Detection of Multidrug-Resistant Organisms in Clinical Isolates: A Systematic Review of Prevalence, Resistance Mechanisms, and Diagnostic Advances

Abstract

Background:
The global rise of multidrug-resistant organisms (MDROs) poses a severe threat to healthcare systems, increasing mortality, prolonging hospital stays, and imposing substantial economic burdens (Marino et al., 2025). Effective infection prevention and control (IPC) and clinical management depend critically on the timely and accurate laboratory detection of these pathogens and their resistance mechanisms in clinical isolates.
Methods:
This systematic review followed PRISMA 2020 guidelines and was prospectively registered on PROSPERO (CRD42025098765). A comprehensive search of five electronic databases identified 20 eligible studies, including observational cohorts, randomized trials, and surveillance reports. Data were extracted on diagnostic accuracy (phenotypic vs. molecular), prevalence, resistance determinants (e.g., blaNDM-1, mcr- 1), risk factors, and patient outcomes across diverse healthcare settings, with special focus on intensive care units (ICUs) and low- and middle-income countries (LMICs).
Results:
Traditional phenotypic methods remain widely applied due to accessibility, yet advanced molecular assays—particularly metagenomic next-generation sequencing (mNGS), plasma cell-free DNA sequencing, and nanopore platforms—demonstrated superior speed and sensitivity in identifying resistance genes. The review also identified striking geographic disparities in prevalence, with carbapenem-resistant Klebsiella pneumoniae and Pseudomonas aeruginosa most prevalent in LMICs, and emerging fungal MDROs such as Candida auris and azole-resistant Aspergillus fumigatus complicating outbreak control.
Conclusion:
A hybrid diagnostic model, combining phenotypic screening with molecular tools for high-risk cases, is essential for timely treatment and stewardship. Strengthening IPC bundles and integrating genomic surveillance into routine workflows are critical steps to contain MDRO spread. Policy frameworks must prioritize equitable access to these innovations, particularly in LMICs, to mitigate the escalating global challenge of antimicrobial resistance.