Molecular Diagnosis of Gastrointestinal Infections

Abstract

Enteric infections cause significant morbidity and mortality and have a significant financial cost worldwide. This chapter discusses the molecular techniques for the clinical identification of the bacteria, viruses, and parasites most commonly responsible for infections of the lower gastrointestinal tract. Numerous studies have reported on the development of PCR assays for the detection of enteric pathogens. Overall, multiplex, real-time PCR assay is favored because of its speed and elimination of postamplification carryover. The chapter summarizes the advancements achieved for the detection of enteric bacterial pathogens by molecular methods and discusses the remaining challenges. It also discusses the special case of hospital-acquired Clostridium difficile infection and the role of molecular methods in its diagnosis. Except for Plesiomonas shigelloides, which causes disease only in some patients, Salmonella, Shigella, and Yersinia enterocolitica are intrinsic enteric pathogens in humans. Importantly, the sequence of the viral capsid protein encoded by open reading frame 2 (ORF2) correlates directly with the serotype, making RT-PCR the most common technique for astrovirus detection and typing. The major pathogenic intestinal coccidia include Cryptosporidium parvum, Cryptosporidium hominis, Cyclospora cayetanensis, and Isospora belli, with Cryptosporidium spp. being the most common. The microsporidia are composed of more than 1,000 species of small, spore-forming, obligate intracellular organisms originally classified as protozoa but now considered fungi.