Samar M. El-Shahidy

Background: Respiratory tract infections (RTIs) remain a major cause of morbidity and mortality, particularly among hospitalized and critically ill patients. The increasing prevalence of multidrug-resistant organisms (MDROs) complicates treatment and highlights the need for local surveillance to guide antimicrobial stewardship. This study investigated the epidemiology, antimicrobial resistance patterns, and seasonal trends of respiratory bacterial pathogens in a tertiary care hospital in Riyadh, Saudi Arabia. Methods: A retrospective observational study was conducted on 5582 respiratory specimens collected between January 2023 and December 2025. Samples included tracheal aspirates, sputum, bronchoalveolar lavage, throat swabs, pleural fluids, ear swabs, and nasal swabs. Bacterial identification and antimicrobial susceptibility testing were performed using the VITEK® 2 Compact system and interpreted according to CLSI M100-S35 guidelines. Statistical analyses included Chi-square tests and logistic regression. Results: Culture positivity was 38.6% (2154/5582), with tracheal aspirates and sputum accounting for the most positive specimens. The predominant pathogens were Pseudomonas aeruginosa (31.9%), Klebsiella spp. (21.3%), Staphylococcus aureus (10.2%), Serratia marcescens (6.3%), Escherichia coli (5.7%) and Acinetobacter baumannii (5.5%). Culture positivity increased significantly with age (p< 0.001), with Gram-negative bacteria predominating in older patients. MDROs were slightly prevalent, including, carbapenem-resistant organisms (22.9%) and ESBL producers (12.3%). The highest MDRO burden occurred in intensive care and other high-acuity wards. Seasonal analysis demonstrated a significant increase in MDRO prevalence during the summer months, with carbapenem-resistant Gram-negative pathogens rising from 18.2% in the winter to 28.7% in the summer (OR 1.82, 95% CI: 1.45– 2.28; p< 0.001). Conclusions: Respiratory pathogens in this Saudi tertiary care hospital exhibited a high prevalence of multidrug resistance, particularly among Gram-negative bacteria and in critical care settings. Seasonal increases in resistance during the summer months suggest the need for intensified infection control measures, strengthened antimicrobial stewardship, and ongoing surveillance to reduce MDRO transmission and optimize patient outcomes.

Background Viral–bacterial co-infections contribute to disease severity in pediatric acute gastroenteritis but are frequently underdiagnosed using routine methods. Enteric viruses, including human adenoviruses (HAdVs), may coexist with bacterial pathogens that influence intestinal pathology through virulence and antimicrobial resistance determinants. This study applied shotgun metagenomic sequencing to characterize concurrent viral and bacterial pathogens in a pediatric prolonged diarrhea. Methods Shotgun metagenomic sequencing was performed on a pediatric diarrheic stool sample, followed by quality filtering, de novo assembly, taxonomic classification, phylogenetic reconstruction, and integrated virulome-resistome profiling, including plasmid-associated resistance elements. Results Routine diagnostics identified adenovirus as the sole pathogen. Metagenomic analysis confirmed human adenovirus F40, showing close phylogenetic relatedness to globally distributed HAdV-F40 reference strains and a clear distinction from HAdV-F41. In addition, metagenomics uniquely detected a co-occurring Clostridium perfringens strain (SAM_A8, ST-5) that was not recovered by culture. The strain lacked the classical enterotoxin gene ( cpe ) but harbored a conserved histotoxic virulence profile, including plc , pfoA , colA , hyaluronidases, and sialidases. Plasmid-associated tetracycline resistance genes ( tetA(P) and tetB(P) ) were also identified. Conclusion Shotgun metagenomic sequencing enabled genomic characterization of a viral–bacterial co-infection missed by conventional diagnostics, highlighting its value for pathogen identification and resistance surveillance.