P329 Stool multiplex molecular PCR assay in comparison to conventional stool tests for detecting gastrointestinal infections as cause of flares in Inflammatory Bowel Disease

Kutar, M.(1)*;Desai, D.(2);Abraham, P.(2);Gupta, T.(2);

(1)P.D. Hinduja Hospital and Medical Research Centre, Gastroenterology, Mumbai, India;(2)P.D Hinduja Hospital and Medical Research Centre, Gastroenterology, Mumbai, India;


Inflammatory bowel disease (IBD) is characterized by unpredictable flares. Other than natural history, flares can be caused by superadded gastrointestinal (GI) tract infections. Diagnosis of infection is conventionally made by microscopy and culture of stool specimens. These are limited by lengthy turnaround time, low sensitivity, inability to detect agents other than bacteria, and effect of pre-test antibiotic usage.Stool multiplex molecular PCR assay allows simultaneous detection of nucleic acids from 23 bacteria, viruses and parasites.


We aimed to:
1. Compare infectious organisms detected by stool multiplex PCR assay and conventional stool tests during flare in patients with IBD.
2. Determine impact of detection of infective agents in the management of flares, as measured by use of anti-infective agents.

In this single centre, prospective, cohort study, every patient underwent conventional stool tests (microscopy, culture and Clostridioides Difficile toxin assay) and multiplex PCR assay by Biofire® FilmArray test. Consenting patients above 18 years with IBD flare were included. Patients with colorectal cancer, toxic megacolon, intestinal perforation, previous IBD surgery were excluded.


Of 60 patients, 53 patients were of Ulcerative colitis (UC) and 7 were of Crohn's disease (CD). The mean age of patients with UC was 42.32 years and that of CD was 37.5 years. Of the patients with UC, 26 were male and 27 were female. In CD, 4 were male and 3 were female.

Stool Biofire® resulted in better organism detection rate (Table 1) and more frequent need for change in management (Table 2) as compared to conventional tests.

Table 1: Organisms detected during flare

  Conventional stool test n (%)Biofire® n (%)P value (Chi-square test)
Organism detected 6 (10) 33 (55) 0.0001
Organism not detected 54 (90) 27 (45)
Total 60 60

Table 2: Change in management based on test findings

  Conventional stool test n (%)Biofire® n (%)P value (Chi-square Test)
Change in management 3 (5) 11 (18.3) 0.023
No management change 57 (95) 49 (81.7)
Positive reports 60 60

The cost per stool Biofire® was INR 12000 (€142) and that of conventional stool tests INR 4300 (€51). However, the cost to achieve one positive result on stool Biofire® that led to change in management was INR 65,454 (€773) as compared to INR 86,000 (€1015) for conventional stool tests.


Stool Biofire® resulted in significantly more organism detection (33 vs 6 pts). It also led to more frequent need for change in management as compared to conventional stools tests (11 vs 3 pts). It also proved more cost-effective than conventional stool tests in terms of change in management of flare in patients with IBD.