Sever acute respiratory infections (SARIs) are a public health issue that are common in children and are associated with an important morbidity and mortality rate worldwide. Although SARI are mainly caused by viruses, they are still a cause of antibiotic overuse. The use of molecular methods especially real-time multiplex PCR allowed to detect a wide range of respiratory viruses and their subtype as well as some atypical bacteria. The aim of this study was to investigate the epidemiology of respiratory pathogens detected in children admitted with SARI and to highlight the role of real-time multiplex PCR in the rapid diagnosis of viral and bacterial SARI. This work is a descriptive observational study from January 2018 to December 2019 including nasopharyngeal secretions collected from 534 children hospitalised in paediatric department. The detection of respiratory viruses and bacteria was performed by the FilmArray® Respiratory Panel. A total of 387 (72.5%) children were tested positive for at least one respiratory pathogen, and 23.3% of them were coinfected with more than one pathogen. Viral aetiology was found in 91.2% (n = 340). The most common viruses detected were HRV (n = 201) and RSV (n = 124), followed by PIV (n = 35) influenza A (n = 29) and human metapneumovirus (n = 27). Bacteria was found in 8.8% (n = 47), and Bordetella pertussis was the most detected. Respiratory syncytial virus and Bordetella pertussis were significantly higher in infants less than 6 months old. The detection of RSV and influenza A presented a pic in winter, and HMPV was statistically significant in spring ( p < 0.01 ). This study described the epidemiology of respiratory pathogens involved in severe respiratory infections in children that were affected by several factors such as season and age group. It also highlighted the importance of multiplex PCR in confirming viral origin, thus avoiding irrational prescription of antibiotics in paediatric settings.

Severe Acute Respiratory Syndrome Virus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19), which was identified at the end of December 2019 in China. Symptoms of COVID-19 can appear after an incubation phase of the virus of 2 to 14 days, the most common being fever, cough, and asthenia. Other specific symptoms may include shortness of breath or difficulty breathing, muscle pain, sore throat, chills, loss of smell or sensation, chest pain, headache, nausea, rash, diarrhea, and vomiting. The severity of these symptoms can be mild or even extreme causing serious damage to several organs, directly and indirectly, namely pulmonary, renal, hepatic, cardiac, digestive, neurological. Some people have only mild symptoms, while others are asymptomatic. Seniors or those at risk for certain chronic diseases, such as massive obesity, diabetes, heart disease, lung disease, kidney disease, immune system abnormalities, and liver disease are more susceptible to COVID-19 and can develop more serious and fatal complications.

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Since the outbreak of the COVID-19 pandemic, a significant decrease in non-COVID-19 respiratory illnesses were observed, suggesting that the implementation of measures against COVID-19 affected the transmission of other respiratory pathogens. The aim of this study was to highlight the changes in the epidemiology of respiratory pathogens in children during the COVID-19 pandemic. All children with Severe Acute respiratory illness admitted to the pediatric departments between January 2018 and December 2021 with negative COVID-19 PCR, were enrolled. The detection of respiratory pathogens was made by the Film Array Respiratory Panel. A total of 902 respiratory specimens were tested. A significantly lower positivity rate during the COVID-19 period was found (p = 0.006), especially in infants under 6 months (p = 0.008). There was a substantial absence of detection of Respiratory Syncytial Virus and Influenza A during the winter season following the outbreak of the pandemic (p < 0.05; p = 0.002 respectively). An inter-seasonal resurgence of Respiratory Syncytial Virus was noted. Human Rhinovirus was detected throughout the year, and more prevalent in winter during COVID-19 (p = 0.0002). These changes could be explained by the impact of the implementation of preventive measures related to the COVID-19 pandemic on the transmission of respiratory pathogens in children.

Introduction: Gastrointestinal infection is a major cause of morbidity worldwide. Culture and microscopy are time consuming and have low diagnostic yield. New rapid molecular methods such as multiplex PCR have recently been introduced for etiological diagnosis. The purpose of this study was to compare the diagnostic yield of the FilmArray gastrointestinal panel with that of standard culture for the etiological diagnosis of gastrointestinal infections. Materials and methods: This is a retrospective study carried out within the Microbiology department of the Arrazi hospital of the CHU Mohamed VI, including all the patients treated for a gastrointestinal infection and having required hospitalization in the various departments within the Arrazi Hospital of the CHU Mohamed VI in Marrakech, over a period of 15 months. Results: During the period studied, 124 patients were sampled. All samples were tested using stool culture and FilmArray. PCR detected significantly more positive samples, with bacterial, viral and/or parasitic infections compared to stool culture (57.3% vs 21%). Additionally, gastrointestinal PCR was able to detect all pathogens implicated in the gastrointestinal FilmArray panel except for Yersinia Enterocolitica, whereas stool culture could only detect three bacterial pathogens (E.coli, Salmonella and Shigella). Additionally, 52.11% of patients had co-infections that were identified only by PCR. Conclusions: The FilmArray GI panel showed very good diagnostic performance compared to culture for the diagnosis of gastrointestinal infections and gave a more detailed picture of the spectrum of pathogens involved. Further studies are needed to determine whether multiplex PCR improves patient outcomes and reduces costs.