Study Design
This was a single centre, stratified (< 18, 18 to 69, and 70 years of age with no fixed ratio) single-masked (patients), controlled, parallel, 2-group, 1:1 allocation, pragmatic randomized trial conducted in Canada. This study followed the Consolidated Standards of Reporting Parallel Group Randomized Trials (CONSORT) guideline.
Study Participants
Eligible participants were any patient admitted to hospital with suspected acute gastroenteritis (AGE) in whom a physician requested a stool test(s) for viruses, bacteria and/or parasites. Stool samples were collected at the earliest time after admission. This study was conducted under a waiver of consent due to minimal risk given that the FGP results have been shown to be concordant with conventional testing (18). To avoid time delays from stool test reporting and decisions regarding contact isolation on the weekends or after 17:00 on weekdays that could confound the primary outcome, only participants whose stools were tested between Monday 08:00 and Friday 15:00 were eligible for inclusion. This was done to ensure that Infection Prevention and Control (IPAC) practitioners were available to review the stool testing results during their working hours (Monday 08:00 to Friday 16:00). In our hospital, IPAC practitioners are responsible for all decisions regarding additional precautions. Exclusion criteria included immunocompromised patients (HIV/AIDS, solid or stem cell transplant, febrile neutropenia, active chemotherapy, steroid treatment equivalent to prednisone ≥ 20 mg/day for ≥ 14 consecutive days preceding admission to hospital, active treatment with any of methotrexate, biologic immunosuppressants or cyclophosphamide), nosocomial Clostridioides difficile infection (defined as positive polymerase chain reaction test in any patient hospitalized ≥ 72 hours who develops diarrhea (≥ 3 loose bowel movements/day) in hospital), or any patient who develops diarrhea regardless of length of hospital stay and had been hospitalized in the preceding 3 months for ≥ 48 hours), or is being investigated as part of a possible diarrheal outbreak by either public health officials or IPAC.
Study Setting
The study took place at the Royal Victoria Regional Health Centre in Barrie, Ontario, Canada. The Royal Victoria Regional Health Centre is a 339-bed acute care, large community-teaching hospital. Barrie is a medium-sized city with a population of 150 000 located 100 kilometres north of Toronto in Central Ontario. Study recruitment started in December 2019. All consecutive patients admitted with acute gastroenteritis who met the eligibility requirements were enrolled in the study.
Study Interventions
All stool samples were collected in enteric pathogen transport Cary-Blair medium and stored at refrigeration temperature (2-8oC) until processing. Eligible participants were randomly allocated to either stool testing with FGP or conventional methods by the microbiology laboratory technologist processing the stool. For the FGP group, 200 μL of stool was added to the BioFire® GI Panel pouch testing system. The pouch was inserted into the BioFire® FilmArray® Instrument. This system can process one stool test every hour. For the conventional group, the microbiology laboratory performed the following investigations as requested by the attending physician:
a) Bacterial culture for Salmonella, Shigella, E.coli O157 and Campylobacter – specimen in Enteric Pathogen Transport (EPT) medium planted to:
i) MacConkey agar, Sorbitol-MacConkey agar, Hektoen agar and Selenite broth (all from ThermoFisher) all incubated overnight at 350C
ii) Campylobacter agar (ThermoFisher) incubated for 48 hours at 420C in a microaerophilic atmosphere
b) Bacterial culture for Yersinia enterocolitica (≤ 18 years old): EPT specimen sent to Dynacare Laboratories (https://www.dynacare.ca/) for processing, results back in 10-14 days
c) Ova & Parasites investigation: Sodium acetate-Acetic Acid-Formalin specimen sent to the Public Health Laboratories (PHL) (https://www.publichealthontario.ca/en/laboratory-services/laboratory-contact) for testing, results back in 7-10 days
d) Viral detection: rarely requested, requires a specimen in a sterile container, sent to the PHL (https://www.publichealthontario.ca/en/laboratory-services/laboratory-contact) for testing, results back in 5-7 days. PHL assay is real-time PCR for adenovirus, norovirus GI & GII, and rotavirus.
e) Clostridioides difficile: specimen in sterile container, results in 1h (GeneXpert Intermedico)
For some pathogens that are detectable in the FGP group, there may not be any conventional testing methods that permit isolation and identification. For both groups, the microbiology laboratory technologists manually inputted all positive and negative stool testing results into the laboratory information system as soon as the test results became available with an estimated delay of ≤ 30 minutes. The results were then automatically downloaded into the patient’s electronic medical record and the IPAC e-surveillance folder. IPAC can access all results as soon as they become available in their e-surveillance folder. The IPAC team used the Provincial Infectious Disease Advisory Council (PIDAC) best practice guidelines to direct the use of additional precautions during the study (19). In general, all patients admitted to hospital with acute diarrhea should receive additional precautions in addition to routine infection control practices. Additional precautions may include private room accommodation, contact precautions with personal protective equipment with gloves, mask and gowns dependent on fecal incontinence, dedicated equipment and additional cleaning measures as needed according to the etiologic pathogen. The decision to discontinue additional precautions is made by the Infection Prevention and Control practitioners in our hospital and is dependent on identification of a pathogen along with control of diarrhea (continence and treatment where applicable). Where additional clarity was needed, the IPAC Medical Director was engaged. Physicians were not able to override any IPAC decisions regarding contact isolation precautions.
Study Outcomes
The primary endpoint with respect to efficacy was the overall hospital costs associated with contact isolation. Differences in overall costs between groups were indirectly measured by assessing the differences in duration of contact isolation precautions (hours). Additional analyses were completed on the differences in antimicrobial, diagnostic imaging, and endoscopy utilization during hospitalization. In addition, physicians’ perceptions of the value added by having the earlier results provided by the FGP assay were assessed using a 2-item questionnaire. Physicians were asked to rank their agreement/disagreement with the following statements using a Likert scale (1=strongly disagree, 2= 2=moderately disagree, 3=neither disagree nor agree, 4=moderately agree, 5=strongly agree): (1) Without the earlier results provided by the FGP assay, my patient would have experienced possible/probable harm, (2) Because of the earlier results provided by the FGP assay, my patient’s treatment plan was changed (for example, change or discontinuation of antibiotic treatment, discontinuation of contact isolation, earlier discharge from hospital).
Sample Size
Sample size that would be required to achieve an assurance of 0.8, or the unconditional probability that the trial would yield a statistically significant difference in the primary outcome, was estimated using a Bayesian approach (20). The primary outcome difference was set $140 (CDN) because this is equivalent to the net cost of the FGP assay at the Royal Victoria Regional Health Centre, the breakeven point for cost-neutrality. Using the estimated costs of a single contact isolation day of $100 (Canadian 2020) (21) and $135 (Canadian 2020) (14) from previous studies, a reduction between 1.04 days (25 hours) and 1.4 days (33.6 hours) per patient would be needed to demonstrate cost-neutrality. Two previous studies had estimated that the reduction in contact isolation days per patient were 0.94 (14) and 0.9 (16). These two estimates of effect size were used as equally weighted prior information in our sample size estimates. Using a posterior standard deviation of $150 (14), the total sample size needed to detect an effect size of $140 (Canadian 2020) with an assurance of 0.8 and two-sided α = 0.05 ranged from 125 to 218 participants assuming that 30% of the PCR-based assays detect Clostridioides difficile infection and that the probability of being placed in contact isolation for patients with a diarrheal illness was 50% (2,14). The total sample size was estimated from the following equation = 2 (groups) * sample size per group * 1.3 (to account for Clostridioides difficile infection rate of 30%) * 2 (for contact isolation rate of 50% of hospitalized patients with a diarrheal illness). It is unlikely that the posterior standard deviation would exceed the difference in contact isolation costs of $150 given that the observed range of contact isolation days in Goldenberg et al. was from 1 to 4 days after excluding isolation due to Clostridioides difficile. nQuery 8 statistical software version 8.6.1.0 was used for all sample size calculations (https://www.statsols.com/).
Randomization and Masking
Permuted block design was used to randomly allocate participants to either FGP or conventional testing in a 1:1 ratio within each stratum. Allocation was stratified by age (<18, 18 to 69 and ≥ 70 years of age). The block size was fixed at 4. There was no a priori fixed ratio for allocation in the different strata. The randomization table was created by an independent statistician using the ralloc command in STATA/MP 16.1 for Mac (https://www.stata.com/). The randomization table was uploaded into a secure, web-based software platform (REDCap®) hosted at the Royal Victoria Regional Health Centre (22). The allocation sequence was concealed from researchers responsible for screening eligibility and enrollment. To enroll patients once they were deemed eligible, these researchers accessed the randomization module in REDCap® to assign patients to either FGP or conventional testing. Patients were masked to the assignment, but outcome assessors, healthcare providers and analysts were not.
Statistical Methods
Continuous variables were summarized using means and standard deviations (sd) or medians and interquartile ranges (iqr) depending on whether they were normally distributed or not, respectively. Frequency data were summarized using proportions. Comparisons of the frequency distribution of categorical data were done using Pearson’s χ2 testing or Fisher’s exact testing. Comparison of means and proportions was done using t-tests and z-tests, respectively. Comparison of medians was done using the Wilcoxon rank-sum test. For the 2-item questionnaire, physicians’ mean scores for questions 1 and 2 were compared to a hypothesized mean = 3 (=neither disagree nor agree). STATA/MP 16.1 for Mac (https://www.stata.com/) was used for all analyses. Statistical significance was defined a priori at p<0.05 (two-tailed) for all comparisons.