madney, Y., L. Shalaby, M. Hammad, M. El anany, R. Hassan, A. Youssef, I. Abdo, A. Zaki, and R. Khedr, "COVID-19-Associated Pulmonary Fungal Infection among Pediatric Cancer Patients, a Single Center Experience.", Journal of fungi (Basel, Switzerland), vol. 8, issue 8, 2022. Abstract

Patients with COVID-19 are at risk of developing secondary complications such as invasive pulmonary aspergillosis and mucormycosis. This is a retrospective study including all cancer children diagnosed with COVID-19-associated pulmonary fungal infection (CAPFI) during the period 2020-2021. A total of 200 patients were diagnosed with COVID-19, out of which 21 (10%) patients were diagnosed with CAPFI, 19 patients (90%) with COVID-aspergillosis (CAPA), and 2 (10%) patients with COVID-mucormycosis (CAM). Patients with CAPFI were classified using the "2020 ECMM/ISHAM consensus criteria"; proven in 2 (10%) patients, probable in 12 (57%), and possible in 7 (33%) patients. Although the hematological malignancy patients were already on antifungal prophylaxis, breakthrough fungal infection was reported in 16/21 (75%), 14 (65%) patients had CAPA while on echinocandin prophylaxis, while 2 (10%) patients had CAM while on voriconazole prophylaxis. Overall mortality was reported in 8 patients (38%) while CAPFI-attributable mortality was reported in 4 patients (20%). In conclusion, clinicians caring for pediatric cancer patients with COVID-19 should consider invasive pulmonary fungal infection, even if they are on antifungal prophylaxis, especially with worsening of the clinical chest condition. A better understanding of risk factors for adverse outcomes may improve clinical management in these patients.

Jalal, D., M. G. Elzayat, H. E. El-Shqanqery, A. A. Diab, A. Yahia, O. Samir, U. Bakry, K. Amer, M. ElNaqeeb, W. Hassan, et al., "SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study.", Scientific reports, vol. 12, issue 1, pp. 14511, 2022. Abstract

A serious global public health emergency emerged late November 2019 in Wuhan City, China, by a new highly pathogenic virus, SARS-CoV-2. The virus evolution spread has been tracked by three developing databases: GISAID, Nextstrain and PANGO to understand its circulating variants. In this study, 110 diagnosed positive COVID-19 patient's samples, were collected from Kasr Al-Aini Hospital and the Children Cancer Hospital Egypt 57357 between May 2020 and January 2021, with clinical severity ranging from mild to severe. The viral genomes were sequenced by next generation sequencing, and phylogenetic analysis was performed to understand viral transmission dynamics. According to Nextstrain clades, most of our sequenced samples belonged to clades 20A and 20D, which in addition to clade 20B were present from the beginning of sample collection in May 2020. Clades 19A and 19B, on the other hand, appeared in the mid and late 2020 respectively, followed by the disappearance of clade 20B at the end of 2020. We identified a relatively high prevalence of the D614G spike protein variant and novel patterns of mutations associated together and with different clades. We also identified four mutations, spike H49Y, ORF3a H78Y, ORF8 E64stop and nucleocapsid E378V, associated with higher disease severity. Altogether, our study contributes genetic, phylogenetic, and clinical correlation data about the spread of the SARS-CoV-2 pandemic in Egypt.

Jalal, D., O. Samir, M. G. Elzayat, H. E. El-Shqanqery, A. A. Diab, L. ElKaialy, A. M. Mohammed, D. Hamdy, I. K. Matar, K. Amer, et al., "Genomic characterization of SARS-CoV-2 in Egypt: insights into spike protein thermodynamic stability.", Frontiers in microbiology, vol. 14, pp. 1190133, 2023. Abstract

The overall pattern of the SARS-CoV-2 pandemic so far has been a series of waves; surges in new cases followed by declines. The appearance of novel mutations and variants underlie the rises in infections, making surveillance of SARS-CoV-2 mutations and prediction of variant evolution of utmost importance. In this study, we sequenced 320 SARS-CoV-2 viral genomes isolated from patients from the outpatient COVID-19 clinic in the Children's Cancer Hospital Egypt 57357 (CCHE 57357) and the Egypt Center for Research and Regenerative Medicine (ECRRM). The samples were collected between March and December 2021, covering the third and fourth waves of the pandemic. The third wave was found to be dominated by Nextclade 20D in our samples, with a small number of alpha variants. The delta variant was found to dominate the fourth wave samples, with the appearance of omicron variants late in 2021. Phylogenetic analysis reveals that the omicron variants are closest genetically to early pandemic variants. Mutation analysis shows SNPs, stop codon mutation gain, and deletion/insertion mutations, with distinct patterns of mutations governed by Nextclade or WHO variant. Finally, we observed a large number of highly correlated mutations, and some negatively correlated mutations, and identified a general inclination toward mutations that lead to enhanced thermodynamic stability of the spike protein. Overall, this study contributes genetic and phylogenetic data, as well as provides insights into SARS-CoV-2 viral evolution that may eventually help in the prediction of evolving mutations for better vaccine development and drug targets.

Hassan, R. M., M. G. El Anany, M. M. Mostafa, R. H. A. Yousef, and S. T. Salem, "Whole genome characterization of methicillin resistant Staphylococcus aureus in an Egyptian Tertiary Care Hospital.", Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi, vol. 56, issue 4, pp. 802-814, 2023. Abstract

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a significant healthcare-associated (HA-MRSA) pathogen due to its increased morbidity and mortality rates. There is a paucity of data regarding MRSA clones circulating in the Middle East in the literature, especially from Egypt. We aimed to identify the pattern of resistance and virulence in the propagating clones using NGS technologies for the whole genome sequence.

METHODS: From an 18-month surveillance program for MRSA-positive patients, 18 MRSA isolates from surgical healthcare associated infections were selected. The Vitek2 system was used to assess antimicrobial susceptibility. The whole genome sequencing was performed using the NovaSeq6000. The reads were mapped to the reference genome (Staphylococcus_aureus_ATCC_BAA_1680), used for variant calling, screened for virulence/resistance genes, and typed using multi-locus sequence typing and spa typing. Correlation between demographic and clinical data and molecular findings were performed.

RESULTS: All the MRSA isolates were highly resistant to tetracycline followed by gentamicin (61%) and highly susceptible to trimethoprim/sulfamethoxazole. Most of the isolates showed a high virulence profile. ST239 was the predominant sequence type (6/18), while t037 was the predominant spa type (7/18). Five isolates shared the same ST239 and spa t037. ST1535, an emerging MRSA strain, was the second most prevalent in our study. One isolate showed a unique pattern of a high abundance of resistance and virulence genes.

CONCLUSION: WGS elucidated the resistance and virulence profiles of MRSA isolated from clinical samples of HAI patients with high-resolution tracking of clones predominant in our healthcare facility.

Reda, N. M., R. M. Hassan, S. T. Salem, and R. H. A. Yousef, "Prevalence and species distribution of Candida bloodstream infection in children and adults in two teaching university hospitals in Egypt: first report of Candida kefyr.", Infection, vol. 51, issue 2, pp. 389-395, 2023. Abstract

BACKGROUND: Candidemia is a pervasive problem associated with significant morbidity and mortality in health care settings. This study aimed to determine the changing distribution of Candida species and the emergence of uncommon species.

METHODS: This was a cross-sectional study performed in two Cairo University hospitals between 2019 and 2020. All Candida species isolates recovered from blood cultures of adults and pediatrics patients admitted to the hospitals were included. Candida isolates were identified by chromogenic Candida agar and Vitek2 YST identification card. Candida kefyr was confirmed by chip array.

RESULTS: Candida species were responsible for 1.6% of bloodstream infections in adults and 10.8% in pediatric patients. C. albicans was the most prevalent species representing 27.8% in adults and 48.3% in pediatrics. Non-albicans species (NAC) represented the most isolated Candida species among adults and pediatrics (72.2% and 51.6%, respectively) with the predominance of C. tropicalis (27.8% and 22.5%, respectively) followed by C. parapsilosis (16.7% and 10.8%, respectively). The uncommon Candida, which is Candida species other than C. albicans, C. parapsilosis, C. tropicalis, C. glabrata, and C. krusei, represents 16.6% and 14% of all candidemia in adults and pediatrics, respectively. Only one of each of C. lusitaniae, C. utilis, and C. kefyr were detected in adults. C. lusitaniae was the most frequently recovered uncommon Candida among pediatrics resulting in 6.4% of candidemia followed by C. famata (4.3%), C. utilis (2.2%), and C. kefyr (1.1%).

CONCLUSIONS: C. albicans is still the primary species isolated from pediatrics and adults with candidemia despite the considerable shift to the non-albicans species. C. tropicalis and C. parapsilosis are the most prevalent NAC. The increased prevalence of uncommon Candida species is alarming and necessitates a prompt stewardship program.

Yang, Y., Y. Yang, M. A. E. - G. El-Sayed, and R. M. Hassan, "Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt", BMC Genomics, vol. 23: BioMed Central, 2022. Abstract

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Jalal, D., M. G. Elzayat, A. A. Diab, H. E. El-Shqanqery, O. Samir, U. Bakry, R. Hassan, M. El anany, L. Shalaby, and A. A. Sayed, "Deciphering Multidrug-Resistant Acinetobacter baumannii from a Pediatric Cancer Hospital in Egypt", mSphere, vol. 6, issue 6: American Society for Microbiology (ASM), 2021. Abstract
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Romeih, M., M. R. Mahrous, L. Shalby, R. Khedr, S. Soliman, R. Hassan, M. G. El-Ansary, A. Ismail, A. Al Halfway, and A. Mahmoud, "Prognostic impact of CT severity score in childhood cancer with SARS-CoV-2", Egyptian Journal of Radiology and Nuclear Medicine, vol. 52, issue 1: SpringerOpen, pp. 1-13, 2021. Abstract
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Hammad, M., L. Shalaby, I. Sidhom, N. Sherief, I. Abdo, S. Soliman, Y. Madeny, R. Hassan, S. Elmeniawy, and N. Khamis, "Management and Outcome of Coronavirus Disease 2019 (COVID-19) in Pediatric Cancer Patients: A Single Centre Experience from a Developing Country", Clinical Lymphoma Myeloma and Leukemia, vol. 21, issue 11: Elsevier, pp. e853-e864, 2021. Abstract
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Fadel, M., M. Nasr, R. M. Hassan, and S. S. Thabet, "Cationic zinc (II) phthalocyanine nanoemulsions for photodynamic inactivation of resistant bacterial strains.", Photodiagnosis and photodynamic therapy, vol. 34, pp. 102301, 2021. Abstract

BACKGROUND: The growing emergence of microbial resistance to antibiotics represents a worldwide challenge. Antimicrobial photodynamic inactivation (aPDI) has been introduced as an alternative technique, especially when combined with nanotechnology. Therefore, this study was designed to investigate the therapeutic merits of combined aPDI and nanoemulsion in infections caused by resistant bacterial strains.

METHODS: Cationic zinc (II) phthalocyanine nanoemulsions (ZnPc-NE) were prepared using isopropyl myristate (IPM) as oil phase, egg phosphatidylcholine (egg PC) as emulsifier, and N-cetyl-N,N,N-trimethyl ammonium bromide (CTAB). Nanoemulsions were characterized for particle size, polydispersity, zeta potential, viscosity, and skin deposition. The in-vitro aPDI was investigated on human resistant pathogens; gram-positive methicillin-resistant Staphylococcus aureus (MRSA) and gram-negative Multidrug-resistant strain of Escherichia coli (MDR E. coli), under different experimental conditions. In addition, in-vivo model of abrasion wound infected by MDR E. coli was induced in rats to investigate the therapeutic potential of the selected formulation.

RESULTS: It was evident that the selected ZnPc formulation (20 % IPM, 2 % egg PC and 0.5 % CTAB) displayed a particle size of 209.9 nm, zeta potential +73.1 mV, and 23.66 % deposition of ZnPc in skin layers. Furthermore, the selected formulation combined with light achieved almost 100 % eradication of the two bacterial strains, with superior bacterial load reduction and wound healing propertiesin-vivo, compared to either the nanoemulsion formulation or laser alone.

CONCLUSION: ZnPc nanoemulsion improved antimicrobial photodynamic therapy in inactivating resistant bacterial infections and provided a promising therapeutic means of treating serious infections, and hence could be applied in diseases caused by other bacterial strains.