4 The analytical stage

Diagnostic techniques range from conventional culture-based identification and AST to molecular diagnostic methods. (These techniques are discussed in detail in the modules Isolating and identifying bacteria and Antimicrobial susceptibility testing, so are not explained here.) Each technique has advantages and disadvantages, and a basic understanding is useful to help clinicians optimise their use of the laboratory.

Culture-based methods are part of routine pathogen detection. They require viable organisms to culture, an incubation period for growth and more than 24 hours for results: this means it can take two to three days between taking a sample and getting the final result – sometimes longer for difficult-to-grow bacteria.

More rapid techniques are available: such as quantitative PCR (qPCR), which can quantify the amount of pathogen genetic material and determine the presence of specific genes and alleles. However, these should be used with care, because genes present are not necessarily expressed, and do not necessarily correlate with phenotype. The rapid test may be useful for initial treatment, but results should be correlated with phenotypic and biochemical tests (Kralik and Ricchi, 2017). qPCR can also be used for typing strains and isolates, and for indicating potential toxin production.

Validated international guidelines are available for standard culture techniques and AST such as disk diffusion and broth microdilution. If these are followed carefully, laboratories can have high confidence in their results, and data can be readily compared between facilities and geographic locations. For AST, the international standards used are CLSI and EUCAST (see the module Antimicrobial susceptibility testing).