Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes.

Monitoring the emergence of new SARS-CoV-2 variants is important to detect potential risks of increased transmission or disease severity. We investigated the identification of SARS-CoV-2 variants from real-time reverse transcriptase polymerase chain reaction (RT-PCR) routine diagnostics data. Cycle threshold (Ct) values of positive samples were collected from April 2021 to January 2022 in the Northern Metropolitan Area of Barcelona (n = 15,254). Viral lineage identification from whole genome sequencing (WGS) was available for 4618 (30.3%) of these samples. Pairwise differences in the Ct values between gene targets (ΔCt) were analyzed for variants of concern or interest circulating in our area. A specific delay in the Ct of the N-gene compared to the RdRp-gene (ΔCtNR) was observed for Alpha, Delta, Eta and Omicron. Temporal differences in ΔCtNR correlated with the dynamics of viral replacement of Alpha by Delta and of Delta by Omicron according to WGS results. Using ΔCtNR, prediction of new variants of concern at early stages of circulation was achieved with high sensitivity and specificity (91.1% and 97.8% for Delta; 98.5% and 90.8% for Omicron). Thus, tracking population-wide trends in ΔCt values obtained from routine diagnostics testing in combination with WGS could be useful for real-time management and response to local epidemics.

Commercial real time PCR implementation for rapid diagnosis of onychomycosis: A new workflow in a clinical laboratory.

INTRODUCTION: Onychomycosis is a frequent and underdiagnosed condition. Approximately 90% of toenail onychomycosis infections are caused by dermatophytes, but classical diagnosis based on culture and microscopy observation is slow and has low sensitivity. Both limitations can be solved incorporating molecular techniques to routine diagnosis of onychomycosis. OBJECTIVE: Prospective evaluation of the utility of incorporating in the clinical laboratory workflow a commercial real time PCR (qPCR) for dermatophytes detection in nails after potassium hydroxide direct observation screening. MATERIALS AND METHODS: 152 nail samples were included (34 KOH negative and 118 KOH positive) and processed by culture and qPCR. RESULTS: In the negative KOH group, only one dermatophyte grew in culture and three were detected by qPCR. In the group of positive KOH, 57 dermatophytes grew in culture and 81 were detected by qPCR. In this group, 25% of diagnosed dermatophytes were detected only by qPCR. The sensitivity of qPCR compared to culture is 92.8% and time of response decreases from days to hours. CONCLUSION: Based in our results, we propose a workflow algorithm for a clinical laboratory that eliminates culture for qPCR positive samples.

PCR a tiempo real comercial para diagnóstico rápido de las onicomicosis: un nuevo algoritmo de trabajo en el laboratorio clínico / Commercial real time PCR implementation for rapid diagnosis of onychomycosis: A new workflow in a clinical laboratory

Introduction: Onychomycosis is a frequent and underdiagnosed condition. Approximately 90% of toenail onychomycosis infections are caused by dermatophytes, but classical diagnosis based on culture and microscopy observation is slow and has low sensitivity. Both limitations can be solved incorporating molecular techniques to routine diagnosis of onychomycosis. Objective: Prospective evaluation of the utility of incorporating in the clinical laboratory workflow a commercial real time PCR (qPCR) for dermatophytes detection in nails after potassium hydroxide direct observation screening. Materials and methods: 152 nail samples were included (34 KOH negative and 118 KOH positive) and processed by culture and qPCR. Results: In the negative KOH group, only one dermatophyte grew in culture and three were detected by qPCR. In the group of positive KOH, 57 dermatophytes grew in culture and 81 were detected by qPCR. In this group, 25% of diagnosed dermatophytes were detected only by qPCR. The sensitivity of qPCR compared to culture is 92.8% and time of response decreases from days to hours. Conclusion: Based in our results, we propose a workflow algorithm for a clinical laboratory that eliminates culture for qPCR positive samples.(AU)

Introducción: La onicomicosis es una patología frecuentemente infradiagnosticada. Aproximadamente el 90% de las infecciones en las uñas del pie están causadas por dermatofitos, pero el diagnóstico microbiológico clásico basado en cultivo y microscopia es lento y tiene una baja sensibilidad. Ambas limitaciones pueden resolverse incorporando técnicas moleculares al diagnóstico de la onicomicosis. Objetivo: Evaluación prospectiva de la utilidad de incorporar en un laboratorio clínico una PCR a tiempo real (qPCR) comercial para detección de dermatofitos en uñas tras cribado por examen directo con hidróxido de potasio (KOH). Materiales y métodos: Se incluyeron 152 muestras de uñas (34 KOH negativas y 118 KOH positivas) y se procesaron mediante cultivo y qPCR. Resultados: En el grupo KOH negativo, solo un dermatofito creció en cultivo y 3 se detectaron mediante qPCR. En el grupo KOH positivo, 57 dermatofitos crecieron en cultivo y 81 se detectaron por qPCR. En este grupo, el 25% de los dermatofitos diagnosticados se detectaron únicamente mediante qPCR. La sensibilidad de la qPCR comparada con el cultivo es del 92,8% y el tiempo de respuesta disminuye de días a horas. Conclusión: En base a nuestros resultados, proponemos un algoritmo de flujo de trabajo para los laboratorios de microbiología clínica, que elimina el cultivo para aquellas muestras con qPCR positiva.(AU)

Pre-Treatment with Grape Seed Extract Reduces Inflammatory Response and Oxidative Stress Induced by Helicobacter pylori Infection in Human Gastric Epithelial Cells.

Helicobacter pylori (H. pylori) is a pathogenic bacteria identified as a potential risk factor for gastritis, gastric ulcers and gastric cancer. During the stomach colonization, H. pylori triggers a strong inflammatory response and subsequent oxidative stress, which are associated with tissue damage. For this reason, it is of particular interest to develop alternative natural tools that enable modulation of the associated damaging immune response. With this purpose, we obtained grape seed extract (GSE) from sweet (not fermented) food grade seeds. The aim of our study was to investigate the effect of GSE and its two enriched procyanidins fractions (OPC and PPC) on the inflammatory process and oxidative stress produced by different H. pylori strains in human gastric epithelial cells (AGS). Anti-inflammatory activity was evaluated by measuring the level of interleukin-8 (IL-8) secretion. IL-8 production was significantly reduced in H. pylori-infected human gastric epithelial cells pre-treated with GSE or its enriched fractions when compared with non-pre-treated infected cells (from 21.6% to 87.8%). Pre-treatment with GSE or its fractions significantly decreased intracellular reactive oxygen species (ROS) production in AGS cells after infection, depending on the H. pylori strain. Our results also showed that GSE and its fractions demonstrate antibacterial activity against all strains of H. pylori used in the study. This work demonstrates the effectiveness of GSE enriched in procyanidins against the main events associated with H. pylori infection.

Retrospective search of SARS-CoV-2 in respiratory samples in Vallès Occidental (Barcelona, Spain) before the first case was reported / Búsqueda retrospectiva del SARS-CoV-2 en muestras respiratorias en el Vallès Occidental (Barcelona, España) antes de que se notificara el primer caso

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Retrospective search of SARS-CoV-2 in respiratory samples in Vallès Occidental (Barcelona, Spain) before the first case was reported / Búsqueda retrospectiva del SARS-CoV-2 en muestras respiratorias en el Vallès Occidental (Barcelona, España) antes de que se notificara el primer caso

No disponible

Ús de la PCR de bacteris atípics en el maneig ambulatori de pacients amb pneumònia adquirida a la comunitat que acudeixen a urgències / Uso de la PCR de bacterias atípicas en el manejo ambulatorio de pacientes con neumonía adquirida en la comunidad que acuden a urgencias / Use of PCR for atypical bacteria in the ambulatory management of patients with community-acquired pneumonia seen in the emergency departament

FONAMENT: Mycoplasma pneumoniae I Chlamydophila pneu-moniae són agents causals freqüents de la pneumònia adquirida a la comunitat (PAC) en pediatria, I les tècniques com la reacció en cadena de la polimerasa (PCR) poden facilitar-ne el diagnòstic etiològic precoç, adequant l'antibioteràpia emprada. OBJECTIU: Descriure l'ús d'aquesta tècnica en el maneig ambulatori dels pacients pediàtrics amb PAC que acudeixen a urgències. MÈTODE: Estudi observacional, retrospectiu I descriptiu de pacients pediàtrics diagnosticats de PAC a urgències amb maneig ambulatori. RESULTATS: De 67 pacients, el 32,8% va obtenir un resultat positiu per a bacteris atípics. El percentatge de resultats positius en <4 anys va ser del 10,0% I en ≥4 anys del 42,6% (p = 0,021). Van rebre antibiòtic empíric a l'alta 49 pacients dels 67 (73,1%): 31 macròlids, 12 betalactàmics I 6 ambdós. Amb el resultat de la PCR, per resultat negatiu es van retirar els macròlids a 25 dels 37 als quals se'ls havia pautat (67,6%) I es va pautar a 10 dels 22 casos positius que no els estaven rebent (45,5%). CONCLUSIONS: La PCR de bacteris atípics facilita el diagnòstic microbiològic ràpid I l'adequació de l'antibioteràpia, i, sobretot, evita l'excés de tractament amb macròlids a les urgències pediàtriques

FUNDAMENTO: Mycoplasma pneumoniae y Chlamydophila pneumoniae son agentes causales frecuentes de la neumonía adquirida en la comunidad (NAC) en pediatría, y las técnicas como la reacción en cadena de la polimerasa (PCR) pueden facilitar su diagnóstico etiológico precoz, adecuando la antibioterapia utilizada. OBJETIVO: Describir el uso de esta técnica en el manejo ambulatorio de los pacientes pediátricos con NAC que acuden a urgencias. MÉTODO: Estudio observacional, retrospectivo y descriptivo de pacientes pediátricos diagnosticados de NAC en urgencias manejados ambulatoriamente. RESULTADOS: De 67 pacientes, el 32,8% obtuvo resultado positivo para bacterias atípicas. El porcentaje de resultados positivos en <4 años fue del 10,0% y en ≥4 años de 42,6% (p = 0,021). Recibieron antibiótico empírico 49 pacientes de los 67 (73,1%): 31 macrólidos, 12 betalactámicos y 6 ambos. Con el resultado de la PCR, por resultado negativo se retiraron los macrólidos a 25 de los 37 a los que se les había pautado (67,6%) y se pautó a 10 de los 22 casos positivos que no los estaban recibiendo (45,5%). CONCLUSIONES: La PCR de bacterias atípicas facilita el diagnóstico microbiológico rápido y la adecuación de la antibioterapia, evitando sobre todo el exceso de tratamiento con macrólidos en urgencias

BACKGROUND: Mycoplasma pneumoniae and Chlamydophila pneu-moniae are frequent causative agents of community-acquired pneumonia (CAP) in children. Techniques such as the polymerase chain reaction (PCR) can facilitate early diagnosis and adequacy of antibiotic therapy. OBJECTIVE: To describe the use of this test in the ambulatory management of children with CAP seen in the emergency room. METHOD: Observational, retrospective and descriptive study of children diagnosed with CAP in the emergency room and managed as outpatients. RESULTS: Sixty-seven patients were recruited and 22 (32.8%) had a positive PCR for atypical bacteria. The percentage of positive results in children <4 years was 10.0% and it was 42.6% in children ≥4 years (p = 0.021). Forty-nine (73.1%) patients received antibiotic treatment: 31 received macrolides, 12 beta-lactams and 6 both. The results of the PCR test resulted in discontinuation of macrolide treatment in 25 of 37 patients (67.6%) after a negative PCR test and in its prescription to 10 of the 22 (45.5%) positive cases that were not receiving it. CONCLUSIONS: The use of PCR for atypical bacteria in the emergency department facilitates rapid microbiological diagnosis and the adequacy of antibiotic therapy, avoiding over-treatment with macrolides