Genotypic Drug Resistance Assays

Abstract

Antimicrobial resistance has become a major public health threat worldwide. Some hospital-acquired pathogens are becoming multiple resistant or totally resistant to antimicrobials. Known examples include vancomycin-resistant Enterococcus faecium and E. faecalis (VRE), methicillinresistant Staphylococcus aureus (MRSA), vancomycinintermediate and -resistant S. aureus (VISA and VRSA), and extended-spectrum β-lactamases (ESBL)-producing Enterobacteriaceae (1). In the community, the prevalence of multidrug resistance in Streptococcus pneumoniae is increasing in some countries and includes resistance to β-lactams (intermediate and high-level resistance to penicillin and cross-resistance to cephalosporins), the macrolides and, more recently, the fl uoroquinolones (2). Furthermore, virulent strains of MRSA that differ from the hospital strains have emerged in the communities of several countries (3). Another major public health problem is the increasing incidence of multidrug-resistant Mycobacterium tuberculosis (4). Physicians practicing in both hospitals and the community must treat infections caused by multiresistant organisms, and new, emerging antimicrobial resistances are becoming more complex to detect (5). With the limited number of antimicrobial agents available to treat the infections caused by multidrug-resistant organisms, the need for rapid and reliable susceptibility testing methods or alternative resistance testing methods for detection of antimicrobial resistance becomes increasingly important. Conventional phenotypic culture-based susceptibility test results are usually obtained in 24–48 h or more after a bacterial culture has been isolated. Moreover, susceptibility tests are not always accurate in diffi cult-to-detect emerging antimicrobial resistance and often more than one method is needed to obtain an accurate susceptibility profi le. The lack of accurate and timely susceptibility data by the microbiology laboratory has consequences on antibiotic usage and prescription. Patients have to be treated empirically and often with broad-spectrum antibiotics, which results in increased resistance rates and healthcare costs (6). The advances in our understanding of the genetic mechanisms of antimicrobial resistance and the progress in sample preparation, nucleic acid–based amplifi cation, and sensitive nucleic acid detection have allowed the development of genotypic methods for rapid detection of antimicrobial resistance. While most genotypic resistance tests are presently performed with pure bacterial culture which requires at least 18–24 h, it is now possible to identify a microorganism and its resistance to antimicrobial agents directly from clinical specimens in 1 h (7, 8). Some genotypic drug resistance assays are increasingly used in the clinical settings, providing more accurate and rapid resistance testing. The purpose of this review is to describe the mechanisms of antimicrobial resistance and to present some genotypic drug resistance assays used to detect antimicrobial resistance. Genotypic drug resistance assays that are increasingly used in the clinical microbiology laboratory and their applications in the clinical settings will be further discussed.