Phenotypic and Molecular Characterization of Multidrug-Resistant Escherichia Coli and Staphylococcus Aureus Strains Isolated from Clinical and Environmental Samples

Background: Today, antimicrobial resistance (AMR) poses a major threat to humanity, resulting in ineffective treatment of bacterial infections. The study aimed to evaluate phenotypic and molecular characteristics of MDR E. coli and S. aureus strains isolated from clinical and environmental samples in a hospital, Calabar, Nigeria. Methods: A total of 240 samples (75.0%, n = 180 clinical samples; 25,0%, n = 60 environmental samples) were collected and cultured. Phenotypic analysis was conducted on 174 E. coli and 193 non-duplicate suspected coagulase-positive S. aureus strains isolated from burn wound, urine, blood, sputum, ear swab, skin swab, catheter and used cotton wool in University of Calabar Teaching Hospital. Presumptive identification was carried out based on microbiological standards. Molecular characterization techniques, such as PCR, single gene 16S rRNA sequencing, and phylogenetic analysis were employed to confirm the identity of two select strains of E. coli and S. aureus. Antibiotic susceptibility testing was evaluated using Kirby Bauer disc diffusion method with a total of fifteen (15) antibiotics belonging to five different classes of antibiotics. The demographic characteristics of age and gender were only applicable to specimens from patients, which included 107 females (59.4%) and 73 males (40.5%); while the median age was 30 years. Results: A total of one hundred and ninety-three (193) S. aureus strains were isolated in this study from different clinical specimens and environmental samples. The highest percentage (23.3%) was recovered from burn wound. The least percentage prevalence (1.6%) of S. aureus strains were recovered from sputum specimen. E. coli isolates recorded highest percentage prevalence (61, 25.4%) from urine specimen, out of a total of 174 isolates obtained from 240 samples collected. The least number of isolates (4, 1.6%) of E. coli strains were recovered from skin swab. S. aureus strain demonstrated resistance to all the β-lactam drugs tested, gentamycin and streptomycin (aminoglycosides), erythromycin (macrolide), and sulphamethoxazole/trimethoprim (sulphonamide). The organism was sensitive to chloramphenicol and levofloxacin with higher percentage resistance rate (66.66%) compared to 53.33% of E. coli. However, E. coli was susceptible to augmentin, oxacillin, streptomycin, chloramphenicol, levofloxacin, and ceftazidime but resistant to ampicillin, amoxicillin, oxacillin, gentamycin, amikacin, erythromycin, norfloxacin and sulphamethoxazole/trimethoprim. Conclusion: This evaluation demonstrates significant occurrence of multidrug-resistant E. coli and S. aureus strains in the study area, suggesting that the current treatment for these bacterial infections in the region is not effective which is a public health concern.