The Utility of Biofire Filmarray in Evaluation of Entero Pathogens Triggers in Patients With Chronic Diarrhea

Chronic diarrhea is a common condition and a key symptom in many disorders. It is a major cause of morbidity and mortality worldwide and one of the most common reasons for referral to a gastroenterology clinic.The prevalence varies depending on population and the definition of diarrhea used. It affects approximately 5% of the population at any given point in time, although the exact prevalence is unknown. Diarrhea is associated with 4 pathophysiological mechanisms: osmotic, secretory, exudative and altered motility. It is more useful to classify patients presenting with symptoms of diarrhea according to ''functional'' or ''organic'' characteristics. It is usually difficult to make a reliable differentiation between organic and functional causes in patients with chronic diarrhea based only on history and physical examination .

The standard evaluation of patients with chronic diarrhea that begins with a detailed history, a careful physical examination and then basic diagnostic tests is critical for optimal treatment and prevention. Initially, thought needs to exclude several other possibilities as (a) fecal incontinence masquerading as diarrhea, (b) iatrogenic diarrhea due to drugs, surgery, or therapeutic radiation, (c) chronic infections, and (d) irritable bowel syndrome with diarrhea (IBS-D).

The detection of a broad array of potentially offending agents has traditionally required a combination of microbiologic approaches, including bacterial culture, antigen detection, microscopy, and polymerase chain reaction (PCR). The new multiplex PCR-based panels have several advantages over conventional methods including (i) reduced sample volume requirements, (ii) broad coverage without the need to select specific tests, (iii) enhanced ability to detect coinfections (iv) increased sensitivity and specificity as high as 97-100% and (v) higher throughput.The food and drug administration (FDA) cleared and recommended the use of FilmArray GI panel (BioFire Diagnostics), which targets 22 analytes (bacteria with bacterial toxin, viruses, and parasites)

Investigations:

• Routine laboratory investigation: Complete blood picture and differential WBCs count, liver, kidney function tests, RBG, Na, K, CRP, ESR.

• Microbilogical Investigations:

To ensure that good specimens are provided for examination, it is important to note the following:

* A sterile clean dry container must be used for the collection of fecal samples.
* The specimen should be brought to the lab as soon as possible.
* The specimen container should be clearly labeled with the patient's name, date, and time of passage of the specimen.

A) Conventional methods:

Stool samples will be cultured on Selenite broth then subcultured on blood agar, chocolate agar, MacConkeys agar, Sorbitol MacConkys agar: Xylose Lysine Deoxycholate agar (XLD) ,Sabouraud dextrose agar (SDA), blood agar with 10um/ml ampicillin , Cambylobacter CVA agar plates.

1. Identification of the bacterial organism:

   Pure colonies of isolated microorganisms were identified by:
   * Morphology on agar.
   * Gram stain film was made from the growth to identify morphology of the organism.
   * Biochemical reactions tests.
2. Detection of antibiotic sensitivity pattern according to CLSI 2019 by disc diffusion method
3. Confirmation of results by automated microbial system VITEK 2Compact.

B) Multiplex PCR: for Identification of different causative organisms by Biofire microarray (BioMerieux,France)

Eligibility Criteria:
Inclusion Criteria:

* Patients with diarrhea \> 4 weeks

Exclusion Criteria:

* Age below 18 years old and diarhhoea \< 4 weeks.