Challenges in identifying antibiotic resistance targets for point-of-care diagnostics in general practice

Mitsakakis, Konstantinos; Kaman, Wendy E; Elshout, Gijs; Specht, Mara; Hays, John P

Phenotypic analysis is a gold standard 'catch-all' technique that determines antibiotic resistance via the inability of a microorganism to replicate in the presence of a minimum inhibitory concentration (MIC) of an antibiotic. However, current problems with phenotypic detection include the 'time to result', sensitivity and the general need for centralized laboratory testing compared with nucleic acid amplification techniques [43] . Additionally, the majority of currently available POC infectious disease diagnostics rely on nucleic acid-based amplification (usually involving polymerase chain reaction (PCR) or isothermal amplification techniques) [44] . The detection of MGE-associated antibiotic resistance genes by nucleic amplification techniques, using conserved regions of DNA as targets, is highly suited to the detection of many (transferable) antibiotic resistance genes. However, antibiotic resistance that occurs due to genetic mutations are less easily detected using standard nucleic acid amplification techniques. This is because these mutations mostly occur in genes normally present in the pathogenic bacterium, for example, ciprofloxacin resistance and the quinolone-resistance determining region, and the detection of the gene per se provides no information on actual phenotypic antibiotic resistance. However, POC diagnostics that detect mutations in combination with gene amplification, for example, gene amplification followed by microarray detection, or gene sequencing [45] , may have a distinct advantage over gene amplification-only POC diagnostics with respect to mutation-associated antibiotic resistance. Essentially, gene amplification-only diagnostics could be perceived as not offering the GP enough clinical information (antibiotic resistance caused by mutations) on which to base an informed antibiotic-prescribing decision. This could seriously impact on the perceived value of a nucleic acid amplification-only diagnostic device to the GP.