Chapter 27 - Molecular detection of antimicrobial resistance

Abstract

Phenotypic methods like growth-based methods have been the gold standard for the detection of resistance mechanisms in clinical microbiology. Despite being the method of choice, reference antimicrobial susceptibility test (AST) methods like broth microdilution or disk diffusion methods to determine susceptible, intermediate and resistant have several limitations, including long-term around time (24–72hours) and significant laboratory hands-on time. Most of the Food and Drug Administration (FDA)-cleared automated AST systems (Vitek, Phoenix, Microscan) have to reduce the hands-on processing time, however, the overall time to get AST results is still relatively long compared to a molecular assay. Genotypic methods like polymerase chain reaction (PCR)-based methods have been used to detect resistance genes and their associated resistance mechanisms. There are many advantages of using a molecular method for the detection of resistance determinants for bacteria, mycobacteria and fungi. The use of molecular methods in the clinical laboratory allows for the rapid identification of resistance determinants for microbial organisms, which is vital for the appropriate management of patients. Recent advances in molecular technologies in the clinical microbiology diagnostics space have simplified that workflow, leading to the implementation of such technologies with little to no training in clinical laboratories. One of the most common molecular methods used by the majority of FDA-cleared assays in the clinical laboratory includes nucleic acid amplification using a PCR method in an end-point or real-time format. Such FDA-approved assays have allowed for a simplified workflow that allows for the detection of single or multiple targets in a direct sample-to-answer format. Access to such user-friendly technologies has shortened the time for the identification of pathogens and detection of resistance markers that can be used to predict AST result for select organisms that have been shown to improve patient outcome and reduce mortality.