Gastrointestinal pathogens detected by multiplex nucleic acid amplification testing in stools of pediatric patients and patients returning from the tropics

Clostridioides difficile Infections in Children: What Is the Optimal Laboratory Diagnostic Method?

The diagnosis of Clostridioides difficile infection (CDI) in the pediatric population is complicated by the high prevalence of asymptomatic colonization, particularly in infants. Many laboratory diagnostic methods are available, but there continues to be controversy over the optimal laboratory testing approach to diagnose CDI in children. We evaluated commonly used C. difficile diagnostic commercial tests in our pediatric hospital population at Sidra Medicine in Doha, Qatar. Between June and December 2023, 374 consecutive stool samples from pediatric patients aged 0-18 years old were tested using: Techlab C. diff Quik Chek Complete, Cepheid GeneXpert C. difficile, QIAstat-Dx Gastrointestinal Panel, and culture using CHROMagar C. difficile. The results of these tests as standalone methods or in four different testing algorithms were compared to a composite reference method on the basis of turnaround time, ease of use, cost, and performance characteristics including specificity, sensitivity, negative predictive value, and positive predictive value. Our study showed variability in test performance of the different available assays in diagnosing CDI. In our population, a testing algorithm starting with Cepheid GeneXpert C. difficile PCR assay or QIAstat-Dx Gastrointestinal panel as a screening test followed by toxin immunoassay for positive samples using the Techlab C. diff Quik Chek Complete kit showed the best performance (100% specificity and 100% positive predictive value) when combined with clinical review of the patient to assess risk factors for CDI, clinical presentation, and alternative causes of diarrhea.

Nucleic acid sample preparation techniques for bead-based suspension arrays

Multiplexing in biological assays allows the simultaneous detection of multiple analytes in a single reaction, which reduces time, labor, and cost as compared to single reaction-based detection methods. Microsphere- or bead-based suspension array technologies, such as the Luminex® xMAP® system, offer high-throughput detection of nucleic acids through a variety of different assay chemistries. Common with most nucleic acid chemistries, for bead-based or other microarray technologies, is the need for efficient extraction and purification of the nucleic acids from the specimen of interest. Often, the optimal method will be dictated by the requirements of the up-front enzymatic chemistry, such as PCR, primer extension, branched DNA (bDNA), etc. For bead-based microarray platforms, the user must also be cognizant of proteins and other contaminants present in reactions that require heat denaturation, as that can lead to bead aggregation or agglutination, preventing the reading of assay results. This review describes and highlights some of the nucleic acid extraction and purification methods that have been used successfully for bead-based nucleic acid analysis, for both prokaryotic and eucaryotic nucleic acids, from a variety of sample types.

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.

Bacterial travellers' diarrhoea: A narrative review of literature published over the past 10 years

Travellers' diarrhoea (TD) is the most frequent illness experienced by international travellers to lower-income countries with bacterial agents considered to account for 80-90% of cases. In this review, we summarise evidence published on bacterial TD over the past 10 years, focusing on the epidemiology and aetiology of TD. Diarrhoeagenic Escherichia coli (DEC) continue to be the most commonly implicated bacteria in TD, although Enteropathogenic E. coli (EPEC) and Enteroaggregative E. coli (EAEC) now appear to be predominant where Enterotoxigenic E. coli (ETEC) was previously considered most prevalent globally. Where fluroquinolone resistance had primarily been documented for Campylobacter in Southeast Asia, widespread resistance has been observed in most regions of the world for multiple enteropathogens, including Shigella, Salmonella, ETEC and EAEC. Implementation of novel molecular methods for pathogen detection has led to identification of bacterial pathogens, including Clostridium difficile (with and without the use of prior antibiotics), Arcobacter species and Bacteroides fragilis, as aetiological agents in TD. The widespread resistance to first-line antibiotics in multiple bacterial enteropathogens warrants continued surveillance and re-evaluation of current treatment practices. Further investigations are required to determine the prevalence and geographical distribution of bacterial enteropathogens that have been more recently implicated in TD.

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.

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

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

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.

Surveillance of enteropathogenic bacteria, protozoa and helminths in travellers returning from the tropics

Diarrhoea is a frequent symptom associated with travelling to tropical regions, but the cause is often not found. Epidemiology was assessed including up-to-date real-time PCR approaches.We analysed datasets of 528 patients who presented at the Bernhard Nocht Institute for Tropical Medicine in Hamburg, Germany, between 2006 and 2010 for screening purposes or because of diarrhoea. Stool samples were obtained and investigated by microscopy, bacterial culture, two PCR assays targeting Entamoeba histolytica, Entamoeba dispar, Giardia duodenalis, and Cryptosporidium parvum, or Salmonella spp., Shigella/EIEC spp., Campylobacter jejuni, and Yersinia spp.Among patients with gastrointestinal symptoms, 51% tested positive for bacteria or parasites, of which 66% had a known enteropathogenic potential. In patients without diarrhoea, 53% (n = 80) were positive, and 33% of these cases harboured agents of pathogenic potential. Association with clinical symptoms was primarily found for bacterial infections. Blastocystis hominis, however, was more frequent in asymptomatic than in symptomatic travellers.In conclusion, the study stresses the etiological relevance of bacterial gastroenteritis in travellers returning from the tropics, the need for molecular approaches to increase diagnostic sensitivity and demonstrates that asymptomatic carriage of enteropathogens after prolonged stays in the tropics is similarly frequent compared with symptomatic infections in travellers.

Traveler's diarrhea in children: New insights and existing gaps

The number of children accompanying their parents in international travel is increasing steadily, and with the rising global migration, children more frequently accompany their parents or caregivers for visiting friends or relatives (VFR). As compared to travel for tourism, VFR children are at higher risk of acquiring local diseases, as they more often stay in rural areas in resource-poor locations, have longer periods of visit, are less likely to attend pre-travel consultations, and less frequently adhere to recommended precautions. Travelers's diarrhea (TD) is the most common travel-associated illnesses in children. This review updates the existing knowledge on TD in children, regarding its distinctive epidemiology, risk factors, preventive measures, clinical manifestations, complications, causative microorganisms and management. Despite the limited focused research on pediatric TD, which challenges the formulation of children-oriented evidence-based guidelines, practical recommendations are suggested.

Identification and Evaluation of Probiotic Potential in Yeast Strains Found in Kefir Drink Samples from Malaysia

Kefir drink is a source of probiotic microorganism with remarkable functional and technological properties. The objective of this work is to isolate yeast strains from Malaysian kefir drink and evaluate them for probiotic potentials. In the present study, nine strains of probiotic yeast were isolated from a Malaysian kefir drink and identified according to their 16S rDNA sequences. Furthermore, their probiotic potential was evaluated. The probiotic properties were tested for aspects of antibiotic susceptibility, antimicrobial activity, and gastrointestinal condition tolerance (pH and temperature). Five isolated strains, M3, Y5, Y9, Y11 and A1, showed good tolerance towards low pH condition while three strains, A1, M1, and M3, showed antimicrobial activity against E. coli, P. aeruginosa, and Salmonella sp. Most isolates were resistant to penicillin, streptomycin, and ampicillin, and grew well at human body temperature. The result of this test indicates that the yeast strains isolated from Malaysian kefir drink have excellent potential for use as probiotics in various products. Lastly, kefir milk is one of the excellent source of probiotic yeast strains and could be used as a new yeast probiotic formulation or in food supplements.

Travelers' diarrhea: update on the incidence, etiology and risk in military and similar populations - 1990-2005 versus 2005-2015, does a decade make a difference?

BACKGROUND

Travelers' diarrhea remains a prevalent illness impacting individuals visiting developing countries, however most studies have focused on this disease in the context of short term travel. This study aims to determine the regional estimates of travelers' diarrhea incidence, pathogen-specific prevalence, and describe the morbidity associated with diarrheal disease among deployed military personnel and similar long term travelers.

METHODS

We updated a prior systematic review to include publications between January 1990 and June 2015. Point estimates and confidence intervals of travelers' diarrhea and pathogen prevalence were combined in a random effects model and assessed for heterogeneity. Eighty-two studies were included in the analysis, including 29 new studies since the prior systematic review.

RESULTS

Military personnel were evaluated in 69% of studies and non-military long term travelers in 34%, with a median duration of travel of 4.9 months, and travel predominantly to the Middle East, Southeast Asia, and Latin America and the Caribbean. Sixty-two percent of tested cases were due to bacterial pathogens, with enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC), and Campylobacter predominating, and significant regional variability. The incidence of TD from studies with longitudinal data was 36.3 cases per 100 person-months, with the highest rates in Southeast Asia, Latin America and the Caribbean, and the Middle East, with higher estimates from those studies using self-reporting of disease. Morbidity remained significant, with 21% being incapacitated or placed sick in quarters (SIQ) by their illness, 15% requiring intravenous fluids, and 3% requiring hospitalization.

CONCLUSIONS

In comparison to results from the prior systematic review, there were no significant differences in incidence, pathogen prevalence, or morbidity; however there was a trend toward improved care-seeking by sick individuals.

Detection of Norovirus by BD MAX™, Xpert® Norovirus, and xTAG® Gastrointestinal Pathogen Panel in stool and vomit samples

BACKGROUND

Norovirus is a leading cause of infectious gastroenteritis, characterized by outbreaks of diarrhoea and vomiting in closed settings. Nucleic acid amplification tests allow rapid and sensitive laboratory diagnosis of norovirus, with a number of commercial platforms now available.

OBJECTIVES

Evaluate the performance of the Becton Dickinson BD-MAX™System, Cepheid Xpert® Norovirus Assay, and Luminex xTAG® Gastrointestinal Pathogen Panel (GPP) for norovirus detection in stool. Assess the performance of the Xpert® Norovirus Assay and BD-MAX™ in vomit samples.

STUDY DESIGN

163 diarrhoeal stool samples were tested on four diagnostic systems (laboratory-defined real time RT-PCR (assigned as gold standard), BD MAX™, Xpert® Norovirus Assay, and xTAG® GPP). A further 70 vomit samples were tested on the Xpert and BD MAX platforms.

RESULTS

In stool, sensitivity and specificity of the BD-MAX™ was 96.8% and 100%, for Xpert® Norovirus Assay was 91.9% and 100%, and for xTAG® GPP was 79.0% and 87.1%. In vomit samples positive and negative percent agreement was 95.6% and 92.0%, between the BD-MAX™ and Xpert® Norovirus.

CONCLUSIONS

The BD-MAX™ System with user defined settings and the Xpert® Norovirus Assay showed acceptable sensitivity and specificity for detection of norovirus from stool and vomit. The xTAG GPP assay was less reliable for norovirus detection but can detect a number of other clinically useful enteropathogens. Clinical laboratories must consider skill mix, budget, and sample throughput to determine the best fit for their service.

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.

Rapid diagnosis of parasitic diseases: current scenario and future needs

BACKGROUND

Parasitic diseases are one of the world's most devastating and prevalent infections, causing millions of morbidities and mortalities annually. In the past, many of these infections have been linked predominantly to tropical or subtropical areas. Nowadays, however, climatic and vector ecology changes, a significant increase in international travel, armed conflicts, and migration of humans and animals have influenced the transmission of some parasitic diseases from 'book pages' to reality in developed countries. It has also been noted that many patients who have never travelled to endemic areas suffer from blood-borne infections caused by protozoa. In the light of existing knowledge, this new trend can be explained by the fact that in the process of migration a large number of asymptomatic carriers become a part of the blood bank donor and transplant donor populations. Accurate and rapid diagnosis represents the crucial weapon in the fight against parasitic infections.

AIMS

To review old and new approaches for rapid diagnosis of parasitic infections.

SOURCES

Data for this review were obtained through searches of PubMed using combinations of the following terms: parasitological diagnostics, microscopy, lateral flow assays, immunochromatographic assays, multiplex-PCR, and transplantation.

CONTENT

In this review, we provide a brief account of the advantages and limitations of rapid methods for diagnosis of parasitic diseases and focus our attention on current and future research in this area. The approximate costs associated with the use of different techniques and their applicability in endemic and non-endemic areas are also discussed.

IMPLICATIONS

Microscopy remains the cornerstone of parasitological diagnostics, especially in the field and low-resource settings, and provides epidemiological assessment of parasite burden. However, increased use and availability of point-of-care tests and molecular assays in modern era allow more rapid and accurate diagnoses and increased sensitivity in the identification of parasitic infections.

Cholera: under diagnosis and differentiation from other diarrhoeal diseases

BACKGROUND

Globally 1.4 billion people are at risk from cholera in countries where the disease is endemic, with an estimated 2.8 million cases annually. The disease is significantly under reported due to economic, social and political disincentives as well as poor laboratory resources and epidemiological surveillance in those regions. In addition, identification of cholera from other diarrhoeal causes is often difficult due to shared pathology and symptoms with few reported cases in travellers from Northern Europe.

METHODS

A search of PubMed and Ovid Medline for publications on cholera diagnosis from 2010 through 2017 was conducted. Search terms included were cholera, Rapid Diagnostic Test (RDT), multiplex PCR and diagnosis of diarrhoea. Studies were included if they are published in English, French or Spanish.

RESULTS

An increase of RDT study publications for diarrhoeal disease and attempted test validations were seen over the publication period. RDTs were noted as having varied selectivity and specificity, as well as associated costs and local resource requirements that can prohibit their use.

CONCLUSIONS

Despite opportunities to employ RDTs with high selectivity and specificity in epidemic areas, or in remote locations without access to health services, such tests are limited to surveillance use. This may represent a missed opportunity to discover the true global presence of Vibrio cholerae and its role in all cause diarrhoeal disease in underdeveloped countries and in travellers to those areas. The wider applicability of RDTs may also represent an opportunity in the wider management of traveller's diarrhoea.

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.

An alternative DNA extraction method for detection of Blastocystis spp. in human fecal samples

Polymerase chain reaction (PCR) is an effective technique for diagnosis of Blastocystis infection. Notably, DNA isolation procedure is extremely critical for the PCR step. In the present study, a recently described extraction procedure, named as the "sand method" was modified and adapted for isolation of Blastocystis DNA. To evaluate its efficacy, the current method and QIAamp DNA Stool Mini Kit (Qiagen) were applied to fresh human stool samples. Our results indicated that, the mean DNA concentrations obtained by the sand method and the commercial kit were 48 and 55 ng/μl, respectively. Also, no DNA inhibitors were detected in two methods. The sand method was capable of detecting 16 parasites per 50 mg feces. DNA samples extracted by both methods were subjected to PCR. Blastocystis spp. were detected in 11 (31.4%) of 35 samples, and perfect agreement (κ: 1.000) was found between the PCR-sand method and PCR-commercial kit method. The samples that were detected positive by PCR-sand method were successfully sequenced, and Blastocystis subtypes (STs) were identified as ST3, ST2 and ST1. In conclusion, the present study indicates that the sand method provides a simple, rapid and inexpensive procedure for reliable extraction of Blastocystis DNA from stool samples.

Advances in the diagnosis and treatment of Clostridium difficile infections

Clostridium difficile is a leading cause of antibiotic-associated diarrhea worldwide. The diagnosis of C. difficile infection (CDI) requires both clinical manifestations and a positive laboratory test for C. difficile and/or its toxins. While antibiotic therapy is the treatment of choice for CDI, there are relatively few classes of effective antibiotics currently available. Therefore, the development of novel antibiotics and/or alternative treatment strategies for CDI has received a great deal of attention in recent years. A number of emerging agents such as cadazolid, surotomycin, ridinilazole, and bezlotoxumab have demonstrated activity against C. difficile; some of these have been approved for limited clinical use and some are in clinical trials. In addition, other approaches such as early and accurate diagnosis of CDI as well as disease prevention are important for clinical management. While the toxigenic culture and the cell cytotoxicity neutralization assay are still recognized as the gold standard for the diagnosis of CDI, new diagnostic approaches such as nucleic acid amplification methods have become available. In this review, we will discuss both current and emerging diagnostic and therapeutic modalities for CDI.

Enterovirus detection in patients with acute gastroenteritis in Switzerland

Acute gastroenteritis (GE) has a major impact on morbidity and mortality worldwide, yet comprehensive data regarding infectious agents including enteroviruses are scarce. We hypothesized that enteroviruses constitute a significant cause of acute GE. We analyzed 677 stool samples from 504 patients, which had been submitted for suspected infectious GE. 0.2 mL of stool suspension was extracted using the Abbott m2000_sp robot and analysed by multiplex nucleic acid testing (NAT) using the Luminex xTAG gastrointestinal pathogen panel (GPP) as well as by specific NATs detecting enteroviruses and polioviruses. Median age of the patients was 6.6 years (IQR 1.1-50.6; pediatric <18 years). 292 of 677 (43%) samples were positive for at least one pathogen. Enterovirus was detected in 5.3% (36/677) as sole pathogen (67%), and more frequently in children (P = 0.0054). Only rotavirus (18.6%) and norovirus (12.1%) were more frequent. Clostridium difficile and Campylobacter jejuni were detected in 5.5% and 2.2% of stools, respectively. Adenovirus, E. coli O157, Salmonella, Shiga toxin-producing E. coli (STEC), Shigella, Giardia lamblia, Cryptosporidium, and Entamoeba histolytica were rare (<1% of samples). Vibrio cholerae, Yersinia enterocolitica, enterotoxigenic E. coli (ETEC) and poliovirus were not detected. Thus, non-polio enteroviruses are the third most frequent pathogen in acute GE suggesting that enteroviruses may play an important role in GE even in developed, industrial health care settings.

Management of Acute Diarrheal Illness During Deployment: A Deployment Health Guideline and Expert Panel Report

BACKGROUND

Acute diarrheal illness during deployment causes significant morbidity and loss of duty days. Effective and timely treatment is needed to reduce individual, unit, and health system performance impacts.

METHODS

This critical appraisal of the literature, as part of the development of expert consensus guidelines, asked several key questions related to self-care and healthcare-seeking behavior, antibiotics for self-treatment of travelers' diarrhea, what antibiotics/regimens should be considered for treatment of acute watery diarrhea and febrile diarrhea and/or dysentery, and when and what laboratory diagnostics should be used to support management of deployment-related travelers' diarrhea. Studies of acute diarrhea management in military and other travelers were assessed for relevance and quality. On the basis of this critical appraisal, guideline recommendations were developed and graded by the Expert Panel using good standards in clinical guideline development methodology.

RESULTS

New definitions for defining the severity of diarrhea during deployment were established. A total of 13 graded recommendations on the topics of prophylaxis, therapy and diagnosis, and follow-up were developed. In addition, four non-graded consensus-based statements were adopted.

CONCLUSIONS

Successful management of acute diarrheal illness during deployment requires action at the provider, population, and commander levels. Strong evidence supports that single-dose antimicrobial therapy is effective in most cases of moderate to severe acute diarrheal illness during deployment. Further studies are needed to address gaps in available knowledge regarding optimal therapies for treatment, prevention, and laboratory testing of acute diarrheal illness.

More Pathogenicity or Just More Pathogens?-On the Interpretation Problem of Multiple Pathogen Detections with Diagnostic Multiplex Assays

Modern molecular diagnostic approaches in the diagnostic microbiological laboratory like real-time quantitative polymerase chain reaction (qPCR) have led to a considerable increase of diagnostic sensitivity. They usually outperform the diagnostic sensitivity of culture-based approaches. Culture-based diagnostics were found to be insufficiently sensitive for the assessment of the composition of biofilms in chronic wounds and poorly standardized for screenings for enteric colonization with multi-drug resistant bacteria. However, the increased sensitivity of qPCR causes interpretative challenges regarding the attribution of etiological relevance to individual pathogen species in case of multiple detections of facultative pathogenic microorganisms in primarily non-sterile sample materials. This is particularly the case in high-endemicity settings, where continuous exposition to respective microorganisms leads to immunological adaptation and semi-resistance while considerable disease would result in case of exposition of a non-adapted population. While biofilms in chronic wounds show higher pathogenic potential in case of multi-species composition, detection of multiple pathogens in respiratory samples is much more difficult to interpret and asymptomatic enteric colonization with facultative pathogenic microorganisms is frequently observed in high endemicity settings. For respiratory samples and stool samples, cycle-threshold-value-based semi-quantitative interpretation of qPCR results has been suggested. Etiological relevance is assumed if cycle-threshold values are low, suggesting high pathogen loads. Although the procedure is challenged by lacking standardization and methodical issues, first evaluations have led to promising results. Future studies should aim at generally acceptable quantitative cut-off values to allow discrimination of asymptomatic colonization from clinically relevant infection.

Rapid diagnosis of gastrointestinal tract infections due to parasites, viruses, and bacteria

Rapid diagnostic techniques are valuable tools in the diagnosis of gastrointestinal infections, especially for the detection of some microorganisms and in certain groups of patients. While antigen detection techniques are widely used in Clinical Microbiology laboratories, for the diagnosis of viruses, some parasites and some bacteria, molecular techniques are routinely used only for some pathogens (such as Clostridium difficile). However, molecular techniques are constantly evolving, and they allow a rapid diagnosis for an increasing number of pathogens, with high sensitivity and specificity. In addition, they are also able to detect virulence factors or resistance mechanisms. Syndromic surveillance systems, which detect different pathogens simultaneously, are very promising because they enable the most frequent pathogens to be diagnosed in a few hours and they can be very useful in certain patients. For the diagnosis of Helicobacter pylori infection, molecular techniques are able to detect bacteria and its resistance to clarithromycin and levofloxacin, allowing the most appropriate treatment to be selected for each patient when bacterial culture is not possible.

Rapid diagnosis of gastrointestinal tract infections due to parasites, viruses, and bacteria

Rapid diagnostic techniques are valuable tools in the diagnosis of gastrointestinal infections, especially for the detection of some microorganisms and in certain groups of patients. While antigen detection techniques are widely used in Clinical Microbiology laboratories, for the diagnosis of viruses, some parasites and some bacteria, molecular techniques are routinely used only for some pathogens (such as Clostridium difficile). However, molecular techniques are constantly evolving, and they allow a rapid diagnosis for an increasing number of pathogens, with high sensitivity and specificity. In addition, they are also able to detect virulence factors or resistance mechanisms. Syndromic surveillance systems, which detect different pathogens simultaneously, are very promising because they enable the most frequent pathogens to be diagnosed in a few hours and they can be very useful in certain patients.

For the diagnosis of Helicobacter pylori infection, molecular techniques are able to detect bacteria and its resistance to clarithromycin and levofloxacin, allowing the most appropriate treatment to be selected for each patient when bacterial culture is not possible.

Guidelines for the prevention and treatment of travelers' diarrhea: a graded expert panel report

BACKGROUND

: Travelers' diarrhea causes significant morbidity including some sequelae, lost travel time and opportunity cost to both travelers and countries receiving travelers. Effective prevention and treatment are needed to reduce these negative impacts.

METHODS

: This critical appraisal of the literature and expert consensus guideline development effort asked several key questions related to antibiotic and non-antibiotic prophylaxis and treatment, utility of available diagnostics, impact of multi-drug resistant (MDR) colonization associated with travel and travelers' diarrhea, and how our understanding of the gastrointestinal microbiome should influence current practice and future research. Studies related to these key clinical areas were assessed for relevance and quality. Based on this critical appraisal, guidelines were developed and voted on using current standards for clinical guideline development methodology.

RESULTS

: New definitions for severity of travelers' diarrhea were developed. A total of 20 graded recommendations on the topics of prophylaxis, diagnosis, therapy and follow-up were developed. In addition, three non-graded consensus-based statements were adopted.

CONCLUSIONS

: Prevention and treatment of travelers' diarrhea requires action at the provider, traveler and research community levels. Strong evidence supports the effectiveness of antimicrobial therapy in most cases of moderate to severe travelers' diarrhea, while either increasing intake of fluids only or loperamide or bismuth subsalicylate may suffice for most cases of mild diarrhea. Further studies are needed to address knowledge gaps regarding optimal therapies, the individual, community and global health risks of MDR acquisition, manipulation of the microbiome in prevention and treatment and the utility of laboratory testing in returning travelers with persistent diarrhea.

Epidemiology of travellers' diarrhea

BACKGROUND

Travellers' diarrhea (TD) continues to be the most frequent health problem in travellers with destinations in lower income parts of the world as compared with where they reside, even if that risk has slightly decreased.

METHODS

A systematic review was published 18 months ago; now PubMed was searched for more recent publications relating to travel, diarrhea, epidemiology, incidence, risk.

RESULTS

A trend to decreasing incidence rates have been noted in this as compared with the last century, but TD remains frequent. The clinical picture varies from a trivial ailment to severe with subsequent hospitalization. Of great concern are long-term sequelae, particularly post-infectious irritable bowel syndrome. The most important risk factors are the destination and duration of exposure among the environmental factors, whereas the age is the most relevant host factor.

CONCLUSIONS

Even if improved hygienic conditions in low-income countries often visited by travellers have resulted in slightly diminished incidence rates of TD, this remains a frequent health problem. Visitors to such destinations must be informed about that health risk and it is beneficial to equip them with instructions and a travel kit to enable them to some extent self-manage TD occurring abroad.

Etiology of travellers' diarrhea

Eleven published studies of the etiology of travellers' diarrhea (TD) were reviewed define the etiology of TD and to exam newly developed technology such as Real-Time multiplex polymerase chain reaction (PCR) to identify multiple pathogens in one assay to define the cause of TD. Using PCR methods bacterial pathogens were found in 72% of patients acquiring diarrhea in Latin America and in 80% in travellers with illness acquired in Southeast Asia). In these studies, enterotoxigenic Escherichia coli as the predominant pathogen (42% in Latin America and 28% in Southeast Asia). Ciprofloxacin-resistant Campylobacter was commonly associated with TD in Southeast Asia. Multiplex PCR has improved the detection of enteropathogens and allowed better assessment returning travellers hospitalized with TD and those with persistent diarrhea.

Current knowledge on the laboratory diagnosis of Clostridium difficile infection

Clostridium difficile (C. difficile) is a spore-forming, toxin-producing, gram-positive anaerobic bacterium that is the principal etiologic agent of antibiotic-associated diarrhea. Infection with C. difficile (CDI) is characterized by diarrhea in clinical syndromes that vary from self-limited to mild or severe. Since its initial recognition as the causative agent of pseudomembranous colitis, C. difficile has spread around the world. CDI is one of the most common healthcare-associated infections and a significant cause of morbidity and mortality among older adult hospitalized patients. Due to extensive antibiotic usage, the number of CDIs has increased. Diagnosis of CDI is often difficult and has a substantial impact on the management of patients with the disease, mainly with regards to antibiotic management. The diagnosis of CDI is primarily based on the clinical signs and symptoms and is only confirmed by laboratory testing. Despite the high burden of CDI and the increasing interest in the disease, episodes of CDI are often misdiagnosed. The reasons for misdiagnosis are the lack of clinical suspicion or the use of inappropriate tests. The proper diagnosis of CDI reduces transmission, prevents inadequate or unnecessary treatments, and assures best antibiotic treatment. We review the options for the laboratory diagnosis of CDI within the settings of the most accepted guidelines for CDI diagnosis, treatment, and prevention of CDI.

xMAP Technology: Applications in Detection of Pathogens

xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays.

Performance of the Verigene® enteric pathogens test, Biofire FilmArray™ gastrointestinal panel and Luminex xTAG® gastrointestinal pathogen panel for detection of common enteric pathogens

BACKGROUND

Multiplex syndromic panels have the capability of identifying causes of diarrheal illness. This study evaluated the performance characteristics of three multiplex molecular assays for the detection of common stool pathogens.

METHODS

A total of 152 stool specimens were tested using three platforms: Verigene Enteric Pathogens Test (Verigene), Biofire FilmArray Gastrointestinal Panel (Biofire) and Luminex xTAG® Gastrointestinal Pathogen Panel (Luminex). Assays were assessed only for the targets common among all three; namely, Campylobacter, Salmonella, Shigella, Shiga toxin-producing E. coli (STEC), norovirus, and rotavirus.

RESULTS

The sensitivities (%) and specificities (%) of the assays were: Campylobacter, Biofire (100,100), Verigene (83.3,99.3), Luminex (91.7,100); Salmonella, Biofire (95.8,100), Verigene (83.3,100), Luminex (79.2,100); Shigella, Biofire (100,100), Verigene (95.4,99.1), Luminex (100,100); STEC, Biofire (100,100), Verigene (91.7,100), Luminex (91.7,100); norovirus, Biofire (94.7,99.3), Verigene (89.0,100), Luminex (89.5,100); and rotavirus, Biofire (100, 98.6), Verigene (71.4,100), Luminex (100,100).

CONCLUSIONS

All multiplex panels detected the majority of gastrointestinal pathogens when compared to conventional methods.

Using Multiplex Molecular Testing to Determine the Etiology of Acute Gastroenteritis in Children

OBJECTIVE

To detect the etiologic agents of acute gastroenteritis (AGE) in children using broad molecular-based techniques, and compare clinical presentations among etiologies.

STUDY DESIGN

This was a prospective population-based surveillance study of children aged <6 years with AGE conducted between 2008 and 2011 as part of the New Vaccine Surveillance Network. Stools from patients and healthy controls were tested for 21 gastrointestinal pathogens using the analyte-specific reagent Gastrointestinal Pathogen Panel and an additional reverse transcription real-time polymerase chain reaction assay for sapovirus and astrovirus.

RESULTS

Of the 216 stool samples from patients with AGE, 152 (70.4%) tested positive for a pathogen, with norovirus genogroup II (n = 78; 36.1%) and Clostridium difficile (n = 35; 16.2%) the most common pathogens detected. Forty-nine patients (22.7%) tested positive for more than 1 pathogen, including 25 (71%) with a C difficile detection. There were no significant clinical differences among the patients with no pathogen detected, those with a single pathogen detected, and those with ≥2 pathogens detected.

CONCLUSION

Using a broad molecular testing approach, high rates of enteropathogens were detected in children with AGE, dominated by norovirus genogroup II and C difficile. Coinfections were common but had no identifiable impact on clinical manifestations. As routine diagnostics of AGE progressively evolve toward nucleic acid-based pathogen detection, ongoing systematic studies are needed to better analyze the clinical significance of results.

Multiplex Molecular Panels for Diagnosis of Gastrointestinal Infection: Performance, Result Interpretation, and Cost-Effectiveness

Gastrointestinal disease is a major cause of morbidity and mortality worldwide, especially among young children and immunocompromised patients. Diarrhea may result from infection with a variety of microbial pathogens, including bacteria, viruses, or parasites. Historically, the diagnosis of infectious diarrhea has been made using microscopy, antigen tests, culture, and real-time PCR. A combination of these traditional tests is often required due to the inability to distinguish between infectious etiologies based on the clinical presentation alone. Recently, several multiplex molecular assays have been developed for the detection of gastrointestinal pathogens directly from clinical stool samples. These panels allow for the detection and identification of up to 20 pathogens in as little as 1 h. This review will focus on the multiplex molecular panels that have received clearance from the FDA for the diagnosis of diarrheal disease and will highlight issues related to test performance, result interpretation, and cost-effectiveness of these new molecular diagnostic tools.

ACG Clinical Guideline: Diagnosis, Treatment, and Prevention of Acute Diarrheal Infections in Adults

Acute diarrheal infections are a common health problem globally and among both individuals in the United States and traveling to developing world countries. Multiple modalities including antibiotic and non-antibiotic therapies have been used to address these common infections. Information on treatment, prevention, diagnostics, and the consequences of acute diarrhea infection has emerged and helps to inform clinical management. In this ACG Clinical Guideline, the authors present an evidence-based approach to diagnosis, prevention, and treatment of acute diarrhea infection in both US-based and travel settings.

Application of a multiplex PCR assay for the detection of gastrointestinal pathogens in a rural African setting

BACKGROUND

Despite high morbidity and mortality, the laboratory diagnosis of gastrointestinal infections is largely neglected in tropical African settings. This study aims to apply the Luminex multiplex PCR assay for the diagnosis of gastrointestinal pathogens in rural Ghana to evaluate its usefulness as a routine method.

METHODS

A case-control study was conducted at the Agogo Presbyterian Hospital in Ghana. Stool samples were collected from children below 6 years of age with (cases) and without (controls) diarrhoea. Samples were screened for 15 different diarrhoeal pathogens by the Luminex xTAG GPP assay and associations between diarrhoea and gastrointestinal infections and fractions attributable to diarrhea (AF) were determined.

RESULTS

The Luminex PCR assay identified organisms in 96.6% (n = 428) of 443 cases and in 92.5% (n = 221) of 239 selected controls. A mean of 2.5 (standard deviation [SD]: ± 1.3) and 2.3 (SD: ± 1.3) organisms per sample were detected in cases and controls respectively. An association with diarrhoea was found for rotavirus (adjusted odds ratio [aOR] = 7.2; 95% confidence interval [CI]: 2.9-18.1), norovirus (aOR = 2.7; 95% CI: 1.4-5.3) and Shigella spp. (aOR = 1.7; 95% CI: 1.2-2.4) with respective AFs of 12.5% (95% CI: 9.6-15.3), 7.9% (95% CI: 3.8-11.7) and 16.9% (95% CI: 6.9-25.9).

CONCLUSION

The high proportion of pathogen-positive stool samples with a high number of co-infections in cases and controls suggests a substantial amount of transient or colonizing microorganisms for which treatment is not necessarily implicated. The use of sequential diagnostic algorithms with pathogen specific or quantitative PCRs might be most appropriate for diagnosing gastrointestinal infections.

Evaluation of the Luminex xTAG®-GPP (Gastrointestinal Pathogen Panel) in the diagnosis of diseases with acute diarrhoea

INTRODUCTION

Most Microbiology laboratories use different techniques for the diagnosis of gastrointestinal infections. Some of which require at least 72 hours to obtain final results.

MATERIAL AND METHODS

The gastrointestinal panel Luminex (xTAG-GPP, Luminex Molecular Diagnostics, Toronto, Canada) is a qualitative multiplex fast and sensitive assay able to detect and to identify the 15 most common pathogens causing gastrointestinal infection simultaneously. We evaluated this multiplex panel comparing it with conventional methods used in our laboratory.

RESULTS

We analyzed 225 samples of feces. Through the conventional methods were positive 74 samples (32.9%). Through the Luminex method were positive 137 samples (60.9%).

CONCLUSIONS

The use of the xTAG^® GPP system in Clinical Microbiology can improve the diagnosis of gastrointestinal infectious because it provides results in less than 8 hours. Some pathogens should be applied with caution and should be interpreted based on the patient́s clinical data.

Diagnostic value of the Vesikari Scoring System for predicting the viral or bacterial pathogens in pediatric gastroenteritis

Purpose

To evaluate the diagnostic value of the Vesikari Scoring System (VSS) as an early predictor of pathogens in children with acute gastroenteritis (AG).

Methods

In this retrospective study, the VSS score, absolute neutrophil count (ANC), and C-reactive protein (CRP) levels were analyzed in 107 hospitalized children with AG, aged 6 months to 17 years. Patients were divided into nonspecific, viral, and bacterial groups according to the pathogens detected using a multiplex polymerase chain reaction (PCR) test.

Results

Patients in the bacterial group had significantly higher CRP values and VSS scores compared to those in the viral group and significantly higher VSS scores compared to those in the nonspecific group (P<0.05). Patients in the viral group had significantly higher VSS scores than those in the nonspecific group (P<0.05). Logistic regression analysis revealed that VSS was the most effective diagnostic tool for predicting the type of pathogen (P<0.05). The area under the receiver operating characteristics curve of VSS was significantly greater than that for ANC and CRP (P<0.05). At a cutoff point of 10 in the VSS, an acceptable diagnostic accuracy could be achieved for distinguishing between bacterial and viral pathogens in AG.

Conclusion

VSS can be considered a useful and reliable infectious marker for pediatric gastroenteritis. VSS may be a good early predictor of the type of pathogen, enabling development of a treatment plan before results from a stool culture or PCR test are available.

Diagnosis of Clostridium difficile Infections in Children

The detection and diagnosis of Clostridium difficile infection in pediatric populations have some unique considerations in comparison to testing in adults. The testing methodologies, including toxigenic culture, cell cytotoxicity, antigen detection, and, more recently, molecular testing, are the same in all age groups. However, limited data exist on the specific performance characteristics in children. In this review, we focus on the challenges of testing in pediatric populations and assess the available data on test performance in these populations. Additionally, a review of the existing guidance for testing is provided.

Tropical and travel-associated norovirus: current concepts

PURPOSE OF REVIEW

We highlight recent advances relevant to understanding norovirus infections in the tropics, both in populations living in developing settings and travelers to these regions.

RECENT FINDINGS

Because of the decrease in diarrheal disease associated with the global rollout of vaccines against rotavirus, norovirus is emerging as the predominant cause of diarrhea morbidity among children in the tropics, and evidence suggests that it contributes to adult disease in endemic populations and travelers. In addition to identifying potential target populations for preventive measures, we provide an update on norovirus vaccine development and concepts related to their implementation in low-income and middle-income countries.

SUMMARY

These current concepts related to norovirus-attributable disease burden, clinical significance, and economic impact can potentially be applied to tailoring efforts to prevent and mitigate the effects of this important enteropathogen.

Norovirus: new developments and implications for travelers' diarrhea

Noroviruses are the leading cause of acute gastroenteritis in the United States and are responsible for at least 50 % of acute gastroenteritis outbreaks occurring worldwide each year. In addition, noroviruses have caused outbreaks on cruise ships, in nursing homes and hospitals, and in deployed military personnel, but its role in the etiology of travelers’ diarrhea is not well defined. The aim of this review is to describe the role of noroviruses in travelers’ diarrhea in terms of epidemiology, current diagnostics, treatment and vaccine development efforts. Studies have shown prevalence rates of noroviruses in travelers’ diarrhea cases ranging from 10–65 %. It is likely that norovirus prevalence rates are highly underestimated in travelers’ diarrhea due to rapid onset, short duration of the illness, limited availability of laboratory facilities, and the fact that most clinical laboratories lack the diagnostic capability to detect noroviruses in stool. Further, additional studies are needed to accurately determine the true prevalence rates of norovirus as an etiologic agent of diarrhea among travelers to different regions around the world. With the rapid progress in the development of a norovirus vaccine, travelers could serve as an ideal population for future norovirus clinical trials.

Evaluation of the xTAG Gastrointestinal Pathogen Panel Assay for the Detection of Enteric Pathogens in Kuwait

OBJECTIVE

To evaluate the utility of the Luminex xTAG gastrointestinal pathogen panel (GPP) assay in the detection of enteric pathogens from diarrheal stool samples in Kuwait.

MATERIALS AND METHODS

The Luminex xTAG GPP assay was used according to the manufacturer's instructions to evaluate single diarrheal stool samples from 109 hospitalized patients at Mubarak Al-Kabeer Hospital, Kuwait, from March 2014 to June 2015. The assay procedure involved nucleic acid extraction from stool samples, amplification of the target by reverse transcriptase polymerase chain reaction, hybridization of the amplified target by probe, detection of the target by the Luminex instrument and computerized data analysis. Conventional microbiological assays were used as the gold standard for comparison.

RESULTS

From the 109 diarrheal stool samples, 20 (18.4%) pathogens were detected by the xTAG GPP assay compared to 10 (9.2%) pathogens using conventional assays. Both methods detected 3 Salmonella spp., 3 Clostridium difficile, 2 rotavirus and 2 norovirus. In addition, the xTAG GPP assay detected 1 Shigella sp., 6 Campylobacter spp., 1 Cryptosporidium sp. and 2 Giardia lamblia which were missed by conventional assays.

CONCLUSIONS

In this study, xTAG GPP detected twice as many pathogens as the conventional assays. We recommend the introduction of this assay in routine diagnostic laboratories for a rapid and better diagnosis and treatment of diarrheal disease.

Molecular genotyping and sub-genotyping of Cryptosporidium spp. isolates from symptomatic individuals attending two major public hospitals in Madrid, Spain

Infections by members of the protozoan genus Cryptosporidium are among the most common causes of human gastrointestinal illness worldwide. In Spain cryptosporidiosis is not a compulsory notifiable disease, so the actual burden of the infection in both clinical and general populations remains largely unknown. We present here data on the diversity and frequency of the Cryptosporidium species and sub-genotypes identified in symptomatic individuals seeking medical care in two major hospitals in Madrid, Spain, between December 2013 and January 2015. Initial detection of the parasite was conducted on a total of 122 stool samples collected from 120 patients by microscopy with modified Ziehl-Neelsen and/or immunochromatographic tests. We used immunofluorescence, PCR-based methods and sequence analyses of the 60-kDa (GP60) glycoprotein and the small subunit ribosomal RNA (SSU rRNA) genes for confirmatory purposes and to characterize Cryptosporidium isolates. A total of 110 patients were confirmed with cryptosporidiosis. Overall, 101 isolates were successfully sub-genotyped at the GP60 locus, and an additional seven at the SSU rRNA locus. The analyses of all amplicons defined 10 distinct sequence types representing the GP60 family sub-genotypes IbA10G2 (78.7%), IeA11G3T3 (3.7%) of C. hominis, and the GP60 family sub-types IIaA15G2R1 (5.6%), IIaA18G6R1 (0.9%), IIcA5G3a (0.9%), IIdA18G1 (0.9%), IIdA19G1 (0.9%), IIdA21G1 (0.9%), and IIdA22G1 (0.9%) of C. parvum. A single isolate was assigned to C. felis (0.9%), two C. parvum isolates (1.9%) could not be characterized at the sub-genotype level and an additional four isolates (3.7%) were not typable. These results strongly suggest that transmission of cryptosporidiosis is mostly anthroponotic in origin in the clinical sample under study. We expect that our molecular epidemiological data will make a significant contribution to unravel the actual epidemiological situation of cryptosporidiosis in Spain, providing health care and policy makers with solid baseline information to unavoidably improve the national surveillance system and allocate additional resources to research, diagnosis, and treatment of cryptosporidiosis.

A controlled, before-and-after trial of an urban sanitation intervention to reduce enteric infections in children: research protocol for the Maputo Sanitation (MapSan) study, Mozambique

INTRODUCTION

Access to safe sanitation in low-income, informal settlements of Sub-Saharan Africa has not significantly improved since 1990. The combination of a high faecal-related disease burden and inadequate infrastructure suggests that investment in expanding sanitation access in densely populated urban slums can yield important public health gains. No rigorous, controlled intervention studies have evaluated the health effects of decentralised (non-sewerage) sanitation in an informal urban setting, despite the role that such technologies will likely play in scaling up access.

METHODS AND ANALYSIS

We have designed a controlled, before-and-after (CBA) trial to estimate the health impacts of an urban sanitation intervention in informal neighbourhoods of Maputo, Mozambique, including an assessment of whether exposures and health outcomes vary by localised population density. The intervention consists of private pour-flush latrines (to septic tank) shared by multiple households in compounds or household clusters. We will measure objective health outcomes in approximately 760 children (380 children with household access to interventions, 380 matched controls using existing shared private latrines in poor sanitary conditions), at 2 time points: immediately before the intervention and at follow-up after 12 months. The primary outcome is combined prevalence of selected enteric infections among children under 5 years of age. Secondary outcome measures include soil-transmitted helminth (STH) reinfection in children following baseline deworming and prevalence of reported diarrhoeal disease. We will use exposure assessment, faecal source tracking, and microbial transmission modelling to examine whether and how routes of exposure for diarrhoeagenic pathogens and STHs change following introduction of effective sanitation.

ETHICS

Study protocols have been reviewed and approved by human subjects review boards at the London School of Hygiene and Tropical Medicine, the Georgia Institute of Technology, the University of North Carolina at Chapel Hill, and the Ministry of Health, Republic of Mozambique.

TRIAL REGISTRATION NUMBER

NCT02362932.

Multiplex polymerase chain reaction tests for detection of pathogens associated with gastroenteritis

A wide range of enteric pathogens can cause infectious gastroenteritis. Conventional diagnostic algorithms are time-consuming and often lack sensitivity and specificity. Advances in molecular technology have provided new clinical diagnostic tools. Multiplex polymerase chain reaction (PCR)-based testing has been used in gastroenterology diagnostics in recent years. This article presents a review of recent laboratory-developed multiplex PCR tests and current commercial multiplex gastrointestinal pathogen tests. It focuses on two commercial syndromic multiplex tests: Luminex xTAG Gastrointestinal Pathogen Panel and BioFire FilmArray gastrointestinal test. Multiplex PCR tests have shown superior sensitivity to conventional methods for detection of most pathogens.