Evaluation of routine enteric pathogens in hospitalized patients: A Canadian perspective

Low Yield of FilmArray GI Panel in Hospitalized Patients with Diarrhea: an Opportunity for Diagnostic Stewardship Intervention

The FilmArray GI panel (BioFire Diagnostics, Salt Lake City, UT) is a multiplex, on-demand, sample-to-answer, real-time PCR assay for the syndromic diagnosis of infectious gastroenteritis that has become widely adopted and, in some instances, has replaced conventional stool culture and parasite exams. Conventional testing has historically been restricted among hospitalized patients due to low diagnostic yield, but it is not known whether use of the FilmArray GI panel should be circumscribed. Cary-Blair stool samples submitted for FilmArray GI panel in adult patients admitted to an academic hospital from August 2015 to January 2017 were included in this study. Of 481 tests performed >72 h after admission, 29 (6.0%) were positive, all for a single target, excluding Clostridium difficile When follow-up tests beyond the first positive per hospitalization were excluded, 20 (4.8%) of 414 tests were positive. There was no difference in yield by immune status. Most targets detected were viral (79% of all positives [n = 23] and 70% in unique patients [n = 14]). All four cases positive for a bacterial target could not be confirmed and presentation was atypical, suggesting possible false positives. After removing potential false positives and chronic viral shedders, the yield was 3.0% (12/406). Repeat testing performed >72 h after admission and following a negative result within the first 72 h was done in 19 patients and 100% (22/22) remained negative. The FilmArray GI panel has low yield in adult patients hospitalized for >72 h, similar to conventional stool microbiology tests, and it is reasonable to restrict its use in this population.

Stool submission data to help inform population-level incidence rates of enteric disease in a Canadian community

Laboratory-based surveillance data is essential for monitoring trends in the incidence of enteric disease. Current Canadian human enteric surveillance systems report only confirmed cases of human enteric disease and are often unable to capture the number of negative test results. Data from 9116 hospital stool specimens from the Waterloo Region in Canada, with a mixed urban and rural population of about 500 000 were analysed to investigate the use of stool submission data and its role in reporting bias when determining the incidence of enteric disease. The proportion of stool specimens positive for Campylobacter spp. was highest in the 15-29 years age group, and in the 5-14 years age group for Salmonella spp. and E. coli O157:H7. By contrast, the age-specific incidence rates were highest for all three pathogens in the 0-4 years age group which also had the highest stool submission rate. This suggests that variations in age-specific stool submission rates are influencing current interpretation of surveillance data.

Differential yield of pathogens from stool testing of nosocomial versus community-acquired paediatric diarrhea

OBJECTIVES

To evaluate the role of routine stool examination for all pathogens in paediatric nosocomial diarrhea (NAD) and community-acquired diarrhea (CAD) over a two-year period at Alberta Children's Hospital and current practices in other Canadian hospitals. A secondary objective was to characterize features that may predict NAD or CAD etiology.

STUDY DESIGN

Retrospective cohort study and telephone survey.

SETTING

Alberta Children's Hospital (retrospective review) and Canadian tertiary care paediatric centres (telephone survey).

METHODS

The health and microbiological records of all children with an admission or discharge diagnosis of diarrhea were reviewed using a standardized data collection form. In addition, a telephone survey of laboratories serving all paediatric hospitals in Canada was conducted using a standard questionnaire to obtain information about practices for screening for pathogens related to NAD.

RESULTS

Four hundred and thirty-four CAD episodes and 89 NAD episodes were identified. Overall, rotavirus and Clostridium difficile were the most commonly identified pathogens. Bacterial culture was positive in 10.6% CAD episodes tested, with Escherichia coli O157:H7 identified as the most common non-C difficile organism. In NAD, no bacteria were identified other than C difficile (toxin). Screening for ova and parasites had negligible yield. Viruses were more frequent in the winter months, while bacterial pathogens were more common in the summer and fall months. Over 50% of Canadian paediatric hospitals still routinely process NAD specimens similarly to CAD specimens.

CONCLUSIONS

There is a need for the re-evaluation of routine ova and parasite screening, and bacterial culture in nonoutbreak episodes of NAD in children.

[When should a stool culture be done in adults with nosocomial diarrhea?]

OBJECTIVE

To assess the diagnostic efficacy, cost and possible corrective measure of the indications for routine stool cultures in nosocomial diarrhoea in adults.

METHODS

A retrospective study over a 10-month period of 660 standard stool cultures, 256 of which were conducted after the 3rd day of hospitalisation, conducted in 528 patients at the hospital centre in Pau.

RESULTS

The positivity rate of the stool cultures was of 26/336 patients (7.7%), and of 37/404 examinations (9%) within the first three days of hospitalisation, versus 2/192 patients (1%) and 3/256 examinations (1%) after the 3rd day of hospitalisation (p<0.05). In 83 patients a stool culture was repeated, and was only positive in one patient with an initially negative culture. If a stool culture had not been performed after the 3rd day, 2 infections would not have been diagnosed (1 salmonella and 1 K. oxytoca) and 256 stool cultures could have been economised (estimated cost: 6,144 euro). Moreover, by eliminating repeated stool cultures, 3 infections would not have been diagnosed (2 salmonella, and 1 K. oxytoca) and 321 stool cultures would have been avoided (estimated cost: 7,704 euro). If the stool cultures had been conducted after the 3rd day of hospitalisation only in those aged over 64 with comorbidity, immunosuppression or within the context of an epidemic, no false negative would have been observed and 149 stool cultures would have been economised (estimated cost: 3,576 euro). The positivity rate of the search for C. difficile, only conducted on explicit request from the practitioners, was of 5/23 (22%) and 4/28 (14%) before and after the 3rd day of hospitalisation (non-significant difference).

CONCLUSION

Restriction of standard stool cultures after the 3rd day of hospitalisation to patients aged over 64 with comorbidity, to the immunodepressed, and within an epidemic context would economise around 4,300 euro per month in a medium-sized general hospital. No systematic restriction should be applied to the search for C. difficile.

Nosocomial salmonellosis: implications for microbiologic processing of stools in hospitalized patients

Many microbiology laboratories are rationalizing their services and are not culturing stool for bacterial and parasitic pathogens from patients hospitalized for more than 3 days. We report a sporadic case of nosocomial salmonellosis that highlights the need for ongoing communication among clinicians, infection control personnel, and laboratories to allow for modification of such a routine laboratory protocol should epidemiologic evidence warrant.