Characterization of Opportunistic Bacterial Strains in Intensive Care Unit patients and Assessment of Natural Crude Extracts for Antibacterial Drugs: A Cross-Sectional Study

Background: The prevalence of opportunistic bacterial infections poses a significant challenge in healthcare facilities worldwide, including in Saudi Arabia. These infections are often associated with increased morbidity and mortality, particularly in vulnerable populations such as intensive care unit (ICU) patients. This study was conducted to characterize the opportunistic bacterial strains that are prevalent in healthcare settings across Saudi Arabia. By identifying these strains and their phylogenetic relationships, the study aims to enhance the understanding of the bacterial diversity in these environments and explore potential natural antibacterial agents. Materials and Methods: This descriptive cross-sectional study involved the collection and analysis of 36 samples from ICU patients across six hospitals in Saudi Arabia. The samples were processed to identify bacterial strains using the VITEK 2 automated system, which provides rapid and accurate identification of bacterial species. To further understand the genetic relationships among the bacterial strains, phylogenetic analyses were performed using 16S rRNA gene sequences. Additionally, ten methanolic extracts from natural crude materials were tested in vitro to assess their antibacterial activity against the isolated bacterial strains using the disc diffusion method. Results: The study revealed that all isolated bacteria were Gram-negative. The most prevalent bacterium identified was Klebsiella pneumoniae, accounting for 30.6% of the isolates. This was followed by Pseudomonas aeruginosa (25%), Proteus mirabilis (19.4%), Escherichia coli (13.9%), Serratia marcescens (8.3%), and Citrobacter koseri (2.8%). The DNA extracted from the samples showed high purity, with a purity ratio ranging from 1.8 to 2.0. Phylogenetic tree analysis revealed significant similarities in the nucleotide base sequences of different bacterial strains, particularly between Escherichia coli and Citrobacter koseri. Among the ten natural extracts tested, only four—Melaleuca cajuputi, Acanthaster planci, Stylissa carteri, and Sonneratia lanceolata—exhibited antibacterial activity. These extracts showed varying degrees of inhibition against all isolated bacteria. Conclusion: This study highlights the predominance of Gram-negative bacteria in the ICU settings of Saudi Arabian hospitals, with Klebsiella pneumoniae being the most frequently isolated pathogen. The phylogenetic analysis uncovered notable similarities in the genetic makeup of different bacterial strains, particularly between Escherichia coli and Citrobacter koseri. The findings also underscore the potential of certain natural compounds as effective antibacterial agents, suggesting their promise for future development as alternative antibiotics. These results emphasize the need for continued surveillance of bacterial strains in healthcare settings and the exploration of natural products as a source of new antibacterial drugs.