Gastroenteritis is a transient illness characterised by the sudden onset of diarrhoea with or without vomiting. It can be caused by infection with bacteria, viruses or parasites. About 20% of the UK population develop gastroenteritis each year (NICE 2014) with an estimated 17 million cases annually in the UK (Tam et al. 2012).

Common bacterial pathogens causing gastroenteritis are Campylobacter, Salmonella, E. coli O157 and Shigella sonnei. Public Health England statistics (Public Health England 2015a) show that in England in 2014 there were:

  • 58,722 positive laboratory reports of Campylobacter

  • 6672 positive laboratory reports of Salmonella

  • 1088 positive laboratory reports of Shigella

  • 891 positive laboratory reports of E. coli O157.

Rarer bacterial pathogens include Shigella boydii, Shigella dysenteriae and Shigella flexneri. Public Health England statistics (Public Health England 2015b) show that in 2014 there were:

  • 711 positive laboratory reports of Shigella flexneri

  • 58 positive laboratory reports of Shigella boydi

  • 29 positive laboratory reports of Shigella dysenteriae.

Polymerase chain reaction (PCR) is a molecular technique that involves the detection and amplification of DNA from clinical samples. In recent years multiplex real‑time PCR has been developed to give rapid, quantitative detection of multiple pathogens from a single sample at the same time (Reddington et al. 2014). Different PCR‑based systems are available, offering different tests with varying levels of automation. PCR‑based detection of pathogens is faster than traditional bacterial culture techniques and in some cases offers greater sensitivity and specificity.

The increased sensitivity of PCR‑based detection of pathogens compared with bacterial culture methods may partly reflect the detection of DNA after an acute infection has resolved. Antibiotic treatment may kill the bacteria, but the bacterial DNA can still be detected by PCR. Persistent detection can occur in chronic and convalescent carriers after an acute infectious episode (Health Protection Agency, now Public Health England, 2013). As such it is possible that increased detection of DNA may result in unnecessary treatment.