Enteric Infection in Relapse of Inflammatory Bowel Disease: The Utility of Stool Microbial PCR Testing

Proton pump Inhibitors and Risk of Enteric Infection in Inflammatory Bowel Disease: A Self-controlled Case Series

BACKGROUND

We tested whether proton pump inhibitors (PPIs) are associated with enteric infections among those with inflammatory bowel disease (IBD), after adequately accounting for baseline differences between PPI users and nonusers.

METHODS

This was a self-controlled case series, with each patient serving as their own control. Ambulatory patients with IBD were included if they were tested for enteric infection by multiplex polymerase chain reaction testing panel (GIPCR) and/or Clostridoides difficile toxin PCR from 2015 to 2019 and received PPIs for some but not all of this period. Rates of enteric infections were compared between the PPI-exposed period vs pre- and post-PPI periods identical in duration to the exposed period. Conditional Poisson regression was used to adjust for time-varying factors.

RESULTS

Two hundred twenty-one IBD patients were included (49% ulcerative colitis, 46% Crohn's disease, and 5% indeterminate colitis). The median PPI duration was 7 months (interquartile range 4 to 11 months). A total of 25 (11%) patients had a positive GIPCR or C. difficile test in the PPI period, 9 (4%) in the pre-PPI period, and 8 (4%) in the post-PPI period. Observed incidence rates for enteric infections were 2.5, 7.4, and 2.2 per 100 person years for the pre-PPI, PPI, and post-PPI periods, respectively (adjusted incidence rate ratios, 2.8; 95% confidence interval [CI] 1.3-6.0) for PPI vs pre-PPI and 2.9 (95% CI, 1.3-6.4) for PPI vs post-PPI). The adjusted absolute excess risk associated with PPIs was 4.9 infections per 100 person years.

CONCLUSIONS

Proton pump inhibitors were associated with a 3-fold increased risk for enteric infection among those with IBD but had a modest absolute risk.

Fecal calprotectin level is nonlinearly associated with GI pathogen detection in patients with and without inflammatory bowel disease

Fecal calprotectin (FCP) is used to monitor inflammatory bowel disease (IBD) activity and can also be elevated in gastrointestinal infections. Our study's objective was to quantify the relationship between FCP levels and lab-confirmed infections in people with and without IBD. We performed a cross-sectional study at a tertiary-care center of all encounters during which FCP and gastrointestinal pathogen polymerase-chain reaction (GI PCR) panel testings were conducted. Using non-parametric tests and quantile regression, we compared the FCP levels by IBD status and pathogen detection. There were 3,347 encounters with FCP and GI PCR testings from 2,780 unique individuals between 1 August 2016 and 17 February 2022. Overall, 54.4% had IBD (n = 1,819). Pathogens were detected in 744 encounters (22.2%), and the detection rate did not differ by IBD status. Median FCP without IBD was significantly elevated when a pathogen was detected (64 vs 41 mg/kg, P = 0.0003, normal ≤50.0 mg/kg), but FCP with IBD was not significantly elevated when a pathogen was detected (299 vs 255 mg/kg, P = 0.207). In quantile regression adjusted for age and IBD, pathogen detection was only significantly associated with higher FCP in the lower two quartiles, though IBD remained significantly associated with higher FCP at all levels (P > 0.001). Pathogen detection by GI PCR is associated with elevated FCP, though this relationship is nonlinear and varies by IBD status. Our findings indicate that FCP may be an adjunct to, but not a substitute for, stool pathogen testing.

Infectious Disease Pathology of the Gastrointestinal Tract: Diagnosing the Challenging Cases

Infectious diseases of the GI tract mimic a variety of other GI diseases, including chronic idiopathic inflammatory bowel disease and ischemia. It can be challenging to identify pathogens in tissue sections as well, as many trainees are not exposed to infectious disease pathology other than in the context of microbiology. Our ability to diagnose infections in formalin fixed, paraffin embedded material has grown exponentially with the advent of new histochemical and immunohistochemical stains, as well as more options for molecular testing. Correlating these diagnostic techniques with morphology has led to increasing understanding of the histologic patterns that are associated with specific pathogens.

Enteric Infection at Flare of Inflammatory Bowel Disease Impacts Outcomes at 2 Years

BACKGROUND

Outcomes of inflammatory bowel disease (IBD) following flare complicated by enteric infection (EI) are limited by follow-up duration and insufficient assessment of the role of non-Clostridioides difficile pathogens. We compared 2-year IBD outcomes following flare with and without EI.

METHODS

We performed a retrospective cohort study of adults evaluated with stool PCR testing for IBD flare. Subjects were stratified by presence of EI at flare and were matched for age, sex, and date to those without EI. The primary outcome was a composite of steroid-dependent IBD, colectomy, and/or IBD therapy class change/dose escalation at 2 years. Additional analyses were performed by dividing the EI group into C. difficile infection (CDI) and non-CDI EI, and further subdividing non-CDI EI into E. coli subtypes and other non-CDI EI.

RESULTS

We identified 137 matched subjects, of whom 62 (45%) had EI (40 [29%] CDI; 17 [12%] E. coli). Enteric infection at flare was independently associated with the primary outcome (adjusted odds ratio, 4.14; 95% confidence interval [CI], 1.62-11.5). After dividing EI into CDI and non-CDI EI, only CDI at flare was independently associated with the primary outcome (adjusted odds ratio, 4.04; 95% CI, 1.46-12.6). After separating E. coli subtypes from non-CDI EI, E. coli infection and CDI at flare were both independently associated with the primary outcome; other EI was not.

CONCLUSIONS

Enteric infection at flare-specifically with CDI-is associated with worse IBD outcomes at 2 years. The relationship between E. coli subtypes at flare and subsequent IBD outcomes requires further investigation.

Bidirectional association between infectious gastroenteritis and inflammatory bowel disease: a population-based study

BACKGROUND

Intertwined association between infectious gastroenteritis (IGE) and inflammatory bowel disease (IBD) has not been investigated clearly. We aimed to examine the bidirectional association between IGE and IBD.

METHODS

A bidirectional study using the Taiwan National Health Insurance Research Database was designed. Through a case-control design, we identified 2899 new IBD cases during 2006-2017 and matched to 28,990 non-IBD controls. We used conditional logistic regression model to estimate odds ratios (OR) of IBD for previous IGE in different exposure time-windows within 5-years before IBD diagnosis and Poisson regression model to estimate incidence rate ratio (IRR) of subsequent IGE for IBD group to non-IBD group.

RESULTS

The mean age at the initial IBD diagnosis was 41 years. More IBD patients (21.49%) than controls (12.60%) had been exposed to IGE during > 6 months to 5 years before IBD diagnosis, the OR of IBD for IGE was 1.89 [95% confidence interval: 1.69-2.11]. Excess OR decreased as IGE exposure time before the index date increased. More IGE episodes were associated with additional increase in IBD risk (OR: 1.64, 2.19, 2.57, 3.50, and 4.57 in patients with 1, 2, 3, 4, and ≥ 5 IGE episodes, respectively). The IRR of having IGE for IBD group to non-IBD group was 2.42 before IBD diagnosis and increased to 5.74 after IBD diagnosis.

CONCLUSIONS

These findings suggested an IGE-IBD bidirectional association. More attention is needed for physicians to develop preventive strategies and be aware of the higher risk of subsequent IGE in IBD patients.

Current insight into enteropathogens in flare-up ulcerative colitis. An observational study

OBJECTIVE

Incidence of ulcerative colitis is globally increased. Enteric infections and their role in ulcerative colitis flares present a common health problem and a unique clinical challenge. We aimed to identify enteropathogens in flared ulcerative colitis patients and their antimicrobial susceptibilities and relation with the disease activity.

METHODS

Stool samples were collected from 95 patients with ulcerative colitis (17 inactive cases and 78 active cases) according to the Mayo score assessment of ulcerative colitis severity. Enteropathogens were examined using an automated VITEK2 system and FilmArray gastrointestinal pathogen panel.

RESULTS

Enteric infections were found in 81 patients (85.3%) with a significantly higher percentage in active ulcerative colitis (96.2% vs. 35.3%, P  < 0.001). In 78 symptomatic patients, (78.7%) of bacteria as enteroaggregative and enteropathogenic E. coli , (11.5%) parasitic as Cryptosporidium and (7.7%) viral as Norovirus were the most detected microbial pathogens. Mixed, multidrug-resistant organisms (MDROs) and opportunistic infections were reported in 70.7%, 52.9% and 46.7% respectively. Raoultella ornithinolytica was reported for the first time as an enteropathogen in ulcerative colitis flare. Multiple organisms, MDROs, extended-spectrum beta-lactamases-producing and AmpC-resistant bacteria were significantly associated with disease severity.

CONCLUSION

Identifying enteropathogens especially opportunistic and MDR organisms as a cause of ulcerative colitis flare-ups is a matter of worry increasing their diagnostic and therapeutic burden. Periodic studies evaluating changes in microbial profiles and their antimicrobial susceptibilities are needed to achieve antibiotic stewardship and improve management.

Role of adherent invasive Escherichia coli in pathogenesis of inflammatory bowel disease

Gut microbiota imbalances play an important role in inflammatory bowel disease (IBD), but no single pathogenic microorganism critical to IBD that is specific to the IBD terminal ileum mucosa or can invade intestinal epithelial cells has been found. Invasive Escherichia coli (E. coli) adhesion to macrophages is considered to be closely related to the pathogenesis of inflammatory bowel disease. Further study of the specific biological characteristics of adherent invasive E. coli (AIEC) may contribute to a further understanding of IBD pathogenesis. This review explores the relationship between AIEC and the intestinal immune system, discusses the prevalence and relevance of AIEC in Crohn's disease and ulcerative colitis patients, and describes the relationship between AIEC and the disease site, activity, and postoperative recurrence. Finally, we highlight potential therapeutic strategies to attenuate AIEC colonization in the intestinal mucosa, including the use of phage therapy, antibiotics, and anti-adhesion molecules. These strategies may open up new avenues for the prevention and treatment of IBD in the future.

Phylogrouping and characterization of Escherichia coli isolated from colonic biopsies and fecal samples of patients with flare of inflammatory bowel disease in Iran

Background

Although the etiopathogenesis of inflammatory bowel disease (IBD) is still poorly understood, Escherichia coli has been described as a potential causative microorganism in IBD pathogenesis and also disease progression, offering a potential therapeutic target for disease management. Therefore, we conducted this study to investigate the pathotypes, phylogenetic groups, and antimicrobial resistance of E. coli isolates from patients with IBD in Iran.

Methods

Fecal and biopsy colonic samples were collected from IBD patients experiencing flare-up episodes referred to Taleghani hospital in Tehran, Iran, between August 2020 and January 2021. Identification of E. coli strains was performed based on biochemical and molecular methods. Antibiotic susceptibility testing was performed as recommended by the Clinical and Laboratory Standards Institute. Phylogrouping and pathotyping of each isolate were carried out using polymerase chain reaction (PCR) and multilocus sequence typing (MLST) assays.

Results

A total of 132 non-duplicate E. coli strains were isolated from 113 IBD patients, including 96 ulcerative colitis (UC), and 17 Crohn’s disease (CD) patients. In our study, 55% of CD-related E. coli and 70.5% of UC-related isolates were non-susceptible to at least three or more unique antimicrobial classes, and were considered as multidrug-resistant (MDR) strains. E. coli strains exhibited a high level of resistance to cefazolin, ampicillin, tetracycline, ceftazidime, ciprofloxacin, and cefotaxime. Enterotoxigenic E. coli (ETEC) and diffusely adherent E. coli (DAEC) were the most prevalent pathotypes, and groups B2 and D were the predominant phylogroups.

Conclusion

In the present study, we found that E. coli strains that colonize the gut of Iranian patients with IBD most frequently belonged to phylogenetic groups B2 and D. We also conclude that E. coli isolates from IBD patients have been revealed to be resistant to commonly used antibiotics, in which most of them harbored strains that would be categorized as MDR.

The role of gastrointestinal pathogen PCR testing in liver transplant recipients hospitalized with diarrhea

BACKGROUND

Diarrhea is a common symptom among liver transplant (LT) recipients and can result in significant morbidity. The utility of PCR-based multiplex gastrointestinal (GI) pathogen panels in this population is unknown.

METHODS

We assessed incidence, predictors, and outcomes of GI PCR positivity among inpatients who underwent stool pathogen testing with the FilmArray multiplex GI PCR panel at our institution within 1 year following LT from April 2015 to December 2019.

RESULTS

112 patients were identified. 14 (12.5%) had a positive PCR for any pathogen. Escherichia coli (n = 9) and Norovirus (n = 5) were the most common pathogens detected. Recipients with a positive PCR were significantly further from LT (median 74.5 vs 15.5 days, p < 0.01) and tested earlier during hospitalization (median 1.0 vs 9.0 days, p < 0.01). C. difficile was positive in 20.0% of patients with a positive PCR and 11.4% with a negative PCR. CMV viremia was observed in 11.6% of patients, all in the negative PCR group. Following a positive PCR, patients were more likely to have a change in antimicrobial regimen (71.4% vs 28.6%, p = 0.02), a shorter length of stay (median 7.5 vs. 17.5 days, p < 0.01), and a trend toward lower rates of readmission and colonoscopy within 30 days.

CONCLUSIONS

In hospitalized LT recipients with diarrhea, GI PCR pathogen identification was associated with the use of targeted antimicrobial therapy and a shorter length of stay. GI PCR testing should be considered early during admission and later in the post-LT period. This article is protected by copyright. All rights reserved.

Intra-abdominal septic complications after ileocolic resection increases risk for endoscopic and surgical postoperative Crohn's disease recurrence

BACKGROUND

Postoperative recurrence [POR] of Crohn's disease following ileocolonic resection is common. The impact of immediate postoperative intra-abdominal septic complications [IASC] on endoscopic and surgical recurrence has not been elucidated.

AIMS

To evaluate if IASC is associated with an increased risk for endoscopic and surgical POR.

METHODS

This was a retrospective study of adult Crohn's disease patients undergoing ileocolonic resection with primary anastomosis between 2009 and 2020. IASC was defined as anastomotic leak or intra-abdominal abscess within 90 days of the date of surgery. Multivariable logistic and Cox proportional hazard modelling were performed to assess the impact of IASC on endoscopic POR [modified Rutgeerts' score ≥ i2b] at index postoperative ileocolonoscopy and long-term surgical recurrence.

RESULTS

In 535 Crohn's disease patients [median age 35 years, 22.1% active smokers, 35.7% one or more prior resection] had an ileocolonic resection with primary anastomosis. A minority of patients [N = 47; 8.8%] developed postoperative IASC. In total, 422 [78.9%] patients had one or more postoperative ileocolonoscopies, of whom 163 [38.6%] developed endoscopic POR. After adjusting for other risk factors for postoperative recurrence, postoperative IASC was associated with significantly greater odds (adjusted odds ratio [aOR]: 2.45 [1.23-4.97]; p = 0.01) and decreased time (adjusted hazards ratio [aHR]: 1.60 [1.04-2.45]; p = 0.03] to endoscopic POR. Furthermore, IASC was associated with increased risk (aOR: 2.3 [1.04-4.87] p = 0.03) and decreased survival-free time [aHR: 2.53 [1.31-4.87]; p = 0.006] for surgical recurrence.

CONCLUSION

IASC is associated with an increased risk for endoscopic and surgical POR of Crohn's disease. Preoperative optimization to prevent IASC, in addition to postoperative biological prophylaxis, may help reduce the risk for endoscopic and surgical POR.

Core indicators of an evaluation and guidance system for quality of care in inflammatory bowel disease centers: A critical review

The mission of the IBD Quality Care Evaluation Center (IBDQCC) is to establish indicators of quality of care (QoC), certify IBD units to generate a network of IBD quality care, and eventually improve the national level of IBD healthcare. The final list of 28 core and 13 secondary IBD QoC indicators suitable for the healthcare system in China were selected using a Delphi consensus methodology. Units that met all core indicators were qualified as "regional"; units that met all core indicators together with more than 50% of the secondary indicators received a rating of "excellence." Using the selected QoC core indicators for certifying IBD units, a network of IBD quality care units covering the majority of IBD patients in China was established.

FUNDING

This work was financially supported by Cultivation Funding for Clinical Scientific Research Innovation, Renji Hospital, School of Medicine, Shanghai Jiaotong University (RJPY-LX-004), National Natural Science Foundation of China (No. 81,770,545), Shanghai Science and Technology Innovation Initiative (21SQBS02302), and Cultivated Funding for Clinical Research Innovation, Renji Hospital, School of Medicine, Shanghai Jiaotong University (RJPY-LX-004).

Critical diagnoses in paediatric gastrointestinal diseases

Gastrointestinal biopsies represent an increasing proportion of the paediatric pathologist's workload, an increase fundamentally due to an expansion of the understanding of the basic clinical, molecular, genetic, and histopathological features of paediatric gastrointestinal disorders. The histological interpretation of endoscopically retrieved gastrointestinal biopsies in children requires a unique set of diagnostic expertise and detailed knowledge of various gastrointestinal disorders that have a predilection for the paediatric population. This article's major role is to highlight the unique problems inherent to paediatric gastrointestinal disorders that require immediate communication with the paediatric surgeon or the gastroenterologist. For this, we tried to cover the most important diseases that a paediatric pathologist might encounter in daily practice. Some of these diseases are relatively rare, such as microvillous inclusion disease and tufting enteropathy, but some are more common such as eosinophilic disorders and inflammatory bowel disease. Awareness of the histopathological features of these diseases, particularly those that are relatively uncommon, is crucial to spare the patient a lengthy and costly evaluation. We made a particular effort to abundantly reference this article should the reader wish to expand on the content of any section.

Is the Medium Still the Message? Culture-Independent Diagnosis of Gastrointestinal Infections

Infectious diarrhea is caused by a variety of pathogens, including viruses, bacteria, and parasitic organisms. Though the causative agent of diarrhea has historically been evaluated via stool cultures, recently, culture-independent diagnostic tests (CIDT) have been developed and utilized with increasing frequency. Current practice guidelines recommend their use as adjuncts to stool cultures for diagnosing acute and chronic diarrhea. The three principal CIDT are microscopy, enzyme-based immunoassays (EIAs), and molecular based polymerase chain reaction (PCR). This review explores the common causes of infectious diarrhea, the basics of stool culture, the diagnostic utility of these three culture-independent modalities, and the strengths and weaknesses of all currently available clinical techniques. It also outlines considerations for specific populations including returning travelers and those with inflammatory bowel disease.

Comparative Evaluation of Conventional Stool Testing and Multiplex Molecular Panel in Outpatients With Relapse of Inflammatory Bowel Disease

BACKGROUND

Differentiating between enteric infection and relapse of inflammatory bowel disease (IBD) is a common clinical challenge. Few studies have evaluated the impact of multiplex gastrointestinal polymerase chain reaction (GI PCR) pathogen panels on clinical practice compared to stool culture. Our aim was to compare the impact of PCR stool testing to conventional stool testing in outpatients presenting with relapse of IBD.

METHODS

In a retrospective cohort study of outpatients with IBD presenting to NYU Langone Health with flare from September 2015 to April 2019, we compared patients who underwent stool testing with GI PCR to age-, sex-, and IBD-subtype-matched patients who underwent culture and ova and parasite exam (conventional testing). The primary outcome was IBD therapy escalation after testing. Secondary outcomes included rates of posttesting endoscopy, abdominal radiography, antibiotics, and IBD-related emergency department visits, hospitalizations, and abdominal surgeries.

RESULTS

We identified 134 patients who underwent GI PCR matched to 134 patients who underwent conventional testing. Pathogens were more frequently identified on GI PCR (26 vs 5%; P < 0.01). We found that GI PCR was associated with less escalation in IBD therapy (16 vs 29%; P < 0.01) and fewer posttest endoscopies (10% vs 18%; P = 0.04), with no differences in IBD outcomes. On multivariate analysis, testing with GI PCR was associated with an odds ratio of 0.26 (95% confidence interval, 0.08-0.84; P = 0.02) for escalation of IBD therapies.

CONCLUSIONS

Testing with GI PCR was associated with higher rates of pathogen detection and lower rates of IBD therapy escalation and endoscopy in the outpatient setting. These changes in management were not associated with a difference in IBD outcomes.

Superimposed Infectious Colitis in Crohn's Disease

The differential diagnosis for an acute Crohn's flare should include enteric infection, a challenging yet critical distinction to make when determining appropriate therapy. Since both present similarly, identification of an enteric infection should be performed with comprehensive stool microbial testing. In the setting of moderate-to-severe disease, patients on biologic therapy may be more prone to infectious complications. We present a patient with chronic Crohn's disease with an unusual, previously undetected enteric infection due to Plesiomonas shigelloides. Once identified, appropriate antibiotic treatment led to resolution of the patient's acute symptomatology. This is the first reported case of P. shigelloides infection in Crohn's disease.

The role of gastrointestinal pathogens in inflammatory bowel disease: a systematic review

The inflammatory bowel diseases (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), are chronic, progressive, inflammatory conditions of the gastrointestinal tract. Imbalance in the gut microbial community, or dysbiosis, and the subsequent immune response, represent the critical relationship between genetic susceptibility, microbes, and environment factors, that result in IBD. Gastrointestinal pathogens - a common cause of dysbiosis - have been implicated as an environmental trigger in new onset IBD, as well as flare of existing IBD. In this article, we systematically review clinical data regarding the association between specific gastrointestinal pathogens and IBD. Numerous bacteria, viruses, fungi, and parasites have been implicated in the pathogenesis of IBD, and exacerbations of existing disease. In this article, we will also specifically discuss the less recognized microbes that have an inverse association with IBD, including certain bacterial pathogens, such as Helicobacter pylori, and parasites, such as Trichuris species. Future prospective and experimental studies are required to establish causality and clarify potential mechanisms of enteric pathogens in modifying the risk and course of IBD.

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.

Systematic review: gastrointestinal infection and incident inflammatory bowel disease

BACKGROUND

The initiating events of chronic gastrointestinal (GI) inflammation in Crohn's disease (CD) and ulcerative colitis (UC) are not well-defined, but GI infections are implicated.

AIMS

To define the role of GI infections in risk of incident inflammatory bowel disease (IBD) and synthesise the current body of relevant translational data to provide biological context for associations between GI infections and IBD risk.

METHODS

We systematically reviewed electronic databases through February 2020. Clinical studies that provided risk estimates of the association between GI infections and incident IBD were included. Inclusion criteria were broader for translational studies aiming to define mechanisms of GI infections and predisposition to or protection from IBD.

RESULTS

Of the studies identified, 63 met full inclusion criteria. Among studies of clinical gastroenteritis, bacteria-specifically, Salmonella species, Campylobacter species and Clostridioides difficile-demonstrated consistent positive associations with risk of incident IBD. Of viruses, norovirus was associated with increased risk of incident CD. Regarding inverse associations with incident IBD, Helicobacter pylori and helminth infections were associated with a generally consistent reduced risk of IBD. Based on a qualitative analysis of the translational data, putative mechanisms involve multiple microbial and immunologic pathways.

CONCLUSIONS

Based on this systematic review, certain enteric pathogens are associated with an increased risk of incident IBD, while others are potentially protective. Prospective studies are required to clarify the clinical implications of these enteric pathogens on the risk and course of IBD, and possible therapeutic or preventative benefit.

Clostridium difficile infection in inflammatory bowel disease: epidemiology over two decades

BACKGROUND

The incidence of Clostridium difficile infection (CDI) has been rising in the overall population as well as in patients with inflammatory bowel disease (IBD). However, the incidence of CDI in IBD may be changing owing to alterations in medical therapies.

OBJECTIVE

The aim of this study was to establish the incidence of CDI in IBD over the past two decades and compare risk factors, disease characteristics and outcomes between IBD and non-IBD patients.

PATIENTS AND METHODS

In this retrospective case-control study, the incidence of CDI in IBD was followed for 18 years. The electronic database of our centre was reviewed for all stool samples received from patients admitted to gastroenterology wards or visiting the outpatient clinic. Diagnosis of CDI was based on diagnostic criteria that evolved throughout the years.

RESULTS

IBD patients (n=44) with CDI were found to be younger (P=0.0001), have less cardiovascular comorbidity (P=0.023), fewer prior hospitalizations (P=0.009) and fewer prior antibiotic use (P=0.005). More IBD patients were on biologic therapy (P=0.0001) or steroids (P=0.001) but less likely taking proton pump inhibitors (P=0.001). The number of stool testing per year increased as well as the median number of positive stool samples for CDI (2% in 2000-2008 to 3% in 2009-2017, P=0.032). Pseudomembranes were only seen in non-IBD patients (28%, P=0.048). There was no difference in the choice of antibiotics between IBD and non-IBD patients [metronidazole (36 vs. 51%) and vancomycin (36 vs. 26%), P=0.090 and 0.190]. The 1-year mortality rate was lower in IBD patients compared with non-IBD patients (0 vs. 32%, P=0.0001).

CONCLUSION

In the past two decades, the incidence of CDI in IBD and non-IBD patients has increased. However, the overall outcome of CDI in IBD patients was favourable compared with non-IBD patients.

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.

Nested case-control study on risk factors for opportunistic infections in patients with inflammatory bowel disease

BACKGROUND

When opportunistic infections occur, patients with inflammatory bowel disease (IBD) commonly display a significantly increased rate of morbidity and mortality. With increasing use of immunosuppressive agents and biological agents, opportunistic infections are becoming a hot topic in the perspective of drug safety in IBD patients. Despite the well-established role of opportunistic infections in the prognosis of IBD patients, there are few epidemiological data investigating the incidence of opportunis-tic infections in IBD patients in China. Besides, the risk factors for opportunistic infection in Chinese IBD patients remain unclear.

AIM

To predict the incidence of opportunistic infections related to IBD in China, and explore the risk factors for opportunistic infections.

METHODS

A single-center, prospective study of IBD patients was conducted. The patients were followed for up to 12 mo to calculate the incidence of infections. For each infected IBD patient, two non-infected IBD patients were selected as controls. A conditional logistic regression analysis was used to assess associations between putative risk factors and opportunistic infections, which are represented as odds ratios (OR) and 95% confidence intervals (CIs).

RESULTS

Seventy (28.11%) out of 249 IBD patients developed opportunistic infections. Clostridium difficile infections and respiratory syncytial virus infections were found in 24 and 16 patients, respectively. In a univariate analysis, factors such as the severity of IBD, use of an immunosuppressant or immunosuppressants, high levels of fecal calprotectin, and C-reactive protein or erythrocyte sedimentation rate were individually related to a significantly increased risk of opportunistic infection. Multivariate analysis indicated that the use of any immunosuppressant yielded an OR of 3.247 (95%CI: 1.128-9.341), whereas the use of any two immunosuppressants yielded an OR of 6.457 (95%CI: 1.726-24.152) for opportunistic infection. Interestingly, when immunosuppressants were used in combination with infliximab (IFX) or 5-aminosalicylic acid, a significantly increased risk of opportunistic infection was also observed. The relative risk of opportunistic infection was greatest in IBD patients with severe disease activity (OR = 9.090; 95%CI: 1.532-53.941, relative to the remission stage). However, the use of IFX alone did not increase the risk of opportunistic infection.

CONCLUSION

Factors such as severe IBD, elevated levels of fecal calprotectin, and the use of immunosuppressive medications, especially when used in combination, are major risk factors for opportunistic infections in IBD patients. The use of IFX alone does not increase the risk of opportunistic infection.

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.

Comparison of Multiplex Gastrointestinal Pathogen Panel and Conventional Stool Testing for Evaluation of Diarrhea in Patients with Inflammatory Bowel Diseases

BACKGROUND AND AIMS

Gastrointestinal pathogen panels (GPPs) are increasingly being used for evaluation of diarrhea. The impact of these tests on patients with inflammatory bowel diseases (IBD) is unknown. We performed a time-interrupted cohort study comparing GPPs and conventional stool evaluation in patients with IBD with diarrhea.

METHODS

We included 268 consecutive patients with IBD who underwent GPP (BioFire Diagnostics^®) (n = 134) or conventional stool culture and Clostridium difficile polymerase chain reaction testing (n = 134) during suspected IBD flare between 2012 and 2016. Primary outcome was composite of 30-day IBD-related hospitalization, surgery, or emergency department visit; secondary outcome was IBD treatment modification.

RESULTS

Overall, 41/134 (30.6%) patients tested positive on GPP (18 C. difficile, 17 other bacterial infections, and 6 viral pathogens) versus 14/134 patients (10.4%, all C. difficile) testing positive on conventional testing. Rate of IBD treatment modification in response to stool testing was lower in GPP group as compared conventional stool testing group (35.1 vs. 64.2%, p < 0.01). On multivariate analysis, diagnostic evaluation with GPP was associated with three times higher odds of IBD-related hospitalization/surgery/ED visit (95% CI, 1.27-7.14), as compared to conventional stool testing. This negative impact was partly mediated by differences in ordering provider specialty, with non-gastroenterologists more likely to order GPP as compared to gastroenterologists.

CONCLUSIONS

In patients with suspected flare of IBD, GPPs have higher pathogen detection rate and lead to lower rate of IBD treatment modification. A diagnostic testing strategy based on GPPs is associated with higher hospital-related healthcare utilization as compared to conventional stool testing, particularly when utilized by non-gastroenterologists.

Enteric Infections Are Common in Patients with Flares of Inflammatory Bowel Disease

OBJECTIVES

Few studies have examined the role of non-Clostridium difficile enteric infections in flares of inflammatory bowel disease (IBD). Our objective was to investigate enteric infection detected by multiplex PCR stool testing in patients with IBD.

METHODS

We performed a cross-sectional analysis of 9403 patients who underwent 13,231 stool tests with a gastrointestinal pathogen PCR panel during a diarrheal illness from March 2015 to May 2017. Our primary outcome was the presence of an infection. Secondary outcomes included endoscopic and histologic predictors of infection, and IBD outcomes following testing.

RESULTS

A total of 277 patients with Crohn's disease (CD), 300 patients with ulcerative colitis (UC), and 8826 patients without IBD underwent 454, 503, and 12,275 tests, respectively. Compared to patients without IBD, patients with IBD were less likely to test positive (CD 18.1%, UC 16.1%, no IBD 26.6%, p < 0.001). Compared to patients without IBD, CD had a higher prevalence of norovirus (p = 0.05) and Campylobacter (p = 0.043), whereas UC had a lower prevalence of norovirus (p = 0.001) and a higher prevalence of Campylobacter (p = 0.013), Plesiomonas (p = 0.049), and Escherichia coli species (p < 0.001). Of 77 patients who underwent endoscopy, there were no major endoscopic or histologic predictors of a positive test. Patients who tested negative were more likely to have IBD therapy escalated (p = 0.004). Enteric infection did not impact IBD outcomes following testing (log-rank 0.224).

CONCLUSIONS

Non-Clostridium difficile enteric infections were identified in 17% of symptomatic patients with IBD. Endoscopic and histologic findings may not differentiate flare from infection. Norovirus and E.coli may play an important role in flare of IBD.

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.

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

BACKGROUND

Gastrointestinal infection is a major cause of morbidity. We sought to characterize the pathogenic etiologies of gastrointestinal infection to identify seasonal patterns and predictors of specific infections utilizing a multiplex PCR assay in clinical practice.

METHODS

We performed a cross-sectional study of 9403 patients who underwent 13,231 stool tests with a FilmArray gastrointestinal pathogen PCR panel during an episode of diarrhea from March 2015 to May 2017. Our primary outcome was the presence of a positive panel. Logistic regression was used to test for associations between season and infections.

RESULTS

A positive result was found in 3426 tests (25.9%) in 2988 patients (31.8%), yielding 4667 pathogens consisting of 1469 viruses (31.5%), 2925 bacteria (62.7%), and 273 parasites (5.8%). Age less than 50 years was associated with a higher prevalence of pathogens compared to age ≥ 50 (p < 0.0001). The overall prevalence of a positive result for bacteria peaked in the summer (635, 29.2%), and the prevalence of viruses peaked in the winter (446, 31.8%). Compared to the winter, testing in the summer yielded a higher prevalence of bacteria (OR 1.52, 95% CI 1.33, 1.73, p < 0.0001) and lower odds of viruses (OR 0.69, 95% CI 0.58, 0.81, p < 0.0001), primarily driven by E. coli species and norovirus.

CONCLUSIONS

Season was a major determinant in detecting specific pathogens. Our substantially lower positivity rate than previous reports in the literature on multiplex PCR assays may more accurately reflect true clinical practice. Recognizing the temporal distribution of enteric pathogens may help facilitate empiric treatment decisions in certain clinical situations.

Risk Factors for Clostridium difficile Isolation in Inflammatory Bowel Disease: A Prospective Study

INTRODUCTION

Clostridium difficile is the most commonly isolated stool pathogen in inflammatory bowel disease (IBD). Traditional risk factors for C. difficile may not exist in patients with IBD, and no prior studies have assessed the risk factors for the isolation of C. difficile in both symptomatic and asymptomatic IBD outpatients.

METHODS

We prospectively recruited consecutive IBD patients presenting to our outpatient clinic between April 2015 and February 2016. We excluded patients with a diverting ostomy or ileoanal pouch. Demographics, healthcare exposures, medical therapies and disease activity were recorded from medical charts or surveys. A rectal swab was performed from which toxigenic culture and PCR analysis for the presence of toxin and fluorescent PCR ribotyping were performed. The primary outcome of interest was isolation of toxigenic C. difficile.

RESULTS

A total of 190 patients were enrolled in this prospective study including 137 (72%) with Crohn's disease and 53 (28%) with ulcerative colitis. At the time of enrollment, 69 (36%) had clinically active disease. Sixteen (8.4%) patients had toxigenic C. difficile isolated on rectal swab at enrollment and four (2.1%) patients had non-toxigenic C. difficile cultured. Mixed infection with more than one toxigenic isolate was present in 5/16 (31.3%) individuals. Patients with CD with a toxin positive isolate were more likely to have a history of CDI in the past 12 months (40 vs. 11.02%, p = 0.027) and an emergency department visit in the past 12 weeks (50 vs. 20.63%, p = 0.048). In UC, individuals with isolation of C. difficile were more likely to be hospitalized within the past 12 months (66.6 vs. 8.51%, p = 0.003). C. difficile isolation at the time of presentation was not associated with a subsequent disease relapse over a 6-month period in CD (p = 0.557) or UC (p = 0.131).

CONCLUSION

Healthcare exposures remain a significant risk factor for C. difficile isolation in the IBD population; however, this was not associated with relapse of disease. Further studies assessing the clinical significance of C. difficile isolation is warranted in IBD.

Non-Clostridium difficile Bacterial Infections Are Rare in Patients With Flares of Inflammatory Bowel Disease

BACKGROUND & AIMS

Clostridium difficile infection (CDI) causes flares in patients with inflammatory bowel disease (IBD). We investigated the frequency and outcomes of non-CDI bacterial enteric infections in symptomatic patients with IBD.

METHODS

We performed a retrospective study of patients with ulcerative colitis (UC) or Crohn's disease (CD) from whom stool samples were collected and analyzed by PCR or culture for bacterial pathogens (Campylobacter jejuni or C coli, Salmonella species, Shigella species, enteroinvasive Escherichia coli, shiga toxin-producing E coli, or Yersinia species) from November 19, 2011, through June 30, 2014. Patients were excluded if they had nonbacterial infections or no symptoms. Data were collected from medical records on IBD duration, treatment, age at diagnosis, and presence of concurrent CDI. Patients were followed for 1 year after the date of infection resolution or until date of last follow-up in the health record. Each patient with an enteric infection was matched with 2 patients with IBD flares and negative results from stool tests (non-infected control) and 2 patients with IBD and CDI (CDI control), adjusted for age (within 5 years at the time of stool test), sex, and IBD subtype. Outcome measures included IBD therapy escalation and hospitalization.

RESULTS

Of 9247 patients with IBD seen during the study period, stool samples were tested from 1345 patients (50% with UC and 50% with CD). There were 3 positive results (detection of bacterial pathogens) from 339 PCR analyses of stool samples from 296 patients with UC (0.88%) and 12 positive results from 486 cultures of stool samples from 418 patients with UC (2.5%). There was 1 positive result from 355 PCR analyses of stool samples from 311 patients with CD (0.28%) and 9 positive results from 496 cultures of stool samples from 413 patients with CD (1.8%). Of the 19 patients followed beyond infection, 9 patients required escalation of their IBD therapy (47%)-most commonly addition of an immunomodulator (5 patients) or a biological agent (3 patients)-compared with 34% of CDI controls and 66% of non-infected controls (P < .001). Higher proportions of patients with non-CDI bacterial infections were in remission 1 year after their infection (89%) than patients with CDI (55%) or negative results of stool tests (63%; P = .04). We did not observe differences in hospitalization, emergency department visits, or surgical interventions among groups.

CONCLUSIONS

In a retrospective study of patients with an IBD flare, we detected non-CDI bacterial infections in fewer than 3% of those who were tested. Higher proportions of patients with non-CDI bacterial infections were in remission in the year after their infection than patients with CDI.