DETECTING ANTIMICROBIAL RESISTANCE

Traditionally, resistance is detected using the disc diffu­sion method, where a lawn of bacterial culture is grown in the presence of paper discs infused with known concen­trations of antibiotics.

DNA methods for detecting and characterising resist­ance in the host and the environment are now widely used (D’Costa et al. 2006; Schmieder and Edwards 2012). Direct PCR tests have been developed for the detection of genes associated with resistance to different classes of antibiotics and these can be performed on bacterial strains or envi- ronmental/faecal/urogenital DNA (Power et al. 2013; Gill­ings et al. 2014; Chen et al. 2015; McDougall et al. 2023). The development of high throughput qPCR and metagen­omics allows the resistome (all resistance genes present) in diverse sample types to be determined (Ferreira et al. 2023). Increasingly, resistant bacterial isolates are under­going whole genome sequencing to identify genetic resist­ance mechanisms (Florensa et al. 2022), which has the added benefit of determining bacterial strain type, patho­genicity and phylogeny (McDougall et al. 2021a). Best practice would be to combine genetic methods with the traditional culture and susceptibility-based screening to determine if the presence of genetic indicators of resist­ance is coupled to a phenotype (Piddock 2016). This meth­odological combination is particularly important given the rapid rate at which new genetic technologies are being applied to pathogen research and diagnosis.

Although there are diverse genes and mechanisms of resistance, those of most concern enable resistance to those antibiotics considered the ‘last-line’ of defence: β-lactams (methicillin, 3rd- to 5th-generation cephalo­sporins and carbapenems), the fluoroquinolones (cipro­floxacin and enrofloxacin) and glycopeptides (vancomycin). The genetic basis of resistance to these different classes is fairly well known.

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