Dalal M. Alkuraythi

Background: Oils from medicinal plants, including thyme (Thymus vulgaris), cinnamon (Cinnamomum verum), and black seed (Nigella sativa), are recognized for their antibacterial and antioxidant properties. While several studies have investigated individual oils and binary combinations, fewer reports have examined ternary mixtures using systematic optimization approaches. Accordingly, the present study aimed to optimize the antibacterial and antioxidant performance of combinations of these three plant-derived oils using a statistical mixture design strategy supported by in silico exploration. Methods: An Augmented Simplex Centroid Mixture Design was applied to evaluate the individual and combined effects of thyme, cinnamon, and black seed oils. Antibacterial activity was assessed by determining the minimum inhibitory concentrations (MICs) against Escherichia coli and Staphylococcus aureus, while antioxidant activity was measured using the DPPH radical scavenging assay (IC₅₀). The experimental data were fitted to a special cubic model, and model validity was verified through ANOVA parameters, including F-values, R², and adjusted R². Multi-response optimization was performed using a desirability function. Potential interactions among oils were further examined using checkerboard assays. Molecular docking and ADMET predictions were conducted as supportive, hypothesis-generating tools. Results: The special cubic model was statistically significant for all responses (p < 0.0001), with R² values of 0.9763, 0.9944, and 0.9841 for MIC_{E. coli}, MIC_{S. aureus}, and DPPH IC₅₀, respectively. Response surface analysis and multi-response optimization identified the optimal oil mixture as thyme (41.7%), cinnamon (41.7%), and black seed (16.7%), achieving MIC values of 0.5 µL/mL for E. coli and 0.517 µL/mL for S. aureus, and a DPPH IC₅₀ of 5.32 ± 0.52 mg/mL. Checkerboard assays confirmed synergistic interactions for the optimized formulation, with ΣFIC values of 0.15 and 0.29 against E. coli and S. aureus, respectively. Cytotoxicity testing of the optimized formulation on WI-38 normal fibroblasts indicated high cell viability (>92%) at all tested concentrations. In silico docking showed favorable binding affinities of major oil constituents with bacterial targets, and ADMET analysis suggested acceptable pharmacokinetic and safety profiles. Conclusions: The study demonstrated that specific combinations of thyme, cinnamon, and black seed oils can synergistically enhance antibacterial and antioxidant activities. The optimized formulation exhibited enhanced antibacterial and antioxidant activities with minimal cytotoxicity, while in silico analyses provided supportive mechanistic insights.

The emergence and expansion of methicillin-resistant Staphylococcus aureus (MRSA) clones in healthcare facilities pose a significant public health concern due to their adaptability and resistance to commonly used antibiotics. In this study, the genomic and epidemiological characteristics of 81 MRSA isolates collected between February and June 2022 were analyzed. ST5 (25.9%) and ST6 (19.7%) emerged as the dominant sequence types, collectively accounting for 45.6% of infections. Whole-genome sequencing and phenotypic analyses revealed that ST5 clone exhibited a broader multidrug-resistant profile compared to ST6 clone, with higher prevalence of β-lactam, tetracycline, and trimethoprim resistance. ST6 clone showed more variable resistance, including aminoglycoside and macrolide genes, suggesting a possible community origin before adaptation to hospital settings. Phylogenetic analysis demonstrated ongoing microevolution within Clonal Complex 5 (CC5), including the identification of novel single-locus variants such as ST8111. Correlation analyses highlighted significant associations between key resistance genes and their phenotypic profiles, reflecting complex co-resistance mechanisms. Additionally, virulence profiling revealed that ST5 uniquely carried tsst -1, whereas PVL genes were absent in both ST5 and ST6 and appeared only in a small subset of other MRSA clones. The emergence of highly resistant clones like ST672 underscores the potential concern for sustained genomic surveillance. The observed clonal shift from ST239 to ST5 and ST6 signals a dynamic MRSA landscape in Saudi Arabia, emphasizing the need for integrated molecular epidemiology and targeted infection control strategies.

Methicillin-resistant Staphylococcus aureus (MRSA) surveillance in regions with mass gatherings presents unique challenges for public health systems. Saudi Arabia, hosting millions of pilgrims annually, provides a distinctive setting for studying how human mobility shapes bacterial populations, yet comprehensive genomic surveillance data from this region remain limited. Here, we present an integrated analysis of S. aureus isolates collected across seven Saudi Arabian regions, combining whole-genome sequencing with extensive antimicrobial susceptibility testing and standardized metadata following findability, accessibility, interoperability and reusability data principles. Our analysis revealed striking differences between pilgrimage and non-pilgrimage cities. Pilgrimage cities showed significantly higher genetic diversity and antimicrobial resistance rates, harbouring numerous international strains, including recognized clones from diverse geographic origins. Reported lineage dynamics are changing, expanding toward community clones. While genomic prediction of antimicrobial resistance showed high accuracy for some antibiotics, particularly beta-lactams, with varying performance for others, it highlights the necessity for phenotypic testing in clinical settings. Our findings demonstrate how mass gatherings drive bacterial population structures and emphasize the importance of integrated surveillance approaches in regions with significant global connectivity and travel.

Escherichia coli , typically harmless, resides in the gut. However, certain strains are lethal pathogens. Here, we report a draft genome sequence of a multidrug resistance E. coli O13/O129 (food source) in Saudi Arabia. O-antigen of E. coli O13/O129 is closely related to Shigella flexneri (causative agent of shigellosis).

In Saudi Arabia, the occurrence of methicillin-resistant Staphylococcus aureus (MRSA) in food and livestock represents a major public health hazard. The emergence of livestock-associated MRSA has heightened the risk of human infection with comparable virulence traits. The lack of information about MRSA transmission in our region hinders accurate risk assessment, despite its detection in food animals and retail foods. Adopting a One Health approach is essential for effectively combating MRSA in Saudi Arabia. This method unites actions in the human, animal, and environmental spheres. To combat MRSA contamination, surveillance measures need strengthening; interdisciplinary collaboration among healthcare professionals, veterinarians, and environmental scientists is crucial, and targeted interventions must be implemented in local food chains and animal populations. Through a holistic strategy, public health and sustainable food production in the region are protected. This review aims to improve public health interventions by increasing understanding of MRSA prevalence and related risks in local food chains and animal populations. Keywords: antibiotic resistance, food-producing animals, livestock-associated methicillin-resistant Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, Saudi Arabia.

Introduction: Staphylococcus aureus is a significant human pathogen that poses a threat to public health due to its association with foodborne contamination and a variety of infections. The factors contributing to the pathogenicity of S. aureus include virulence, drug resistance, and toxin production, making it essential to monitor their prevalence and genetic profiles. This study investigated and compared the genomic characteristics of S. aureus isolates from retail meat and patients in Saudi Arabia.Methods: A total of 136 S. aureus isolates were obtained between October 2021 and June 2022:84 from patients and 53 from meat samples in Riyadh, Saudi Arabia. S. aureus isolates were identified using conventional methods and MALDI-TOF MS, and methicillin-resistant S. aureus (MRSA) was identified using VITEK2 and BD Phoenix systems. MRSA was confirmed phenotypically using chromogenic agar, and genotypically by detecting mecA. Genomic data were analyzed using BactopiaV2 pipeline, local BLAST, and MLST databases.Results: Antibiotic resistance genes were prevalent in both meat and patient S. aureus isolates, with high prevalence of tet38, blaZ, and fosB. Notably, all S. aureus isolates from patients carried multidrug-resistant (MDR) genes, and a high percentage of S. aureus isolates from meat also harbored MDR genes. Phenotypically, 43% of the S. aureus isolates from meat and 100% of the patients’ isolates were MDR. Enterotoxin genes, including selX, sem, and sei, exhibited high compatibility between meat and patient S. aureus isolates. Virulence genes such as cap, hly/hla, sbi, and isd were found in all S. aureus isolates from both sources.Conclusion: Our study established a genetic connection between S. aureus isolates from meat and patients, showing shared antibiotic resistance and virulence genes. The presence of these genes in meat derived isolates underscores its role as a reservoir. Genomic relatedness also suggests potential transmission of resistance between different settings. These findings emphasize the necessity for a comprehensive approach to monitor and control S. aureus infections in both animals and humans.

In this study, we investigated both meat-derived and methicillin-resistant Staphylococcus aureus (MRSA), exploring their genetic relatedness to patient-derived MRSA isolates in Saudi Arabia. We collected 250 meat samples and identified 53 S. aureus isolates, with 79% being methicillin-sensitive Staphylococcus aureus (MSSA) and 21% being MRSA. Moreover, we included 80 clinically confirmed patient-derived MRSA isolates. We identified the most common S. aureus clone in both patients and retail meat. In meat, ST6 and ST97 were the most common clones in 55% of the MRSA isolates, and ST1153 and ST672 were the most common in 21% and 17% of the MSSA isolates. In patients, ST5 and ST6 were the predominant clones in 46% of the S. aureus isolates. CC5/ST5-SCCmecVc-t311 and CC361/ST672-SCCmecV-t3841 were common MRSA clones in both meat and patients. CC97 and CC361 clones were the second most prevalent S. aureus clones in meat and were relatively common in patients. Furthermore, we sequenced and characterized novel S. aureus strains ST8109, ST8110, and ST8111. The genomic similarities between meat- and patient-derived S. aureus isolates suggest that retail meat might be a reservoir for S.aureus and MRSA transmission. Therefore, a structured One Health approach is recommended for S. aureus dissemination, genetic characterization, antibiotic resistance, and impact on human health.

Hospitals and communities are significant hubs for antibiotic-resistant staphylococcal infections, but recently there have been spread of the Staphylococci to other settings including farms and food chains. This study aimed to compare the methicillin-resistant Staphylococcus aureus (MRSA) isolates from humans and food to understand the genetic characteristics and similarities between the circulating clones across both groups. A total of 250 samples of meat (camel, beef, chicken, fish, and lamb) were collected from different retailers in Riyadh, Saudi Arabia. Culture, and Genomics analysis of the isolates yielded 53 S . aureus out of which (42/53; 79%) were methicillin-sensitive S . aureus (MSSA) and (11/53; 21%) were MRSA in addition to to other Staphylococci. 80 clinically confirmed MRSA isolates were obtained from patients in the same city. The most common S. aureus clone in patients and retail meat belonged to clonal complex (CC5). In meat, ST6 and ST97 were the most common clones found in (6/11; 54.5%) of MRSA isolates, and ST1153 (9/42; 21.42%), ST672 (7/42; 16.66%) of MSSA isolates. The majority of MRSA isolates in meat carried SCC mec type V, which was observed in (6/11; 54.54%) of isolates. While in patients, ST5 and ST6 were the predominant clones found in (37/80; 46%) of MRSA isolates. The most prevalent SCC mec types in MRSA isolates from patients were SCC mec type IVa, which was observed in (39/80; 48.7%) of isolates. While there was no MRSA found in beef, camel meat had the highest prevalence of MRSA ST6-t2450 contamination. The other two clones, CC97 and CC361, were the second-most prevalent clones in meat and were relatively common among patients. Novel S. aureus lineages were sequenced and characterized for the first time ST8109 from meat and ST8110 and ST8111 from patients. A structured One Health approach on S. aureus considering its dissemination, genetic characterization, antibiotic resistance, and overall impact on food intended for human consumption and its effect on human health is advised.