5.2 Identification to genus and species level

If the identification of a pathogen’s species requires costly or time-consuming testing schemes or expertise only available in specialised laboratories, the identification may be limited to the genus level. For example, animal diagnostic laboratories often report ‘Salmonella spp.’ (i.e. genus-level), and sometimes the serogroup (for example, ‘Group D’ Salmonella). The identification of Salmonella to species and serovar levels is often performed at reference laboratories.

The professional requesting the tests is responsible for the interpretation of the bacteriological results. For instance, a laboratory report of the isolation of a coagulase-positive Staphylococcus from a case of bovine mastitis is usually interpreted as an infection with the species S. aureus, as non-aureus coagulase-positive staphylococci are extremely uncommon in cows.

Lastly, some bacterial groups include species with broadly overlapping phenotypes, making it difficult to distinguish between them using phenotypic keys. In these cases, the species could be defined using genetic markers or advanced techniques, as you will learn in Sections 7.4–7.5.