Covid-19 in Egyptian hemodialysis and kidney transplant children: retrospective analysis of single center experience.

BACKGROUND: Chronic kidney disease stage 5 (CKD 5) populations have peculiar risk for severe Covid-19 infection. Moreover; pediatric data are sparse and lacking. The aim of this study is to report our experience in CKD 5 children treated by hemodialysis (CKD 5D) and CKD 5 children after kidney transplantation (KTR) during one year of Covid-19 pandemic. METHODS: Retrospective analysis of 57 CKD 5 children with Covid-19 like symptoms during 1 year pandemic was performed. A cohort of 19 confirmed patients (13 CKD 5D and 6 KTR) was analyzed in details as regard clinical, laboratory, radiological criteria, management and their short term outcome. RESULTS: CONCLUSION: Pediatric patients on regular HD (CKD 5D) are at higher risk and worse outcome of Covid-19 infection than KT recipients (KTR). Pre-existing HTN and shorter duration after KT are potential risk factors. Reversible AGD after KT and CVC related infections in HD patients are additional presenting features of Covid-19 infection.

MALDI-TOF MS Overcomes Misidentification of the Uncommon Human Pathogen Candida famata by Routine Phenotypic Identification Methods.

Candida famata has been associated with the identifiable Candida infections that takes place in human and the identification error of this species possibly will result in misinterpretation of antifungal susceptibility and improper diagnosis; which will have a major effect on the prognosis and therapy of patients. Our objective is to correctly identify Candida spp. collected from patients at the intensive care units, New Cairo University teaching hospital in Cairo-Egypt using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Hundred clinically isolated yeast strains were identified using API 20C AUX obtained from patients receiving care at intensive care units. ATB FUNGUS 3 strips were used to detect the minimum inhibitory concentration. Thirty-three non duplicate strains identified as C. famata were subjected to re-identification by MALDI-TOF MS. Our results revealed that isolates were initially identified as C. famata 33%, C. tropicalis 15%, C. albicans 12% and C. parapsillosis 10% using the phenotypic techniques. MALDI-TOF MS analyses results showed that the 33 C. famata isolates are C. tropicalis (n = 29), Trichosporon asahii (n = 2), C. parapsilosis (n = 1), and Aeromonas sobria (n = 1). Antifungal resistance was low in the Candida species, except for reduced susceptibility to itraconazole among C. krusei strains. This report shows that misidentification of C. famata is frequent when using conventional phenotypic methods of identification which result in challenges in treating fungal infections. MALDI-TOF MS is an accurate convenient substitute to classical approaches for fungal identification. In general, antifungal multidrug resistance is uncommon in our studied Candida species and yeast isolates.

A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions.

The novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is causing an unprecedented pandemic, threatening planetary health, society, and economy. Genomic surveillance continues to be a critical effort toward tracking the virus and containing its spread, and more genomes from diverse geographical areas and different time points are needed to provide an appropriate representation of the virus evolution. In this study, we report the successful assembly of one single gapless, unambiguous contiguous sequence representing the complete viral genome from a nasopharyngeal swab of an infected health care worker in Cairo, Egypt. The sequence has all typical features of SARS-CoV-2 genomes, with no protein-disrupting mutations. However, three mutations are worth highlighting and future tracking: a synonymous mutation causing a rare spike S813I variation and two less frequent ones leading to an A41V variation in NSP3, encoded by ORF1a (ORF1a A895V), and a Q677H variation in the spike protein. Both affected proteins, S and NSP3, are relevant to vaccine and drug development. Although the genome, named CU_S3, belongs to the prevalent global genotype, marked by the D614G spike variation, the combined variations in the spike proteins and ORF1a do not co-occur in any of the 197,000 genomes reported to date. Future studies will assess the biological, pathogenic, and epidemiological implications of this set of genetic variations. This line of research is needed to inform vaccine and therapeutic innovation to stem the COVID-19 pandemic.