The Distribution of Enteric Infections Utilizing Stool Microbial Polymerase Chain Reaction Testing in Clinical Practice

Review of the role of gastrointestinal multiplex polymerase chain reaction in the management of diarrheal illness

Acute and chronic diarrheal illness secondary to gastrointestinal infection is a significant cause of morbidity and mortality around the world. A cornerstone of management includes prompt diagnosis and appropriate treatment of culprit pathogens. Timely diagnosis can improve patient care, assist in infection control, and prevent disease outbreaks. Historical methods of diagnosis include traditional culture methods and stool analysis. These are limited by long turnaround time and inability to simultaneously assess multiple pathogens. The advent of multiplexed nucleic acid amplification tests first began with the Food and Drug Administration-approved respiratory virus multiplex polymerase chain reaction (PCR) panel in 2009, followed by gastrointestinal infections in 2013, and neurological infections in 2014. We conducted a review of current literature pertaining to the clinical utility of a gastrointestinal multiplex PCR in management of acute and chronic diarrhea in patients. To date, seven platforms approved by the US Food and Drug Administration are used in detection of various bacterial, viral, and parasitic causative organisms for diagnosis of gastrointestinal infections. The sensitivity and specificity of each assay vary depending on the tested organism. Interpretation of a positive result has to be tailored to the clinical context. Further studies are required to establish the utility of gastrointestinal multiplex PCR from a cost-based perspective, whether specific enteropathogens such as Clostridioides difficile are better assessed with toxin gene detection and whether new parameters such as cycle threshold values can improve clinical application of test results.

Clinical Implications of Multiplex Pathogen Panels for the Diagnosis of Acute Viral Gastroenteritis

Acute gastroenteritis remains a significant cause of morbidity and mortality in both high- and low-resource settings. The development of nucleic acid-based testing has demonstrated that viruses are a common, yet often undetected, cause of acute gastroenteritis. The development of multiplex pathogen PCR panels makes it possible to detect these viral pathogens with greater sensitivity and rapidity than with previous methods. At present, there is insufficient evidence to recommend the routine use of these panels for the average patient with acute gastroenteritis. However, there are specific scenarios and patient populations, such as epidemiology/outbreak surveillance, antimicrobial stewardship, and the care of immunocompromised patients, where these tests could be clinically useful today. Further research on the effect of these syndromic panels on provider antibiotic prescribing behavior and patient length of stay will be necessary to know their ultimate role in clinical practice.

Prevalence and Effect of Intestinal Infections Detected by a PCR-Based Stool Test in Patients with Inflammatory Bowel Disease

BACKGROUND

The advent of PCR-based stool testing has identified a greatly increased number of infectious agents in IBD, but their clinical significance is unknown.

AIMS

To determine the infectious agent prevalence and the clinical significance of these infectious agents in IBD patients.

METHODS

This cross-sectional study compared the prevalence of GI infections among IBD patients with active and quiescent disease versus healthy controls. Among actively inflamed patients, we compared clinical characteristics, medication use, and disease course between those with positive and negative tests.

RESULTS

Three hundred and thirty-three IBD patients and 52 healthy volunteers were included. The IBD group was divided into active Crohn's disease (CD, n = 113), inactive CD (n = 53), active ulcerative colitis (UC, n = 128), and inactive UC (n = 39). A significantly higher percentage of actively inflamed patients had positive stool tests (31.1%) compared to those with quiescent disease (7.6%, P = < 0.001) and healthy controls (13.5%, P = 0.01). In actively inflamed patients, shorter symptom duration and the use of multiple immunosuppressive agents were significantly associated with positive stool tests. Escalation of immunosuppressive therapy was less frequent in those with positive (61.3%) than with negative tests (77.7%, P = < 0.01). However, the need for surgery (13.3% vs. 18.7%, respectively, P = 0.31) and hospitalization (14.7% vs. 17.5%, respectively, P = 0.57) in 90 days was not significantly different.

CONCLUSION

GI infections are common in IBD patients with active disease. Evaluating patients for infection may help avoid unnecessary escalation of immunosuppressants, especially during an acute flare or combination immunosuppression.

Gastrointestinal Infection Increases Odds of Inflammatory Bowel Disease in a Nationwide Case-Control Study

BACKGROUND & AIMS

Gastrointestinal infections have been associated with later development of inflammatory bowel diseases (IBD). However, studies have produced conflicting results. We performed a nationwide case-control study in Sweden to determine whether gastroenteritis is associated with the development of Crohn's disease (CD) or ulcerative colitis (UC).

METHODS

Using the Swedish National Patient Register, we identified 44,214 patients with IBD (26,450 with UC; 13,387 with CD; and 4377 with IBD-unclassified) from 2002 to 2014 and matched them with 436,507 individuals in the general population (control subjects). We then identified patients and control subjects with reported episodes of gastroenteritis (from 1964 to 2014) and type of pathogen associated. We collected medical and demographic data and used logistic regression to estimate odds ratios (ORs) for IBD associated with enteric infection.

RESULTS

Of the patients with IBD, 3105 (7.0%) (1672 with UC, 1050 with CD, and 383 with IBD-unclassified) had a record of previous gastroenteritis compared with 17,685 control subjects (4.1%). IBD cases had higher odds for an antecedent episode of gastrointestinal infection (aOR, 1.64; 1.57-1.71), bacterial gastrointestinal infection (aOR, 2.02; 1.82-2.24), parasitic gastrointestinal infection (aOR, 1.55; 1.03-2.33), and viral gastrointestinal infection (aOR, 1.55; 1.34-1.79). Patients with UC had higher odds of previous infection with Salmonella, Escherichia coli, Campylobacter, or Clostridium difficile compared to control subjects. Patients with CD had higher odds of previous infection with Salmonella, Campylobacter, Yersinia enterocolitica, C difficile, amoeba, or norovirus compared to control subjects. Increasing numbers of gastroenteritis episodes were associated with increased odds of IBD, and a previous episode of gastroenteritis remained associated with odds for IBD more than 10 years later (aOR, 1.26; 1.19-1.33).

CONCLUSIONS

In an analysis of the Swedish National Patient Register, we found previous episodes of gastroenteritis to increase odds of later development of IBD. Although we cannot formally exclude misclassification bias, enteric infections might induce microbial dysbiosis that contributes to the development of IBD in susceptible individuals.

Impact of Gastrointestinal Panel Implementation on Health Care Utilization and Outcomes

PCR-based multiplex gastrointestinal (GI) pathogen panels have started to replace stool culture and ova and parasite exam as a rapid and accurate means of diagnosing acute gastroenteritis. However, there are limited data on the impact of panel testing on patient outcomes. The objective of this study was to evaluate the management and health care utilization of patients following GI panel compared with conventional stool testing. We performed a retrospective comparative analysis of 9,402 patients who underwent testing with the FilmArray GI panel from March 2015 through May 2017 and 5,986 patients who underwent conventional stool testing from December 2012 through February 2015. GI panel was positive in 2,746 exams (29.2%) compared with 246 exams (4.1%) with conventional testing. Within 30 days following stool testing, compared with patients who received a conventional stool test, patients who received a GI panel were less likely to undergo any endoscopic procedure (8.4% GI panel versus 9.6% stool culture, P = 0.008) or any abdominal radiology (29.4% GI panel versus 31.7%, P = 0.002). Within 14 days following stool testing, patients who received a GI panel were less likely to be prescribed any antibiotic (36.2% GI panel versus 40.9%, P < 0.001). The implementation of multiplex PCR stool testing was associated with a reduction in the utilization of endoscopy, abdominal radiology, and antibiotic prescribing.

Gut colonization with vancomycin-resistant Enterococcus and risk for subsequent enteric infection

Background

Gut colonization with vancomycin-resistant Enterococcus (VRE) is associated with poor outcomes. This study evaluated the impact of VRE colonization on subsequent acquisition of enteric pathogens.

Methods

We performed a retrospective cohort study of adults admitted to an ICU from 2012 to 2017 who were screened for VRE colonization and subsequently underwent stool testing with a gastrointestinal pathogen PCR panel (GI PCR) with or without PCR testing for Clostridium difficile. Our primary outcome was the presence of any enteric pathogen. Cox proportional hazards modeling was used to adjust for factors associated with enteric infection.

Results

Of 761 patients who underwent VRE screening and subsequent GI PCR, 131 (17%) were colonized with VRE. Patients with VRE colonization were less likely to test positive on GI PCR compared to patients without VRE (9.2% vs 18%, p = 0.01); specifically for E. coli species (p = 0.03) and viral (p = 0.04) enteric infections. In 716 patients who underwent C. difficile testing, there was a trend towards more C. difficile infections in patients colonized with VRE (15% vs 10%, p = 0.11). On multivariable analysis, patients with VRE had a decreased risk of a positive GI PCR (aHR 0.47, 95% CI 0.25-0.88, p = 0.02) but not C. difficile infection, effects which persisted during 5 years of follow-up. Among positive tests, there was a greater proportion of C. difficile with VRE (57% vs 28%, p < 0.01).

Conclusions

VRE colonization was associated with a decreased risk of subsequent non-C. difficile enteric infection. VRE domination of the gut microbiome may protect against acquisition of common enteric pathogens.