Aims: The coronavirus disease 2019 (COVID-19) is a contagious respiratory disease. The massive use of antibiotics during COVID-19 treatment induced the problem of antibiotic resistance among different strains of microbiome. The current study was conducted to evaluate the level of antibiotic resistance among pathogenic and microbiome bacteria isolated from the blood and upper respiratory tract of COVID-19 patients and its correlation with the case fatality rate in each patient. Methodology and results: COVID-19 patients were diagnosed using real-time reverse transcription-polymerase chain reaction (RT-PCR) technique. Swabs and blood samples were collected from each patient to isolate bacteria and every isolate identification was performed using the bioMérieux VITEK® 2 system. The case fatality rate among the study group was 50% for patients whose isolates were highly antibiotic-resistant. Blood culture was positive in 2.5% compared to nasal swab culture in 65%. Results of nasal swab culture revealed growth of Gram-positive bacteria isolated from 17.1% of patients, Gram-negative isolates were found in 9.75% and fungal isolates formed 9.75%. Most of the isolates were reflective of normal microbiomes; unfortunately, isolates were 100% resistant to penicillins, cephalosporins, azithromycin and amoxicillin-clavulanate. On the other hand, isolates were 100% sensitive to daptomycin. Conclusion, significance and impact of study Results were alarming and there is a need to take measures to prevent the increase in bacterial resistance to antibiotics and limit the excessive use of it. It is crucial to monitor the rise in fungal infections among patients and consider it a risk factor for increasing the case fatality rate.