Noha Salah Soliman

Background: Of all blood stream infections (BSI), candidaemia poses the greatest threat with a high fatality rate among children. There has been an increase in the number of reports of non- C. albicans species and antifungal resistance has progressively emerge. Aim: The present study aimed to demonstrate the prevalence of candidaemia among children and to characterize the involved species and their susceptibility to antifungal agents. Methodology: Microbes were isolated from blood samples and identified via standard microbiological procedures. Chromogenic media was used to characterize the Candida species. The susceptibility of the isolates to the antifungal agents; caspofungin, amphotericin, itraconazole, and fluconazole was determined with the E-test. Statistical methods: The data were analysed with Statistical Package for the Social Science SPSS; SPSS Inc., Chicago, IL, USA) version 15 for Microsoft Windows. Comparisons between the study groups were performed using the Chi square (χ 2 ) test. p -values less than 0.05 were considered significant. Results: Candidaemia accounted for 17.3% of all BSIs. C. albicans and non- C. albicans species accounted for 36% and 64% of the cases of candidaemia, respectively. Caspofungin, amphotericin, itraconazole, and fluconazole antifungals had activities of 99%, 97%, 73% and 64%, respectively. In total, 64% of patients with candiaemia died. Conclusion: The prevalence of candidaemia was high, the fatality rate was alarming and non- C. albicans species were predominant. Fluconazole was the least effective of the tested antifungal agents owing to the high level of resistance. Keywords: candidaemia, chromogenic agar, antifungal

Background: Multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of Pseudomonas aeruginosa are the leading cause of healthcare-associated infections worldwide. Objective: The aim was to identify the resistant phenotypes among P. aeruginosa and to characterize different aminoglycosides and carbapenem resistance genes as major mechanisms of resistance in these isolates, in Theodor Bilharz Research Institute (TBRI), a tertiary care hospital in Cairo, Egypt. Methods: During a period of 11 months, 42 P. aeruginosa clinical isolates were collected from the microbiology laboratory by routine culture. Antimicrobial sensitivity testing to the aminoglycosides gentamicin and amikacin, and other classes of antibiotics, was performed by a disk diffusion method. Isolates were tested for aminoglycoside resistance genes, aac(6ʹ)-lb , aac-(3)-lla , rmtB , rmtC , armA , rmtD , and rmtF , and carbapenemase resistance genes bla NDM , bla VIM , and bla IMP , using conventional PCR. Results: Thirty-three (78.5%) of the clinical P. aeruginosa isolates showed MDR and XDR phenotypes at 42.4% and 57.65%, respectively, and these were included in the study. Aminoglycoside resistance was found in 97%, whereas carbapenem resistance was found in 81% of the isolates phenotypically. Only 59.4% (19/26) of the aminoglycoside-resistant isolates harbored resistance genes; none of the amikacin-susceptible isolates harbored any of the tested aminoglycoside resistance genes. Aminoglycoside resistance genes rmtB , armA , aac(6ʹ)-lb , and rmtF were found at rates of 17/33 (51.5%), 3/33 (9%), 2/33 (6%), and 2/33 (6%), respectively, whereas rmtD , acc(3)-II , and rmtC were not detected. Only 40.7% (11/27) of the carbapenem-resistant isolates harbored resistance genes. Carbapenem resistance genes, bla NDM and bla VIM , were found at rates of 7/33 (21.2%) and 6/33 (18.1%), respectively, and bla IMP was not detected. Conclusion: Rates of MDR and XDR P. aeruginosa and resistance to aminoglycosides and carbapenems in our setting are high. Methyltransferases and metallo-beta-lactamases are the main mechanisms of resistance to aminoglycosides and carbapenems, respectively. The presence of bla NDM and rmtF in the strains confirms their rapid dissemination in the Egyptian environment. Keywords: aminoglycosides, carbapenems, antibiotic resistance, Pseudomonas aeruginosa , MDR, XDR, rmtB , rmtF , NDM

healthcare-associated infections. This study combined whole-genome sequencing, bioinformatics, and statistical analyses to identify the phylogeny, resistome, virulome and potential genotype-phenotype-clinical correlation among 18 clinical isolates of MRSA in a tertiary hospital in Cairo, Egypt. The ST1535-V MRSA clone was the most frequently isolated (16.6%), followed by ST5-VI, ST1-V and ST239-III (11.1% each). SCCmec V, VI, IV and III types were detected at frequencies of 50%, 16.6%, 11.1% and 11.1%, respectively. None of the tested virulence genes were detected in all isolates, but they ranged in distribution from 1/18 to 17/18. The Panton-Valentine leukocidin (PVL)-encoding genes were detected in only four isolates and were enriched in isolates causing non-severe cases. Phylogenetic analysis revealed relatedness between three ST1535-Vs, two ST5-VIs, two ST239-IIIs and two ST1-Vs; however, only the two genetically related ST1-V isolates were epidemiologically linked. While disease outcome and source of infection had no correlation with a particular genotypic pattern, the sequence type was the most correlated factor with phylogeny and genotypic patterns, and a few genes were associated with non-severe cases.

Nucleic acid and antibody detection assays have been utilized in COVID-19 laboratory diagnosis. However, the use of viral antigenic proteins for diagnosis has not been successfully developed. Using viral antigen allows rapid direct viral detection earlier than production of antibodies. The present study was aimed at evaluating the performance of two COVID-19 rapid antigen detection tests, which are BIOCREDIT COVID-19 Ag (RapiGEN Inc., Korea) and Standard Q COVID-19 Ag (SD Biosensor, Korea), in comparison with RT-PCR. These tests were performed on 80 COVID-19 RT-PCR positive respiratory samples and 20 RT-PCR negative control samples. BIOCREDIT COVID-19 Ag and SD Biosensor RAD kits recorded total sensitivities of 52.5% and 68.7% and specificities of 46% and 96%, respectively. In high viral load samples, BIOCREDIT COVID-19 Ag and SD Biosensor RAD kits recorded higher sensitivities of 60% and 77%, compared to 45% and 60% in normal viral load samples, respectively. Sensitivity and specificity of the 2 antigen kits varied significantly with <i>P</i> values of <0.000001 and 0.0135, respectively. The evaluated RAD tests presented promising performance which was relatively better for SD-Biosensor than BIOCREDIT RAD tests, especially in high viral load samples. However, antigen tests are still considered substandard in comparison with RT-PCR in detecting SARS-CoV-2.