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Chapter 74 : Detection and Characterization of Antimicrobial Resistance Genes in Pathogenic Bacteria *
This chapter focuses specifically on genotypic methods for detecting and characterizing antimicrobial-resistant bacterial pathogens. There are four major reasons to use genetic tests to identify antimicrobial resistance genes or mutations associated with resistance in bacterial isolates. DNA sequence analysis has been particularly helpful for identifying point mutations in genes associated with extended-spectrum-β-lactamases (ESBLs) and resistance to carbapenems, fluoroquinolones, oxazolidinones, and antimycobacterial drugs. There are several potential pitfalls associated with using genetic tests to detect resistant organisms. The plethora of novel resistance mechanisms, as outlined in this chapter, suggests that phenotypic methods to identify resistance in the organism groups will continue to have value at least for the next decade. In sections, the chapter reviews applications of molecular diagnostic methods for specific classes of resistance determinants. The rapid detection of klebsiella pneumoniae carbapenemases (KPC)-containing isolates may also be facilitated by using one of several real-time polymerase chain reaction (PCR)-based assays. Mupirocin is an antistaphylococcal agent that is used to suppress or eliminate nasal carriage of staphylococci among colonized patients and hospital personnel. All PCR assays for antimicrobial resistance genes, whether sold commercially or developed in-house, must be validated before use.