Agreement between gastrointestinal panel testing and standard microbiology methods for detecting pathogens in suspected infectious gastroenteritis: Test evaluation and meta-analysis in the absence of a reference standard

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.

Utility and Recommendations for the Use of Multiplex Molecular Gastrointestinal Pathogen Panels

BACKGROUND

Many molecular gastrointestinal pathogen panels (GIPs) are Food and Drug Administration (FDA) cleared but it is still unclear how to best utilize these new diagnostic tools. GIPs are highly sensitive and specific, simultaneously detect multiple pathogens in one reaction, and can shorten the overall time of diagnosis for infectious gastroenteritis but are also expensive with relatively poor insurance reimbursement.

CONTENT

In this review, we take a comprehensive approach to discuss issues with utilization of GIPs from a physician perspective, and implementation from a laboratory perspective. The information presented is to assist physicians in deciding on appropriate use of GIPs in diagnostic algorithms for their patients, and to provide information to laboratories that may be considering the addition of these powerful diagnostic assays to their test menu. Some of the important topics discussed are inpatient vs outpatient use, the appropriate panel size and organisms to include, interpretation of results, laboratory validation, and reimbursement.

SUMMARY

The information in this review provides clear guidance to both clinicians and laboratories in deciding the best use of GIPs for a specific patient population. While this technology provides many benefits over traditional methods, it can also complicate result interpretation and comes with a high cost, which necessitates the need for use recommendations.

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

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

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

OBJECTIVE

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

METHODS

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

RESULTS

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

CONCLUSION

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

Successful management of life-threatening post-COVID-19 cryptosporidiosis in a renal transplant patient: a case report

Worldwide, Cryptosporidium spp. is a common parasite that affects domestic and wild animals, including humans, and causes diarrhea in both immunocompetent and immunocompromised hosts. The fecal-oral pathway accounts for the majority of its transfer. Although C. parvum and C. hominis are the most common zoonotic species in humans, other zoonotic species can also infect immunocompetent and immunocompromised people. Patients undergoing renal transplants are more likely to contract cryptosporidiosis, which can cause severe and potentially fatal diarrhea. A 41-year-old male patient who presented to the emergency department complained of a sudden onset, severe and continuous fatigue, and a feverish sensation of two-day duration. Two days prior to the current admission, the patient started to complain of weakness affecting his whole body, as well as a fever of 39°C and continuous yellowish diarrhea occurring 4-5 times daily without blood. Stool analysis revealed a cryptosporidium infection. The patient underwent surgery for kidney transplantation. The donated kidney was the left one from his brother and was attached to the patient´s right groin. As illustrated by our example, cryptosporidiosis should be considered a significant cause of acute, persistent, watery diarrhea in immunocompromised kidney transplant recipients. Patients undergoing renal transplants should be instructed to wash their hands frequently, stay away from young animals, sick people, and swimming pools in order to lower their risk of infection.

Comparative Evaluation of Luminex xTAG® Gastrointestinal Pathogen Panel and Direct-From-Stool Real-Time PCR for Detection of C. difficile Toxin tcdB in Stool Samples from a Pediatric Population

Detection of Clostridioides difficile toxins in patients with gastroenteritis has increasingly been accomplished through the use of enteric multiplex syndromic panels. Comparisons of the performance of these panels to both direct-from-stool (DFS) and culture-enriched stools followed by polymerase chain reaction (PCR) methods in pediatric populations are limited. Here, we compare the performance of the Luminex xTAG^® Gastrointestinal Pathogen Panel (GPP) to our DFS in-house real-time PCR (DFS RT-PCR) assay for the detection of C. difficile toxin gene, tcdB, using 2641 stool specimens collected from children enrolled in the Alberta Provincial Pediatric EnTeric Infection Team (APPETITE) study in Alberta, Canada. We used culture enrichment followed by in-house RT-PCR to resolve discordant results between the two assays. We found excellent agreement (k = 0.89) between the GPP and our DFS RT-PCR assay: the positive percent agreement between the two assays was 97%, and the negative percent agreement was 99%. GPP, a multi-analyte platform can easily be implemented into a routine diagnostic laboratory for detecting enteric pathogens including C. difficile.

Diagnostic accuracy of multiplex nucleic acid amplification tests for Campylobacter infection: a systematic review and meta-analysis

Campylobacter infection is one of the most frequently reported foodborne diseases with approximately 230,000 and 1.5 million cases each year in Europe and the USA, respectively. Culture methods are the reference for the diagnosis of Campylobacter infections; however, these methods are complex and time-consuming. Multiplex nucleic acid amplification test is favored due to its rapidity, automatization in the procedure followed and the quick simultaneous testing of numerous foodborne pathogens. The aim of this meta-analysis was to evaluate the accuracy of these tests for the diagnosis of Campylobacter infection. Scopus, Science Direct, PubMed, Web of Science, and Mendeley were searched for peer-reviewed articles. The split component synthesis method with the use of the inverse variance heterogeneity model was chosen for the quantitative meta-analysis. Sensitivity analysis was performed by age category and index test. The literature search found 34 studies involving 28,105 patients with suspected gastroenteritis. The sensitivity and specificity were 95.3% (92.3; 97.1) and 97.1% (95.1; 98.3), respectively, and AUC (area under the curve) was 0.963 (0.947; 0.974). Pediatric patients had a lower sensitivity (87.4, 48.2; 98.1) and higher specificity (99.2, 91.6; 99.9) estimate compared to all ages category (sensitivity 95.3, 91.3; 97.5, specificity 96.7, 93.7; 98.3). Among the various index tests, Seeplex/Allplex and Amplidiag/Novodiag had the lowest estimate for sensitivity (88.9, 73.8; 95.8) and specificity (95.2, 86; 98.4), respectively. BDMax had the highest (sensitivity 98.1, 96.1; 99 and specificity 98.5, 97; 99.3). Multiplex nucleic acid tests showed excellent accuracy and could play an influential role in diagnosing Campylobacter infections.

[Usefulness of Stool Multiplex Polymerase Chain Reaction Assays in Patients with Acute Diarrhea]

Background/Aims

There is a recent increase in the use of stool multiplex PCR assay-based diagnostic tests in patients with acute diarrhea. We used multiplex PCR assays to analyze the distribution of diarrhea-causing bacteria and viruses, as well as the clinical features of patients with acute diarrhea.

Methods

We retrospectively reviewed stool specimens of inpatients complaining of acute diarrhea from October 2018 to July 2020. The stool specimens had been tested for bacteria and viruses using multiplex PCR assays.

Results

A total of 414 stool specimens from 346 patients were tested, and 152 pathogens were detected in 131 stool samples (131/414, 31.6%). Co-infection was detected in 20 patients (20/346, 5.8%). The common pathogens detected as causes of acute diarrhea, including co-infection, were Clostridium perfringens (34.9%), Clostridioides difficile (19.7%), and Campylobacter spp. (18.4%). The average age of patients with multiplex PCR-positive tests was lower than those with multiplex PCR-negative tests (p=0.001). In patients with suspected C. difficile infection (CDI), the RT-PCR for toxin gene assay was performed in 370 stool samples, 35 of which were positive (9.5%). Furthermore, 16 of the 35 samples were positive on the multiplex PCR assay (45.7%).

Conclusions

The multiplex PCR assay revealed that C. perfringens was the most common diarrhea-causing pathogen. In addition, in patients with suspected CDI, the multiplex PCR assay alone was insufficiently sensitive to detect pathogens and a conventional CDI test was additionally required.

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.

Effects of an urban sanitation intervention on childhood enteric infection and diarrhea in Maputo, Mozambique: A controlled before-and-after trial

We conducted a controlled before-and-after trial to evaluate the impact of an onsite urban sanitation intervention on the prevalence of enteric infection, soil transmitted helminth re-infection, and diarrhea among children in Maputo, Mozambique. A non-governmental organization replaced existing poor-quality latrines with pour-flush toilets with septic tanks serving household clusters. We enrolled children aged 1-48 months at baseline and measured outcomes before and 12 and 24 months after the intervention, with concurrent measurement among children in a comparable control arm. Despite nearly exclusive use, we found no evidence that intervention affected the prevalence of any measured outcome after 12 or 24 months of exposure. Among children born into study sites after intervention, we observed a reduced prevalence of Trichuris and Shigella infection relative to the same age group at baseline (<2 years old). Protection from birth may be important to reduce exposure to and infection with enteric pathogens in this setting.

Assessors assemble: the need for harmonised external quality assessment schemes for emerging diagnostic methodologies in the field of parasitology

Global travel and migration trends have meant a huge increase in the numbers of people exposed to tropical parasitic diseases. Thus, there is an increasing need for robust, reproducible and reliable diagnostic techniques in the field. Advanced molecular and lateral flow techniques have pushed the boundaries of clinical parasite diagnostics with their enhanced sensitivities and specificities. These emerging technologies are, however, not without their challenges, and recently there has been multiple evidence of a lack of consensus among protocols and results obtained by quality assessment of these novel technologies. This commentary discusses findings from some recent quality assessment studies in the field of blood and faecal parasitology. The article also makes recommendations for a unified and harmonised approach towards delivering high-quality clinical parasitology diagnoses, especially through the use of proficiency testing.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

Diagnostic stewardship of Clostridioides difficile polymerase chain reaction results from syndromic diarrhea panel and implications for patient outcomes

BACKGROUND

A syndromic gastrointestinal pathogen panel (GIP) was implemented in May 2018. All positive (+) GIP and standard-of-care (SOC) C. difficile results were reviewed.

METHODS

A single-center audit of adult patients with GIP results was conducted May-December 2018. We reviewed GIP(+)/SOC(+/-) and GIP(-)/SOC(-) tests (control group) for clinical outcomes.

RESULTS

We reviewed 269 GIP(+) patients. Of 119 GIP(+)/SOC(+) patients, 44 (37%) were positive by toxin A/B enzyme immunoassay, and 75 (63%) by PCR only. Thirty-day mortality and re-admission were not significantly different between groups. CDI rates within 6 months were not significantly different between GIP(+)/SOC(-) and controls (p-value = 0.39). Those with initial SOC(+) tests had more true CDI events within 6 months, compared to controls (p-values < 0.001).

CONCLUSIONS

Forty percent of patients with GIP(+) C. difficile were (-) by SOC test, suggesting that true CDI was not present. Additional PCR-based testing may not impact outcomes.

Evaluation of the Vibrant DNA microarray for the high-throughput multiplex detection of enteric pathogens in clinical samples

Background

Rapid detection of a wide range of etiologic agents is essential for appropriate treatment and control of gastrointestinal (GI) infections. A variety of microbial species including bacteria, viruses, parasites, and fungi have been recognized as diarrheagenic enteric pathogens. However, multiplex testing of various targets in a single reaction needs further improvement because of its limitation in species and throughput.

Results

This study aims at developing and evaluating a DNA microarray-based qualitative multiplexed polymerase chain reaction (PCR) assay, Vibrant GI pathogen panel (GPP), for simultaneous detection of 27 enteric GI pathogenic targets (16 bacteria, 5 viruses, 4 parasites, and 2 fungi) directly from stool specimens. Limits of detection ranged from 10² to 10⁴ cells/mL for bacteria, 10² to 10³ cells/mL for parasites, 10² to 10³ RNA copies/mL for viruses, and 10² to 10³ cells/mL for fungi. Performance characteristics were determined using 27 Quantitative Genomic DNAs, 212 spiked stool specimens, 1067 clinical and archived stool specimens. Overall sensitivity was 95.9% (95% CI 92.4–98.1) and specificity was 100% (95% CI 99.9–100). Polymicrobial detections contained either two or three organisms was 20.2% (35/173) of positive clinical specimens and 3.3% (35/1055) of all clinical specimens.

Conclusion

The Vibrant GPP is a comprehensive, high-throughput, and rapid DNA microarray to provide etiologic diagnosis of GI infections in the laboratory setting.

Case Report: Diagnosis of Cryptosporidiosis in Renal Transplantation in a Low-Prevalence Setting

In high prevalence settings, cryptosporidiosis is commonly implicated as a cause of a gastroenteritis syndrome in the organ transplant population. Stool microscopy is predominant diagnostic modality. Therapeutic options in this group of patients are limited, making their management exceptionally challenging. We describe a case of a renal transplant recipient with cryptosporidiosis confirmed by the stool FilmArray gastrointestinal panel (GIP) nucleic acid-based assay and stool microscopy, describe our institutional experience in diagnosing cryptosporidiosis in a low-prevalence setting, and review the available literature on management of this condition in the organ transplant population. In a low-prevalence setting, the GIP can serve as a rapid screening tool in the diagnosis of cryptosporidiosis.

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

OBJECTIVES

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Benefits and risks of standardization, harmonization and conformity to opinion in clinical laboratories

Large laboratory systems that include facilities with a range of capabilities and capacity are being created within consolidated healthcare systems. This paradigm shift is being driven by administrators and payers seeking to achieve resource efficiencies and to conform practice to the requirements of computerization as well as the adoption of electronic medical records. Although standardization and harmonization of practice improves patient care outcomes and operational efficiencies, administratively driven practice conformity (conformity to opinion) also has serious drawbacks and may lead to significant system failure. Juxtaposition of the distinct philosophical approaches of physicians and scientists (i.e. "professionalism") versus administrators and managers (i.e. "managerialism") towards bringing about conformity of the laboratory system inherently creates conflict. Despite an administrative edict to "perform all tests using the same methods" regardless of available "best practice" evidence to do so, medical/scientific input on these decisions is critical to ensure quality and safety of patient care. Innovation within the laboratory system, including the adoption of advanced technologies, practices, and personalized medicine initiatives, will be enabled by balancing the relentless drive by non-medical administration to meet "business" requirements, the medical responsibility to provide the best care possible, and customizing practice to meet individual patient care needs.

Comparative Evaluation of Enteric Bacterial Culture and a Molecular Multiplex Syndromic Panel in Children with Acute Gastroenteritis

Although enteric multianalyte syndromic panels are increasingly employed, direct comparisons with traditional methods and the inclusion of host phenotype correlations are limited. Luminex xTAG gastrointestinal pathogen panel (GPP) and culture results are highly concordant. However, phenotypic and microbiological confirmatory testing raises concerns regarding the accuracy of the GPP, especially for Salmonella spp. A total of 3,089 children with gastroenteritis submitted stool specimens, rectal swab specimens, and clinical data. The primary outcome was bacterial pathogen detection agreement for shared targets between culture and the Luminex xTAG GPP. Secondary analyses included phenotype assessment, additional testing of GPP-negative/culture-positive isolate suspensions with the GPP, and in-house and commercial confirmatory nucleic acid testing of GPP-positive/culture-negative extracts. The overall percent agreement between technologies was >99% for each pathogen. Salmonella spp. were detected in specimens from 64 participants: 12 (19%) by culture only, 9 (14%) by GPP only, and 43 (67%) by both techniques. Positive percent agreement for Salmonella spp. was 78.2% (95% confidence interval [CI], 64.6%, 87.8%). Isolate suspensions from the 12 participants with specimens GPP negative/culture positive for Salmonella tested positive by GPP. Specimens GPP positive/culture negative for Salmonella originated in younger children with less diarrhea and more vomiting. GPP-positive/culture-negative specimen extracts tested positive using additional assays for 0/2 Campylobacter-positive specimens, 0/4 Escherichia coli O157-positive specimens, 0/9 Salmonella-positive specimens, and 2/3 Shigella-positive specimens. For both rectal swab and stool samples, the median cycle threshold (C_T ) values, determined using quantitative PCR, were higher for GPP-negative/culture-positive samples than for GPP-positive/culture-positive samples (for rectal swabs, 36.9 [interquartile range {IQR}, 33.7, 37.1] versus 30.0 [IQR, 26.2, 33.2], respectively [P = 0.002]; for stool samples, 36.9 [IQR, 33.7, 37.1] versus 29.0 [IQR, 24.8, 30.8], respectively [P = 0.001]). GPP and culture have excellent overall agreement; however, for specific pathogens, GPP is less sensitive than culture and, notably, identifies samples false positive for Salmonella spp.

A Meta-analysis of Diagnostic Test Agreement Between Eucapnic Voluntary Hyperventilation and Cardiopulmonary Exercise Tests for Exercise-Induced Bronchoconstriction

INTRODUCTION

Exercise-induced bronchoconstriction (EIB) is very common in athletes. Cardiopulmonary exercise tests (CPET) have traditionally been used for the diagnosis of EIB. However, alternative indirect bronchoprovocation tests have recently been used as surrogate tests. One of these is the eucapnic voluntary hyperventilation (EVH). This meta-analysis studied the agreement between the two tests.

METHODS

An extensive search in PubMed and Medline was conducted for studies where participants underwent both CPET and EVH with measurement of forced expiratory volume in 1-second (FEV₁). After extracting data using two-by-two contingency tables, pooled positive and negative agreements were first calculated between the two tests, with EVH benchmarked against CPET, and then, pooled positive and negative agreements were calculated with CPET benchmarked against EVH.

RESULTS

The pooled positive and negative agreements between EVH and CPET (with CPET as the reference) were 0.62 [(95% confidence interval 0.54-0.70), I² 77%] and 0.61 [(0.56-0.65)), I² 81%]. The pooled positive and negative agreements between CPET and EVH (with EVH as the reference) were 0.36 [(0.30-0.42), I² 93%] and 0.82 [(0.77-0.86), I² 78%]. The average of positive test results with EVH across all studies was greater than that of CPETs (58.84% vs. 39.51%).

CONCLUSIONS

Results of this meta-analysis show poor positive agreement between the two tests but high negative agreement (specifically using EVH as reference), suggesting that either test can be used for correctly identifying those without EIB. Results also suggest that the chances of a test resulting positive are higher with EVH than with CPET.

Impact of Gastrointestinal Panel Implementation on Health Care Utilization and Outcomes

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

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

BACKGROUND AND AIMS

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Clinical application of a multiplex genetic pathogen detection system remaps the aetiology of diarrhoeal infections in Shanghai

Background

Culture-based diagnostic methods cannot achieve rapid and precise diagnoses for the identification of multiple diarrhoeal pathogens (DPs). A high-throughput multiplex genetic detection system (HMGS) was adapted and evaluated for the simultaneous identification and differentiation of infectious DPs and a broad analysis of DP infection aetiology.

Results

DP-HMGS was highly sensitive and specific for DP detection compared with culture-based techniques and was similar to singleplex real-time PCR. The uniform level of sensitivity of DP-HMGS for all DPs allowed us to remap the aetiology of acute diarrhoeal infections in Shanghai, correcting incidences of massively underdiagnosed DP species with accuracy approaching that of sequencing-based methods. The most frequent DPs were enteropathogenic Escherichia coli, rotavirus and Campylobacter jejuni. DP-HMGS detected two additional causes of infectious diarrhoea that were previously missed by routine culture-based methods: enterohemorrhagic E. coli and Yersinia enterocolitica. We demonstrated the age dependence of specific DP distributions, especially the distributions of rotavirus, intestinal adenovirus and Clostridium difficile in paediatric patients as well as those of dominant bacterial infections in adults, with a distinct “top 3” pattern for each age group. Finally, the multiplexing capability and high sensitivity of DP-HMGS allowed the detection of infections co-induced by multiple pathogens (approximately 1/3 of the cases), with some DPs preferentially co-occurring as infectious agents.

Conclusions

DP-HMGS has been shown to be a rapid, specific, sensitive and appropriate method for the simultaneous screening/detection of polymicrobial DP infections in faecal specimens. Widespread use of DP-HMGS is likely to advance routine diagnostic and clinical studies on the aetiology of acute diarrhoea.

Electronic supplementary material

The online version of this article (10.1186/s13099-018-0264-7) contains supplementary material, which is available to authorized users.

Detection of common diarrhea-causing pathogens in Northern Taiwan by multiplex polymerase chain reaction

Conventional methods for identifying gastroenteritis pathogens are time consuming, more likely to result in a false-negative, rely on personnel with diagnostic expertise, and are dependent on the specimen status. Alternatively, molecular diagnostic methods permit the rapid, simultaneous detection of multiple pathogens with high sensitivity and specificity. The present study compared conventional methods with the Luminex xTAG Gastrointestinal Pathogen Panel (xTAG GPP) for the diagnosis of infectious gastroenteritis in northern Taiwan. From July 2015 to April 2016, 217 clinical fecal samples were collected from patients with suspected infectious gastroenteritis. All specimens were tested using conventional diagnostic techniques following physicians' orders as well as with the xTAG GPP. The multiplex polymerase chain reaction (PCR) approach detected significantly more positive samples with bacterial, viral, and/or parasitic infections as compared to conventional analysis (55.8% vs 40.1%, respectively; P < .001). Moreover, multiplex PCR could detect Escherichia coli O157, enterotoxigenic E coli, Shiga-like toxin-producing E coli, Cryptosporidium, and Giardia, which were undetectable by conventional methods. Furthermore, 48 pathogens in 23 patients (10.6%) with coinfections were identified only using the multiplex PCR approach. Of which, 82.6% were from pediatric patients. Because the detection rates using multiplex PCR are higher than conventional methods, and some pediatric pathogens could only be detected by multiplex PCR, this approach may be useful in rapidly diagnosing diarrheal disease in children and facilitating treatment initiation. Further studies are necessary to determine if multiplex PCR improves patient outcomes and reduces costs.

Multiplex tests to identify gastrointestinal bacteria, viruses and parasites in people with suspected infectious gastroenteritis: a systematic review and economic analysis

BACKGROUND

Gastroenteritis is a common, transient disorder usually caused by infection and characterised by the acute onset of diarrhoea. Multiplex gastrointestinal pathogen panel (GPP) tests simultaneously identify common bacterial, viral and parasitic pathogens using molecular testing. By providing test results more rapidly than conventional testing methods, GPP tests might positively influence the treatment and management of patients presenting in hospital or in the community.

OBJECTIVE

To systematically review the evidence for GPP tests [xTAG^® (Luminex, Toronto, ON, Canada), FilmArray (BioFire Diagnostics, Salt Lake City, UT, USA) and Faecal Pathogens B (AusDiagnostics, Beaconsfield, NSW, Australia)] and to develop a de novo economic model to compare the cost-effectiveness of GPP tests with conventional testing in England and Wales.

DATA SOURCES

Multiple electronic databases including MEDLINE, EMBASE, Web of Science and the Cochrane Database were searched from inception to January 2016 (with supplementary searches of other online resources).

REVIEW METHODS

Eligible studies included patients with acute diarrhoea; comparing GPP tests with standard microbiology techniques; and patient, management, test accuracy or cost-effectiveness outcomes. Quality assessment of eligible studies used tailored Quality Assessment of Diagnostic Accuracy Studies-2, Consolidated Health Economic Evaluation Reporting Standards and Philips checklists. The meta-analysis included positive and negative agreement estimated for each pathogen. A de novo decision tree model compared patients managed with GPP testing or comparable coverage with patients managed using conventional tests, within the Public Health England pathway. Economic models included hospital and community management of patients with suspected gastroenteritis. The model estimated costs (in 2014/15 prices) and quality-adjusted life-year losses from a NHS and Personal Social Services perspective.

RESULTS

Twenty-three studies informed the review of clinical evidence (17 xTAG, four FilmArray, two xTAG and FilmArray, 0 Faecal Pathogens B). No study provided an adequate reference standard with which to compare the test accuracy of GPP with conventional tests. A meta-analysis (of 10 studies) found considerable heterogeneity; however, GPP testing produces a greater number of pathogen-positive findings than conventional testing. It is unclear whether or not these additional 'positives' are clinically important. The review identified no robust evidence to inform consequent clinical management of patients. There is considerable uncertainty about the cost-effectiveness of GPP panels used to test for suspected infectious gastroenteritis in hospital and community settings. Uncertainties in the model include length of stay, assumptions about false-positive findings and the costs of tests. Although there is potential for cost-effectiveness in both settings, key modelling assumptions need to be verified and model findings remain tentative.

LIMITATIONS

No test-treat trials were retrieved. The economic model reflects one pattern of care, which will vary across the NHS.

CONCLUSIONS

The systematic review and cost-effectiveness model identify uncertainties about the adoption of GPP tests within the NHS. GPP testing will generally correctly identify pathogens identified by conventional testing; however, these tests also generate considerable additional positive results of uncertain clinical importance.

FUTURE WORK

An independent reference standard may not exist to evaluate alternative approaches to testing. A test-treat trial might ascertain whether or not additional GPP 'positives' are clinically important or result in overdiagnoses, whether or not earlier diagnosis leads to earlier discharge in patients and what the health consequences of earlier intervention are. Future work might also consider the public health impact of different testing treatments, as test results form the basis for public health surveillance.

STUDY REGISTRATION

This study is registered as PROSPERO CRD2016033320.

FUNDING

The National Institute for Health Research Health Technology Assessment programme.

Molecular versus culture-based testing for gastrointestinal infection

PURPOSE OF REVIEW

Molecular-based diagnostic methods for the detection of gastrointestinal pathogens are becoming increasingly commonplace in microbiology laboratories. This review aims to summarize recent developments in this field and discuss the clinical application and limitations of implementing these techniques.

RECENT FINDINGS

Recent evaluations of multiplex PCR assays show increased sensitivity whenever compared with standard microbiological culture-based methods. In addition to shorter turnaround times, assays can detect an increased repertoire of pathogens from a single specimen and provide useful information for infection prevention and control practices. There are many limitations, however, associated with their use, including clinical interpretation of results and lack of concordance between different test panels. Newer technologies, such as metagenomic analysis, can provide comprehensive information useful to both patient management and public health surveillance.

SUMMARY

Molecular techniques are capable of replacing culture in the diagnosis of gastrointestinal infections. Whether all positive results, however, represent true infection is still debateable, as is the clinical significance of identifying more than one pathogen. As it currently stands, microbiological culture remains vital for public health surveillance, monitoring antibiotic resistance and managing outbreaks.