A Gastrointestinal PCR Panel Improves Clinical Management and Lowers Health Care Costs

Multiplexed Gastrointestinal PCR Panels for the Evaluation of Diarrhea in Hematopoietic Stem Cell Transplantation Recipients

Multiplexed gastrointestinal PCR panels (MGPPs) are frequently used to aid the diagnosis and management of diarrhea in hematopoietic stem cell transplantation (HCT) recipients. Many issues related to the optimal use of MGPPs in HCT patients remain to be clarified. We aimed to better define MGPP diagnostic and therapeutic stewardship in HCT recipients, including indications for and benefits of testing, optimal timing of tests, and interpretation of results. We retrieved 463 consecutive MGPPs ordered on 651 consecutive first HCT (312 allogeneic, 339 autologous) performed at our institution between June 2015 and June 2023. One hundred and sixteen of the 463 MGPPs (25%) identified at least 1 diarrheagenic pathogen, and 12 (3%) identified more than 1 diarrheagenic pathogen. A positive result was more likely if the test was ordered within 48 hours of a hospital admission (41%; 32 of 78) or as an outpatient (41%; 46 of 111) compared with evaluation of hospital-onset diarrhea (14%; 38 of 274). Among the positive results, the most frequent pathogens identified included Clostridioides difficile (64%), diarrheagenic Escherichia coli (20%), norovirus (9%), and adenovirus 40/41 (5%). Thirty-eight percent of the positive C. difficile MGPP determinations were associated with a positive test for toxin. In our allogeneic HCT cohort, 3% of MGPPs for hospital-onset diarrhea yielded an organism other than C. difficile. Fifty-six percent of positive and 14% of all submitted tests resulted in a change in treatment. For organisms other than C. difficile, only 1% of all tests and 5% of positive tests resulted in initiation of therapy. For patients at risk for acute graft-versus-host disease (aGVHD), a positive or negative MGPP result was not predictive of a new diagnosis of aGVHD in proximity to diarrhea onset. These results suggest that MGPP testing is most useful when performed at hospital admission or on an outpatient basis. Because MGPPs are sensitive and do not distinguish between colonization and causes of diarrhea, caution is needed when interpreting results, especially for toxin-negative C. difficile and diarrheagenic gram-negative organisms.

Navigating Viral Gastroenteritis: Epidemiological Trends, Pathogen Analysis, and Histopathological Findings

BACKGROUND

Gastroenteritis is a common cause of morbidity and mortality globally. Its cause encompasses a spectrum of agents, including viruses, bacteria, parasites, toxins, and drugs. Viruses account for a considerable portion of gastroenteritis cases across all age groups, typically presenting with symptoms like nausea, vomiting, diarrhea, dehydration, anorexia, and weight loss. While sporadic cases occur, viral gastroenteritis is more frequently observed in outbreaks within closely knit communities such as daycare facilities, nursing homes, and cruise ships. Therefore, it becomes necessary to determine when healthcare providers should consider this condition in their differential diagnosis and to develop the most effective strategy to confirm the diagnosis.

METHODS

De-identified data of patients with gastroenteritis were collected over a five-year period utilizing the Patient Cohort Explorer, an electronic health record at the University of Mississippi Medical Center. Confirmatory laboratory tests employed the BioFire® FilmArray® multiplex polymerase chain reaction for gastrointestinal pathogens. Out of the 22 most common agents associated with gastroenteritis, only viral pathogens, specifically adenovirus, astrovirus, norovirus, rotavirus, and sapovirus, were included in the analysis. When available, histopathology was reviewed.

RESULTS

Among the various causes of gastroenteritis, both infectious and non-infectious, our findings revealed that 25.46% of the cases were linked to viral pathogens. This included a significantly higher percentage of pediatric patients (72.73%) when compared to adults (27.07%), with a p-value of 0.015. Norovirus genogroups I and II emerged as the most frequently detected viruses across all age groups, with a significant prevalence among adults. No discernible gender-based differences were observed. The histopathological findings included inflammation, ulceration, erosion, architectural distortion, and the pathognomonic viral inclusion bodies associated with adenovirus.

CONCLUSION

Our comprehensive analysis of viral gastroenteritis cases highlights the substantial burden of this condition, particularly among pediatric patients. Norovirus emerges as a prevalent culprit which emphasizes the importance of vigilant surveillance and timely diagnosis, especially in settings where outbreaks are common.

Optimizing Antimicrobial Stewardship in the Emergency Department

Antibiotic stewardship is a core component of emergency department (ED) practice and impacts patient safety, clinical outcomes, and public health. The unique characteristics of ED practice, including crowding, time pressure, and diagnostic uncertainty, need to be considered when implementing antibiotic stewardship interventions in this setting. Rapid advances in pathogen detection and host response biomarkers promise to revolutionize the diagnosis of infectious diseases in the ED, but such tests are not yet considered standard of care. Presently, clinical decision support embedded in the electronic health record and pharmacist-led interventions are the most effective ways to improve antibiotic prescribing in the ED.

Clinical Impact of Multiplex Molecular Diagnostic Testing in Children With Acute Gastroenteritis Presenting to an Emergency Department: A Multicenter Prospective Study

BACKGROUND

Multiplex molecular diagnostic panels have greatly enhanced detection of gastrointestinal pathogens. However, data on the impact of these tests on clinical and patient-centered outcomes are limited.

METHODS

We conducted a prospective, multicenter, stepped-wedge trial to determine the impact of multiplex molecular testing at 5 academic children's hospitals on children presenting to the emergency department with acute gastroenteritis. Caregivers were interviewed on enrollment and 7-10 days after enrollment to determine symptoms, risk factors, subsequent medical visits, and impact on family members. During the pre-intervention period, diagnostic testing was performed at the clinician's discretion . During the intervention period, multiplex molecular testing was performed on all children, with results available to clinicians. The primary outcome was return visits to a healthcare provider within 10 days of enrollment.

RESULTS

Potential pathogens were identified by clinician-ordered tests in 19 of 571 (3.3%) in the pre-intervention period compared with 434 of 586 (74%) in the intervention period; clinically relevant pathogens were detected in 2.1% and 15%, respectively. In the multivariate model, the intervention was associated with a 21% reduction in the odds of any return visit (odds ratio, 0.79; 95% confidence interval, .70-.90) after adjusting for potential confounders. Appropriate treatment was prescribed in 11.3% compared with 19.6% during the intervention period (P = .22).

CONCLUSIONS

Routine molecular multiplex testing for all children who presented to the ED with acute gastroenteritis detected more clinically relevant pathogens and led to a 21% decrease in return visits. Additional research is needed to define patients most likely to benefit from testing. Clinical Trials Registration. NCT02248285.

Multicenter evaluation of BioCode GPP for syndromic molecular detection of gastrointestinal pathogens from stool specimens

Acute gastroenteritis (AGE) is a leading cause of morbidity and mortality worldwide across all age groups that disproportionally affects young children in low- and middle-income countries and immunocompromised patients in high-income countries. Regional outbreaks of AGE are typically detected by traditional microbiological detection methods that target limited organisms and are associated with low sensitivity and lengthy time-to-results. Combined, these may result in repeat testing, imprecise or delayed treatment, and delayed recognition of outbreaks. We conducted a multi-site prospective study comparing the BioCode Gastrointestinal Pathogen Panel (BioCode GPP) for the detection of 17 common bacterial, viral, and protozoan causes of gastroenteritis with reference methods, including stool culture, enzyme immunoassays, pathogen-specific PCR assays, and sequencing. One thousand five hundred fifty-eight residual, de-identified stool samples (unpreserved stool and stool in Cary-Blair transport medium) were enrolled and tested for 11 bacterial, 3 viral, and 3 protozoan pathogens. BioCode GPP and reference methods were positive for 392 (25.2%) and 283 (18.2%) samples, respectively (P < 0.0001). In this study, the BioCode GPP and reference methods detected 69 and 65 specimens positive for Clostridioides difficile, 51 and 48 for enteroaggregative Escherichia coli, 33 and 27 for enterotoxigenic E. coli, 50 and 47 for norovirus GI/GII, and 30 and 22 for rotavirus A, respectively. The BioCode GPP showed good positive and negative agreements for each pathogen ranging from 89.5% to 100%, with overall sensitivity and specificity of 96.1% and 99.7%, post adjudication. The BioCode GPP detected >1 pathogens in 49 samples, representing 12.5% of the total 392 positive specimens.

IMPORTANCE

This study highlights performance of a novel technology for timely and accurate detection and differentiation of 17 common bacterial, viral, and protozoan causes of gastroenteritis. Utilizing molecular tests such as the BioCode Gastrointestinal Pathogen Panel may improve the detection of gastrointestinal pathogens and provide actionable results, particularly for patient populations at most risk.

An overview of point-of-care testing for infections in critically ill patients

INTRODUCTION

Molecular diagnostic systems for point-of-care (POC) testing are nowadays routinely used and are part of many labs. Although often intended for bedside use outside of the microbiology lab, there is still room for expansion.

AREAS COVERED

This review discusses the two techniques that are currently the most widespread, real-time polymerase-chain reaction (RT-PCR) and loop-mediated isothermal amplification (LAMP). An overview is provided of the various manufacturers and products as well as the evidence and current use in clinical practice. The article further sheds light on some newer techniques, such as CRISPR-based diagnostics and lab-on-a-chip, which are still in development.

EXPERT OPINION

With many new platforms and techniques still in the pipeline and their potential currently not yet fully exploited, we expect the use of molecular POC testing to increase in the years to come. However, even when used in hospital - in lab, the main advantages of the tests being fast and easy to perform already provide significant benefits in terms of patient outcome.

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.

Comparative evaluation of the detection rate, workflow and associated costs of a multiplex PCR panel versus conventional methods in diagnosis of infectious gastroenteritis

Introduction. Infectious gastroenteritis is a common reason for consulting a physician. Although most cases of gastrointestinal illness are self-limiting, the identification of the etiologic pathogen by stool specimen analysis is important in cases of more severe illness and for epidemiological reasons.Due to the broad range of causative pathogens, the conventional examination of a stool specimen is labour-intensive and usually requires different diagnostic methods. Multiplex PCR tests [e.g. BioFire Gastrointestinal (GI) Panel] allow the rapid detecting of up to 22 pathogens in one test.Hypothesis. Using a multiplex PCR panel to test stool specimens for infectious gastroenteritis pathogens can improve the detection rate, reduce the time-to-result and hands-on time and lower the costs of a microbiology laboratory.Aim. This study was aimed at evaluating the detection rate, the workflow and associated costs of stool specimen management using the BioFire GI Panel versus conventional methods.Methodology. Stool specimens were evaluated prospectively during the routine operation. Pathogen detection rate, hands-on time, time-to-result and material and personnel costs were determined for the BioFire GI Panel and conventional methods-the latter based on physician request and excluding viral testing.Results. Analysing 333 specimens collected between 2019 and 2020, the detection rate of enteropathogens was significantly higher with a positivity rate of 39.9 % using the multiplex PCR panel compared with 15.0 % using the conventional methods. The BioFire GI Panel presented results in a median time of 2.2 h compared with 77.5 h for culture and 22.1 h for antigen testing, noting that no tests were performed at weekends except for toxinogenic Clostridioides difficile. Based on list prices, the BioFire GI Panel was nine times more expensive compared with conventional methods, whereas hands-on-time was significantly lower using the BioFire GI Panel.Conclusion. Multiplex PCR panels are valuable tools for laboratory identification of infectious agents causing diarrhoea. The higher costs of such a multiplex PCR panel might be outweighed by the higher detection rate, ease of handling, rapid results and most likely improved patient management. However, these panels do not provide information on antimicrobial susceptibility testing. Therefore, if this is necessary for targeted therapy or if outbreak monitoring and control is required, specimens must still be cultured.

Clinical performance evaluation of TAQPATH Enteric Bacterial Select Panel for the detection of common enteric bacterial pathogens in comparison to routine stool culture and other qPCR-based diagnostic tests

IMPORTANCE

Enteric bacterial infections caused by Salmonella, Shigella, pathogenic Escherichia coli, and Campylobacter represent one of the most common causes of infectious enteritis worldwide. The timely and accurate diagnosis of pathogens causing gastroenteritis is crucial for patient care, public health, and disease surveillance. While stool culture has long been the standard and highly specific method for detecting enteric pathogens, it is labor-intensive and time-consuming with limited sensitivity. To improve patient outcomes, there is a need to implement new cost-effective approaches for the detection of bacterial enteric pathogens with higher sensitivity and faster time to result. This study shows that multiplex real-time polymerase chain reaction-based tests, such as the TAQPATH Enteric Bacterial Select Panel, are accurate and cost-effective diagnostic alternatives for the detection and differentiation of the most common enteric bacterial pathogens, offering quicker time to result and higher sensitivity compared to routine stool culture.

Rapid detection of gastrointestinal pathogens using a multiplex polymerase chain reaction gastrointestinal panel and its role in antimicrobial stewardship

OBJECTIVES

The FilmArray gastrointestinal panel (FAGIP) is widely used to detect infectious diarrhoea due to its outstanding sensitivity compared to conventional methods, but there is geographic variation, such as in the distribution of pathogens, among populations.

METHODS

This was a retrospective study that analysed patients with acute diarrhoea who underwent FAGIP tests from all age groups during 2022. We compared positive rates of FAGIP between paediatric (n = 245) and adult patients (n = 242) of different origins. The targeted therapy rate and antimicrobial agent use rate were also analysed.

RESULTS

Among the 487 stool samples evaluated, the overall, community-origin (CO), and nosocomial (NC) positivity rates of paediatric patients were significantly higher than those of adults (73.9 % vs. 43.0 %, p = 0.000; 76.2 % vs. 51.7 %, p = 0.000; 50.0 % vs. 19.7 %, p = 0.000). Salmonella was the most frequently detected pathogen (35.9 %) in children, while the predominant pathogen in adult patients was toxin A/B-genic Clostridioides difficile (13.2 %). There was a significantly lower antimicrobial agent use rate after FAGIP results were available (79.1 % vs. 64.5 %, p = 0.000) and a higher rate of targeted therapy towards C. difficile infection in adults than in children (84.4 % vs. 69.0 %, p = 0.011).

CONCLUSION

Paediatric diarrhoea patients showed higher positivity rates than adult patients. Application of FAGIP for acute diarrhoea might lower unnecessary antimicrobial use.

Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology

The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.

QIAstat-Dx gastrointestinal panel and Luminex xTAG gastrointestinal pathogen panel comparative evaluation

The diagnosis of acute gastroenteritis is an ongoing clinical challenge in terms of identification of the etiologic agent, time to results, and appropriate treatment. Rapid detection of gastrointestinal pathogens is needed to improve patient care. This study evaluates the performance of the QIAstat-Dx gastrointestinal panel (Q-GP; Investigational Use Only) compared to the Luminex xTAG gastrointestinal pathogen panel (L-GPP; US-IVD). Using 245 stool specimens, we evaluated 10 different targets including rotavirus, norovirus, Salmonella, Shigella, Campylobacter, Giardia, Cryptosporidium, Escherichia coli O157, enterotoxigenic E. coli (ETEC), and Shiga toxin-producing E. coli (STEC). For the viral targets, the percent positive agreement (PPA) for rotavirus was 100% (n = 19) and that for norovirus was 91% (20/22). For the parasitic targets, the PPA was 100% for Giardia and Cryptosporidium (n = 18 and n = 23, respectively). The PPA was 96% for Salmonella (22/23) and Campylobacter (22/23), and the PPA for Shigella was 100% (n = 23). For the E. coli targets, a PPA of 94% was achieved for STEC (32/34) and 96% for ETEC (24/25). We did not assess PPA for the E. coli O157 target as the Q-GP O157 call is stx dependent. The negative percent agreement across all targets was 99.1%. Our study suggests that QIAstat-Dx GP provides comparable results to Luminex GPP based on the analysis of targets found on both panels.

Evaluating outpatient diagnostic stewardship of comprehensive polymerase chain reaction Clostridioides difficile testing in a regional health system

Objective

We examined the use of comprehensive and targeted polymerase chain reaction (PCR) of Clostridioides difficile infection (CDI) among immunocompetent patients with and without CDI risk factors across different outpatient settings. A priori, we expected patients with higher CDI risk to be associated with targeted testing to reflect providers incorporating pretest risk factors in their choice of test assay.

Design

Retrospective analysis of adult patients from clinic, emergency room, and non-medically acute inpatient settings.

Setting

A tertiary academic medical center offering inpatient and outpatient medical, surgical, mental health, and rehabilitation services to Veterans across the Puget Sound region.

Patients

Immunocompetent adult patients with ≥1 stool PCR assay performed between January 2016 and December 2019.

Intervention

Patients were tested with either a specific tcdB PCR assay or a comprehensive gastrointestinal PCR panel that tests for 22 pathogens.

Results

A total of 2,717 tests (74% targeted, 26% comprehensive) were obtained from 2,156 patients, among which 13% detected C. difficile and 7% detected other organisms. The proportion of comprehensive PCR tests increased nearly four-fold from 2016 to 2019 in clinic and emergency room settings, independent of CDI risk factors. Only two CDI risk factors (prior history of CDI and antibiotic use within three months before testing) were associated with increased targeted testing.

Conclusion

The use of comprehensive GI PCR among immunocompetent adults with diarrhea is increasing in the outpatient setting. There may be an opportunity for diagnostic stewardship by nudging providers to consider all CDI risk factors at the time of test selection.

Gastrointestinal Infection in South African Children under the Age of 5 years: A Mini Review

Objective

To estimate gastroenteritis disease and its etiological agents in children under the age of 5 years living in South Africa.

Methods

A mini literature review of pertinent articles published in ScienceDirect, PubMed, GoogleScholar, and Scopus was conducted using search terms: "Gastroenteritis in children," "Gastroenteritis in the world," Gastroenteritis in South Africa," "Prevalence of gastroenteritis," "Epidemiological surveillance of gastroenteritis in the world," and "Causes of gastroenteritis".

Results

A total of 174 published articles were included in this mini review. In the last 20 years, the mortality rate resulting from diarrhea in children under the age of 5 years has declined and this is influenced by improved hygiene practices, awareness programs, an improved water and sanitation supply, and the availability of vaccines. More modern genomic amplification techniques were used to re-analyze stool specimens collected from children in eight low-resource settings in Asia, South America, and Africa reported improved sensitivity of pathogen detection to about 65%, that viruses were the main etiological agents in patients with diarrhea aged from 0 to 11 months but that Shigella, followed by sapovirus and enterotoxigenic Escherichia coli had a high incidence in children aged 12-24 months. In addition, co-infections were noted in nearly 10% of diarrhea cases, with rotavirus and Shigella being the main co-infecting agents together with adenovirus, enteropathogenic E. coli, Clostridium jejuni, or Clostridium coli.

Conclusions

This mini review outlines the epidemiology and trends relating to parasitic, viral, and bacterial agents responsible for gastroenteritis in children in South Africa. An increase in sequence-independent diagnostic approaches will improve the identification of pathogens to resolve undiagnosed cases of gastroenteritis. Emerging state and national surveillance systems should focus on improving the identification of gastrointestinal pathogens in children and the development of further vaccines against gastrointestinal pathogens.

Laboratory assessment of a multi-target assay for the rapid detection of viruses causing vesicular diseases

BACKGROUND

The recent mpox outbreak has highlighted the need to rapidly diagnose the causative agents of viral vesicular disease to inform treatment and control measures. Common causes of vesicular disease include Monkeypox virus (MPXV), clades I and II, Herpes simplex viruses Type 1 and Type 2 (HSV-1, HSV-2), human herpes virus 6 (HHV-6), Varicella-zoster virus (VZV) and Enteroviruses (EVs). Here, we assessed a syndromic viral vesicular panel for rapid and simultaneous detection of these 7 targets in a single cartridge.

OBJECTIVE

The aim of this study was to evaluate the QIAStat-Dx ® viral vesicular (VV) panel and compare with laboratory developed tests (LDTs). Limit of detection, inter-run variability, cross-reactivity and specificity were assessed. Positive and negative percent agreement, and correlation between assays was determined using 124 clinical samples from multiple anatomical sites.

RESULTS

The overall concordance between the QIAstat and LDTs was 96%. Positive percent agreement was 82% for HHV-6, 89% for HSV-1 and 100% for MPXV, HSV-2, EV and VZV. Negative percent agreement was 100% for all targets assessed. There was no cross-reactivity with Vaccinia, Orf, Molluscum contagiosum viruses, and a pooled respiratory panel.

CONCLUSION

The QIAstat VV multi-target syndromic panel combine ease of use, rapid turnaround, good sensitivity and specificity for enhanced diagnosis, clinical care and public health responses.

Clinical Impact of Multiplex Molecular Diagnostic Testing in Children with Acute Gastroenteritis Presenting to An Emergency Department: A Multicenter Prospective Study

Background

Multiplex molecular diagnostic panels have greatly enhanced detection of gastrointestinal pathogens. However, data on the impact of these tests on clinical and patient-centered outcomes are limited.

Methods

We conducted a prospective, multicenter, stepped-wedge trial to determine the impact of multiplex molecular testing at five academic children's hospitals in children presenting to the ED with acute gastroenteritis. Caregivers were interviewed on enrollment and again 7-10 days after enrollment to determine symptoms, risk factors, subsequent medical visits, and impact on family members. During the pre-intervention period, diagnostic testing was performed at the discretion of clinicians. During the intervention period, multiplex molecular testing was performed on all children with results available to clinicians. Primary outcome was return visits to a health care provider within 10 days of enrollment.

Results

Potential pathogens were identified by clinician ordered tests in 19/571 (3.3%) in the pre-intervention period compared to 434/586 (74%) in the intervention period; clinically relevant pathogens were detected in 2.1% and 15% respectively. In the multivariate model adjusting for potential confounders, the intervention was associated with a 21% reduction in the odds of any return visit (OR 0.79; 95% CI 0.70-0.90). Appropriate treatment was prescribed in 11.3% compared to 19.6% during the intervention period(P=0.22).

Conclusions

Routine molecular multiplex testing for all children presenting to the ED with AGE detected more clinically relevant pathogens and led to a 21% decrease in return visits. Additional research is needed to define patients most likely to benefit from testing.

Comparison of a Rapid Multiplex Gastrointestinal Panel with Standard Laboratory Testing in the Management of Children with Hematochezia in a Pediatric Emergency Department: Randomized Controlled Trial

Advances in diagnostic microbiology allow for the rapid identification of a broad range of enteropathogens; such knowledge can inform care and reduce testing. We conducted a randomized, unblinded trial in a tertiary-care pediatric emergency department. Participants had stool (and rectal swabs if stool was not immediately available) tested using routine microbiologic approaches or by use of a device (BioFire FilmArray gastrointestinal panel), which identifies 22 pathogens with a 1-h instrument turnaround time. Participants were 6 months to <18.0 years and had acute bloody diarrhea. Primary outcome was performance of blood tests within 72 h. From 15 June 2018 through 7 May 2022, 60 children were randomized. Patients in the BioFire FilmArray arm had a reduced time to test result (median 3.0 h with interquartile range [IQR] of 3.0 to 4.0 h, versus 42.0 h (IQR 23.5 to 47.3 h); difference of -38.0 h, 95% confidence interval [CI] of -41.0 to -22.0 h). Sixty-five percent (20/31) of participants in the BioFire FilmArray group had a pathogen detected-most frequently enteropathogenic Escherichia coli (19%), Campylobacter (16%), and Salmonella (13%). Blood tests were performed in 52% of children in the BioFire FilmArray group and 62% in the standard-of-care group (difference of -10.5%, 95% CI of -35.4% to 14.5%). There were no between-group differences in the proportions of children administered intravenous fluids, antibiotics, hospitalized, or who had diagnostic imaging performed. Testing with the BioFire FilmArray reduced the time to result availability by 38 h. Although statistical significance was limited by study power, BioFire FilmArray use was not associated with clinically meaningful reductions in health care utilization or improved outcomes. IMPORTANCE Advances in diagnostic microbiology now allow for the faster and more accurate detection of an increasing number of pathogens. We determined, however, that in children with acute bloody diarrhea, these advances did not necessarily translate into improved clinical outcomes. While a greater number of pathogens was identified using a rapid turnaround multiplex stool diagnostic panel, with a reduction in the time to stool test result of over 1.5 days, this did not alter the practice of pediatric emergency medicine physicians, who continued to perform blood tests on a large proportion of children. While our conclusions may be limited by the relatively small sample size, targeted approaches that educate clinicians on the implementation of such technology into clinical care will be needed to optimize usage and maximize benefits.

Impact of Rapid Molecular Multiplex Gastrointestinal Pathogen Testing in Management of Children during a Shigella Outbreak

Fecal culture for isolation and identification of Shigella may take days. The BioFire FilmArray Gastrointestinal (GI) panel (bioMérieux, France) is a PCR-based assay that detects enteric pathogens including Shigella/enteroinvasive Escherichia coli (EIEC) in about an hour. The aim of this study was to evaluate the impact of GI panel detection of Shigella in a pediatric emergency department (ED) during an outbreak. Stool samples from children with acute gastroenteritis were tested by the GI panel. Test results were either withheld in preintervention (PRE) or reported to clinicians/families in the postintervention (POST) period. The impact of the GI panel testing on patient management and outcomes was measured. Shigella/EIEC was identified by the GI panel in the PRE (n = 30) and POST (n = 21) phase. The GI panel detected more Shigella infections than did culture; six of 31 (19.4%) Shigella GI panel-positive patients who also had stool cultures were missed by culture. Azithromycin therapy was prescribed for 20% of subjects in the PRE phase and 71.4% of subjects in the POST phase (P < 0.001). Time from the clinical encounter until starting azithromycin therapy was shorter in the POST phase (n = 9), 8.25 h (range, 6.37 to 52.37 h), than in the PRE phase (n = 1), 72 h. Six subjects in the PRE phase visited additional providers compared with one in the POST phase. Prompt diagnosis of shigellosis with the GI panel may provide the opportunity for prompt antimicrobial therapy and avoid additional visits to providers due to early definitive diagnosis. Prompt diagnosis of Shigella at an ED visit may optimize patient management and reduce transmission.

The Impact of a Positive Biofire® FilmArray® Gastrointestinal Panel Result on Clinical Management and Outcomes

The gold standard diagnostic method for gastrointestinal infections is stool culture, which has limited sensitivity and long turnaround time. Infection diagnosis recently shifted to syndrome-based panel assays. This study employed the FilmArray® Gastrointestinal Panel, which detects 22 pathogens simultaneously, to investigate gastrointestinal infection and pathogen distribution in 91 stool samples of patients hospitalized at the Tzafon Medical Center, Israel, during 2020, and to compare the clinical and demographic data of negative vs. positive samples. Among the 61 positive samples (67%), the most common pathogen was Campylobacter (34.4%). Positive test results were associated with a slightly younger patient age (p = 0.012), significantly higher post-diagnosis use of antibiotics (63.9% vs. 36.7%; p = 0.014), and shorter length of stay and time to discharge (p = 0.035, p = 0.003, respectively) than negative test results. To conclude, the FilmArray® Gastrointestinal Panel enabled the early identification of causative infectious agents and enhanced clinical management and outcomes.

Clinical impact of biofire gastrointestinal panel testing for hospitalised children with acute gastroenteritis

AIM

To investigate the clinical impact of BioFire FilmArray Gastrointestinal Panel (FGP) testing in real-life diarrhoeal episodes of hospitalised paediatric patients.

METHODS

Children hospitalised between October 2018 and September 2020 for whom stool specimens for FGP were submitted at the clinician's discretion were retrospectively observed. For each episode, demographics, clinical information and stool tests were collected.

RESULTS

The clinical impact for each case was evaluated by changing the antibiotic prescription, following the result of the FGP testing. Out of 140 diarrhoeal episodes, 25 pathogens were found in 24 cases using conventional methods, whereas, FGP testing identified 75 pathogens in 56 cases (p < 0.05). The pathogens more frequently identified by FGP testing were Campylobacter, Shigella, Rotavirus, Giardia lamblia and Cryptosporidium. The clinical impact of FGP testing was observed in 17/140 (12%) diarrhoeal episodes, and higher rates in previously healthy (19%) and solid organ-transplanted children (15%).

CONCLUSION

We found that using FGP testing for hospitalised children with diarrhoeal episodes could increase pathogen identification and impact clinical decisions, especially in healthy and transplant patients.

Relationship between Diagnostic Method and Pathogen Detection, Healthcare Resource Use, and Cost in U.S. Adult Outpatients Treated for Acute Infectious Gastroenteritis

A retrospective observational study was performed to assess the relationship between diagnostic method (traditional work-up [TW], multiplex PCR panel with < 12 target pathogens [PCR < 12], or multiplex PCR panel with ≥ 12 target pathogens [PCR12]), and diagnostic yield, health care resource use (HRU), and cost in adult outpatients visiting U.S. hospitals for acute infectious gastroenteritis (AGE). Using data from PINC AI Healthcare Database during January 1, 2016-June 30, 2021, we analyzed adult patients with an AGE diagnosis and stool testing performed during an outpatient visit. Detection rates for different pathogens were analyzed for those with microbiology data available. Among 36,787 patients, TW was most often performed (57.0%). PCR12 testing was more frequent in patients from large, urban, and teaching hospitals, compared to TW (all P < 0.01). PCR12 was associated with a higher mean index visit cost (by $97) but lower mean 30-day AGE-related follow-up cost (by $117) than TW. Patients with PCR12 had a lower 30-day AGE-related hospitalization risk than TW (1.7% versus 2.7% P < 0.01). Among the 8,451 patients with microbiology data, PCR12 was associated with fewer stool tests per patient (mean 1.61 versus 1.26), faster turnaround time (mean 6.3 versus 25.7 h) and lower likelihood of receiving in-hospital antibiotics (39.4% versus 47.1%, all P < 0.01) than TW. A higher percentage of patients with PCR12 had a target pathogen detected (73.1%) compared to PCR < 12 (63.6%) or TW (45.4%, P < 0.01). Thus, we found that large multiplex PCR panels were associated with lower 30-day AGE-related follow-up cost and risk of AGE-related hospitalization, and increased diagnostic yield compared to TW.

Foodborne and Waterborne Illness

Safe water and food are impactful public health measures that improved significantly during the past century in the United States. But waterborne and foodborne illnesses continue to cause significant morbidity and mortality despite existing public health control measures and regulations. It was estimated that each year in the United States, 31 pathogens caused 37.2 million illnesses, with 36.4 million domestically acquired. Of those, 9.4 million were foodborne: 59% were caused by viruses, 39% by bacteria, and 2% by parasites. The pathogens that caused the most foodborne illnesses were norovirus (58%), nontyphoidal Salmonella species (11%), Clostridium perfringens (10%), and Campylobacter species (9%). Unspecified agents caused an estimated 38.4 million episodes of domestically acquired foodborne gastroenteritis, 258,033 hospitalizations, and 3,574 deaths. The estimate for illnesses caused by waterborne transmission was 7.15 million. The diseases that caused the greatest number were otitis externa (n = 4.67 million), norovirus (n = 1.33 million), giardiasis (n = 415,000), and cryptosporidiosis (n = 322,000). An important aspect of management and prevention is health-care provider reporting of foodborne and waterborne illnesses. Health-care provider reporting of reportable diseases has been inconsistent, infrequent, and delayed. Education efforts concerning reporting need to be enhanced, and physicians should report suspected cases before laboratory confirmation to enhance the timeliness of outbreak investigation and possibly prevent subsequent cases.

BD MAX Enteric Bacterial, Bacterial Plus, and Virus Panels for Diagnosis of Acute Infectious Gastroenteritis: a Cost-Benefit Analysis

Economic assessment is required to gauge the value of implementing PCR syndromic platforms in the microbiology laboratory for the diagnosis of community-acquired acute gastroenteritis (AGE) in pediatric and adult in- and outpatients. A cost-benefit analysis was conducted from a health care system perspective using BD MAX Enteric Bacterial, Bacterial Plus, and Virus panels. Two 6-month periods were selected, in which either conventional procedures (in 2017) or BD MAX PCR multiplex panels (in 2018) were used. We retrospectively reviewed medical records of all patients with positive results and a representative sample of negative ones. A Markov model was used to represent transition probabilities between different health care states from time of stool microbiological study until completion of AGE-episode-associated health care. A total of 1,336 medical records were reviewed (829 in 2018 and 507 in 2017), showing overall a significantly higher positivity rate in 2018 than in 2017 (26% versus 6%, P < 0.001). The total cost per individual associated with health care for AGE was €314 in 2018 and €341 in 2017; when we only considered the pediatric cohort, the figures were €271 and €456, respectively. Using Tornado sensitivity analyses, we found that the three variables that most influenced the model in descending order of weight were the probability of longer hospital stays, the probability of returning to the emergency room (ER), and the probability of hospitalization from the ER. Use of BD MAX enteric PCR platforms for the diagnosis of community-acquired AGE instead of a non-PCR-based conventional approach results in an incremental benefit from a health care perspective in the general population, particularly children. IMPORTANCE The implementation of multiplex molecular panels allows microbiological laboratories to quickly, sensitively, and accurately diagnose acute infectious gastroenteritis. This methodology therefore allows faster decisions regarding treatment and infection control measures. Economic evaluations are required to gauge the value of implementing these syndromic PCR platforms in a community-based acute gastroenteritis setting. We studied the potential clinical and cost benefits, in terms of both their impact on laboratory costs and the subsequent costs of managing patients.

The Efficacy of the BioFire FilmArray Gastrointestinal Panel to Reduce Hospital Costs Associated With Contact Isolation: A Pragmatic Randomized Controlled Trial

Background: Molecular syndromic panels can rapidly detect common pathogens responsible for acute gastroenteritis in hospitalized patients. Their impact on both patient and healthcare system outcomes is uncertain compared to conventional stool testing. This randomized trial evaluates the impact of molecular testing on in-hospital resource utilization compared to conventional stool testing.

Methods: Hospitalized patients with acute diarrheal illness were randomized 1:1 to either conventional or molecular stool testing with the BioFire FilmArray gastrointestinal panel (FGP). The primary outcome was the duration of contact isolation, and secondary outcomes included other in-hospital resource utilization such as diagnostic imaging and antimicrobial use.

Results: A total of 156 patients were randomized. Randomization resulted in a balanced allocation of patients across all three age strata (<18, 18-69, ≥70 years old). The proportion of positive stools was 20.5% vs 29.5% in the control and FGP groups, respectively (p=0.196). The median duration of contact isolation was 51 hours (interquartile range [iqr] 66) and 69 hours (iqr 81) in the conventional and FGP groups, respectively (p=0.0513). There were no significant differences in other in-hospital resource utilization between groups.

Conclusions: There were no differences in in-hospital resource utilization observed between the FGP and conventional stool testing groups.

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.

Mapping of etiologies of computed tomography-proven acute colitis: a prospective cohort study

Our objective was to describe the etiologies of acute colitis and to identify patients who require diagnostic endoscopy. Patients with symptoms of gastrointestinal infection and colonic inflammation on CT were prospectively included. Those immunosuppressed, with history of colorectal cancer or inflammatory bowel disease (IBD), were excluded. Microbiological analysis of the feces was performed using PCR assays BD-Max and FilmArray (GI panel,) and fecal cultures. Fecal calprotectin was determined. Patients with negative BD-Max underwent colonoscopy. One hundred and seventy-nine patients were included. BD-Max was positive in 93 patients (52%) and FilmArray in 108 patients (60.3%). Patients with infectious colitis (n = 103, 57.5%) were positive for Campylobacter spp. (n = 57, 55.3%), Escherichia coli spp. (n = 8, 7.8%), Clostridioides difficile (n = 23, 22.3%), Salmonella spp. (n = 9, 8.7%), viruses (n = 7, 6.8%), Shigella spp. (n = 6, 5.8%), Entamoeba histolytica (n = 2, 1.9%) and others (n = 4, 3.9%). Eighty-six patients underwent colonoscopy, which was compatible with ischemic colitis in 18 patients (10.1%) and IBD in 4 patients (2.2%). Fecal calprotectin was elevated in all patients, with a mean concentration of 1922.1 ± 2895.6 μg/g, and was the highest in patients with IBD (8511 ± 9438 μg/g, p < 0.001). After exclusion of patients with infectious etiology, a fecal calprotectin > 625 μg/g allowed identifying patients with IBD with an area under ROC curve of 85.1%. To conclude, computed tomography-proven colitis was of infectious etiology in 57.5% of patients. The main pathogens identified were Campylobacter spp. (55.3%), Clostridioides difficile (22.3%) and Salmonella spp. (8.7%). Ischemic colitis (10.1%) and IBD (2.2%) were seldom represented. No colorectal cancer was found.

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.

Faster infection diagnostics for intensive care unit (ICU) patients

INTRODUCTION

: The patient admitted to intensive care units (ICU) is critically ill, to some extent immunosuppressed, with a high risk of infection, sometimes by multidrug-resistant microorganisms. In this context, the intensivist expects from the microbiology service quick and understandable information so that appropriate antimicrobial treatment for that particular patient and infection can be initiated.

AREAS COVERED

: In this review of recent literature (2015-2021), we identified diagnostic methods for the most prevalent infections in these patients through a search of the databases Pubmed, evidence-based medicine online, York University reviewers group, Cochrane, MBE-Trip, and Sumsearch using the terms: adult, clinical laboratory techniques, critical care, early diagnosis, microbiology, molecular diagnostic techniques, spectrometry and metagenomics.

EXPERT OPINION

: There has been an exponential surge in diagnostic systems used directly on blood and other samples to expedite microbial identification and antimicrobial susceptibility testing of pathogens. Few studies have thus far assessed their clinical impact; final outcomes will also depend on preanalytical and post-analytical factors. Besides, many of the resistance mechanisms cannot yet be detected with molecular techniques, which impairs the prediction of the actual resistance phenotype.

Nonetheless, this is an exciting field with much yet to explore.

The Cutting Edge of Gastroenteritis: Advances in Understanding of Enteric Infection

ABSTRACT

In recent years, multiple advances have been made in the care, diagnosis, and mechanistic understanding of acute gastroenteritis (AGE). In this review, we discuss the current state of the art of diagnosis and management, as well as how changes in practice can improve care and decrease costs. We will discuss present study demonstrating the effect of AGE on the microbiome and how that may be linked to secondary effects or long-term changes. We will explore the use of novel technologies to further our capacity to understand how gastrointestinal infections occur and promulgate. Finally, will discuss advances in our understanding of how gastrointestinal infections capacitate other changes such as post-viral motility or other post viral intestinal dysfunction.

Approach to fever in patients with neutropenia: a review of diagnosis and management

Febrile neutropenia (FN) is associated with mortality rates as high as 40%, highlighting the importance of appropriate clinical management in this patient population. The morbidity and mortality of FN can be attributed largely to infectious processes, with specific concern for infections caused by pathogens with antimicrobial resistance. Expeditious identification of responsible pathogens and subsequent initiation of empiric antimicrobial therapy is imperative. There are four commonly used guidelines, which have variable recommendations for empiric therapy in these populations. All agree that changes could be made once patients are stable and/or with an absolute neutrophil count (ANC) over 500 cells/mcL. Diagnostic advances have the potential to improve knowledge of pathogens responsible for FN and decrease time to results. In addition, more recent data show that rapid de-escalation or discontinuation of empiric therapy, regardless of ANC, may reduce days of therapy, adverse effects, and cost, without affecting clinical outcomes. Antimicrobial and diagnostic stewardship should be performed to identify, utilize, and respond to appropriate rapid diagnostic tests that will aid in the definitive management of this population.

Syndromic diagnostic testing: a new way to approach patient care in the treatment of infectious diseases

Advanced microbiology technologies such as multiplex molecular assays (i.e. syndromic diagnostic tests) are a novel approach to the rapid diagnosis of common infectious diseases. As the global burden of antimicrobial resistance continues to rise, the judicious use of antimicrobials is of utmost importance. Syndromic panels are now being recognized in some clinical practice guidelines as a 'game-changer' in the diagnosis of infectious diseases. These syndromic panels, if implemented thoughtfully and interpreted carefully, have the potential to improve patient outcomes through improved clinical decision making, optimized laboratory workflow, and enhanced antimicrobial stewardship. This paper reviews the potential benefits of and considerations regarding various infectious diseases syndromic panels, and highlights how to maximize impact through collaboration between clinical microbiology laboratory and antimicrobial stewardship programmes.

Relationship of Multiplex Molecular Pneumonia Panel Results With Hospital Outcomes and Clinical Variables

Background

Antibiotic treatment decisions in severely ill patients must often be made in the absence of microbiologic results. The recently Food and Drug Administration-cleared BioFire FilmArray Pneumonia Panel (PN) detects 15 bacteria semiquantitatively, 3 atypical pneumonia bacteria, 8 viruses, and 7 antimicrobial resistance markers by multiplex PCR in ~1 hour in the laboratory. Previous reports have shown that the PN Panel bacterial detections are highly accurate, even when routine culture had no growth.

Methods

Consecutive bronchoalveolar lavage and endotracheal specimens submitted for culture between June and September 2018 from 270 patients with sufficient clinical and laboratory data were tested with the PN Panel. Patients were divided into 3 groups: (1) both culture and PN Panel positive, (2) PN Panel positive but culture uninformative (no growth or normal flora), and (3) patients with no PN Panel detections.

Results

Groups 1 and 2 had significantly higher maximum temperatures on the day of culture (P = .00036, analysis of variance [ANOVA] with Bonferroni correction), higher levels of an inflammatory response as measured by percent polymorphonuclear leukocytes in bronchoalveolar lavage (P = .00025, ANOVA with Bonferroni correction), and gram stain report of white blood cells, as previously reported [1].

Conclusions

Both group 1 (culture and PN Panel positive), and group 2 (PN Panel positive but culture uninformative) had higher levels of host response inflammatory responses compared with group 3, which had no targets detected, suggesting that PN Panel detections need to be interpreted in the clinical context, even if cultures are discordant. Depending on laboratory turnaround time, there could be opportunities for improved diagnosis and antibiotic stewardship.

Evaluation of the Genmark ePlex® and QIAstat-Dx® respiratory pathogen panels in detecting bacterial targets in lower respiratory tract specimens

Background

The ePlex® and QIAstat-Dx® respiratory pathogen panels detect multiple respiratory pathogens, mainly viruses but also Legionella pneumophila, Mycoplasma pneumoniae and Bordetella pertussis. The assays have been marketed for use in nasopharyngeal swab specimens. For diagnosing bacterial pneumonia, lower respiratory tract (LRT) specimens are indicated. Aim of this study was to evaluate the performance of these syndromic panels for these three bacterial targets in samples from the LRT. Fifty-six specimens were collected from our repositories, five negative samples and fifty-one samples which had been previously tested positive with the routine diagnostic real-time PCR assays for Legionella spp. (N = 20), Bordetella spp. (N = 16) or M. pneumoniae (N = 15).

Results

The QIAstat-Dx Respiratory Panel V2 (RP) assay detected all of the L. pneumophila and B. pertussis positive samples but only 11/15 (73.3 %) of the M. pneumoniae targets. The ePlex Respiratory Pathogen Panel (RPP) assay detected 10/14 (71.4 %) of the L. pneumophila targets, 8/12 (66.7 %) of the B. pertussis positive samples and 13/15 (86.7 %) of the M. pneumoniae targets.

Conclusions

No false-positive results were reported for all three bacterial pathogens by both assays. The clinical performance of both assays depended highly on the bacterial load in the sample and the type of specimen under investigation.

Diagnostic syndromic multiplex approaches for gastrointestinal infections

Introduction: Gastrointestinal diseases due to infectious pathogens currently represent an important global health concern, especially in children and developing countries. Early and accurate detection of gastrointestinal pathogens is important to initiate the appropriate type of therapy. Multiplex molecular gastrointestinal panels rapidly detect several gastrointestinal pathogens at once with high sensitivity.Areas covered: We assess the scope and limitations of several multiplex gastrointestinal panels approved by the Food and Drug Administration or marked by Conformité Européenne-in vitro diagnostic. We compare 10 syndromic gastrointestinal panels, 14 bacteria-specific multiplex panels, seven parasite-specific multiplex panels, and eight virus-specific multiplex panels.Expert opinion: Thanks to the advances made in the diagnostic approaches for gastrointestinal infections, there are various panels to choose. The choice of a specific syndromic gastrointestinal multiplex panel should be made to improve patient care. Diagnostic syndromic multiplex approaches for gastrointestinal infections should be customized; each hospital should develop its diagnostic algorithm for gastrointestinal infections tailored to its setting, study population, and geographical site. Current multiplex gastrointestinal panels could be improved by including the detection of antimicrobial resistance, toxigenic Clostridioides difficile, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus responsible for the COVID-19 pandemic).

New Developments in PCR-Based Diagnostics for Bacterial Pathogens Causing Gastrointestinal Infections-A Narrative Mini-Review on Challenges in the Tropics

The application of modern PCR approaches for the diagnosis of bacterial gastrointestinal pathogens is on the rise due to their rapidly available results combined with high sensitivity. While multiple studies describe the ongoing implementation of this technique for routine diagnostic purposes in laboratories in Western industrialized countries, reports on successful and also sustainable respective approaches in resource-poor tropical settings are still scarce. In order to shed light on potential reasons for this marked discrepancy, this narrative review summarizes identified challenges for the application of diagnostic PCR targeting bacterial gastrointestinal pathogens from stool samples in the tropics. The identified and discussed issues comprise the lack of generally accepted definitions for (1) minimum standards regarding sample acquisition, storage and transport time for diagnostic PCR analyses in the tropics, (2) nucleic acid extraction standards allowing an optimum detection of all types of pathogens which may be responsible for gastroenteritis in the tropics, (3) validation standards to ensure comparable quality of applied diagnostic assays, and (4) cut-offs for a reliable discrimination of infection and mere colonization in areas where semi-immunity due to repeated exposition associated with poor hygiene conditions has to be expected. Further implementation research is needed to solve those issues.

Fatal infection with enterocolitis from methicillin-resistant Staphylococcus aureus and the continued value of culture in the era of molecular diagnostics

MRSA enterocolitis is under-recognized in the setting of PCR testing. In this case report, we describe risk factors, the importance of stool culture, and the third published case of MRSA enterocolitis in a patient with leukemia. In addition, we performed a retrospective analysis of all stool cultures at our institution that have grown Staphylococcus aureus, and we describe an additional five cases. We also report the diagnostic yield of organisms detected by culture, but not on the FilmArray panel. While rare, these cases demonstrate that MRSA in stool may indicate a severe and potentially life-threatening infection, particularly in immunocompromised persons.

Rapid molecular syndromic testing for aetiological diagnosis of gastrointestinal infections and targeted antimicrobial prescription: experience from a reference paediatric hospital in Spain

Aetiological diagnosis of gastrointestinal infections is challenging since a wide range of bacteria, parasites and viruses can be causal agents and derived clinical manifestations appear quite similar. Our aim was to evaluate contribution of the novel QIAstat-DxGastrointestinal Panel (GIP) to aetiological diagnosis of gastrointestinal infections and rational antimicrobial prescription in a reference paediatric hospital. Evaluation included comparison of diagnostic yield and agreement of results of QIAstat-Dx GIP and conventional microbiological methods. Parallel testing was performed on stool samples collected prospectively from children admitted to Sant Joan de Deu Barcelona Hospital (Spain) during the period February-March 2019. Influence of the panel test use on antimicrobial prescription was assessed using a pre-post study design. Eighty-six (68.8%) out of 125 specimens were positive by QIAstat-Dx GIP versus 44 (35.2%) positive by a composite of conventional methods (p<0.001). Global agreement of panel test results with rotavirus-adenovirus antigen detection (92.8%) and a two-step antigen/toxin and PCR-based algorithm for toxigenic Clostridioides difficile detection (87.5%) was greater than that with bacterial culture (76.0%) and parasite microscopic identification (64.3%). Panel test results orientated antimicrobial prescription changes in 18 (14.4%) patients, including antimicrobial start in 11 cases initially untreated, targeted antimicrobial prescription in 5 and discontinuation in 2 cases empirically treated. Results showed that QIAstat-Dx GIP significantly expanded aetiological diagnosis of gastrointestinal infections compared to conventional microbiological methods while orientating a more judicious use of antimicrobial drugs in hospitalised children.

Implementation of infectious diseases rapid molecular diagnostic tests and antimicrobial stewardship program involvement in acute-care hospitals

A survey of acute-care hospitals found that rapid molecular diagnostic tests (RMDTs) have been widely adopted. Although many hospitals use their antimicrobial stewardship team and/or guidelines to help clinicians interpret results and optimize treatment, opportunities to more fully achieve the potential benefits of RMDTs remain.

Real-time gastrointestinal infection surveillance through a cloud-based network of clinical laboratories

Acute gastrointestinal infection (AGI) represents a significant public health concern. To control and treat AGI, it is critical to quickly and accurately identify its causes. The use of novel multiplex molecular assays for pathogen detection and identification provides a unique opportunity to improve pathogen detection, and better understand risk factors and burden associated with AGI in the community. In this study, de-identified results from BioFire^® FilmArray^® Gastrointestinal (GI) Panel were obtained from January 01, 2016 to October 31, 2018 through BioFire^® Syndromic Trends (Trend), a cloud database. Data was analyzed to describe the occurrence of pathogens causing AGI across United States sites and the relative rankings of pathogens monitored by FoodNet, a CDC surveillance system were compared. During the period of the study, the number of tests performed increased 10-fold and overall, 42.6% were positive for one or more pathogens. Seventy percent of the detections were bacteria, 25% viruses, and 4% parasites. Clostridium difficile, enteropathogenic Escherichia coli (EPEC) and norovirus were the most frequently detected pathogens. Seasonality was observed for several pathogens including astrovirus, rotavirus, and norovirus, EPEC, and Campylobacter. The co-detection rate was 10.2%. Enterotoxigenic E. coli (ETEC), Plesiomonas shigelloides, enteroaggregative E. coli (EAEC), and Entamoeba histolytica were detected with another pathogen over 60% of the time, while less than 30% of C. difficile and Cyclospora cayetanensis were detected with another pathogen. Positive correlations among co-detections were found between Shigella/Enteroinvasive E. coli with E. histolytica, and ETEC with EAEC. Overall, the relative ranking of detections for the eight GI pathogens monitored by FoodNet and BioFire Trend were similar for five of them. AGI data from BioFire Trend is available in near real-time and represents a rich data source for the study of disease burden and GI pathogen circulation in the community, especially for those pathogens not often targeted by surveillance.

Impact of a Multiplexed Polymerase Chain Reaction Panel on Identifying Diarrheal Pathogens in Hematopoietic Cell Transplant Recipients

BACKGROUND

Diarrhea is common and associated with substantial morbidity among hematopoietic cell transplant (HCT) recipients, but the etiology is often not identified. Multiplexed polymerase chain reaction (PCR) assays increase the detection of diarrheal pathogens, but the impact of this technology in this population has not been evaluated.

METHODS

Our center replaced stool cultures and other conventional microbiologic methods with the FilmArray Gastrointestinal Panel (GI PCR) in June 2016. We reviewed all adult patients who received an HCT from June 2014-May 2015 (pre-GI PCR, n = 163) and from June 2016-May 2017 (post-GI PCR, n = 182) and followed them for 1 year after transplantation. Clostridioides difficile infection was diagnosed by an independent PCR test in both cohorts.

RESULTS

The proportion of patients with ≥1 identified infectious diarrheal pathogen increased from 25% to 37% after implementation of GI PCR (P = .01). Eight patients (5%) in the pre-GI PCR cohort tested positive for a pathogen other than C. difficile versus 49 patients (27%) in the post-GI PCR cohort (P < .001). The most common non-C. difficile diarrheal pathogens in the post-GI PCR cohort were enteropathogenic Escherichia coli (n = 14, 8%), norovirus (n = 14, 8%), and Yersinia enterocolitica (n = 7, 4%). The percentage of diarrheal episodes with an identified infectious etiology increased from 14% to 23% (P = .001). Median total costs of stool testing per patient did not increase (pre: $473; post: $425; P = .25).

CONCLUSIONS

Infectious etiologies of diarrhea were identified in a higher proportion of HCT recipients after replacing conventional stool testing with a multiplexed PCR assay, without an increase in testing costs.

Syndromic Multiplex Polymerase Chain Reaction (mPCR) Testing and Antimicrobial Stewardship: Current Practice and Future Directions

PURPOSE OF REVIEW

Syndromic multiplex polymerase chain reaction (mPCR) panels offer the antimicrobial steward a rapid tool for optimizing and de-escalating antimicrobials. In this review, we analyze the role of syndromic mPCR in respiratory, gastrointestinal, and central nervous system infections within the context of antimicrobial stewardship efforts.

RECENT FINDINGS

For all mPCR syndromic panels, multiple studies analyzed the pre-and-post implementation impact of mPCR on antimicrobial utilization. Prospective studies and trials of respiratory mPCR stewardship interventions, including diagnostic algorithms, educational efforts, co-testing with procalcitonin, and targeted provider feedback currently exist. For gastrointestinal and cerebrospinal fluid mPCR, fewer peer-reviewed reports exist for the use of mPCR in antimicrobial stewardship. These studies demonstrated an inconsistent trend towards decreasing antibiotic use with mPCR. This is further limited by a lack of statistical significance, the absence of controlled, prospective trials, and issues with data generalizability.

SUMMARY

Antibiotic overuse may improve when mPCR is coupled with electronic medical record algorithm-based approaches and direct provider feedback by an antimicrobial stewardship professional. mPCR may prove a useful tool for antimicrobial stewardship but future studies are needed to define the best practice for its utilization.

Etiological Spectrum of Infective Diarrhea in Renal Transplant Patient by Stool PCR: An Indian Perspective

Introduction:

Diarrhea is a common cause of morbidity and mortality among renal transplant patients. The etiological spectrum of pathogens varies with regional diversity, socioeconomic conditions, sanitation, and eating habits. We aimed to delineate the etiological profile of gastrointestinal pathogens in renal transplant patients using the stool Polymerase chain reaction.

Methods:

In this single-center, retrospective analysis of patients from January 2016 to January 2018, all renal transplant patients who were admitted with severe diarrhea and underwent the stool Polymerase chain reaction (PCR) were included. In the control group, we included patients from the general population who were admitted with similar complaints in the general medicine ward and underwent stool PCR over the same duration.

Results:

One hundred ten admissions occurred over 2 years in the transplant group. 86% of samples were positive for infection. More than one organism was seen in 68% of the patient. Norovirus was the most common organism isolated. Giardia lamblia with Norovirus was the most common coinfection among the transplant population. In the control group, 87% of samples tested positive, with 53% of patients having more than one organism. Enteroaggregative E. coli was the common organism, Enteroaggregative E. coli with Enteropathogenic E. coli and Enterotoxigenic E. coli were the most common organism in combination. Both the groups had similar incidence of infection with multiple organisms.

Conclusion:

The etiological profile of gastrointestinal pathogens differs significantly between the transplant and general population. Coinfections are common in both populations. Norovirus is the most common pathogen in the transplant population, presenting as isolated as well as in coinfections.

Rate and consequences of missed Clostridioides (Clostridium) difficile infection diagnosis from nonreporting of Clostridioides difficile results of the multiplex GI PCR panel: experience from two-hospitals

INTRODUCTION

It is common among microbiology laboratories to blind the Clostridioides difficile (C. difficile) BioFire FilmArray GI Panel result in fear of overdiagnosis.

METHODS

We examined the rate of missed community-onset C. difficile infection (CDI) diagnosis and associated outcomes. Adult patients with FilmArray GI Panel positive for C. difficile on hospital admission who lacked dedicated C. difficile testing were included.

RESULTS

Among 144 adults with a FilmArray Panel positive for C. difficile, 18 did not have concurrent dedicated C. difficile testing. Eight patients were categorized as possible, 5 as probable and 4 as definite cases of missed CDI diagnosis. We observed associated delays in initiation of appropriate therapy, intensive care unit admissions, hospital readmissions, colorectal surgery and death/discharge to hospice. Five out of 17 lacked risk factors for CDI.

CONCLUSION

The practice of concealing C. difficile FilmArray GI Panel results needs to be reconsidered in patients presenting with community-onset colitis.

Oxford nanopore sequencing in clinical microbiology and infection diagnostics

Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.

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.

Evaluating appropriateness and diagnostic stewardship opportunities of multiplex polymerase chain reaction gastrointestinal testing within a hospital system

Objective:

This single-center, retrospective, observational cohort study evaluates the appropriateness of the BioFire® FilmArray® Gastrointestinal (GI) multiplex PCR panel testing at a community-teaching hospital.

Methods:

All adult, hospitalized patients at Prisma Health Richland Hospital with a documented GI multiplex PCR panel from 1 April 2015 through 28 February 2018 were included in the analysis. Inappropriate use of the GI panel was defined as a test obtained without documented diarrhea, greater than 2 days of hospitalization, redundant use with other diagnostic tests (e.g. Clostridioides difficile PCR), or laxative use in the preceding 48 h. Antibiotic use and host variables were compared between groups with positive and negative results.

Results:

During the study period, 442 GI panels were obtained, among which 268 (61%) were deemed inappropriate. Primary reasons for inappropriate testing were lack of documented diarrhea (n = 92), greater than 2 days of hospitalization (n = 116), having a duplicate C. difficile PCR test ordered (n = 118), or laxative use in the 48 h before testing (n = 36). A total of 141 (32%) GI panels were positive. The most frequently identified pathogens were C. difficile (51.1%, n = 72), Enteropathogenic Escherichia coli (17.7%, n = 25), and Norovirus GI/GII (12.1%, n = 17). Patients with negative GI panel results were initiated on antibiotics significantly less frequently than those with positive GI panels (62.5% versus 80.2%, p < 0.00001).

Conclusion:

Stewardship opportunities exist to optimize the diagnostic application of the GI multiplex PCR panel.

Point-of-care multiplex-PCR enables germ identification in haemolytic uremic syndrome 94 h earlier than stool culture

Haemolytic uremic syndrome often affects children causing a relevant morbidity and mortality. We compared the time to diagnosis by multiplex-PCR and stool culture in 15 children from two centres. Multiplex-PCR accelerated the time to diagnosis by 94 (95% confidence interval, 80-119; P = 0.0007) hours. Multiplex-PCR offers a time advantage of stool culture that may aid in earlier identification of outbreak clusters.

Panels and Syndromic Testing in Clinical Microbiology

Syndromic panels have allowed clinical microbiology laboratories to rapidly identify bacteria, viruses, fungi, and parasites and are now fully integrated into the standard testing practices of many clinical laboratories. To maximize the benefit of syndromic testing, laboratories must implement strict measures to ensure that syndromic panels are being used responsibly. This article discusses commercially available syndromic panels, the benefits and limitations of testing, and how diagnostic and laboratory stewardship can be used to optimize testing and improve patient care while keeping costs at a minimum.