Molecular Identification of Pathogenic Bacteria in Hospital Environments: Implications for Infection Control and Patient Safety - A Narrative Review

Nathan Rimamsanati Yohanna; Micheal Abimbola Oladosu; Moses Adondua Abah; Joseph  Oteng; Patrick Chimuanya Etus; Sunday Agbo Okabeonye; Oluwadamilola  Zainab  Yakub; Olabisi O. Ogunlewe; Sarah Oluwaseun Julius; Olaide Ayokunmi Oladosu

doi:10.5455/EJMID.20250603023055

Abstract
Abstract
Healthcare-associated infections (HAIs) impose substantial clinical and economic burdens globally, affecting approximately 7% of hospitalized patients in developed countries and causing over 99,000 deaths annually in the United States alone. This narrative review critically evaluates molecular techniques for detecting and identifying nosocomial pathogens, emphasizing their integration into infection surveillance and control strategies. Key bacterial agents examined include spore-forming organisms like Clostridioides difficile, Gram-positive pathogens such as Staphylococcus aureus and Enterococcus species, and Gram-negative bacteria including Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii. Advanced diagnostic modalities assessed include polymerase chain reaction (PCR), 16S rRNA gene sequencing, whole-genome sequencing (WGS), matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), metagenomics, and emerging CRISPR-Cas-based diagnostics. Environmental sampling challenges, biofilm-associated resistance mechanisms, and high-touch surface contamination are analyzed. Integration of molecular diagnostics into routine surveillance has demonstrated significant improvements in outbreak detection (reducing identification time by 48-72 hours), transmission tracking accuracy (>40% improvement in epidemiological investigations), and targeted intervention implementation. Current limitations include cost barriers, technical expertise requirements, and standardization challenges. Future directions encompass artificial intelligence-assisted outbreak prediction, point-of-care molecular diagnostics, and automated environmental monitoring systems. This review underscores the critical role of molecular surveillance in contemporary HAI prevention and provides evidence-based recommendations for clinical implementation.

Key words: Healthcare-associated infections, molecular diagnostics, pathogen identification, infection control, antimicrobial resistance, environmental surveillance