celulosa y se evaluaron diferentes parámetros (buffers de lisis/lavado, número de discos y elución de ADN). El método se acopló a una amplificación directa por PCR en tiempo real (qPCR) y se estimó el rendimiento utilizando hisopados nasofaríngeos que fueron positivos (n=100) y negativos (n=50) para ADN B. pertussis por qPCR, comparado con el método basado en columnas de sílice. Se calculó el grado de concordancia, sensibilidad, especificidad, valor predictivo positivo (VPP) y valor predictivo negativo (VPN). Se evaluó la factibilidad del método rápido para ser acoplado a un ensayo colorimétrico de amplificación isotérmica mediada por lazo (LAMP). Resultados. El método rápido con un disco de celulosa y buffer de lisis y lavado conteniendo PVP-40 y Tween 20, respectivamente, mostró una mayor capacidad para purificar ADN amplificable de B. pertussis. El método tuvo una sensibilidad de 89,0% (IC95%, 80,2%-94,9%) y una especificidad de 98,5% (IC95%, 92,1%-100,0%), con un buen grado de concordancia (Kappa=0,867; IC95% 0,788 - 0,946), respecto al método referencial. Los VPP y VPN fueron 98,6% (IC95%, 92,7,2%-100,0%) y 88,2% (IC95%, 78,7%-94,4%), respectivamente. Se evidenció una amplificación exitosa por LAMP, y se obtuvieron resultados comparables con el método por columnas de sílice. Conclusión. El método desarrollado es simple, de bajo costo y libre de equipos para la obtención rápida (60 segundos) de ADN en el punto de atención, y puede ser implementado en diversas técnicas moleculares orientados al diagnóstico oportuno y al estudio epidemiológico de tos ferina.
ABSTRACT Objective. To develop and evaluate a low-cost cellulose-based method for rapid purification and direct amplification of Bordetella pertussis DNA from nasopharyngeal swabs. Materials and methods. We prepared cellulose discs and evaluated different parameters (lysis/wash buffers, number of discs and DNA elution). The method was coupled to a direct real-time PCR (qPCR) amplification and the performance was estimated using nasopharyngeal swabs that were positive (n=100) and negative (n=50) for B. pertussis DNA by qPCR, compared to the silica column-based method. We calculated sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) and the degree of agreement. The feasibility of the rapid method to be coupled to a loop-mediated isothermal amplification colorimetric assay (LAMP) was evaluated. Results. The rapid method, with a cellulose disk and lysis and wash buffer containing PVP-40 and Tween 20, respectively, showed a greater capacity to purify amplifiable DNA from B. pertussis. The method had a sensitivity of 89.0% (95%CI: 80.2%-94.9%) and a specificity of 98.5% (95%CI: 92.1%-100.0%), with a good degree of agreement (Kappa=0.867; 95%CI: 0.788 - 0.946), compared to the reference method. The PPV and NPV were 98.6% (95%CI: 92.7.2%-100.0%) and 88.2% (95%CI: 78.7%-94.4%), respectively. Successful amplification by LAMP was evident, and comparable results were obtained with the silica column method. Conclusion. The developed method is simple, low-cost and equipment-free for rapid (60 seconds) DNA collection at the point of care, and can be implemented in various molecular techniques aimed at the timely diagnosis and epidemiological study of pertussis.
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Humans , Bordetella pertussis , DNA , Molecular Diagnostic Techniques , Cellulose , Whooping Cough , Evaluation Study , Real-Time Polymerase Chain Reaction , Point-of-Care TestingABSTRACT
ABSTRACT Introduction: The coronavirus disease 2019 (COVID-19) pandemic has required changes in the management of pediatric cardiac surgery. We would like to share the patient treatment and surgical management strategies employed in our Pediatric Cardiovascular Surgery Clinic during the COVID-19 pandemic. Methods: A total of 112 patients were followed up in our clinic between 11.03.2020 and 02.07.2020. Their mean age was 1,118 (4-5,740) days. Management and treatment were performed by our pediatric heart team (pediatric cardiac anesthetists, general pediatricians, pediatric cardiologists, pediatric cardiac surgeons, and an infectious diseases specialist). We prepared new protocols and a surveillance system specific to the pandemic to prevent in-hospital transmission and reduce postoperative mortality and morbidity; our operations were performed according to these protocols. All decisions pertaining to the operation timing and treatment strategy of our COVID-19-positive patients were made by the same team. Results: During the study period, a total of 112 patients, 69 boys and 43 girls, were hospitalized in our clinic. A total of 333 COVID-19 real-time polymerase chain reaction tests were performed on patients and accompanying persons; positive results were found in three patients and two accompanying individuals. Conclusion: By employing new protocols and a surveillance system throughout the healthcare system, we think that early diagnosis and treatment of the pediatric congenital heart disease population, which is susceptible to infections, can continue unperturbed. This and similar approaches can increase postoperative success and prevent transmission in the pediatric population - which are frequently COVID-19 asymptomatic.
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ABSTRACT Introduction: Congenital syphilis is a major public health problem, and early diagnosis and treatment are necessary to prevent it. Penicillin G benzathine is the treatment of choice in pregnant women; however, it may fail to prevent fetal infection, as in the present case. Case presentation: Male newborn, son of an HIV negative mother with gestational syphilis (venereal disease research laboratory (VDRL) 1:4 dilution, positive treponemal test) diagnosed at week 21 of gestation and treated with three doses of 2 400 000 IU of penicillin G benzathine. At delivery, the mother presented VDRL 1:1 dilution. The newborn was diagnosed with congenital syphilis due to VDRL 1:4 dilution, positive treponemal test, elevated aspartate aminotransferases, hypos-thenuria, proteinuria, hematuria, and leukocyturia that resolved after treatment with crystalline penicillin for 10 days. The molecular testing in blood showed a high treponemal load. The VDRL test at 3 months was non-reactive. Conclusions: Preventing congenital syphilis with the recommended treatment for gestational syphilis may fail. Moreover, diagnosing this condition in an asymptomatic newborn is difficult. Therefore, clinical and serological tests are recommended to confirm whether maternal treatment was effective in the fetus.
RESUMEN Introducción. La sífilis congénita es un importante problema de salud pública y para prevenirla es necesario diagnosticar y tratar la sífilis gestacional de forma temprana. En el presente caso la gestante recibió el tratamiento de elección (penicilina benzatínica), pero este no previno la infección fetal. Presentación del caso. Recién nacido masculino, hijo de una madre con serología negativa para el virus de la inmunodeficiencia humana y positiva para sífilis gestacional diagnosticada en la semana 21 (prueba VDRL con dilución 1:4 y prueba treponémica rápida positiva) y tratada con tres dosis de 2 400 000 UI de penicilina benzatínica. En el parto, la madre presentó VDRL con dilución 1:1 y el recién nacido fue diagnosticado con sífilis congénita por presentar VDRL con dilución 1:4, prueba treponémica rápida positiva, niveles de aspartato aminotransferasa elevados, hipostenuria, proteinuria, hematuria y leucocituria, condiciones que se resolvieron luego de recibir tratamiento con penicilina cristalina durante 10 días. El estudio molecular en sangre realizado al momento del nacimiento evidenció una alta presencia de Treponema pallidum. La prueba VDRL a los 3 meses fue no reactiva. Conclusiones. Prevenir la sífilis congénita con el tratamiento recomendado para sífilis gestacional puede fallar, además, diagnosticar sífilis congénita en un recién nacido asintomático es difícil, por lo cual se recomienda hacer un seguimiento clínico y serológico para confirmar si el tratamiento materno fue efectivo en el feto.
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La necesidad de un diagnóstico rápido, sensible y específico para tuberculosis es apremiante; se estiman 4 000 muertes cada día y aproximadamente 28 000 personas se contagian de esta enfermedad. La prueba Xpert®MTB/RIF consiste en un ensayo de diagnóstico in vitro de reacción en cadena de la polimerasa (PCR) en tiempo real automatizada, semicuantitativa, que en tan solo dos horas, permite detectar el ácido desoxirribonucleico (ADN) del complejo Mycobacterium tuberculosis (MTB) y mutaciones asociadas a la resistencia a rifampicina. Objetivo: Describir la experiencia del ensayo Xpert®MTB/ RIF y su valor diagnóstico en Dpto. de Microbiología del Instituto Médico La Floresta, desde abril 2012 hasta abril 2021. Métodos: Estudio descriptivo de muestras respiratorias y de otras procedencias, de pacientes con sospecha de tuberculosis, ensayadas por PCR a través del Xpert®MTB/RIF. Adicionalmente se realizó Ziehl-Neelsen y cultivo por el método de Ogawa Kudoh modificado, dependiendo del volumen de muestra recibida. Resultados: De 618 PCR realizadas, 58 muestras fueron positivas (9,4 %), 56 correspondieron a adultos y 2 a niños, 81 % se clasificaron como tuberculosis pulmonar y 19 % como extrapulmonar. A 37 se les realizó cultivo, de las cuales 10 no desarrollaron crecimiento, y a 33 adicionalmente Ziehl-Neelsen, de las cuales 12 presentaron baciloscopias negativas. En cinco de las muestras se detectó resistencia a rifampicina. Conclusiones: A través de la prueba Xpert®MTB/RIF fue posible detectar MTB en aquellas con baciloscopias negativas, en las que no desarrollaron crecimiento en el cultivo y permitió la rápida instauración de tratamiento en la tuberculosis multirresistente.
The rapid, sensitive, and specific diagnosis for tuberculosis is urgent; 4 000 deaths are estimated every day and approximately 28 000 people are infected with this disease. The Xpert®MTB/RIF test consists of an automated, semi-quantitative real-time polymerase chain reaction (PCR) in vitro diagnostic assay that, in just two hours, allows the detection of Mycobacterium tuberculosis complex (MTB) DNA and mutations associated with resistance to rifampicin. Objective: To describe the experience of the Xpert®MTB/RIF assay and its diagnostic value in the Department of Microbiology of the La Floresta Medical Institute, from April 2012 to April 2021. Methods: Descriptive study of respiratory samples and other sources, from patients with suspected of tuberculosis, assayed by PCR through Xpert®MTB/RIF. Additionally, Ziehl-Neelsen and culture were performed by the modified Ogawa Kudoh method, depending on the volume of sample received. Results: Of 618 PCR performed, 58 samples were positive (9.4 %), 56 corresponded to adults and 2 to children, 81 % were classified as pulmonary tuberculosis and 19 % as extrapulmonary. Culture was performed on 37, of which 10 did not develop growth, and on 33 additionally Ziehl-Neelsen, of which 12 presented negative bacilloscopy. Rifampicin resistance was detected in five of the samples. Conclusions: Through the Xpert®MTB/RIF test, it was possible to detect MTB in those with negative bacilloscopy, in which they did not develop growth in the culture and allowed the rapid establishment of treatment in multidrug-resistant tuberculosis.