FilmArray™ GI panel performance for the diagnosis of acute gastroenteritis or hemorragic diarrhea

Value of a commercial multiplex molecular panel for the diagnosis of cholera in an outbreak setting in Hammanskraal, Tshwane, South Africa

Cholera is not endemic in South Africa. However, between February and July 2023, 1073 suspected cholera cases, and 198 laboratory-confirmed cases were reported nationally. This is the first report of the use of a commercial, rapid diagnostic assay in an outbreak setting. This method evaluation study was conducted at the National Health Laboratories Service (NHLS) Tshwane Microbiology laboratory in Pretoria, South Africa, during the outbreak period. Eighteen retrospective stored culture-positive Vibrio cholerae isolates and 102 prospective clinical specimens were processed on the EntericBio® Dx panel (Serosep, Limerick, Ireland) as well as the gold standard of culture. For the EntericBio® processing, stools were processed according to the manufacturer's instructions. Real time polymerase chain reaction (PCR) was performed on the Roche LightCycler®. The diagnostic performance was compared between culture and the EntericBio® Dx assay. All discrepant results were resolved at a referral laboratory using an in-house PCR assay. The mean time to results using EntericBio® was 48 h earlier than culture results. Overall, the EntericBio® Dx panel demonstrated a sensitivity of 100 % for the detection of Vibrio species when compared to culture. Although the EntericBio® platform reported the results as Vibrio species, the pre-test probability was high for V. cholerae in an outbreak setting. Further serotyping methods have confirmed this. The quick turnaround time and excellent sensitivity of the EntericBio® platform expedites patient treatment and institution of appropriate infection control practices and has potential to rapidly control such outbreaks.

FilmArray® effectively detects all clades of F41 but encounters challenges with other adenovirus species

The BioFire FilmArray® Gastrointestinal (GI) Panel, a widely used diagnostic tool, is designed to detect the genetic material of 22 common pathogens responsible for gastroenteritis, including viruses, bacteria, and parasites. It can detect human adenovirus (HAdV) species F, particularly serotypes F40 and F41, which are the major causes of diarrhea and mortality in children. However, its potential shortcomings in detecting other HAdV species limit its effectiveness in broader HAdV detection in clinical settings and outbreak investigations. The aim of this study was to evaluate the ability of the GI Panel to detect three clades of HAdV-F41 and other HAdV species (viz., A31, B3, C1, C2, C5, C2/6, and D56) in Japan. Eighteen stool samples were analyzed, five of which contained HAdV-F41, and 13 contained other HAdV species, as confirmed via PCR and sequencing. Although the GI Panel reliably detected all clades of HAdV-F41, it failed to detect any other species, highlighting its limited diagnostic utility beyond F40/41 serotypes. Considering the high false-negative rate for non-F40/41 species, integrating complementary diagnostic methods such as PCR is crucial for comprehensive HAdV detection. These findings underscore the limitations of the GI Panel in detecting non-F40/41 species, such as HAdV-C (commonly associated with pediatric gastroenteritis) and other species that are important in immunocompromised patients. Complementary diagnostic methods, such as PCR or immunochromatographic assays, are essential to ensure accurate HAdV detection, especially in vulnerable populations.

Clinical and microbiological profile of patients with diarrhea evaluated using the gastrointestinal panel in a high-complexity center

INTRODUCTION

Gastrointestinal infections represent a worldwide public health problem. In Colombia, the incidence reaches 21.4 cases per 1,000 inhabitants. Given the limitations of traditional diagnostic methods in terms of sensitivity and specificity, the gastrointestinal panel (GIP) has emerged as a promising tool, allowing rapid detection of 22 pathogens. This study aimed to describe the clinical and microbiological characteristics of immunosuppressed and immunocompetent adult patients with diarrhea and the influence of the gastrointestinal panel in their treatment in a high-complexity hospital in Colombia.

MATERIALS AND METHODS

A cross-sectional observational study was carried out including 350 adult patients treated at the Fundación Valle del Lili hospital between 2021 and 2022. Demographic and clinical variables, GIP findings and treatment were analyzed by univariate and bivariate analysis. We compare immunocompromised and immunocompetent adult patients using Chi-square tests, Fisher's F test for qualitative variables, Student's t-test, and the Mann-Whitney U test for quantitative variables. A significance level of 5% was applied to demonstrate the significance of the variables in all the tests used.

RESULTS

The results showed that 52% were men, with an average age of 52 years. 72.0% presented acute diarrhea, being inflammatory in 60.1%. 39.1% of the patients were immunosuppressed, mainly transplant recipients (31.3%). 53% of the GIPs were positive, with up to 5 pathogens per sample. Bacteria were detected in 80%, viruses in 14.4%, and parasites in 5.5%. The most frequent bacteria were enteropathogenic E. coli (43.0%), enteroaggregative E. coli (18.6%), and C. difficile (17.4%). Norovirus was the predominant virus (67.7%) and Cryptosporidium the most common parasite (41.7%). A higher frequency of Vibrio spp. was observed in non-immunosuppressed patients (p = 0.004) and of enterotoxigenic E. coli in immunosuppressed patients. 41.0% of patients received antibiotic/antiviral therapy, 83% empirically. GIP influenced the treatment of 56.7% of patients, with a 90.0% recovery rate.

CONCLUSION

This study confirms that GIP is a valuable diagnostic tool in the management of adult patients with diarrheal disease, particularly in immunocompromised patients. In our setting it is still a costly and difficult to access test, which makes it necessary to standardize the indications for its application. Future studies could evaluate its cost-effectiveness in our context.

Clinical Performance of the LiquidArray® Gastrointestinal VER 1.0 Assay in Patients with Suspected Gastroenteritis

BACKGROUND/OBJECTIVES

Rapid and accurate pathogen identification is essential for the proper management of patients with infectious gastroenteritis, as well as for a better control of disease outbreaks. This observational, non-interventional, single-site study evaluated the diagnostic accuracy of LiquidArray® Gastrointestinal VER 1.0, a multiplex PCR syndromic panel capable of detecting up to 26 clinically relevant enteropathogens.

METHODS

Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and likelihood ratio (LR) were evaluated using stool samples from 1512 patients with suspected gastroenteritis and were compared to seven competitor assays.

RESULTS

LiquidArray® Gastrointestinal VER 1.0 showed a very low invalid rate (0.5% at initial testing, down to 0% after repeat) and high sensitivity (>90% for most detected targets) and specificity (>99% for all detected targets). Accordingly, the PPV and NPV were high (>90% for most targets and >99% for all targets, respectively). The analytical performance of LiquidArray® Gastrointestinal VER 1.0 was also excellent as to co-amplification capability, cross-reactivity and assay precision.

CONCLUSIONS

This study demonstrates the excellent clinical performance of LiquidArray® Gastrointestinal VER 1.0 and its suitability for implementation in clinical routine for the rapid and accurate diagnosis of infectious gastroenteritis.

Multiplex Gastrointestinal Panel Testing in Hospitalized Patients With Acute Diarrhea in Thailand

Background

Multiplex gastrointestinal (GI) panel testing is widely used for outpatient diagnosis of diarrhea. However, the clinical practicality of multiplex testing in hospitalized diarrheal subjects has not yet been thoroughly elucidated.

Methods

We enrolled hospitalized subjects with acute diarrhea. The subjects' stool samples were collected in triplicate; 1 sample was tested using traditional diagnoses, and the other 2 were tested using Allplex (AP) and FilmArray (FA) GI panel testing. Clinical data were reviewed and analyzed.

Results

Of the 199 subjects, 92 (46.5%) were male, and the mean age was 66.3 years. The median (interquartile range) onset of diarrhea was 6 (2--14) days after hospitalization. One hundred fifty-one patients (75.9%) had sepsis, and 166 (83.4%) had received prior or were receiving current antimicrobial therapy. Positive stool cultures were obtained from 4/89 (4.5%), and Clostridioides difficile toxin gene tests were positive in 14/188 (7.4%) patients. AP and FA multiplex tests were positive for GI pathogens in 49/199 (24.6%) and 40/199 (20.1%), respectively. The target most frequently detected by AP was Aeromonas spp. Both assays commonly detected enteropathogenic E. coli (EPEC), C. difficile toxin gene, and Salmonella spp.; neither assay detected pathogens in 75.4% and 79.9%. Fever (odds ratio [OR], 2.05; 95% CI, 1.08-3.88; P = .028), watery diarrhea (OR, 2.69; 95% CI, 1.25-5.80; P = .011), and antimicrobial therapy (OR, 2.60; 95% CI, 1.18-5.71; P = .018) were independent factors associated with the negative multiplex test result.

Conclusions

Multiplex GI panel testing effectively detects enteric pathogens associated with diarrhea in hospitalized subjects. The etiology remains undiagnosed in >75% of cases. Factors contributing to negative test results should be considered before implementing the tests.

Gastrointestinal Panel Performance for the Diagnosis of Acute Gastroenteritis in Pediatric Patients

BACKGROUND

Various methods are used to identify the causative organisms of acute gastroenteritis (AGE) in children. The gastrointestinal (GI) panel has the potential to detect up to 22 pathogens rapidly through the multiplex real-time PCR test. We studied the impact of the GI panel on clinical management in the pediatric population.

METHODS

A retrospective study was conducted to collect data on GI panel results and clinical details of inpatient children presenting with AGE at King Hamad University Hospital, Kingdom of Bahrain, over the course of one year.

RESULTS

One hundred nine samples were collected. The GI panel was positive in 96 samples (88.1%), with the majority detected in the toddler age group. Forty-one (42.7%) samples were positive for at least one organism. Salmonella was the most frequently encountered bacteria as a single isolate, 10/55 (18.2%), while enteropathogenic Escherichia coli was the most common co-infected organism, 16/41 (39%). Norovirus was the most common virus among the viruses. Bacterial detection peaked from July to October, while viral detection plateaued throughout the year. The GI panel and stool culture were positive for the same organism in 17 samples, versus one sample with a different organism. Sixty-two (56.9%) samples had a positive GI panel but negative stool cultures and stool analysis, and half of those detected viruses. The GI panel was positive in 86.2% of severely ill patients; the majority were bacteria. Bacterial detection was associated with a higher CRP compared to viruses.

CONCLUSION

The GI panel is an informative tool for detecting the causative pathogen of AGE in children. However, it can detect multiple organisms, indicating a possible carrier status, which points toward future studies.

Evaluation of non-invasive diagnostic tools for diarrhea: a systematic review of point-of-care tests and biomarkers

Background

Diarrhea is a prevalent condition affecting millions worldwide. However, current standard diagnostic methods have many drawbacks. This review examines various non-invasive point-of-care (POC) tests and biomarkers aiding rapid diagnosis of diarrhea from different causes.

Methods

PubMed, PubMed Central, ScienceDirect, Cochrane Library, and Google Scholar were searched from 2013 to present for relevant literature. Two reviewers independently assessed included studies' quality using the Critical Appraisal Skills Programme (CASP) checklist.

Results

The search yielded 1453 studies, of which 39 were included after screening and applying eligibility criteria. Polymerase chain reaction (PCR) was the POC test in 25 studies, providing consistent sensitivity and specificity. For biomarkers, C-reactive protein (CRP), fecal calprotectin, and procalcitonin offered high sensitivity and specificity for conditions like acute pediatric diarrhea, microscopic colitis, and inflammatory diarrhea, respectively.

Conclusion

PCR proved the ideal POC test for rapid diarrhea diagnosis, while the procalcitonin biomarker helps differentiate inflammatory from non-inflammatory diarrhea. Other reviewed tools also demonstrated promising diagnostic performance, though improvements in sensitivity, specificity, and usability are still needed.

A metagenomic approach to unveil the association between fecal gut microbiota and short-chain fatty acids in diarrhea caused by diarrheagenic Escherichia coli in children

Diarrheagenic Escherichia coli (DEC) is the main cause of diarrhea in children under five years old. The virulence of DEC is tightly regulated by environmental signals influenced by the gut microbiota and its metabolites. Short-chain fatty acids (SCFAs) are the main metabolic product of anaerobic fermentation in the gut, but their role in DEC diarrhea has not yet been established. In this study, we determine the levels of acetate, propionate, and butyrate in stool samples from children with diarrhea caused by DEC, and we identify bacteria from the fecal gut microbiota associated with the production of SCFAs. The microbiota and SCFAs levels in stool samples obtained from 40 children with diarrhea and 43 healthy children were determined by 16S rRNA gene sequencing and HPLC, respectively. Additionally, shotgun metagenomics was used to identify metagenome-assembled genomes (MAGs) in a subgroup of samples. The results showed significantly higher levels of all SCFAs tested in diarrheal samples than in healthy controls. The abundance of Streptococcus sp., Limosilactobacillus, Blautia, Escherichia, Bacteroides, Megamonas, and Roseburia was higher in the DEC group than in healthy individuals. Functional analysis of bacteria and their main metabolic pathways made it possible to identify species MAGs that could be responsible for the detected SCFAs levels in DEC-positive diarrhea. In conclusion, based on our results and published data, we suggest that SCFAs may be important in the crosstalk between the microbiota and DEC pathogens in the gut.

Epidemiological Characterization of Respiratory Pathogens Using the Multiplex PCR FilmArray™ Respiratory Panel

Various pathogens can cause upper respiratory tract infections, presenting challenges in accurate diagnosis due to similar symptomatology. Therefore, rapid and precise diagnostic tests are crucial for effective treatment planning. Traditional culture-based methods for diagnosis are limited by their reliance on skilled personnel and lengthy processing times. In contrast, multiplex polymerase chain reaction (PCR) techniques offer enhanced accuracy and speed in identifying respiratory pathogens. In this study, we aimed to assess the efficacy of the FilmArray™ Respiratory Panel (RP), a multiplex PCR test capable of simultaneously screening 20 pathogens. This retrospective analysis was conducted at Dankook University Hospital, South Korea, between January 2018 and December 2022. Samples from patients with upper respiratory tract infections were analyzed. Results revealed adenovirus as the most prevalent pathogen (18.9%), followed by influenza virus A (16.5%), among others. Notably, a 22.5% co-infection rate was observed. The FilmArray™ RP method successfully identified 20 pathogens within 2 h, facilitating prompt treatment decisions and mitigating unnecessary antibiotic prescriptions. This study underscores the utility of multiplex PCR in respiratory pathogen identification, offering valuable insights for epidemiological surveillance and diagnosis.

Clinical decision support for gastrointestinal panel testing

Objective

This study aimed to assess the impact of clinical decision support (CDS) to improve ordering of multiplex gastrointestinal polymerase chain reaction (PCR) testing panel ("GI panel").

Design

Single-center, retrospective, before-after study.

Setting

Tertiary care Veteran's Affairs (VA) Medical Center provides inpatient, outpatient, and residential care.

Patients

All patients tested with a GI panel between June 22, 2022 and April 20, 2023.

Intervention

We designed a CDS questionnaire in the electronic medical record (EMR) to guide appropriate ordering of the GI panel. A "soft stop" reminder at the point of ordering prompted providers to confirm five appropriateness criteria: 1) documented diarrhea, 2) no recent receipt of laxatives, 3) C. difficile is not the leading suspected cause of diarrhea, 4) time period since a prior test is >14 days or prior positive test is >4 weeks and 5) duration of hospitalization <72 hours. The CDS was implemented in November 2022.

Results

Compared to the pre-implementation period (n = 136), fewer tests were performed post-implementation (n = 92) with an IRR of 0.61 (p = 0.003). Inappropriate ordering based on laxative use or undocumented diarrhea decreased (IRR 0.37, p = 0.012 and IRR 0.25, p = 0.08, respectively). However, overall inappropriate ordering and outcome measures did not significantly differ before and after the intervention.

Conclusions

Implementation of CDS in the EMR decreased testing and inappropriate ordering based on use of laxatives or undocumented diarrhea. However, inappropriate ordering of tests overall remained high post-intervention, signaling the need for continued diagnostic stewardship efforts.

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.

The role of rapid syndromic diagnostic testing of gastrointestinal pathogens as a clinical decision support tool in a pediatric emergency department

PURPOSE

This study aimed to investigate the role of rapid syndromic diagnostic testing of gastrointestinal pathogens as a clinical decision support tool in a pediatric emergency department (ED) by comparing clinical decision and patient outcome parameters pre- and post-implementation.

METHODS

This was a big data analytical study of children < 18 years old without any underlying diseases, that visited the ED with acute moderate to severe diarrhea during a 34-month period from 2018 to 2022 using Seoul St. Mary's hospital's healthcare corporate data warehouse to retrieve demographic, clinical, and laboratory parameters. Outcome measures pre- and post-implementation of a rapid syndromic multiplex gastrointestinal panel (GI panel) were compared.

RESULTS

A total of 4,184 patients' data were included in the analyses. Broad spectrum antibiotics were prescribed at a significantly lower rate to patients presenting with acute infectious diarrhea at discharge from the ED (9.9% vs 15.8%, P < 0.001) as well as upon admission (52.2% vs 66.0%, P < 0.001) during the post-implementation period compared to the pre-implementation period. Although the duration of ED stay was found to be significantly longer (6.5 vs 5.5 h, P < 0.0001), the rate of ED revisit due to persistent or aggravated symptoms was significantly lower (Δ in intercept, β = -0.027; SE = 0.013; P = 0.041), and the admission rate at follow up after being discharged from the ED shown to be significantly lower during the post-implementation period compared to the pre-implementation period (0.8% vs. 2.1%, P = 0.001, respectively). No significant difference in disease progression was observed (P = 1.000).

CONCLUSION

Using the GI panel in the ED was shown to decrease broad spectrum antibiotic prescribing practices and reduce revisits or admission at follow up by aiding clinical decisions and improving patient outcome.

Prevalence of Enteric Infections in Patients on Immune Checkpoint Inhibitors and Impact on Management and Outcomes

BACKGROUND

Stool pathogen testing is recommended as part of the initial evaluation for patients with new-onset diarrhea on immune checkpoint inhibitors (ICIs), yet its significance has not been well-studied. We aimed to determine the impact of multiplex gastrointestinal (GI) pathogen PCR testing on the clinical course and use of immunosuppressive therapy in patients who develop diarrhea on ICIs.

METHODS

This retrospective cohort included individuals who underwent GI pathogen panel PCR for diarrhea on ICIs at Memorial Sloan Kettering between 7/2015 and 7/2021. The primary outcome was use of immunosuppressive therapy for suspected immunotherapy-related enterocolitis (irEC). Secondary outcomes included diarrhea severity and endoscopic and histologic disease patterns.

RESULTS

Among 521 ICI-treated patients tested for GI pathogens, 61 (11.7%) had a positive PCR. Compared to patients without detectable infections, patients with infections had more frequent grades 3-4 diarrhea (37.7% vs. 19.6%, P < .01) and colitis (39.3% vs. 14.7%, P < .01). However, patients with infections did not have higher rates of persistent or recurrent diarrhea and were less likely to receive steroids (P < .01) and second-line immunosuppressive agents (P = .03). In 105 patients with lower endoscopy, similar trends were observed and no differences in endoscopic severity or histologic patterns were noted between groups.

CONCLUSIONS

GI infections in ICI-treated patients presenting with diarrhea are linked to more severe but self-limited clinical presentations and may be optimally treated with observation and supportive care alone. Routine and timely stool pathogen testing may help avert unnecessary empiric immunosuppression for suspected irEC, which has been linked to blunted antitumor responses and numerous adverse effects.

Gastrointestinal PCR panel results and antibiotic use in acute gastroenteritis cases: How appropriate are we in our usage?

BACKGROUND

We aimed to determine the pathogens detected by the Gastrointestinal (GI) PCR panel in patients with acute gastroenteritis (AGE), the evaluation of antibiotic use in these patients, and the investigation of the role of laboratory parameters in differentiating viral and bacterial etiologies.

METHODS

The demographic characteristics, GI PCR panel results, laboratory investigations, antibiotic usage, and appropriateness of antibiotic treatment were investigated in AGE patients.

RESULTS

A total of 175 adult patients with AGE and GI PCR panel results were included in the study. The most common pathogens were EPEC (24.6%) and C. difficile (18.3%). Among the 102 patients receiving antibiotic treatment, 34.3% were evaluated as inappropriate antibiotic use. WBC, CRP, procalcitonin, CRP/albumin ratio, and procalcitonin/albumin ratio were found to be significantly higher in cases with bacterial origin.

CONCLUSIONS

The utilization of GI PCR panels in AGE patients has revolutionized the field of diagnostics by providing rapid and accurate identification of pathogens. In units without the possibility of GI PCR testing, CRP, procalcitonin, CRP/albumin ratio and procalcitonin/albumin ratio may be useful in the decision of antibiotic treatment.

Development and validation of a bacterial gastrointestinal multiplex RT-PCR assay for use on a fully automated molecular system

PCR-based enteric multiplex panels represent a rapid and reliable alternative to conventional "classical" phenotypic stool diagnostics. The aim of this study was to establish a laboratory-developed non-commercial multiplex Real-Time-PCR panel for the detection of the most important bacterial stool pathogens, Salmonella spp., Shigella spp., Yersinia enterocolitica/ pseudotuberculosis and Campylobacter jejuni/coli. on the "open" cobas omni Utility Channel (UC) of the cobas 6800 system (Roche). The aim was to replace the laborious phenotypical stool diagnostics with a high throughput Real-Time PCR method. The respective primers and probes were designed to cover conserved genomic regions of the pathogens and validated using Ultramer oligonucleotides, positive stool material and reference strains. To further validate the multiplex PCR-assay, the following parameters were evaluated: analytical-sensitivity and -specificity, cross-reactivity, linearity and inter- and intra-assay variance as well as limit of detection (LOD). In addition a retrospective analysis of culture positive and negative samples from daily routine was performed using 745 native stool samples. The Gastro assay was linear over a 5-log-unit and within the expected dynamic range with amplification efficiencies ranging from 94.6% to 120%. In addition, all targets showed excellent coefficients of repeatability (≤ 1.11%), intermediate precision (≤ 1.02%) and total variance (≤ 1.39%). In terms of analytical sensitivity the assay demonstrated detection limits ranging from 7.83 copies per reaction to 14.4 copies per reaction. The assay showed excellent agreement with culture methods (>95%) and a 100% sensitivity and specificity after resolution of discrepant results. The multiplex-PCR assay provides a comprehensive, rapid and sensitive alternative to conventional methods for the detection of the major bacterial stool pathogens in diagnostic laboratories.

High Burden of Co-Infection with Multiple Enteric Pathogens in Children Suffering with Diarrhoea from Rural and Peri-Urban Communities in South Africa

Infectious diarrhoea contributes to high morbidity and mortality in young children from sub-Saharan Africa. The aim of this study was to assess the prevalence of single and multiple diarrhoeal-causing pathogen combinations in children suffering from diarrhoea from rural and peri-urban communities in South Africa. A total of 275 diarrhoea stool specimens were collected between 2014 and 2016 from Hospitals and Primary Health Care clinics. The BioFire^® FilmArray^® Gastrointestinal panel was used to simultaneously detect 22 diarrhoea pathogens (viruses, bacteria, parasites) known to cause diarrhoea. A total of 82% (226/275) enteric pathogens were detected in the stool specimens. The two most detected bacterial, viral and parasitic pathogens each included: EAEC (42%), EPEC (32%), Adenovirus F40/41 (19%), Norovirus (15%), Giardia (8%) and Cryptosporidium (6%), respectively. Single enteric pathogen infections were recorded in 24% (65/275) specimens with EAEC, and Norovirus was found in 26% (17/65) and 14% (9/65) of the specimens, respectively. Multiple enteric pathogen combinations were recorded in 59% (161/275) of the stool specimens with 53% (85/161) containing two pathogens, 22% (35/161) containing three pathogens and 25% (41/161) containing four or more pathogens. The results from this study demonstrated the complex nature of pathogen co-infections in diarrhoeal episodes which could have an impact on treatment effectiveness.

Pathogen-Specific Alterations in the Gut Microbiota Predict Outcomes in Flare of Inflammatory Bowel Disease Complicated by Gastrointestinal Infection

INTRODUCTION

Enteric infection with Clostridioides difficile , Escherichia coli subtypes, and norovirus is commonly detected in flares of inflammatory bowel disease (IBD). We associated the gut microbiome during flare complicated by a gastrointestinal pathogen with outcomes of IBD.

METHODS

We performed a cross-sectional study of 260 patients (92 IBD and 168 non-IBD) with a gastrointestinal polymerase chain reaction panel positive for C. difficile, E. coli , or norovirus, or negative during an episode of diarrhea from 2018 to 2020, and 25 healthy controls. Clinical variables, IBD status, and 2-year outcomes were collected. Using 16S rRNA sequencing, we measured the effect size of the gut microbiome on IBD characteristics and outcomes.

RESULTS

There were major differences in the gut microbiome between patients with and without a pathogen and IBD. In IBD, a higher proportion of patients without a pathogen required hospitalization and IBD therapies at flare and within the 2 years after flare, driven by a milder disease course in flares complicated by an E. coli subtype or norovirus. Examining the contribution of clinical covariates, the presence of IBD, and C-reactive protein, C. difficile had a greater relative influence on the gut microbiome compared with the presence of an E. coli subtype or norovirus. In patients with C. difficile or no pathogen, lower microbiome diversity at flare was associated with adverse IBD outcomes over 2 years.

DISCUSSION

Distinctive pathogen-specific gut microbiomes were associated with subsequent IBD outcomes. These findings may have direct implications for the management of IBD flares complicated by enteric pathogens.

Investigation of the use of multiplex PCR in childhood diarrhea with clinical and epidemiological features

INTRODUCTION

Acute gastroenteritis is one of the most common causes of hospital admission in children. Treatment regimens differ depending on the pathogen. In our study, we aimed to evaluate the epidemiological and clinical features of pediatric patients whose gastrointestinal agents were detected by multiplex PCR.

MATERIALS AND METHODS

The study included 131 pediatric patients who were followed up at Eskişehir Osmangazi University, Pediatric Department between January 2018 and December 2021.Gastrointestinal pathogens were detected in stool samples by multiplex PCR. The epidemiological and clinical features were reviewed retrospectively.

RESULTS

A total of 203 gastrointestinal pathogens were detected from the stool samples of 131 cases. Of these cases, 56% were male and 44% were female. The mean age was 66 (2-204) months. The most common symptoms were diarrhea, fever, vomiting and abdominal pain. The pathogen detection rate was 69% by multiplex PCR. A single pathogen was detected in 85 (65%) cases and multiple pathogens were detected in 46 (35%) cases. The most common pathogens were enteropathogenic Escherichia coli (EPEC, 23%), Clostridium difficile (21%), norovirus (17%), rotavirus (15%), salmonella (12%) and enterotoxigenic E. coli (ETEC, 11%). Stool culture was positive in 16 (12%) cases and microscopic examination positive in 17 (13%) cases. Probiotic treatment was given to 119 (92%) cases and antimicrobial treatment (metroinidazole, ceftriaxone, azithromycin and oral vancomycin) to 34 (26%) cases. Of the cases, 56 (42%) had chronic disease, 40 (30%) had a history of previous antibiotic use and 17 (13%) had a history of hospitalization in the intensive care unit.

CONCLUSION

The sensitivity of the multiplex PCR in the detection of acute gastroenteritis agents is higher than stool microscopy, stool culture and stool antigen tests. However, due to the inability to distinguish between colonization, carrier state and pathogenicity, it should be evaluated together with other diagnostic tests and clinical findings in order to determine whether the determined agent is pathogenic or not and in the regulation of antimicrobial therapy.

Detection of Foodborne Pathogens in Acute Gastroenteritis Patient’s Stool Samples Using the BioFire® FilmArray® Gastrointestinal PCR Panel in the Republic of Trinidad and Tobago, West Indies

In 2009, the burden of illness study for acute gastroenteritis in Trinidad and Tobago highlighted that ~10% of stool samples tested were positive for a foodborne pathogen. The study also noted that limited laboratory screening for pathogens contributed to a lack of etiology as public health hospitals only routinely tested for Salmonella and Shigella, and sometimes for Escherichia coli and Campylobacter. To better understand the foodborne pathogens responsible for acute gastroenteritis, enhanced testing using the BioFire® FilmArray® Gastrointestinal PCR panel was used to screen diarrheal stool samples for 22 pathogens from patients in 2018. The five general public health hospitals (San Fernando, Mt. Hope, Port of Spain, Sangre Grande, and Tobago) were notified of research activities and diarrheal stool samples were collected from all acute gastroenteritis patients. A total of 66 stools were screened and ~30% of samples tested positive for a foodborne pathogen. The current study showed that a much wider range of enteric pathogens were associated with acute gastroenteritis in Trinidad and Tobago than previously reported in 2009. These findings can be used by health officials to guide appropriate interventions, as well as to provide evidence for adoption of the PCR panel detection method at public health hospitals to benefit patient care.

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.

Clinical impact of a gastrointestinal PCR panel in children with infectious diarrhoea

OBJECTIVES

Multiplex gastrointestinal PCR (GI-PCR) allows fast and simultaneous detection of 22 enteric pathogens (including Campylobacter, Salmonella, Shigella/enteroinvasive Escherichia coli (EIEC), among other bacteria, parasites and viruses). However, its impact on the management of children with infectious diarrhoea remains unknown.

PATIENTS/DESIGN

All children eligible for stool culture from May to October 2018 were prospectively included in a monocentric study at Robert-Debré University-Hospital.

INTERVENTION

A GI-PCR (BioFire FilmArray) was performed on each stool sample.

MAIN MEASURES

Data on the children's healthcare management before and after GI-PCR results were collected. Stool culture results were also reported.

RESULTS

172 children were included. The main criteria for performing stool analysis were mucous/bloody diarrhoea and/or traveller's diarrhoea (n=130). GI-PCR's were positive for 120 patients (70%). The main pathogens were enteroaggregative E. coli (n=39; 23%), enteropathogenic E. coli (n=34; 20%), Shigella/EIEC (n=27; 16%) and Campylobacter (n=21; 12%). Compared with stool cultures, GI-PCR enabled the detection of 21 vs 19 Campylobacter, 12 vs 10 Salmonella, 27 Shigella/EIEC vs 13 Shigella, 2 vs 2 Yersinia enterocolitica, 1 vs 1 Plesiomonas shigelloides, respectively. Considering the GI-PCR results and before stool culture results, the medical management was revised for 40 patients (23%): 28 initiations, 2 changes and 1 discontinuation of antibiotics, 1 hospitalisation, 2 specific room isolations related to Clostridioides difficile infections, 4 additional test prescriptions and 2 test cancellations.

CONCLUSION

The GI-PCR's results impacted the medical management of gastroenteritis for almostone-fourth of the children, and especially the prescription of appropriate antibiotic treatment before stool culture results.

The influence of hospitalization and HIV severity on gastrointestinal PCR panel evaluation of HIV-related acute diarrhea in New York City: a retrospective, cross-sectional study

INTRODUCTION

Diarrhea is common in persons living with HIV (PLWH)/AIDS. With the increasing utilization of multiplex gastrointestinal PCR panel (GI panel) testing, we aimed to characterize the roles of CD4 count and hospitalization in GI panel assessments of PLWH with acute diarrhea.

METHODS

We performed a cross-sectional study of adult PLWH with acute diarrhea who underwent GI panel testing at two urban academic centers. Demographic, HIV disease, GI panel result, and hospitalization data were collected, and patients were cohorted by CD4 count (CD4 < 200, CD4 200-499, CD4 > = 500). The primary outcome was enteric infection as detected by GI panel, and hospitalization.

RESULTS

Of 298 PLWH, 119 (39.9%) had a CD4 count below 200, 195 (65.4%) were hospitalized, and 137 (46.0%) had enteric infection. Bacterial infection correlated with higher CD4 count (41.9% (CD4 > = 500) vs 31.2% (CD4 200-499) vs 25.2% (CD4 < 200), p = 0.041). Hospitalization correlated with poorly controlled HIV and fewer enteric infections (34.4% vs 68.0%, p < 0.001). After adjusting for HIV disease severity, a negative GI panel remained independently associated with hospitalization (adjusted odds ratio (aOR) 5.32, 95% confidence interval (CI) 2.72-10.9), even in patients tested within 72 hours of hospitalization. Despite better HIV control, men who have sex with men (MSM) had more frequent infectious diarrhea, including from E. coli, giardiasis, and multiple pathogens. MSM status independently predicted enteric infection (aOR 1.93, 95% CI: 1.02-3.67).

CONCLUSIONS

GI panel results vary by HIV disease severity and hospitalization in PLWH. Clinicians - especially in the inpatient setting - should carefully consider these factors when interpreting GI panel results. Further characterization of diarrheal etiology in PLWH with a negative GI panel is needed.

PLAIN LANGUAGE SUMMARY

PCR stool test results are affected by certain factors in HIV-related diarrhea Diarrhea is common in people living with HIV (PLWH) and has a variety of causes, including infections, medications, and HIV itself. Multiplex polymerase chain reaction (PCR) stool testing simultaneously evaluates for a variety of common viral, bacterial, and parasitic infections of the gastrointestinal tract, and is increasingly being used in patients with diarrhea. However, patients with HIV and diarrheal illness may have uncommon infections not typically present in those with normal immune function - and thus not routinely evaluated for in stool testing. It is not known what factors, if any, might affect the results of PCR testing in HIV-related diarrhea.In this study, we examined all PLWH who underwent stool PCR testing for diarrhea over a 4-year period. We separated the patients into groups based on HIV disease severity as measured by CD4 T-cell count, or the count of the immune cells affected by HIV. We examined whether there were differences among groups in infection rates as detected by PCR stool testing. Separately, we studied the role of hospitalization in stool PCR test results.Of 298 PLWH who underwent stool PCR testing for diarrhea, 119 had a CD4 count less than 200 (low CD4 count), 195 were hospitalized at time of testing, and 137 had a positive stool PCR test. Compared to those with a low CD4 count, subjects with less severe HIV disease were more likely to have a bacterial infection on stool PCR testing and less likely to be hospitalized. Hospitalized patients were more likely to have a negative PCR stool test, regardless of CD4 count. Many patients with a low CD4 count had diarrheal etiologies not evaluated by multiplex stool PCR. In PLWH who experience diarrhea, stool PCR testing results vary by CD4 count and hospitalization. Providers should be mindful of these factors when interpreting stool PCR test results.

Clinical Factors Associated With Positive Stool PCR for Gastrointestinal Pathogens in Celiac and Inflammatory Bowel Disease

GOALS

We aimed to identify the clinical factors of celiac disease (CeD) and inflammatory bowel disease (IBD) associated with positive stool gastrointestinal (GI) polymerase chain reaction (PCR) test.

BACKGROUND

Understanding the pattern of enteric infections in CeD and IBD may allow further insight into microbiome-mediated pathogeneses.

STUDY

This was a retrospective study of adult patients (age 18 y or above) with CeD and IBD at a large quaternary care institution. We identified patients with CeD or IBD who underwent stool GIPCR evaluation as outpatients (office visit or at endoscopy) between March 2015 and March 2019. Patients with a negative GIPCR test within the study time frame were randomly chosen as controls (1 : 1). The independent relationship between clinical characteristics and positive GIPCR was evaluated using multivariable logistic regression.

RESULTS

A total of 266 patients met criteria for the study, including 92 (35%) with CeD and 174 (65%) with IBD. On multivariable analysis of factors associated with positive GIPCR test, CeD patients were more likely to have diarrheal presentation of illness [odds ratio (OR): 2.61, 95% confidence interval (CI) 1.05-6.72], experience extraintestinal manifestations (OR: 2.49, 95% CI: 1.01-6.31), and practice a gluten-free diet for at least 5 years (OR: 4.00, 95% CI: 1.36-11.67), relative to those with a negative GIPCR test. IBD patients with positive GIPCR were more likely to be on corticosteroids (OR: 2.23, 95% CI: 1.02-5.4.84), experience extraintestinal manifestations (OR: 2.60, 95% CI: 1.22-5.53), and use proton-pump inhibitors (OR: 4.07, 95% CI: 1.69-9.77).

CONCLUSIONS

Intestinal infections in CeD and IBD are associated with important disease-specific characteristics.

Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool

Stool culture is the gold standard method to diagnose enteric bacterial infections; however, many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is rapid, accurate, and affordable, yet does not yield subtyping information critical for foodborne disease surveillance. A metagenomics-based stool testing approach could simultaneously provide diagnostic and public health information. Here, we evaluated shotgun metagenomics to assess the detection of common enteric bacterial pathogens in stool. We sequenced 304 stool specimens from 285 patients alongside routine diagnostic testing for Salmonella spp., Campylobacter spp., Shigella spp., and shiga-toxin producing Escherichia coli. Five analytical approaches were assessed for pathogen detection: microbiome profiling, Kraken2, MetaPhlAn, SRST2, and KAT-SECT. Among analysis tools and databases compared, KAT-SECT analysis provided the best sensitivity and specificity for all pathogens tested compared to culture (91.2% and 96.2%, respectively). Where metagenomics detected a pathogen in culture-negative specimens, standard PCR was positive 85% of the time. The cost of metagenomics is approaching the current combined cost of PCR, reflex culture, and whole genome sequencing for pathogen detection and subtyping. As cost, speed, and analytics for single-approach metagenomics improve, it may be more routinely applied in clinical and public health laboratories.

Evaluation of a new fast in-house Real-Time PCR assay for detecting both Norovirus and toxigenic Clostridium difficile using fecal sample and rectal swab

BACKGROUND

Norovirus and toxigenic Clostridium difficile infections are the 2 most common causes of infectious gastroenteritis. Rapid and reliable detection of these to microorganisms is important to assess if contact precautions are indicated to prevent spreading and reduce cost of isolation.

METHODS

This study determines sensitivity and specificity of a new fast in-house PCR assay used on BD MAX platform to detect both norovirus and C difficile in 1 turn-over in clinical context. Furthermore, fecal samples as well as rectal swabs were used as analysis material to determine the accuracy of the new assay on a fecal samples and rectal swabs compared with standard methods.

RESULTS

From 227 included patients, 143 rectal swabs and 135 fecal samples obtained. The new in-house PCR showed a sensitivity of 73.3% and a specificity of 99.2% for norovirus on a fecal sample and a sensitivity of 57.1% and specificity 99.1% of for norovirus on a rectal swab. For C difficile a sensitivity of 100% and specificity of 100% on a fecal sample and a sensitivity of 90.9% and a specificity of 99.1% on a rectal swab was shown. The time consumption for detecting the 2 enteropathogens was reduced by half by using the new assay.

CONCLUSIONS

The new assay shows an acceptable sensitivity and specificity for C difficile and an acceptable specificity for norovirus when analysis was done on fecal samples and reduces half of the time consumption. Further research is needed to improve the accuracy of the new in-house PCR before clinical implication.

The Distribution of Gastrointestinal Pathogens on Stool PCR Prior to the Development of IBD

GOALS

We investigated the distribution of pathogens on stool gastrointestinal (GI) polymerase chain reaction (PCR) testing in those who subsequently developed inflammatory bowel disease (IBD).

BACKGROUND

Infectious gastroenteritis has been associated with later development of IBD.

STUDY

This retrospective study includes patients of all ages hospitalized for diarrhea with positive GIPCR panel and subsequently a new diagnosis of IBD [confirmed by chart review and International Classification of Disease, Clinical Modification code for Crohn's disease (CD) or ulcerative colitis (UC)], between March 2015 to September 2019 at our quaternary care institution. Patients with IBD diagnosis before GIPCR were excluded. Descriptive statistics characterized the distribution of microbial pathogens in relation to later IBD diagnosis.

RESULTS

Fifty-four participants were eligible (UC 44%; CD 56%). Median age at time of IBD diagnosis was 35 years [interquartile range (IQR) 18 to 65]. Median time between GIPCR and IBD diagnosis was 3 months (IQR 2 to 9) for all patients. When stratified by organism class, median time to diagnosis was 6 months (IQR 2 to 10) for patients with bacteria, 3 months (IQR 1 to 8) for patients with viruses, and 1 month (IQR 0.75 to 1) for patients with parasites (log-rank P=0.001). Sixty-nine unique pathogens (83% bacteria) were identified on all tests. Escherichia coli was the most common species (71%), of which enteropathogenic E. coli was predominant (38%).

CONCLUSIONS

The E. coli species, specifically enteropathogenic E. coli, may be implicated in the development of IBD. This is one of the first studies to evaluate the results of stool GIPCR in the link between the microbiome and IBD pathogenesis.

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.

Detection of potential enteric pathogens in children with severe acute gastroenteritis using the filmarray: Results from a three - years hospital-based survey in Northern Italy

Acute gastroenteritis (AGE) are leading causes of morbidity and mortality in children. Therefore, rapid pathogens identification is needed. The AGE aetiology was investigated from 2018 to 2020 in 2,066 children in Parma (Italy) by FilmArray Gastrointestinal Panel and Enterovirus-targeting RT-PCR. Pathogens were detected in 1,162 (56.2%) stool samples from as many children; 798 (68.7%) were single and 364 (31.3%) mixed infections (68.7% vs 31.3%, P < 0.0001). Children aged 0-5 years showed the highest infection incidence (66.1%). The most frequent pathogens were Enteropathogenic Escherichia coli (EPEC; 19.14%), Clostridioides difficile (10.42%), Norovirus (10.36%), Enterovirus (9.44%), and Campylobacter (9.21%). EPEC, Campylobacter, enteroaggregative E. coli, Norovirus, and Rotavirus showed seasonality. The incidence of pathogens detected decreased between 2018 and 2020 (42.7% vs 20.8%, P < 0.0001), seemingly for the preventive measures imposed by the severe acute respiratory syndrome coronavirus-2 pandemic. A putative aetiology in half the children examined and an estimate of enteric pathogens epidemiology were assessed.

Performance of four commercial real-time PCR assays for the detection of bacterial enteric pathogens in clinical samples

OBJECTIVES

Many laboratories use culture-independent diagnostic tests for bacterial gastroenteritis (ie. real-time polymerase chain reaction [RT-PCR]) instead of culture because of better sensitivity, automation, and faster turnaround times. To address some gaps in initial evaluations and lack of intraassay comparisons for many commercial RT-PCRs we compared the ability of four commercially available RT-PCR tests (Ridagene, Fast Track Diagnostics, BD Max, and Prodesse Progastro) to detect five major bacterial enteric pathogens: Campylobacter, Salmonella, Shiga-toxin producing E. coli (STEC), Shigella and Yersinia.

METHODS

Clinical stool specimens and contrived samples comprising commonly circulating species, serotypes, biovars and/or toxin subtypes were used for the comparison.

RESULTS

Concordance rates for RT-PCR and culture using culture positive and negative clinical stools were greater than 90% for Campylobacter (97.5-100%), Salmonella (97.5-100%), Shigella (100%) and STEC (90-100%). However, the agreement between RT-PCR and culture for Y. enteroccolitica ranged from 70-90%. For the contrived sample set, stx_2f was detected by only 1 of 4 assays. Of note, no assay could detect Yersinia non-enterocolitica and C. upsaliensis.

CONCLUSIONS

Depending on the prevalence of certain stx sub-types, Yersinia and Campylobacter species in a laboratory's jurisdiction, culture methods remain critical for the detection of these pathogens without further improvement in PCR assays.

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.

Improved diagnosis of gastrointestinal infections using a semi-automated multiplex real-time PCR for detection of enteropathogens

Introduction. The identification of enteropathogens is critical for the clinical management of patients with suspected gastrointestinal infection. The FLOW multiplex PCR system (FMPS) is a semi-automated platform (FLOW System, Roche) for multiplex real-time PCR analysis.Hypothesis/Gap Statement. FMPS has greater sensitivity for the detection of enteric pathogens than standard methods such as culture, biochemical identification, immunochromatography or microscopic examination.Aim.The diagnostic performance of the FMPS was evaluated and compared to that of traditional microbiological procedures.Methodology. A total of 10 659 samples were collected and analysed over a period of 7 years. From 2013 to 2018 (every July to September), samples were processed using standard microbiological culture methods. In 2019, the FMPS was implemented using real-time PCR to detect the following enteropathogens: Shigella spp., Salmonella spp., Campylobacter spp., Giardia intestinalis, Entamoeba histolytica, Blastocystis hominis, Cryptosporidum spp., Dientamoeba fragilis, adenovirus, norovirus and rotavirus. Standard microbiological culture methods (2013-2018) included stool culture, microscopy and immunochromatography.Results. A total of 1078 stool samples were analysed prospectively using the FMPS from July to September (2019): bacterial, parasitic and viral pathogens were identified in 15.3, 9.71 and 5.29 % of cases, respectively. During the same period of 6 years (2013-2018), the proportion of positive identifications using standard microbiological methods from 2013 to 2018 was significantly lower. A major significant recovery improvement was observed for all bacteria species tested: Shigella spp./enteroinvasive Escherichia coli (EIEC) (P <0.05), Salmonella spp. (P <0.05) and Campylobacter spp. (P <0.05). Marked differences were also observed for the parasites G. intestinalis, Cryptosporidium spp. and D. fragilis.Conclusion. These results support the value of multiplex real-time PCR analysis for the detection of enteric pathogens in laboratory diagnosis with outstanding performance in identifying labile micro-organisms. The identification of unsuspected micro-organisms for less specific clinical presentations may also impact on clinical practice and help optimize patient management.

Approach to the adult patient with chronic diarrhea: A literature review

Chronic diarrhea is defined by symptoms lasting longer than 4 weeks. It is a common problem that affects up to 5% of the adult population. Different pathophysiologic mechanisms involve numerous causes, including drug side effects, postoperative anatomic and physiologic alterations, intestinal and colonic wall abnormalities, inflammatory or malabsorption causes, pancreatobiliary diseases, and functional or gut-brain axis disorders associated with dysbiosis or gastrointestinal motility alterations. Due to such a broad differential diagnosis, it is important to categorize chronic diarrhea into five main groups: drug side effect, postoperative, postinfectious, malabsorptive, inflammatory, and functional. The present review is a narrative analysis of the diagnostic approach, emphasizing key aspects of the clinical history, the utility of biomarkers (in breath, stool, urine, and serology) and malabsorption and motility tests, the role of radiologic and endoscopic studies, and the most common histologic findings. A diagnostic algorithm aimed at determining etiology and personalizing therapy is also proposed.

Quality Improvements in Management of Children with Acute Diarrhea Using a Multiplex-PCR-Based Gastrointestinal Pathogen Panel

Conventional methods for etiologic diagnoses of acute gastroenteritis (AGE) are time consuming and have low positive yield leading to limited clinical value. This study aimed to investigate quality improvements in patient management, antibiotic stewardship, and in-hospital infection transmission prevention using BioFire^® FilmArray^® Gastrointestinal Panel (GI Panel) in children with acute diarrhea. This was a prospective study recruiting children < 19 years old with new onset diarrhea during the study period, and a matched historical cohort study of children diagnosed with AGE during the 4 years prior. Patients in the prospective cohort underwent stool testing with GI Panel and conventional methods. A total of 182 patients were included in the prospective cohort, of which 85.7% (n = 156) had community-onset and 14.3% (n = 26) had hospital-onset diarrhea. A higher pathogen positivity rate for community-onset diarrhea was observed by the GI Panel (58.3%, n = 91) compared to conventional studies (42.3%, n = 66) (p = 0.005) and historical cohort (31.4%, n = 49) (p < 0.001). The stool tests reporting time after admission was 25 (interquartile range, IQR 17-46) hours for the GI Panel, and 72 (IQR 48-96) hours for the historical cohort (p < 0.001). A significant reduction in antibiotic use was observed in the prospective cohort compared to historical cohort, 35.3% vs. 71.8%; p < 0.001), respectively. Compared to the GI Panel, norovirus ICT was only able to detect 4/11 (36.4%) patients with hospital-onset and 14/27 (51.8%) patients with community-onset diarrhea. The high positivity rate and rapid reporting time of the GI Panel had clinical benefits for children admitted for acute diarrhea, especially by reducing antibiotic use and enabling early adequate infection precaution and isolation.

Approach to the adult patient with chronic diarrhea: a literature review

Chronic diarrhea is defined by symptoms lasting longer than 4 weeks. It is a common problem that affects up to 5% of the adult population. Different pathophysiologic mechanisms involve numerous causes, including drug side effects, postoperative anatomic and physiologic alterations, intestinal and colonic wall abnormalities, inflammatory or malabsorption causes, pancreatobiliary diseases, and functional or gut-brain axis disorders associated with dysbiosis or gastrointestinal motility alterations. Due to such a broad differential diagnosis, it is important to categorize chronic diarrhea into five main groups: drug side effect, postoperative, postinfectious, malabsorptive, inflammatory, and functional. The present review is a narrative analysis of the diagnostic approach, emphasizing key aspects of the clinical history, the utility of biomarkers (in breath, stool, urine, and serology) and malabsorption and motility tests, the role of radiologic and endoscopic studies, and the most common histologic findings. A diagnostic algorithm aimed at determining etiology and personalizing therapy is also proposed.

Mapping of aetiologies of gastroenteritis: a systematic review and meta-analysis of pathogens identified using a multiplex screening array

OBJECTIVE

Emergence of molecular methods to screen stools could provide a more complete picture of pathogens causing gastroenteritis, allowing to adequately treat patients whenever required but, so far, no aggregate data have been released. Our objective was to report pathogens identified in patients suffering from gastroenteritis using a multiplex molecular array.

DESIGN

Medline and Embase were searched for original publications reporting pathogens identified with FilmArray GI panel in patients suffering from gastroenteritis. Proportions of pathogens were extracted and pooled using a model with random effects.

RESULTS

Fourteen studies (17,815 patients) were included in the analysis. Among the 7,071 patients (39.7%) with positive FilmArray, identified pathogens were EPEC (27.5%), Clostridium difficile (19.3%), Norovirus (15.1%), EAEC (15%), Campylobacter spp (11.8%), Salmonella spp (8.1%), ETEC (7.3%), Rotavirus (7.3%), Sapovirus (7.1%), STEC (5.2%), Shigella/EIEC (4.9%), Giardia lamblia (4%), Adenovirus (3.8%), Cryptosporidium spp (3.8%), Astrovirus (2.8%), Yersinia enterocolitica (1.7%), Escherichia coli O157 (1.1%), Plesiomonas shigelloides (1.1%), Cyclospora cayetanensis (0.7%), Vibrio spp (0.5%), Vibrio cholerae (0.3%) and Entamoeba histolytica (0.3%). When considering only studies with control group (microbiological examination of the stools performed by other methods), FilmArray identified at least one pathogen in 48.2% of patients versus 16.7% when using comparative diagnostic methods.

CONCLUSIONS

FilmArray GI panel was positive in 39.7% of patients suffering from gastroenteritis. This proportion has to be mitigated by the carriage rates of identified organisms. Ultimately, restricted ordering of molecular panels to those patients who might benefit from specific treatment could provide medical value by swift identification of the pathogen and more targeted therapy.

FilmArray GI-panel performance for the rapid and multiple detection of gastrointestinal microorganisms in foodborne illness outbreaks in Shenzhen during 2018-2019

Foodborne illness outbreaks can be caused by a great many of gastrointestinal microorganisms including bacteria, viruses and parasites. Acute gastroenteritis is most commonly found in such patients infected with at least one pathogen through food intake. The stool culture has been conventionally used to guide a single diagnosis and therapy. However, traditional methods for identification of a pathogen are time-consuming and have limited sensitivity, leading to false negatives and co-infection omission. The aim of this study was to characterize the multiple etiology of each foodborne illness outbreak in Shenzhen during 2018-2019 by the FilmArray GI panel, and to reveal the seasonality of each causative organism incurring outbreaks. All patients included had a FilmArray GI panel performance and the seasonal characteristics were recorded. A total of 173 patients suffered from foodborne illnesses in 32 outbreaks in Nanshan District of Shenzhen. In total, 365 microorganisms were detected of which 83.8% (306/365) corresponded to bacteria and 16.2% (59/365) to viruses. Co-infections with more than one microorganism were detected in 81.3% (26/32) of the outbreaks. In 153 (88.4%) of 173 patients at least two pathogens were identified. The most common diarrheal pathogen related to outbreaks was EPEC (56%), followed by ETEC (38%), Norovirus (34%), EAEC (28%), Vibrio (25%), Salmonella (22%), P. shigelloides (22%), C. difficile (16%), STEC (3%) and Sapovirus (3%). Bacterial outbreaks occurred with a seasonal distribution with the exception of C. difficile whereas Norovirus outbreaks predominated during the autumn-winter months. The use of the FilmArray GI panel has given us worthy information regarding the epidemiology of pathogens detected in patients with acute diarrhea. It also highlights the importance of multi-pathogen infections and the frequency of diarrheogenic E. coli in foodborne disease outbreaks. More significantly, the rapid and multiple findings may help quickly taking an appropriate precaution, control and treatment.

Molecular and non-molecular approaches to etiologic diagnosis of gastroenteritis

Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures, reducing hospital length of stay, and reducing overall medical costs. Although stool culture and microscopic examination of diarrheal stool has been the primary method for laboratory diagnosis, culture-independent proteomic and genomic tests are receiving increased attention. Antigen tests for stool pathogens are routinely implemented as rapid and simple analytics whereas molecular tests are now available in various formats from high complexity to waived point-of-care tests. In addition, metagenomic next-generation sequencing stands poised for use as a method for both diagnosis and routine characterization of the gut microbiome in the very near future. Analysis of host biomarkers as indicators of infection status and pathogenesis may also become important for prediction, diagnosis, and monitoring of gastrointestinal infection. Here we review current methods and emerging technologies for the etiologic diagnosis of gastroenteritis in the clinical laboratory. Benefits and limitations of these evolving methods are highlighted.

Use of BioFire FilmArray gastrointestinal PCR panel associated with reductions in antibiotic use, time to optimal antibiotics, and length of stay

BACKGROUND

Rapid and accurate diagnostic tools are needed for appropriate management of infectious diarrhea.

METHODS

We evaluated the impact of the introduction of rapid multiplex PCR testing using the FilmArray gastrointestinal (GI) panel (BioFire Diagnostics, LLC, Salt Lake City, UT) at our institution, and compared the results to those of standard stool cultures.

RESULTS

The most common pathogens detected by the FilmArray GI panel were Clostridium difficile (55.0%), Campylobacter species (20.9%), Salmonella species (12.4%), and Shigella/EIEC species (12.4%). Rates of reproducibility in stool culture for these pathogens ranged from 56.3 to 77.8%. Co-detection of two or more organisms was common (24.2%), most commonly involving EPEC, EAEC, ETEC, and STEC. The time from arrival in the Emergency Department to discharge or admission to the hospital was unchanged after the introduction of FilmArray GI panel, but length of hospital stay was shorter (3 vs. 7.5 days, p = 0.0002) for the FilmArray group. The time to empiric antibiotics did not differ significantly, but optimal antibiotics were started earlier after introduction of the FilmArray GI panel (hospital day 1 vs. 2, p < 0.0001). More patients were discharged without antibiotics after introduction of the FilmArray GI panel (14.0% vs. 4.5%; p < 0.001).

CONCLUSION

Our results demonstrate that the FilmArray GI panel is an important tool for improving both patient care and antibiotic stewardship, despite the tendency for positive results with multiple pathogens.

Diagnostic Test Accuracy of Commercial Tests for Detection of Shiga Toxin-Producing Escherichia coli: A Systematic Review and Meta-Analysis

BACKGROUND

Rapid detection of Shiga toxin-producing Escherichia coli (STEC) enables appropriate monitoring and treatment. We synthesized available evidence to compare the performance of enzyme immunoassay (EIA) and PCR tests for the detection of STEC.

METHODS

We searched published and gray literature for studies of STEC EIA and/or PCR diagnostic test accuracy relative to reference standards including at least one nucleic acid amplification test. Two reviewers independently screened studies, extracted data, and assessed quality with the second version of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Bivariate random effects models were used to meta-analyze the clinical sensitivity and specificity of commercial EIA and PCR STEC diagnostic tests, and summary receiver operator characteristic curves were constructed. We evaluated the certainty of evidence with the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach.

RESULTS

We identified 43 articles reflecting 25 260 specimens. Meta-analysis of EIA and PCR accuracy included 25 and 22 articles, respectively. STEC EIA pooled sensitivity and specificity were 0.681 (95% CI, 0.571-0.773; very low certainty of evidence) and 1.00 (95% CI, 0.998-1.00; moderate certainty of evidence), respectively. STEC PCR pooled sensitivity and specificity were 1.00 (95% CI, 0.904-1.00; low certainty of evidence) and 0.999 (95% CI, 0.997-0.999; low certainty of evidence), respectively. Certainty of evidence was downgraded because of high risk of bias.

CONCLUSIONS

PCR tests to identify the presence of STEC are more sensitive than EIA tests, with no meaningful loss of specificity. However, given the low certainty of evidence, our results may overestimate the difference in performance.

Prolonged Fever, Diarrhea, Abdominal Pain, and Joint Pain in a 9-Year- Old Boy

A 9-year-old African American boy was admitted to hospital with a 12-day history of fevers, diarrhea, abdominal pain and a 1-day history of joint pain. His abdominal pain and diarrhea resolved within the first few days of admission, but he continued with high-grade fevers and intermittent joint pain. The joints affected included the right first interphalangeal joint, right wrist, right elbow, and left knee joint. His initial laboratory tests revealed normal complete blood count, comprehensive metabolic panel, and C-reactive protein. Consequently, he developed fatigue, lower back pain, and bicytopenias. After 19 days of fevers, a multispecialty collaborative evaluation arrived at a final diagnosis and treatment plan. In this article, we discuss the child's hospital course and our clinical thought process. Written consent was obtained from the family.

Comparison of Multiplex Gastrointestinal Pathogen Panel and Conventional Stool Testing for Evaluation of Patients With HIV Infection

BACKGROUND

Gastrointestinal pathogen panels (GPPs) are increasingly used to identify stool pathogens, but their impact in people with HIV (PWH) is unknown. We performed a retrospective cohort study comparing GPP and conventional stool evaluation in PWH.

METHODS

We included all PWH who underwent GPP (Biofire Diagnostics; implemented September 15, 2015) or conventional testing, including stool culture, Clostridium difficile polymerase chain reaction testing, fluorescent smears for Cryptosporidium or Giardia, and ova and parasite exams (O&P) from 2013 to 2017. A total of 1941 specimens were tested, with 169 positive specimens detected in 144 patients. We compared result turnaround time, pathogen co-infection, antibiotic treatment, and treatment outcomes between positive specimens detected by conventional testing vs GPP.

RESULTS

Overall, 124 patient samples tested positive by GPP, compared with 45 patient specimens by conventional testing. The GPP group demonstrated a higher co-infection rate (48.4% vs 13.3%; P < .001) and quicker turnaround time (23.4 vs 71.4 hours; P < .001). The GPP identified 29 potential viral infections that were undetectable by conventional stool tests. Unnecessary anti-infective therapy was avoided in 9 of 11 exclusively viral infections. Exclusively nonpathogenic parasites (n = 13) were detected by conventional stool tests, the majority of which were treated with metronidazole. There were no significant differences in clinical outcomes between groups.

CONCLUSIONS

In PWH, GPP implementation improved antibiotic stewardship through shorter turnaround times and detection of enteric viral pathogens.

Evaluation of the BioFire FilmArray Gastrointestinal Panel and Real-Time Polymerase Chain Reaction Assays for the Detection of Major Diarrheagenic Pathogens by a Multicenter Diarrheal Disease Surveillance Program in China

In the field of the detection of pathogens responsible for infectious diarrhea, multiplex nucleic acids detection technology has attracted attention due to its ability to simultaneously screen a wide range of pathogens, its simplicity to operate and a faster turnaround time. We conducted a three-center evaluation that compared the BioFire FilmArray gastrointestinal panel (FA GI) and real-time polymerase chain reaction (PCR) assays for the detection of pathogens from 462 clinical diarrhea specimens, and characterized the distribution of various pathogens that were analyzed. The sensitivity of FA GI was 100% for 13 pathogens and 93.8-98.3% for 4 pathogens, but low for Salmonella (60.5%) and adenovirus (88.9%). The sensitivity per pathogen of real-time PCR assays was lower than that observed with FA GI. The specificity of FA GI and real-time PCR assays per pathogen was greater than 94.5% and 99%, respectively. FA GI and real-time PCR assays detected ≥1 pathogen in 339 (73.4%) and 297 (64.3%) samples, respectively, and 324 (70.1%) samples were considered as positive according to the reference standard. Multiple pathogens were detected in 37.2% and 24.9% of samples by FA GI and real-time PCR assays, respectively. Norovirus GI/GII and Campylobacter were less associated with coinfections. The positive rates of some pathogens varied among the three regions of China. Molecular methods can help squickly identify the cause of diarrhea and provide valuable information for early diagnosis and optimal patient therapy.

Enteropathogens in paediatric gastroenteritis: comparison of routine diagnostic and molecular methods

OBJECTIVES

Studies of acute gastroenteritis (AGE) are hampered by the lack of routine diagnostic methods with good sensitivity and specificity. Molecular methods are increasingly used for clinical purposes, but the clinical significance of a positive result remains a challenge. In this study we aimed to compare results of routine diagnostic methods and molecular methods in symptomatic children and asymptomatic controls.

METHODS

Patients presenting to the pediatric emergency departments of two university hospitals in Brussels with AGE were recruited prospectively from May 2015 to October 2016; asymptomatic controls were recruited from the same hospitals. Stool analyses were performed for all participants for common pathogenic bacteria (culture), virus (immunochromatography) and parasites (microscopy). Stools were also analysed with the Luminex Gastrointestinal Pathogen Panel, a multiplex-PCR for common enteropathogens.

RESULTS

Stools from 178 patients and 165 controls were analysed. An enteropathogen was detected in 62.4% (111/178) of cases when combining the two methods (56.2% (100/178) by Luminex, 42.7% (76/178) with routine methods) and 29.1% (48/165) of controls (24.2% (40/165) by Luminex and 10.3% (17/165) by routine methods). Some pathogens were detected more often with Luminex than with routine methods, such as Salmonella (16.3% (29/178) with Luminex and 3.9% (7/178) with routine method, p < 0.05), whereas others identified by culture methods, such as Campylobacter, Shigella, Yersinia, were missed by Luminex.

CONCLUSIONS

Molecular tools seem attractive methods, providing high positivity and a rapid turn-around time for the diagnosis of AGE. However, high rates of positivity in both cases and controls highlight the difficulty in interpreting results. Pathogens missed by Luminex but detected by culture methods raise more questions about the true clinical interest of the technique for our patients.

Whole-Genome Single-Nucleotide Polymorphism (SNP) Analysis Applied Directly to Stool for Genotyping Shiga Toxin-Producing Escherichia coli: an Advanced Molecular Detection Method for Foodborne Disease Surveillance and Outbreak Tracking

Whole-genome sequencing (WGS) of pathogens from pure culture provides unparalleled accuracy and comprehensive results at a cost that is advantageous compared with traditional diagnostic methods. Sequencing pathogens directly from a primary clinical specimen would help circumvent the need for culture and, in the process, substantially shorten the time to diagnosis and public health reporting. Unfortunately, this approach poses significant challenges because of the mixture of multiple sequences from a complex fecal biomass. The aim of this project was to develop a proof of concept protocol for the sequencing and genotyping of Shiga toxin-producing Escherichia coli (STEC) directly from stool specimens. We have developed an enrichment protocol that reliably achieves a substantially higher DNA yield belonging to E. coli, which provides adequate next-generation sequencing (NGS) data for downstream bioinformatics analysis. A custom bioinformatics pipeline was created to optimize and remove non-E. coli reads, assess the STEC versus commensal E. coli population in the samples, and build consensus sequences based on population allele frequency distributions. Side-by-side analysis of WGS from paired STEC isolates and matched primary stool specimens reveal that this method can reliably be implemented for many clinical specimens to directly genotype STEC and accurately identify clusters of disease outbreak when no STEC isolate is available for testing.

Epidemiology and genetic screening of diarrheagenic Escherichia coli among symptomatic and asymptomatic children

PURPOSE

Enteropathogens are frequently associated with diarrheal disease. Knowledge of their etiology and epidemiology is essential for the prevention and control of the sickness. This study describes the microbiological and epidemiological features of diarrheal disease in 197 symptomatic and 223 asymptomatic under-five-year-old children from southeastern Brazil, between January 2015 and September 2016.

METHODS

Isolation of Escherichia coli, Salmonella, Shigella and Campylobacter was realized by culture. E. coli strains were screened by multiplex PCR, PFGE and O:H serotyping. Antimicrobial susceptibility testing was also performed.

RESULTS

Most of the 127 enteropathogens isolated were diarrheagenic E. coli (96.1 %), with predominance of several serotypes of enteropathogenic E. coli (EPEC) and enteroaggregative E. coli (EAEC). Age, sex, rotavirus vaccination, recent use of antibiotics and previous contact with pets, were factors that revealed no significant effects on the probability of infection by the predominant pathogens. Even so, higher incomes could be related to a lesser chance of testing positive for EPEC. Evidence of possible EAEC clonal spread was detected, as well as genetic similarity among strains from both symptomatic and asymptomatic children. Resistance to antimicrobial agents was more pronounced among EAEC than EPEC.

CONCLUSION

The occurrence of genetically similar diarrheagenic E. coli in both groups of children, likewise resistant to these agents, underscores the importance of establishing strategies for the prevention of outbreaks, especially among low-income households.

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.