Stool culture versus FilmArray gastrointestinal PCR in the diagnosis of gastrointestinal infections

Introduction: Gastrointestinal infection is a major cause of morbidity worldwide. Culture and microscopy are time consuming and have low diagnostic yield. New rapid molecular methods such as multiplex PCR have recently been introduced for etiological diagnosis. The purpose of this study was to compare the diagnostic yield of the FilmArray gastrointestinal panel with that of standard culture for the etiological diagnosis of gastrointestinal infections.

Materials and methods: This is a retrospective study carried out within the Microbiology department of the Arrazi hospital of the CHU Mohamed VI, including all the patients treated for a gastrointestinal infection and having required hospitalization in the various departments within the Arrazi Hospital of the CHU Mohamed VI in Marrakech, over a period of 15 months.

Results: During the period studied, 124 patients were sampled. All samples were tested using stool culture and FilmArray. PCR detected significantly more positive samples, with bacterial, viral and/or parasitic infections compared to stool culture (57.3% vs 21%). Additionally, gastrointestinal PCR was able to detect all pathogens implicated in the gastrointestinal FilmArray panel except for Yersinia Enterocolitica, whereas stool culture could only detect three bacterial pathogens (E.coli, Salmonella and Shigella). Additionally, 52.11% of patients had co-infections that were identified only by PCR.

Conclusions: The FilmArray GI panel showed very good diagnostic performance compared to culture for the diagnosis of gastrointestinal infections and gave a more detailed picture of the spectrum of pathogens involved. Further studies are needed to determine whether multiplex PCR improves patient outcomes and reduces costs.