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

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

Background

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

Methods

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

Results

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

Conclusions

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

[The new guideline for gastrointestinal infections]

Gastrointestinal infections are still responsible for around 60% of the infectious diseases that must be reported in Germany and are probably among the most common gastroenterological diseases. The main therapy for gastrointestinal infections remains oral fluid replacement. The recommendations for Clostridioides difficile infections (CDI) have been adapted according to the current data and based on international guidelines; vancomycin or, especially if there is an increased risk of recurrence, fidaxomicin should now be used primarily in CDI. In the case of febrile diarrhea and/or bloody diarrhea, malaria diagnosis should be carried out immediately.

The Performance of Different Parametric Ultrasounds in Prostate Cancer Diagnosis: Correlation with Radical Prostatectomy Specimens

BACKGROUND

Prostate cancer is a prevalent cancer among men. Multiparametric ultrasound [mpUS] is a diagnostic instrument that uses various types of ultrasounds to diagnose it. This systematic review aims to evaluate the performance of different parametric ultrasounds in diagnosing prostate cancer by associating with radical prostatectomy specimens.

METHODOLOGY

A review was performed on various ultrasound parameters using five databases. Systematic review tools were utilized to eliminate duplicates and identify relevant results. Reviewers used the Quality Assessment of Diagnostic Accuracy Results [QUADAS-2] to evaluate the bias and applicability of the study outcomes.

RESULT

Between 2012 and 2023, eleven studies were conducted to evaluate the performance of the different ultrasound parametric procedures in detecting prostate cancer using grayscale TRUS, SWE, CEUS, and mpUS. The high sensitivity of these procedures was found at 55%, 88.6%, 81%, and 74%, respectively. The specificity of these procedures was found to be 93.4%, 97%, 88%, and 59%, respectively. This high sensitivity and specificity may be associated with the large lesion size. The studies revealed that the sensitivity of these procedures in diagnosing clinically significant prostate cancer was 55%, 73%, 70%, and 74%, respectively, while the specificity was 61%, 78.2%, 62%, and 59%, respectively.

CONCLUSIONS

The mpUS procedure provides high sensitivity and specificity in PCa detection, especially for clinically significant prostate cancer.

A multicenter evaluation of the QIAstat-Dx meningitis-encephalitis syndromic test kit as compared to the conventional diagnostic microbiology workflow

PURPOSE

Rapid diagnosis and treatment of infectious meningitis and encephalitis (ME) is critical to minimize morbidity and mortality. Recently, Qiagen introduced the CE-IVD QIAstat-Dx ME panel (QS-ME) for syndromic diagnostic testing of meningitis and encephalitis. Some data on the performance of the QS-ME in comparison to the BioFire FilmArray ME panel are available. In this study, the performance of the QS-ME is compared to the current diagnostic workflow in two academic medical centers in the Netherlands.

METHODS

A total of 110 cerebrospinal fluid samples were retrospectively tested with the QS-ME. The results obtained were compared to the results of laboratory-developed real-time PCR assays (LDTs), IS-pro, bacterial culture, and cryptococcal antigen (CrAg) testing. In addition, the accuracy of the QS-ME was also investigated using an external quality assessment (EQA) panel consisting of ten samples.

RESULTS

Four of the 110 samples tested failed to produce a valid QS-ME result. In the remaining 106 samples, the QS-ME detected 53/53 viral targets, 38/40 bacterial targets, and 7/13 Cryptococcus neoformans targets. The discrepant bacterial results consisted of two samples that were previously tested positive for Listeria monocytogenes (CT 35.8) and Streptococcus pneumoniae (CT 40), respectively. The QS-ME detected one additional result, consisting of a varicella-zoster virus signal (CT 35.9), in a sample in which both techniques detected Streptococcus pyogenes. Finally, 100% concordance was achieved in testing a blinded bacterial ME EQA panel.

CONCLUSION

The QS-ME is a relevant addition to the syndromic testing landscape to assist in diagnosing infectious ME.

Laboratory Criteria for Exclusion and Readmission of Potentially Infectious Persons in Sensitive Settings in the Age of Culture-Independent Diagnostic Tests: Report of a Multidisciplinary Workgroup

Culture-independent diagnostic tests (CIDTs) are increasingly used for clinical diagnosis of gastrointestinal diseases such as salmonellosis, Shiga toxin-producing E. coli disease, and shigellosis because of their speed, convenience, and generally high-performance characteristics. These tests are also used to screen potentially infectious asymptomatic persons during outbreak investigations in sensitive settings such as childcare, food service, and healthcare. However, only limited performance data are available for CIDTs used on specimens from asymptomatic persons. The Association of Public Health Laboratories (APHL) and Council of State and Territorial Epidemiologists (CSTE) convened a workgroup to examine the available scientific data to inform interim decision-making related to exclusion and readmission criteria for potentially infectious persons in sensitive settings, the risks and benefits of different testing strategies, and to identify knowledge gaps for further research. This is the report on the Workgroup findings.

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.

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.

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

INTRODUCTION

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

METHODS

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

RESULTS

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

DISCUSSION

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

Diagnosis of gastrointestinal infections: comparison between traditional microbiology and a commercial syndromic molecular-based panel

Traditional diagnosis of infectious gastroenteritis is based on culture, microscopy and antigen detection. The development of gastrointestinal syndromic panels based on molecular techniques have allowed rapid and simultaneous identification of multiple pathogens. The objective was to evaluate the implementation of Allplex™ Gastrointestinal Panel Assays (AGPA): Allplex™ GI-Virus, Allplex™ GI-Bacteria (I) and Allplex™ GI-Parasite by comparing with traditional diagnosis. A retrospective comparative study was conducted at Hospital Universitario La Paz, between the first year of implementation of the AGPA (April 1, 2018 to March 31, 2019) and the results obtained during the previous year with traditional methods (April 1, 2017 to March 31, 2018). With the implementation of AGPA we obtained an increase in the detection of rotavirus and adenovirus, being statistically significant for rotavirus ([CI95%:3.60-6.79]; P < 0.05) and an increase in the positivity rates of all the bacteria tested, with the exception of Salmonella spp. ([CI95%:3.60-6.79]; P < 0.05). Comparing the bacteria recovered by culture, we obtained an increase in the case of Shigella spp. cultivation during the AGPA period. Regarding protozoa, we achieved a significant increase in the positivity rates for Cryptosporidium spp. ([CI95%:1.98-3.01] P < 0.05), Giardia intestinalis ([CI95%:3.94-5.25]; P < 0.05) and Blastocystis spp. ([CI95%:9.44-11.36]; P < 0.05). There was an improvement in report turnaround time when comparing molecular diagnosis to bacterial culture and concentration plus microscopy for parasites; but not compared with antigen detection. The molecular diagnosis approach with AGPA were more sensitive and had a faster turnaround time for some targets, and in our setting, enabled an increased diagnostic capacity for viruses and protozoa.

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.

Low postoperative complication rate with high survival rate and good clinical outcome 9 years after autologous chondrocyte transplantation of the knee joint

PURPOSE

To investigate postoperative complications and associated risk factors for failure following autologous chondrocyte transplantation ("ACT") as well as its long-term survival and clinical function. It was hypothesized that ACT is a safe technique for cartilage repair with a low incidence of postoperative complications and rare rates of revision surgery combined with a high long-term survival and good to excellent clinical outcome in long-term-follow-up.

METHODS

All patients undergoing ACT-Cs of the knee joint between 2006 and 2012 at the author's institution were included in this retrospective study. Concomitant procedures had been performed if necessary. Early postoperative complications, revision surgeries, failure and risk factors for those events were evaluated 6 months after the surgery. Long-term clinical outcome was assessed using the Lysholm Score, the Tegner Score, a 10-grade scale for satisfaction and the Visual Analogue Scale (VAS) at a minimum follow-up of 9 years postoperatively. Long-term survival was calculated using revision surgeries, clinical failures and conversion procedures to create a Kaplan-Meier analysis. A subgroup analysis for different defect locations was performed. 139 patients were included in this study (27% female/ 73%male; age 26.7 [21.7; 35.2] years). The median defect size was 4.0 [3.0; 6.0] cm² (40% medial femoral condyle (MFC), 17% lateral femoral condyle (LFC), 36% patella, 19% trochlea). 97 (70%) of the patients had undergone previous surgery and 84 (60%) underwent concomitant procedures.

RESULTS

Postoperatively, 8% of patients had complications (4% bleeding, 2% arthrofibrosis, 2% infection), 7% of patients needed revision surgery. 12% of patients had a prolonged deficit in ROM, that did not require revision surgery. No significant difference in terms of complications was found between the patellofemoral and femorotibial group. Patients demonstrated good patient reported long-term outcomes 9-15 years after the index surgery (Tegner: 4.7 ± 1.8; VAS: 2.4 ± 2.1; Lysholm: 80 ± 14; satisfaction with operation: 7.3 ± 1.9). Survival rates were 88% at 9 years, 85% at 11 years, and 85% at 13 years after the index procedure. Reasons for failure included debridement of ACT (n = 4; 5%), revision ACT (n = 3, 3%), conversion to total knee arthroplasty (n = 3, 3%) and conversion to High tibial osteotomy (HTO) (n = 1; 1%)).

CONCLUSION

The present study indicates ACT as an effective treatment option for femorotibial- as well as patellofemoral cartilage defects with a high long-term survival and low conversion rate as well as good long-term results regarding knee function and satisfaction. Postoperative complications needing revision surgery are rare. Prolongated deficits of range of motion appear frequently up to six months especially in patellofemoral defects, but can often be successfully addressed by intensified physiotherapy without requiring an arthrolysis.

LEVEL OF EVIDENCE

Level III.

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

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

The 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.

Prediction of Gestational Diabetes Mellitus under Cascade and Ensemble Learning Algorithm

Gestational diabetes mellitus (GDM) is one of the risk factors for fetal dysplasia and maternal pregnancy difficulties. Therefore, the prediction of the risk of GDM in advance has become a big demand for millions of families. Therefore, machine learning technology is adopted to study GDM prediction. Firstly, the data is preprocessed, and the mean value is used for outlier processing. After preprocessing of the data, the IV value method is used to screen the features. Of the 83 features in the original sample data, 40 important features are screened out through feature engineering. On this basis, Logistics regression model, Lasso-Logistics, Gradient Boosting Decision Tree (GBDT), Extreme Gradient Boosting (Xgboost), Light Gradient Boosting Machine (Lightgbm), and Gradient Boosting Categorical Features (Catboost) are established, and multiple learners are integrated. Finally, the constructed model is tested on data sets. The accuracy of the proposed model is 80.3%, the accuracy is 74.6%, the recall rate is 79.3%, and the running time is only 2.53 seconds. This means that the proposed model is superior to the previous models in terms of accuracy, precision, recall rate, and F1 value, and the time consumption is also in line with the actual engineering requirements. The proposed scheme provides some ideas for the research of machine learning technology in disease prediction.

Potentially Pathogenic Organisms in Stools and Their Association With Acute Diarrheal Illness in Children Aged <2 Years

BACKGROUND

Acute diarrheal illness (ADI) causes a substantial disease burden in high-income countries. We investigated associations between potentially pathogenic organisms in stools and ADI by polymerase chain reaction (PCR) in Australian children aged <2 years.

METHODS

Children in a community-based birth cohort had gastrointestinal symptoms recorded daily and stool samples collected weekly until their second birthday. Diarrhea was defined as ≥3 liquid or looser than normal stools within a 24-hour period. PCR assays tested for 11 viruses, 5 bacteria, and 4 protozoa. Detections of a new organism or of the same following at least 2 negative tests were linked to ADIs, and incidence rates and estimates of association with ADI were calculated.

RESULTS

One hundred fifty-four children provided 11 111 stool samples during 240 child-years of observation, and 228 ADIs were linked to samples. Overall, 6105 (55%) samples tested positive for a target organism. The incidence rate of 2967 new detections was 11.9 (95% confidence interval 11.4-12.3) per child-year, with 2561 (92%) new detections unrelated to an ADI. The relative risk of an ADI was 1.5-6.4 times greater for new detections of adenovirus, enterovirus, norovirus GII, parechovirus A, wild-type rotavirus, sapovirus GI/II/IV/V, Salmonella, Blastocystis, and Cryptosporidium, compared to when these were absent.

CONCLUSIONS

Wild-type rotavirus, norovirus GII, sapovirus GI/II/IV/V, adenovirus 40/41, and Salmonella were associated with ADI in this age group and setting. However, high levels of asymptomatic shedding of potential pathogens in stools from children may contribute to diagnostic confusion when children present with an episode of ADI.

Acute Viral Gastrointestinal (GI) Infections in the Tropics-A Role for Cartridge-Based Multiplex PCR Panels?

Acute gastroenteritis (AGE) contributes to increased morbidity and mortality worldwide. In particular, children in resource-poor settings suffer from frequent episodes of diarrhea. A variety of pathogens, including bacteria, viruses, fungi, and protozoa, can cause AGE. Common viruses associated with AGE are norovirus, rotavirus, astrovirus, adenovirus, and sapovirus. Due to their similar clinical presentation, AGE pathogens cannot be distinguished on clinical grounds rendering the etiological diagnosis challenging. However, reliable diagnosis is essential for individual and public health reasons, e.g., to limit transmission, for appropriate antibiotic use, prognostic appreciation, and vaccination programs. Therefore, high-quality data derived by accurate diagnostics are important to improve global health. In Western industrialized countries, diagnosis relies on microbiological testing, including culture methods, microscopy, immunochromatography, and single-target molecular methods. Recently, multiplex PCR or syndromic panels have been introduced, which simultaneously analyze for multiple pathogens in a very short time. A further technological advancement is cartridge-based syndromic panels, which allow for near patient/point-of-care testing independently from a laboratory. In resource-poor tropical regions, however, laboratory diagnosis is rarely established, and there are little routine laboratory data on the epidemiology of viral AGE pathogens. Limiting factors for the implementation of syndromic panels are high costs, sophisticated equipment, and the need for trained personnel. In addition, pilot studies have shown a large number of viral (co-)detections among healthy controls, thus further challenging their clinical utilization. Hence, there are little evidence-based data on the impact of multiplex syndromic panels from resource-limited regions. Here, we aim to provide a brief overview of what is known about the use of syndromic panels for virus-associated AGE in tropical regions and to address future challenges.

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

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

Alternative Causes of Infectious Diarrhea in Patients with Negative Tests for Clostridoides Difficile

BACKGROUND

Hospitalized patients with diarrhea who have a negative Clostridoides difficile (C. difficile) test are not routinely evaluated for alternative causes of infectious diarrhea. This study assessed for potential infectious causes of diarrhea in hospitalized patients with an order for repeat C. difficile toxin enzyme immunoassay (tEIA) testing after an initial tEIA test was negative.

METHODS

For patients age ≥18 years who had a second C. difficile tEIA test ordered within 96 h after a negative tEIA test, remnant fecal specimens from the first (negative) tEIA test were evaluated using the BioFire FilmArray Gastrointestinal Panel PCR, C. difficile toxigenic culture, and culture on a blood agar plate (BAP) to identify other potential causes of infectious diarrhea. Growth of organisms on the BAP was also used to assess potential disruptions in the gastrointestinal microbiota.

RESULTS

Among 84 remnant specimens, toxigenic C. difficile was identified in 9 (11%) by culture or PCR, while potential alternative causes of infectious diarrhea, including norovirus, rotavirus, enteropathogenic Escherichia coli, and Salmonella, were identified in 11 specimens (13%) by PCR. For the majority of patients, no infectious cause of diarrhea was identified, but 84% exhibited disrupted gastrointestinal microbiota, which may contribute to diarrhea.

CONCLUSIONS

When a hospitalized patient has a negative C. difficile tEIA test but continues to have diarrhea, alternative infectious and noninfectious causes of diarrhea should be considered. If the patient has clinical signs and symptoms suggestive of infection or risk factors for gastrointestinal infection, laboratory testing for other etiologic agents may be appropriate.

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.

Detection of pathogens in blood or feces of adult horses with enteric disease and association with outcome of colitis

Background

Rates of detecting ≥1 potential enteric pathogens (PEP) or toxins (PEP‐T) in feces, blood, or both of horses ≥6 months of age with enteric disease and impact of multiple detections on outcome of horses with colitis has not been reported.

Objective

To determine detection rates of PEP/PEP‐T in feces, blood, or both of horses with enteric disease and effect of detecting multiple agents on outcome of horses with colitis.

Animals

Thirty‐seven hundred fifty‐three fecal samples submitted to IDEXX Laboratories and 239 fecal and blood samples submitted to Michigan State University's Veterinary Diagnostic Laboratory (MSUVDL).

Methods

Retrospective evaluation of PEP/PEP‐T testing results was performed to determine rates of detection of 1 or more PEP/PEP‐T. Impact of detecting multiple agents on outcome was assessed in 239 horses hospitalized for colitis.

Results

One or more PEP/PEP‐T was detected in 1175/3753 (31.3%) and 145/239 (60.7%) of samples submitted to IDEXX Laboratories and MSUVDL, respectively. In a hospitalized cohort, survival to discharge was lower (76%) in horses with 1 agent, compared to horses with either no (88%) or multiple (89%) agents. There was no difference (P = .78) in days of hospitalization between horses with 0 (1–17), 1 (1–33), and > 1 positive (1–20) result. There was no difference in cost of hospitalization (P = .25) between horses with 0 ($2357, $1110‐15 553), 1 ($2742, $788‐11 005), and >1 positive ($2560, $1091‐10 895) result.

Conclusions and Clinical Importance

Detection rates of PEP/PEP‐T in horses with colitis vary with cohorts and tests performed. Detection of more than 1 PEP or PEP‐T did not affect outcome.

Diagnóstico molecular de parasitosis intestinales

Infections causes by parasites of the gastrointestinal tract are a global public health problem. In industrialised countries, their particular epidemiological (low general prevalence of enteroparasites), economic (high labour costs) and clinical characteristics (constant increase in the number of samples and diagnostic determinations to be performed) have led molecular techniques to progressively replace conventional microscopy as the first-line diagnostic method of these pathogens in modern clinical laboratories. PCR-based techniques, particularly those developed for the simultaneous detection of the various agents that can cause the same infectious disease (syndromic diagnosis), already represent a cost-effective option that allow process automisation, workflow optimisation, and comparison of results among different laboratories, and facilitate accreditation of diagnostic procedures. This review clearly and concisely discusses the current situation of the molecular diagnosis of the main species of intestinal parasites in humans, particularly the enteric protozoans causing diarrhoea (Cryptosporidium spp., Giardia duodenalis, Entamoeba histolytica), the most important members the Microsporidia phyla (Enterocytozoon bieneusi) and Stramenopiles phyla (Blastocystis sp.), as well as the helminths transmitted by soil (Ancylostoma spp., Ascaris lumbricoides, Necator americanus, Strongyloides stercoralis and Trichuris trichiura) and food (Anisakis spp., Clonorchis sinensis, Fasciola spp., Taenia solium, and Trichinella spiralis). Special attention is paid to the description of available techniques and formats, to their diagnostic benefits and the most widely used genetic markers for their detection, both in clinical laboratories and genotyping in referral and research centres.

Clinical Implications of Multiplex Pathogen Panels for the Diagnosis of Acute Viral Gastroenteritis

Acute gastroenteritis remains a significant cause of morbidity and mortality in both high- and low-resource settings. The development of nucleic acid-based testing has demonstrated that viruses are a common, yet often undetected, cause of acute gastroenteritis. The development of multiplex pathogen PCR panels makes it possible to detect these viral pathogens with greater sensitivity and rapidity than with previous methods. At present, there is insufficient evidence to recommend the routine use of these panels for the average patient with acute gastroenteritis. However, there are specific scenarios and patient populations, such as epidemiology/outbreak surveillance, antimicrobial stewardship, and the care of immunocompromised patients, where these tests could be clinically useful today. Further research on the effect of these syndromic panels on provider antibiotic prescribing behavior and patient length of stay will be necessary to know their ultimate role in clinical practice.

The Need for Dedicated Microbiology Leadership in the Clinical Microbiology Laboratory

Clinical microbiology laboratories play a crucial role in patient care using traditional and innovative diagnostics. Challenges faced by laboratories include emerging pathogens, rapidly evolving technologies, health care-acquired infections, antibiotic-resistant organisms, and diverse patient populations. Despite these challenges, many clinical microbiology laboratories in the United States are not directed by doctoral level microbiology-trained individuals with sufficient time dedicated to laboratory leadership. The manuscript highlights the need for medical microbiology laboratory directors with appropriate training and qualifications.

Sapovirus: an emerging cause of childhood diarrhea

PURPOSE OF REVIEW

Sapovirus, a genus in the Caliciviridae family alongside norovirus, is increasingly recognized as an important cause of childhood diarrhea. Some challenges exist in our ability to better understand sapovirus infections, including the inability to grow sapovirus in cell culture, which has hindered diagnosis and studies of immunity. Another challenge is that individuals with sapovirus infection are commonly coinfected with other enteric pathogens, complicating our ability to attribute the diarrhea episode to a single pathogen.

RECENT FINDINGS

Development of molecular methods for sapovirus detection has increased our ability to measure disease prevalence. The prevalence of sapovirus varies between 1 and 17% of diarrhea episodes worldwide, with the highest burden in young children and older adults. Further, epidemiological studies have used novel approaches to account for the presence of coinfections with other enteric pathogens; one multisite cohort study of children under two years of age found that sapovirus had the second-highest attributable incidence among all diarrheal pathogens studied.

SUMMARY

Especially in settings where rotavirus vaccines have been introduced, efforts to reduce the overall burden of childhood diarrhea should focus on the reduction of sapovirus transmission and disease burden.

Crosstalk Between Mesenchymal Stromal Cells and Chondrocytes: The Hidden Therapeutic Potential for Cartilage Regeneration

Cartilage injuries following trauma create a puzzling clinical scenario. The finite reparative potential of articular cartilage is well known, and injuries are associated with an increased risk of osteoarthritis. Cell-based therapies have spotlighted chondrocytes and mesenchymal stromal cells (MSCs) as the functional unit of articular cartilage and the progenitor cells, respectively. The available clinical treatments cannot reproduce the biomechanical properties of articular cartilage and call for continuous investigations into alternative approaches. Co-cultures of chondrocytes and MSCs are an attractive in vitro system to step closer to the in vivo multicellular environment's complexity. Research on the mechanisms of interaction between both cell types will reveal essential cues to understand cartilage regeneration. This review describes the latest discoveries on these interactions, along with advantages and main challenges in vitro and in vivo. The successful clinical translation of in vitro studies requires establishing rigorous standards and clinically relevant research models and an organ-targeting therapeutic strategy.

Diagnostic Accuracy of the Synovial Fluid α-Defensin Lateral Flow Test in Periprosthetic Joint Infection: A Meta-analysis

Objectives

There is a controversy on the diagnostic reliability and accuracy of synovial fluid α‐defensin in periprosthetic joint infection (PJI). We performed this meta‐analysis to evaluate the diagnostic accuracy of the α‐defensin lateral flow test in PJI.

Methods

PubMed, Embase, and the Cochrane library were systematically searched, and articles (up to January 2020) on the diagnosis of hip and knee PJIs using the α‐defensin Synovasure lateral flow test were included. The diagnostic accuracy of the α‐defensin lateral flow test in PJI was evaluated using meta‐analysis. The pooled sensitivity, specificity, accuracy, positive and negative likelihood ratio, diagnostic odds ratio, and post‐test probabilities were calculated.

Results

Seventeen studies including 1443 cases were included. Meta‐analysis showed the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and a diagnostic odds ratio was 0.83 (95% CI 0.77, 0.88), 0.95 (95% CI 0.93, 0.97), 16.86 (95% CI 11.67, 24.37), 0.17 (95% CI 0.13, 0.24) and 85.30 (95% CI 47.76, 152.35), respectively. The area under the hierarchical summary receiver operating characteristic curve was 0.97 (95% CI 0.95, 0.98). Subgroup analysis also confirmed the high efficiency of α‐defensin Synovasure lateral flow test in diagnosing PJIs, irrespective of ethnicity. Fagan's nomogram analysis there was a high positive post‐test probability of 94% and a low negative post‐test probability of 15%.

Conclusions

We indicated that the α‐defensin lateral flow test had a high accuracy for diagnosing PJI. Large‐scale studies are needed to validate its significance in PJI diagnosis.

Accuracy and comparison of two rapid multiplex PCR tests for gastroenteritis pathogens: a systematic review and meta-analysis

Objectives

The primary aim is to provide a summary of evidence for the diagnostic accuracies of multiplex PCR gastrointestinal (GI) panels—BioFire FilmArray and Luminex xTAG on the detection of gastroenteritis pathogens. The secondary aim is to compare the performance of these GI panels head to head.

Methods

A comprehensive search up to 1 December 2019 was conducted on PubMed, Embase, Ovid Medline and Web of Science for studies that used FilmArray or Luminex xTAG Gastrointestinal Pathogen Panel (GPP) for diagnosis of acute gastroenteritis. A summary of diagnostic accuracies for the 16 pathogens were calculated by comparing the GI panels to the current gold standards (conventional standard microbiology techniques such as culture or PCR for bacteria, PCR or enzyme immunoassay (EIA) for viruses, microscopy or EIA for parasite). Hierarchical summary receiver operating characteristic (HSROC) curve analysis, pretest and post-test probabilities were used for estimating the pathogen detection performance.

Results

A total of 11 studies with 7085 stool samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with specificity ≧0.98 and area under the ROC curve (AUROC) ≧0.97 for all the pathogens except for Yersinia enterocolitica (AUROC 0.91). The FilmArray panel demonstrated a higher sensitivity than xTAG GPP for most of the pathogens with the exception of Rotavirus A (xTAG GPP and FilmArray were both 0.93).

Conclusions

This is the first meta-analysis that is a head-to-head comparison examining the performance of the novel multiplex PCR-based tests Luminex xTAG GPP and FilmArray GI panel in detecting each pathogen. Point estimates calculated from eligible studies showed that both GI panels are highly accurate and may provide important diagnostic information for early identification of gastroenteritis. In addition, although FilmArray has higher sensitivity and post-test probability than xTAG GPP for most of the pathogens, how this will translate to a clinical setting remains unclear.

Patient-specific metal implants for focal chondral and osteochondral lesions in the knee; excellent clinical results at 2 years

PURPOSE

Surgical treatment options for the management of focal chondral and osteochondral lesions in the knee include biological solutions and focal metal implants. A treatment gap exists for patients with lesions not suitable for arthroplasty or biologic repair or who have failed prior cartilage repair surgery. This study reports on the early clinical and functional outcomes in patients undergoing treatment with an individualised mini-metal implant for an isolated focal chondral defect in the knee.

METHODS

Open-label, multicentre, non-randomised, non-comparative retrospective observational analysis of prospectively collected clinical data in a consecutive series of 80 patients undergoing knee reconstruction with the Episealer® implant. Knee injury and Osteoarthritis Outcome Score (KOOS) and VAS scores, were recorded preoperatively and at 3 months, 1 year, and 2 years postoperatively.

RESULTS

Seventy-five patients were evaluated at a minimum 24 months following implantation. Two patients had undergone revision (2.5%), 1 declined participation, and 2 had not completed the full data requirements, leaving 75 of the 80 with complete data for analysis. All 5 KOOS domain mean scores were significantly improved at 1 and 2 years (p < 0.001-0.002). Mean preoperative aggregated KOOS4 of 35 (95% CI 33.5-37.5) improved to 57 (95% CI 54.5-60.2) and 59 (95% CI 55.7-61.6) at 12 and 24 months respectively (p < 0.05). Mean VAS score improved from 63 (95% CI 56.0-68.1) preoperatively to 32 (95% CI 24.4-38.3) at 24 months. The improvement exceeded the minimal clinically important difference (MCID) and this improvement was maintained over time. Location of defect and history of previous cartilage repair did not significantly affect the outcome (p > 0.05).

CONCLUSION

The study suggests that at 2 years, Episealer® implants are safe with a low failure rate of 2.5% and result in clinically significant improvement. Individualised mini-metal implants with appropriate accurate guides for implantation appear to have a place in the management of focal femoral chondral and osteochondral defects in the knee.

LEVEL OF EVIDENCE

IV.

Cost Consequences for the NHS of Using a Two-Step Testing Method for the Detection of Clostridium difficile with a Point of Care, Polymerase Chain Reaction Test as the First Step

Clostridium difficile infection (CDI) is a common healthcare-associated infection. Current practice for diagnosing CDI in the Newcastle upon Tyne Hospitals NHS Foundation Trust involves a three-step, laboratory testing strategy using glutamate dehydrogenase (GDH) enzyme immunoassay (EIA), followed by a polymerase chain reaction (PCR) test then a toxin EIA. However, a PCR point of care test (POCT) for the C. difficile tcdB gene for screening suspected CDI cases, may provide a more efficient way of facilitating an equally effective, two-step, testing strategy with a toxin EIA. This study evaluated the cost consequences of changing from the three-step to a two-step testing strategy. A cost-consequences model was developed to compare the costs and consequences of the two strategies. Uncertainties in the model inputs were investigated with one- and two-way sensitivity analysis. The two-step, POCT strategy was estimated to save £283,282 per 1000 hospitalized NHS patients with suspected infectious diarrhea. Sensitivity analysis indicated that the turnaround time for the POCT was the largest driver for cost savings. Providing the POCT has sufficiently high diagnostic accuracy for detecting C. difficile, the two-step, POCT strategy for CDI identification is likely to be cost saving for NHS hospitals with an offsite laboratory.

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.

Stool-Based Pathogen Detection Offers Advantages as an Outcome Measure for Water, Sanitation, and Hygiene Trials

Most health impact trials of water, sanitation, and hygiene use caregiver-reported diarrhea in children as the primary outcome; this measure is known to be subject to considerable bias, especially when used in unblinded trials. Detection of enteric pathogens in stool or fecal waste via multiplex molecular methods may offer advantages over—and is complementary to—caregiver-reported diarrhea because these measures are objective, on the causal pathway from exposures of interest to disease outcomes, and increasingly feasible in high-burden countries.

Infectious disease diagnosed by fine needle aspiration biopsy

INTRODUCTION

Fine needle aspiration biopsies (FNABs) have become increasingly important in the assessment of infectious diseases. We assess the ability of cytopathology to predict the presence of a pathogen and review how often neoplasia occurs concurrently with infection.

MATERIALS AND METHODS

A 3-year retrospective review of FNABs with concurrent culture results was performed at the Zuckerberg San Francisco General Hospital and Trauma Center. Rapid onsite evaluation was performed for all cases by a pathologist. The results of the special and immunohistochemical stains and polymerase chain reaction testing were correlated, when available.

RESULTS

A total of 231 samples from 11 different tissue sites were submitted for microbial culture, of which 49 (21%) were positive for pathogenic organisms. Only 2 false-negative cases by cytology were found in immunosuppressed patients. A total of 38 patients had a diagnosis of neoplasia, with 2 (5%) having concurrent infection. Overall, the sensitivity and specificity of cytology in predicting the presence of infection was 96% (95% confidence interval, 86%-100%) and 42% (95% confidence interval, 34%-50%), respectively. Molecular testing was performed in 11 cases, 2 of which were positive for Mycobacterium tuberculosis complex and had cytologic findings of necrosis. Polymerase chain reaction and other ancillary tests were unable to further characterize 2 cases with acid-fast bacilli.

CONCLUSIONS

Our study has shown that FNABs have high sensitivity in detecting infection and that negative cytology findings will correlate with a negative infectious workup. Although infection in the setting of neoplasia is uncommon, it should be considered if clinical data are available to suggest infection.

Workflow optimization for syndromic diarrhea diagnosis using the molecular Seegene Allplex™ GI-Bacteria(I) assay

Syndromic panel-based molecular testing has been suggested to improve and accelerate microbiological diagnosis. We aimed to analyze workflow improvements when using the multiplex Seegene Allplex™ GI-Bacteria(I) assay as a first-line assay for bacterial diarrhea. Technical assay evaluation was done using spiked stool samples and stored patient samples. After implementation of the assay in the routine clinical workflow, an analysis of 5032 clinical samples analyzed by the Seegene assay and 4173 control samples examined by culture in a similar time period 1 year earlier was performed. Sensitivity of the assay was shown to be between 0.4 and 95.9 genome equivalents/PCR. For 159 positive patient samples with a composite reference of culture and/or a molecular assay, the sensitivity of the assay was 100% for Campylobacter, 92% for Salmonella, 89% for Aeromonas, and 83% for Shigella. Sensitivity for C. difficile toxin B detection was 93.9%. The comparison of clinical samples obtained in two 8-month periods showed increased detection rates for Aeromonas (2.90%vs. 0.34%), Campylobacter spp. (2.25% vs. 1.34%), Shigella spp. (0.42% vs. 0.05%) whereas detection of Salmonella was slightly decreased (0.46% vs. 0.67%) when using the Seegene assay. An analysis of the time-to-result showed that the median dropped from 52.7 to 26.4 h when using the molecular panel testing. The Seegene Allplex™ GI-Bacteria(I) assay allows accelerated, reliable detection of major gastrointestinal bacteria roughly within 1 day. Workload is reduced, specifically in a low-prevalence setting.

Impact of the BioFire FilmArray gastrointestinal panel on patient care and infection control

Objectives

Conventional routine PCR testing for gastrointestinal infections is generally based on pathogen related panels specifically requested by clinicians and can be erroneous and time consuming. The BioFire FilmArray gastrointestinal (GI) panel combines 22 pathogens into a single cartridge-based test on a random-access system, thereby reducing the turnaround time to less than 2 hours. We described the clinical impact of implementing the BioFire FilmArray on patients with gastroenteritis in our hospital.

Methods

Patients attending a Dutch tertiary care center (Radboud University Medical Center), from whom stool samples were obtained, were eligible for inclusion. The clinicians selected one or a combination of different routinely performed PCR panels (bacterial panel, viral panel, clostridium testing, and three parasitic panels) based on clinical history and symptoms. All samples were in parallel tested with the FilmArray. We retrospectively collected patient data regarding infection control and patient management to assess the potential impact of implementing the FilmArray.

Results

In total 182 patients were included. Routine PCR detected one or more pathogens in 52 (28.6%) patients compared to 72 (39.6%) using the FilmArray. Turnaround time (including transport) decreased from median 53 hours for the routine PCR to 16 hours for the FilmArray. Twenty-six patients could have been removed from isolation 29 hours sooner, 3.6 antibiotic days could have been saved and in five patients additional imaging testing (including colonoscopies) could have been prevented.

Conclusion

The theoretical implementation of the BioFire FilmArray GI panel in patients with clinical suspicion of gastroenteritis resulted in a significant better patient management.

Prospective Investigation of an Automated PCR/Nucleic Acid Microarray-Based Platform for Enteric Pathogen Testing

BACKGROUND

The Verigene Enteric Pathogens Test (Luminex Corporation) is a polymerase chain reaction (PCR)/nucleic acid microarray-based assay targeting 8 bacterial and viral pathogens that cause diarrhea.

OBJECTIVE

To compare traditional enteric culture methods with stool testing by Verigene EP (PCR/microarray).

METHODS

Tests were performed using PCR/microarray between February and August 2016. All specimens also underwent culture for Salmonella and Shigella; specimens that tested positive for bacterial pathogen(s) had confirmatory cultures.

RESULTS

Valid results were obtained for 99.3% of the 3795 stool specimens. Among these, 497 (13.2%) specimens tested positive for at least 1 pathogen by PCR/microarray; 45.5% of these tested positive for 1 or more bacterial pathogens. Agreement between positive bacterial PCR/microarray results and culture-based testing was 85.3%. Compared with cultures, PCR/microarray demonstrated 95.2% and 87.5% sensitivity and 99.8% and 99.8% specificity for Salmonella and Shigella, respectively.

CONCLUSIONS

The Verigene EP generated evaluable results for most stool specimens tested and demonstrated good agreement with bacterial cultures.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Use of Decision Modelling in Economic Evaluations of Diagnostic Tests: An Appraisal and Review of Health Technology Assessments in the UK

Diagnostic tests play an important role in the clinical decision-making process by providing information that enables patients to be identified and stratified to the most appropriate treatment and management strategies. Decision analytic modelling facilitates the synthesis of evidence from multiple sources to evaluate the cost effectiveness of diagnostic tests. This study critically reviews the methods used to model the cost effectiveness of diagnostic tests in UK National Institute for Health Research (NIHR) Health Technology Assessment (HTA) reports. UK NIHR HTA reports published between 2009 and 2018 were screened to identify those reporting an economic evaluation of a diagnostic test using decision analytic modelling. Existing decision modelling checklists were identified in the literature and a modified checklist tailored to diagnostic economic evaluations was developed, piloted and used to assess the diagnostic models in HTA reports. Of 728 HTA reports published during the study period, 55 met the inclusion criteria. The majority of models performed well with a clearly defined decision problem and analytical perspective (89% of HTAs met the criterion). The model structure usually reflected the care pathway and progression of the health condition. However, there are areas requiring improvement. These are predominantly systematic identification of treatment effects (20% met), poor selection of comparators (50% met) and assumed independence of tests used in sequence (32% took correlation between sequential tests into consideration). The complexity and constraints of performing decision analysis of diagnostic tests on costs and health outcomes makes it particularly challenging and, as a result, quality issues remain. This review provides a comprehensive assessment of modelling in HTA reports, highlights problems and gives recommendations for future diagnostic modelling practice.

Clinical Utility of Advanced Microbiology Testing Tools

Advanced microbiology technologies are rapidly changing our ability to diagnose infections, improve patient care, and enhance clinical workflow. These tools are increasing the breadth, depth, and speed of diagnostic data generated per patient, and testing is being moved closer to the patient through rapid diagnostic technologies, including point-of-care (POC) technologies.

Advanced microbiology technologies are rapidly changing our ability to diagnose infections, improve patient care, and enhance clinical workflow. These tools are increasing the breadth, depth, and speed of diagnostic data generated per patient, and testing is being moved closer to the patient through rapid diagnostic technologies, including point-of-care (POC) technologies. While select stakeholders have an appreciation of the value/importance of improvements in the microbial diagnostic field, there remains a disconnect between clinicians and some payers and hospital administrators in terms of understanding the potential clinical utility of these novel technologies. Therefore, a key challenge for the clinical microbiology community is to clearly articulate the value proposition of these technologies to encourage payers to cover and hospitals to adopt advanced microbiology tests. Specific guidance on how to define and demonstrate clinical utility would be valuable. Addressing this challenge will require alignment on this topic, not just by microbiologists but also by primary care and emergency room (ER) physicians, infectious disease specialists, pharmacists, hospital administrators, and government entities with an interest in public health. In this article, we discuss how to best conduct clinical studies to demonstrate and communicate clinical utility to payers and to set reasonable expectations for what diagnostic manufacturers should be required to demonstrate to support reimbursement from commercial payers and utilization by hospital systems.

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.

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.

Multiplex Nucleic Acid Amplification Testing to Diagnose Gut Infections: Challenges, Opportunities, and Result Interpretation

Multiplex nucleic acid testing is increasingly used to diagnose childhood gastroenteritis. The advantages of this disruptive technology include rapidity, sensitivity, and ability to detect pathogenic viruses, bacteria, and parasites simultaneously. The drawbacks are its capacity to identify organisms of uncertain clinical significance in North American children, cost, and inability to provide viable bacteria for strain typing by public health authorities. However, this technology will certainly improve our knowledge of the causes of human gut infections. As data emerge, physicians should interpret results cautiously, and, most important, consider the context of the presentation before making clinical decisions based on the readouts.