Methicillin-resistant Staphylococcus aureus (MRSA) strains are associated with serious complications and poor clinical outcome. In Egypt, they contribute to more than 70% of S. aureus 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.

The treatment failure recorded among patients and animals infected with diarrheagenic Escherichia coli (DEC) was increased due to the presence of specific virulence markers among these strains. These markers were used to classify DEC into several pathotypes. We analyzed the correlations between DEC pathotypes and antimicrobial resistances, the existence of virulence genes, serotypes, and hosts. The ETEC pathotype was detected with a high prevalence rate (25%). Moreover, the ETEC and EPEC pathotypes were highly associated with human infections in contrast to the EIEC and EAEC phenotypes, which were commonly recognized among animal isolates. Interestingly, the antimicrobial resistance was affected by E. coli pathotypes. With the exception of EIEC and STEC, imipenem represented the most effective antibiotic against the other pathotypes. There were fixed correlations between the DEC pathotypes and the presence of virulence markers and hosts; meanwhile, their correlation with serotypes was variable. Additionally, the vast majority of our isolates were highly diverse, based on both phenotypic and ERIC molecular typing techniques. Our promising results gave a clear indication for the heterogeneity and weak clonality of DEC pathotypes in Egypt, which can be utilized in the evaluation of the current therapeutic protocols and infection control guidelines.

There is growing concern regarding biofilm-producing methicillin-resistant Staphylococcus aureus (MRSA) due to the sudden rise in infection rates and associated morbidity and mortality. Therefore, epidemiological studies, including molecular typing and correlation analysis, are essential for understanding this pathogen. This cross-sectional study investigated epidemiological factors and correlations in MRSA isolates. A total of 300 clinical samples were collected between January and March 2023 from 2 healthcare facilities, including various sample types such as sputum, blood, urine, pus, wound swabs, and other body fluids. This study employed various phenotypic and genotypic methodologies, including adherence assays using standard microtiter plates, the Congo red agar method, antimicrobial resistance and virulence profiling, and multi-locus sequence typing. Among 300 clinical samples from 2 healthcare facilities in Egypt, 94 MRSA isolates were confirmed as biofilm producers. Phylogenetic analysis revealed 8 distinct sequence types (ST8, ST80, ST239, ST15, ST22, ST113, ST398, ST984), found in surgical unit samples across both facilities. Notably, ST22-MRSA was present in all departments, indicating its widespread nature and potential for cross-departmental transmission. ST239-MRSA, the most prevalent strain (22.3%), was found in all departments except burn units. Alarmingly, 95.7% of isolates exhibited multidrug-resistant patterns. However, resistance to vancomycin and imipenem was low among biofilm-producing isolates. The high diversity of MRSA strains suggests multiple sources of infection rather than a single origin. Although most isolates were unrelated, the presence of 2 ST80 isolates in sputum samples from the same unit underscores the importance of targeted infection control within and between hospital areas. ST8-MRSA strains carrying the vanA gene were predominantly identified in body fluid samples, highlighting the need for regular testing in such cases. The diversity of MRSA strains across hospital departments indicates a complex infection landscape with no single source. Although certain genetic markers are linked to specific sequence types, they are not reliable indicators of MRSA clonality. These findings emphasize the need for strict infection control measures and regular testing, particularly for ST8-MRSA in body fluids.