There are a number of enteric pathogens normally present within the GI tract, along with resident flora, that play an important role in digestion and in forming a protective, structural and metabolic barrier against the growth of potentially pathogenic bacteria (Chernecky and Berger [32], Tortora and Derrickson [243]). Pathogenic agents that disrupt the balance within the GI tract manifest in symptoms such as prolonged diarrhoea, bloody diarrhoea, nausea, vomiting, abdominal pain and/or fever. Bacteria in faeces are representative of the bacteria present in the GI tract, so the culture of a faecal sample is necessary for identification of GI tract colonization (Chernecky and Berger [32], Keogh [114], Pagana and Pagana [177]).

Laboratory investigations are requested for bacterial infections such as Salmonella spp., Campylobacter spp., Helicobacter spp., Shigella spp., Escherichia coli and Clostridioides difficile; viral infections such as norovirus and rotavirus; and parasitic pathogens such as protozoa, tapeworms and amoebiasis (HPA 2014c, Weston [255]).

Diarrhoea can be defined as an unusual frequency of bowel actions with the passage of loose, unformed faeces and may be associated with other symptoms such as nausea, abdominal cramping, fever and malaise. It may be attributable to a variety of bacterial, viral or parasitic pathogens and may be associated with antibiotic use, food or travel‐related agents (HPA 2014c, [93]). Prompt collection of a faecal sample for microbiological investigation is essential in determining the presence and identification of such agents.