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

Diagnosing gastrointestinal infections based on cycle threshold cut-offs of PCR

This study compared the performance of molecular vs stool culture assays for gastrointestinal infection (GII) detection, with focus on defining cycle threshold (Ct) cut-off values for positive culture results. A total of 6,000 records of patients with suspected GII between October 2022 and February 2023 and registered at Clalit HealthCare Services in Haifa, Israel, were reviewed. Stool samples were collected from all patients with suspected GII. PCR was performed with the Seegene Allplex GI-Bacteria (I) assay kit. PCR-positive samples were cultured on bacteria-specific agar media. Out of 356 PCR-positive samples, 196 (55.1%) were culture-positive. Significant differences were noted between the mean Ct of culture-positive vs culture-negative samples for Shigella spp. (P < 0.0001), E. coli O157 (P = 0.0001), and Campylobacter spp. (P = 0.004). Shigella had the lowest Ct cutoff (27.14). Negative culture results for PCR-positive samples may result from low bacterial load. At the same time, false-positive PCR results may exist. Thus, PCR result should be considered along with clinical presentation and with Ct value consideration.IMPORTANCEGII diagnostic procedures have shifted from traditional- to molecular-based assays, which may increase missdiagnosis due to the high PCR sensitivity and false positives. This study suggests to consider a Ct threshold for each pathogen in order to reduce inaccurate diagnosis. Alternatively, culture should be performed for PCR-positive samples.

Comparison of AccuPower Diarrhea V1&V2 RT-PCR to a Chromatographic Immunoassay for Detecting Viral Pathogens from Human Diarrheal Stool Specimens

Viruses are a frequent cause of self-limited diarrhea, with more severe outcomes in immunocompromised patients. This study aimed to compare the performance of Real-Time RT-PCR to chromatographic immunoassays (CIAs) for detecting the major gastrointestinal viruses in human stool. This study was conducted at the University Hospital of Split, Croatia, from October 2023 to May 2024. Stool samples were simultaneously analyzed with CIA (Acro Biotech Rotavirus and Adenovirus Combo Rapid Test Cassette, USA and JusChek Norovirus Rapid Test Cassette, China) and Real-Time RT-PCR (AccuPower Diarrhea V1&V2 Real-Time RT-PCR, Bioneer, Republic of Korea), according to the manufacturers' instructions. Positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement (OPA) were calculated. For norovirus, CIA had a low PPA (25%), indicating that it missed 75% of norovirus-positive cases identified by RT-PCR. Adenovirus detection by CIA showed poor agreement with RT-PCR (PPA 0%; NPA 100%). Rotavirus detection presented a relatively better performance with CIA (PPA 90.9% and OPA 84.13%). However, the presence of false positives (15.8%) highlights the need for confirmatory RT-PCR testing. One specimen was sapovirus-RT-PCR-positive, marking the first documented case from human specimens in Croatia. Although CIA provided rapid results, limitations regarding reliability highlight the value of RT-PCR, particularly in the case of ambiguous clinical cases with negative antigenic test results and newly emerged viruses. A two-step diagnostic approach, with initial CIA screening followed by confirmatory RT-PCR, could balance cost-effectiveness with diagnostic accuracy.

Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens

BACKGROUND

Accurate and comprehensive identification of enteropathogens, causing infectious gastroenteritis, is essential for optimal patient treatment and effective isolation processes in health care systems. Traditional diagnostic techniques are well established and optimised in low-cost formats. However, thorough testing for a wider range of causal agents is time consuming and remains limited to a subset of pathogenic organisms. Metagenomic next-generation sequencing (mNGS) allows the identification of all pathogens in a sample in a single test, without a reliance on culture or introduction of target selection bias. This study aims to determine the ability to routinely apply mNGS testing, in comparison to traditional culture or polymerase chain reaction (PCR) based tests, for the identification of causal pathogens for gastrointestinal infections.

RESULTS

The performance of mNGS, PCR and microscopy, culture and sensitivity (MCS) assays was established using 2,619 prospectively collected faecal samples from patients with symptomology indicative of infectious gastroenteritiss. Commonly experienced pathogens including Aeromonas spp, Campylobacter spp, Salmonella spp and Giardia spp, in single and co-infected patients, were used to establish test outcomes. When testing for these organisms, using the combined result from either or both PCR and MCS testing as the comparator, the mNGS assay had clinically acceptable sensitivity (89.2-100%). Further, the mNGS assay detected 14 additional enteropathogens, that were either not detected or not tested, by initial PCR/MCS testing.

CONCLUSIONS

The advantage of mNGS compared to other syndromic testing systems is the broad range of detectable targets and the ability to interrogate samples without clinician informed or assay specific bias. With the development of newer sequencing assays, it is now feasible to test for a wide range of target organisms in a sample using a single mNGS test. Overall, the mNGS based approach enabled pathogen detection that was comparable to conventional diagnostics and was shown to have the potential to be extended for the detection of many pathogens and genes of clinical interest. In conclusion, the mNGS assay offers an easy, sample to answer workflow with rapid detection of enteropathogens and has the potential to improve diagnosis, therapy and infection control precautions.

Etiological, Clinical, and Epidemiological Characteristics of Acute Viral Gastroenteritis in an Adult Population in a Tertiary Level Hospital in Spain

INTRODUCTION

Acute gastroenteritis (AGE) represents a significant global health burden, with enteric viruses being a leading cause of gastroenteritis worldwide. Despite advances in diagnosis and treatment, there are limited data on adults seeking care due to AGE of viral etiology. This study aimed to describe the etiological, clinical, and epidemiological characteristics of viral AGE in adult patients presenting for medical consultation in a tertiary hospital over a 2-year period.

METHODS

A retrospective cross-sectional study was conducted, with 8886 stool samples from 8356 adult patients presenting acute diarrhea between January 2021 and December 2022. A molecular real-time RT-PCR panel was used to screen for common bacterial, parasitic, and viral pathogens. Clinical and demographic data were collected, and statistical analysis was performed to evaluate possible associations.

RESULTS

Enteric viruses constituted 10.3% (307 cases) of all AGE of known etiology, with norovirus being the predominant pathogen (196, 63.8%), followed by rotavirus (82, 26.7%) and adenovirus (29, 9.4%). The different viruses showed a distinct seasonal predominance. Coinfection with other microorganisms was common. Most cases exhibited a self-limiting course. Mortality and hospitalization rates were high in patients with higher comorbidity indices, mainly in individuals with immunosuppression.

CONCLUSIONS

Viruses are an important cause of acute gastroenteritis in adults presenting for medical consultation. The new multiplex molecular tests with high sensitivity and specificity allow early differential diagnosis in AGE. It is therefore necessary to identify which special populations particularly with higher comorbidity indices, would benefit from the implementation of these techniques, to guide decision-making related to appropriate treatments and avoid unnecessary interventions.

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.

Viral gastroenteritis

Since the discovery of norovirus in 1972 as a cause of what was contemporarily known as acute infectious non-bacterial gastroenteritis, scientific understanding of the viral gastroenteritides has continued to evolve. It is now recognised that a small number of viruses are the predominant cause of acute gastroenteritis worldwide, in both high-income and low-income settings. Although treatment is still largely restricted to the replacement of fluid and electrolytes, improved diagnostics have allowed attribution of illness, enabling both targeted treatment of individual patients and prioritisation of interventions for populations worldwide. Questions remain regarding specific genetic and immunological factors underlying host susceptibility, and the optimal clinical management of patients who are susceptible to severe or prolonged manifestations of disease. Meanwhile, the worldwide implementation of rotavirus vaccines has led to substantial reductions in morbidity and mortality, and spurred interest in vaccine development to diminish the impact of the most prevalent viruses that are implicated in this syndrome.

Present and Future Non-Culture-Based Diagnostics: Stewardship Potentials and Considerations

The medical microbiologist plays a key role in the transition from culture-based to molecular test methods for diagnosis of infectious diseases. They must understand the scientific and technical bases underlying these tests along with their associated benefits and limitations and be able to educate administrators and patient providers on their proper use. Coordination of testing practices between clinical departments and the spectrum of public health and research laboratories is essential to optimize health care delivery.

The effect of the transition to molecular diagnosis on the epidemiology and the clinical characteristics of bacterial gastroenteritis in Northern Israel

BACKGROUND

The transition to PCR-based diagnosis of bacterial gastroenteritis (BGE) can increase the sensitivity but might reduce the clinical specificity. The aims of this study were (1) to compare the effect of the change from culture to PCR-based diagnostics on the reported incidence and positivity rates of BGE due to Salmonella, Shigella and Campylobacter species and (2) to compare the demographics, medical background, clinical characteristics and pre-analytic variables between cases with PCR-positive, culture-negative samples to cases with PCR-positive, culture-positive samples.

METHODS

The study was performed at the Emek Medical Centre that serves a population of 0.5 million people in Northern Israel. The study included two parts: (1) a retrospective cohort study, comparing the incidence and positivity rates of laboratory-diagnosed BGE from January 2016 until December 22nd, 2019 when culture was the sole method to January 2020 until April 2023 when PCR was used; (2) a prospective cohort study, conducted between November 2020 until April 2023 that compared the demographics and clinical characteristics of BGE cases that were diagnosed by PCR alone versus cases that were diagnosed by both PCR and culture.

RESULTS

The incidence rate between-periods comparability ratio was only 113% since the incidence rate did not increase during 2020, the first year of the COVID-19 pandemic. The sample positivity rate increased since 2020, with between-periods comparability ratio of 159%. In the second period, the sample positivity rates of culture vs. PCR alone differed between the pathogens and were 90.2%, 63.8% and 54.2% for Salmonella, Campylobacter and Shigella species, respectively (p < 0.001). The following variables were identified as independent predictors of culture positivity: (1) Salmonella infection (O.R. = 10.6, 95% C.I. 3.6-31.1, p < 0.001); (2) Shigella infection (O.R. = 0.46, 95% C.I.0.23-0.93, p = 0.032); (3) time from sample submission to culture (O.R.=0.73, 95% C.I. 0.58-0.92, p = 0.008); (4) the presence of abdominal pain (O.R. = 1.98, 95% C.I. 1.04-3.79, p = 0.038) and the PCR mean Ct value (O.R. = 0.89, 95% C.I.0.85-0.94, p < 0.001).

CONCLUSIONS

The use of PCR had led to improved sensitivity, without noticeable decrease in the clinical specificity. This was especially important in the case of the more fastidious organisms.

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.

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.

Micronucleus assay of DNA damage among welders: effects of welding processes

Metal fumes, gases, noise, and radiation are hazardous occupational exposures that may be encountered by welders. We have evaluated DNA damage among welders; the buccal micronucleus cytome (BMCyt) assay was used. Thirty-four exposed welders (cases) and an equal number of non-welders (controls) participated in this study. Cell types including basal, early and late differentiated cells with micronucleus (MN), dense chromatin, karyorrhectic, pyknotic, karyolitic, and binucleated cells (NBUD) were measured. Damage levels among, arc, argon, and CO₂ welders were statistically significantly higher, compared to the control group. Results showed that mean of MN and NBUDs as indicators of DNA damages among arc, argon and CO₂ welding's were significantly higher compared to control group. Also, the mean of DNA damage levels were statistically higher among the arc welders than among the argon or CO₂ welders; and levels were higher among the argon welders than the CO₂ welders. Preventative measures need to be implemented to reduce exposure to harmful agents during welding.

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.

ImmunoDisk—A Fully Automated Bead-Based Immunoassay Cartridge with All Reagents Pre-Stored

In this paper, we present the ImmunoDisk, a fully automated sample-to-answer centrifugal microfluidic cartridge, integrating a heterogeneous, wash-free, magnetic- and fluorescent bead-based immunoassay (bound-free phase detection immunoassay/BFPD-IA). The BFPD-IA allows the implementation of a simple fluidic structure, where the assay incubation, bead separation and detection are performed in the same chamber. The system was characterized using a C-reactive protein (CRP) competitive immunoassay. A parametric investigation on air drying of protein-coupled beads for pre-storage at room temperature is presented. The key parameters were buffer composition, drying temperature and duration. A protocol for drying two different types of protein-coupled beads with the same temperature and duration using different drying buffers is presented. The sample-to-answer workflow was demonstrated measuring CRP in 5 µL of human serum, without prior dilution, utilizing only one incubation step, in 20 min turnaround time, in the clinically relevant concentration range of 15–115 mg/L. A reproducibility assessment over three disk batches revealed an average signal coefficient of variation (CV) of 5.8 ± 1.3%. A CRP certified reference material was used for method verification with a concentration CV of 8.6%. Our results encourage future testing of the CRP-ImmunoDisk in clinical studies and its point-of-care implementation in many diagnostic applications.