Respiratory tract infection is a major cause of hospitalization in children. Although most such infections are viral in origin, it is difficult to differentiate bacterial and viral infections, as the clinical symptoms are similar. Multiplex polymerase chain reaction (PCR) methods allow testing for multiple pathogens simultaneously and are, therefore, gaining interest. This prospective case-control study was conducted from October 2013 to February 2014. Nasopharyngeal (NP) and oropharyngeal (throat) swabs were obtained from children admitted with severe acute respiratory infection (SARI) at a tertiary hospital. A control group of 40 asymptomatic children was included. Testing for 16 viruses was done by real-time multiplex PCR. Multiplex PCR detected a viral pathogen in 159/177 (89.9 %) patients admitted with SARI. There was a high rate of co-infection (46.9 %). Dual detections were observed in 64 (36.2 %), triple detections in 17 (9.6 %), and quadruple detections in 2 (1.1 %) of 177 samples. Seventy-eight patients required intensive care unit (ICU) admission, of whom 28 (35.8 %) had co-infection with multiple viruses. AdV, HBoV, HRV, HEV, and HCoV-OC43 were also detected among asymptomatic children. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. AdV, HBoV, HRV, HEV, and HCoV-OC43 were also detected in asymptomatic children, resulting in challenges in clinical interpretation. Studies are required to provide quantitative conclusions that will facilitate clinical interpretation and application of the results in the clinical setting.

Background Diarrhoea is still a major public health issue in developing countries, and it is one of the leading causes of morbidity and mortality in children. We aimed to assess the use of a multiplex reverse transcription polymerase chain reaction (RT-PCR) assay for the detection of five viruses, including rotavirus, norovirus (genogroups 1 and 2), astrovirus, and adenovirus, responsible for gastroenteritis in children under 5 years old in primary care centres in Upper Egypt. Subjects and methods A total of 500 stool samples were collected. Fifty samples were randomly selected for viral examination using multiplex RT-PCR for the detection of rotavirus, norovirus (genogroups 1 and 2), astrovirus, and adenovirus, causing diarrhoea. Results Viruses were detected in 45 (90%) of the 50 stool samples. The most frequently identified virus was norovirus G2, followed by Group A rotavirus, astrovirus and adenovirus. Mixed infection by two and three viruses was observed in 7/50 cases (14%) and 2/50 cases (4%), respectively. Norovirus G1 was not detected in the samples examined. Conclusion Our study reveals that multiplex PCR allows for the detection of multiple viral targets in only one reaction, rendering the assay easier to perform compared to existing testing methodologies (RT-PCR and electron microscopy). Additionally, most of the viruses were detected in summer, and the highest prevalence was in the age group less than 1 year. Norovirus G2 and rotavirus were the most frequent agents and the most common coinfections responsible for gastroenteritis in children.

Background: Rapid antigen detection tests for SARS-CoV-2 infection could promote the clinical and public health policies to handle the COVID-19 pandemic. Rapid antigen detection and molecular approaches could expand entry to checking and initial evidence of issues and playing an essential role in public health managing choices that may decrease the transmission. Objectives: We evaluated the diagnostic accurateness of couple of rapid antigen recognition tests equated with the molecular-based assays for verdict of SARS-CoV-2 infection. Methods: The 100 nasopharyngeal swabs were verified by the SARS-CoV-2 RT-PCR kit as a gold standard for COVID-19 recognition. SARS-CoV-2 antigen (Ag) was evaluated in the nasopharyngeal swabs using iFlash and UNICELL-2019-nCoV antigen methods. The iFlash-2019-nCoV antigen assay, which is a chemiluminescent immunoassay (CLIA), was used to qualitatively determine the nucleocapsid protein antigen, where the other one was used to identify the nucleocapsid protein antigen by lateral flow immunofluorescent test. Results: Out of the 100 samples, 62% were positive by RT-PCR. Amongst 62 confirmed COVID-19 cases, 43 (69.4%) were positive by iFlash and 40 samples (64.5%) were positive by the UNICELL-2019-nCoV antigen assay. The specificity of both I Flash-2019-nCoV antigen assay & UNICELL-2019-nCoV antigen assay with RT-PCR were 100% and sensitivity were 69.35 and 64.52%, respectively. This sensitivity was augmented to 100% compared with the PCR with Ct-value of ≤25 and specificity of 80.28 and 84.51%, respectively. Conclusion: Antigen detection rapid diagnostic tests may be motivating in the initial stage of the infection when the viral load is elevated, and the risk of SARS-CoV-2 transmission be high.

BackgroundCarbapenem--resistant Enterobacteriaceae constitute an urgent public health problem worldwide. In 2018, carbapenem--resistant Klebsiella pneumoniae (CR-KP) caused outbreaks of infection in 4 intensive-care units (ICUs)in a tertiary-care hospital in Egypt. We aimed to identify the clonal relatedness of isolates by whole genome (WGS).MethodsIdentification and antibiotic susceptibility testing was done by VITEK-2. Eleven isolates showed identical resistance pattern (resistant to Amikacin, gentamicin, Imipenem, meropenem, levofloxacin, and Piperacillin/Tazobactam) and were susceptible only to colistin. Caba-NP test was positive for carbapenemase production. The 11 isolates were studied by WGS by Illumina Miseq in a reference lab in Cairo University Hospital.ResultsIn only one ICU, WGS identified 4 outbreak isolates of CR-KP that group together as a tight clonal cluster, suggestive of intra-ward transmission event. The outbreak isolates belonged to MLST 147. All isolates carried blaCTXM-15, blaoxa-48, and blaNDM1 encoding ESBL and carbapenemase activity. Other identified resistance genes were Str, AadA, MsrE, Tet, and DfrA, encoding resistance to aminoglycosides, macrolide–lincosamide–streptogramin, tetracycline and trimethoprim/sulphonamides. Virulence genes included Yersiniabactin, aerobactin, rmpA, rmpA2 and wzi64, which has been associated with pathogenicity and hypervirulent K. pneumoniae lineages. No clonal relationships were identified between the isolates from other ICUs.ConclusionWGS is a powerful tool that goes beyond high-resolution tracking of transmission events into identifying the genetic basis of drug-resistance and virulence.Disclosures All authors: No reported disclosures.