Chapter 32 : Detection of Antimicrobial Resistance Genes and Mutations Associated with Antimicrobial Resistance in Bacteria

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During the past several years, commercial products for direct detection of antimicrobial-resistant microorganisms, antimicrobial resistance genes, and mutations associated with antimicrobial resistance have been introduced into the clinical laboratory market. In this chapter, a variety of methods of detecting resistant microorganisms are explored and several novel mechanisms of antimicrobial resistance are reviewed. Commercial real-time PCR assays to detect resistant bacteria directly in clinical samples are now used in many laboratories worldwide to detect methicillin-resistant (MRSA) strains in nasal samples and vancomycin-resistant enterococci (VRE) in stool samples. Detection of mutations associated with resistance can be accomplished by pyrosequencing, line probes, molecular beacons, microarrays, or a variety of other technologies. Phenotypic detection of oxacillin resistance in staphylococci, which is mediated primarily by the mecA determinant, has improved with the substitution of cefoxitin for oxacillin in disk diffusion and MIC testing protocols, particularly with the coagulase-negative strains. While DNA sequencing remains the gold standard for analyzing novel β-lactamase genes, novel microarrays can also be used to identify β-lactamase genes. Additional methods, such as pyrosequencing and microarrays, will soon be available commercially to detect mutations associated with resistance. Thus, rapid detection of antimicrobial-resistant bacteria is likely to become a standard practice in most clinical laboratories, which should have a positive impact on both infection control practices and improvement of anti-infective therapy.

Citation: Tenover F, Rasheed J. 2011. Detection of Antimicrobial Resistance Genes and Mutations Associated with Antimicrobial Resistance in Bacteria, p 507-524. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch32
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PCR assays for antimicrobial resistance genes

Citation: Tenover F, Rasheed J. 2011. Detection of Antimicrobial Resistance Genes and Mutations Associated with Antimicrobial Resistance in Bacteria, p 507-524. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch32
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Multiplex PCR assays for detection of antimicrobial resistance genes

Citation: Tenover F, Rasheed J. 2011. Detection of Antimicrobial Resistance Genes and Mutations Associated with Antimicrobial Resistance in Bacteria, p 507-524. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch32
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Novel amplification methods for detecting antimicrobial resistance genes or mutations associated with resistance

Citation: Tenover F, Rasheed J. 2011. Detection of Antimicrobial Resistance Genes and Mutations Associated with Antimicrobial Resistance in Bacteria, p 507-524. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch32

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