Comparison of rectal swabs and faeces for real-time PCR detection of enteric agents in Rwandan children with gastroenteritis

Shigella Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): Shigella Surveillance Study

Background

Quantitative polymerase chain reaction (qPCR) targeting ipaH has been proven to be highly efficient in detecting Shigella in clinical samples compared to culture-based methods, which underestimate Shigella burden by 2- to 3-fold. qPCR assays have also been developed for Shigella speciation and serotyping, which is critical for both vaccine development and evaluation.

Methods

The Enterics for Global Health (EFGH) Shigella surveillance study will utilize a customized real-time PCR-based TaqMan Array Card (TAC) interrogating 82 targets, for the detection and differentiation of Shigella spp, Shigella sonnei, Shigella flexneri serotypes, other diarrhea-associated enteropathogens, and antimicrobial resistance (AMR) genes. Total nucleic acid will be extracted from rectal swabs or stool samples, and assayed on TAC. Quantitative analysis will be performed to determine the likely attribution of Shigella and other particular etiologies of diarrhea using the quantification cycle cutoffs derived from previous studies. The qPCR results will be compared to conventional culture, serotyping, and phenotypic susceptibility approaches in EFGH.

Conclusions

TAC enables simultaneous detection of diarrheal etiologies, the principal pathogen subtypes, and AMR genes. The high sensitivity of the assay enables more accurate estimation of Shigella-attributed disease burden, which is critical to informing policy and in the design of future clinical trials.

Asymptomatic norovirus infection during outbreaks in China: A systematic review and meta-analysis

Acute gastroenteritis outbreaks may be caused by the excretion of norovirus (NoV) from asymptomatic individuals. Despite numerous studies involving asymptomatic NoV infection during outbreaks in China, a comprehensive assessment of its role has not been conducted, which is critical for emergency management. Our objective was to assess the prevalence of asymptomatic NoV infection during outbreaks in China. We conducted a comprehensive search of multiple databases, including PubMed, Web of Science, Cochrane Library, China National Knowledge Infrastructure, China Wanfang, and China Weipu, between January 1, 1997 and June 19, 2023. The retrieved articles and their references underwent screening, which utilized polymerase chain reaction-based assays for the detection of NoV in asymptomatic individuals during outbreaks that occurred in China. The primary summary data were the prevalence of asymptomatic NoV infection in outbreaks. We generated pooled estimates of asymptomatic prevalence in the population as a whole and in subgroups by using random-effect models. Of the 97 articles included, the pooled asymptomatic prevalence of NoV among 5117 individuals in outbreaks was 17.6% (95% confidence interval [CI]: 14.1-21.3). The asymptomatic prevalence of NoV GII (17.1%, 95% CI: 12.9-21.5) was similar to that of NoV GI (22.0%, 95% CI: 12.8-32.4). However, the proportion of asymptomatic individuals involved in NoV GII (57.44%) was significantly higher than that of NoV GI (5.12%), and NoV GII (75.26%) was reported much more frequently than NoV GI (14.43%) in the included articles. Meta-regression analysis of 11 possible influencing factors (geographic region, setting, season, sample type, genotype, transmission route, occupation, age, per capita income, study quality, and cases definition) showed that the source of heterogeneity might be related to the outbreak settings, per capita income, and study quality (p = 0.037, 0.058, and 0.026, respectively). Of particular note was the asymptomatic prevalence peaked in preschoolers (27.8%), afterward, it fell into trough in elementary and junior school children (10.5%), before the second peak located in adults (17.8%), and the elderly (25.2%). Prevalent genotypes reported include GII.4, followed by GII.17, GII.2, GII.3, GII.6, and so forth. The estimated asymptomatic prevalence of NoV during outbreaks in China was as high as 17.6%, with NoV GII dominating. In addition, genetic subtypes of NoV in outbreaks should be detected whenever possible. The role of asymptomatic individuals in NoV outbreaks cannot be ignored. This knowledge will help governments develop public health policies and emergency response strategies for outbreaks, assess the burden, and develop vaccines.

Global prevalence of asymptomatic norovirus infection in outbreaks: a systematic review and meta-analysis

BACKGROUND

Although many studies on asymptomatic norovirus infection in outbreaks have been conducted globally, structured data (important for emergency management of outbreaks) on the prevalence of this epidemic are still not available. This study assessed the global prevalence of asymptomatic norovirus infection in outbreaks.

METHODS

We identified publications on asymptomatic infections from norovirus outbreaks by searching the PubMed, Embase, Cochrane Library, Medline, and Web of Science databases and screening references from the articles reviewed. Prevalence of asymptomatic norovirus infection in outbreaks was employed as the primary summary data. The random-effects model of the meta-analysis was fitted to generate estimates of the prevalence in the overall and subgroup populations.

RESULTS

In total, 44 articles with a sample size of 8,115 asymptomatic individuals were included. The estimated pooled prevalence of asymptomatic norovirus infection in outbreaks was 21.8% (95%CI, 17.4-27.3). The asymptomatic prevalence of norovirus GII (20.1%) was similar to that of GI (19.8%); however, the proportion prevalence of asymptomatic individuals involved in the former (33.36%) was significantly higher than that of in the latter (0.92%) and the former (93.18%) was reported much more frequently than the latter (15.91%) in the included articles. These studies had significant heterogeneity (I2 = 92%, τ2 = 0.4021, P < 0.01). However, the source of heterogeneity could not be identified even after subgroup analysis of 10 possible influencing factors (geographical area, outbreak settings, outbreak seasons, sample types, norovirus genotypes, transmission routes, subjects' occupations, subjects' age, per capita national income, and clear case definition). Meta-regression analysis of these 10 factors demonstrated that the geographical area could be partly responsible for this heterogeneity (P = 0.012).

CONCLUSIONS

The overall pooled asymptomatic prevalence of norovirus in outbreaks was high, with genome II dominating. Asymptomatic individuals may play an important role in norovirus outbreaks. This knowledge could help in developing control strategies and public health policies for norovirus outbreaks.

Stool biomarkers as measures of enteric pathogen infection in infants from Addis Ababa informal settlements

Frequent enteric infections in children may be an important cause of growth faltering; however, we do not fully understand the mechanisms by which pathogen infections and the physiological responses to these infections result in poorer growth. Commonly used protein fecal biomarkers (anti-alpha trypsin, neopterin, and myeloperoxidase) provide broad immunological information on an inflammatory response; however, they do not provide information on non-immune processes (e.g., gut integrity) that may be important indicators of chronic end states such as environmental enteric dysfunction (EED). To explore how additional biomarkers will better inform which physiological pathways (both immune and non-immune) are impacted by pathogen exposure we added to the traditional panel of 3 protein fecal biomarkers 4 novel fecal mRNA transcript biomarkers (sucrase isomaltase, caudal homeobox 1, S100A8, and mucin 12) and analyzed stool samples from infants living in informal settlements in Addis Ababa, Ethiopia. To test how this expanded biomarker panel captures distinct pathogen exposure processes we used two different scoring systems. First, we used a theory-based approach to assign each biomarker to specific physiological attributes based on prior understanding of each biomarker. Second, we used data reduction methods to categorize biomarkers and then assign physiological attributes to those categories. We used linear models to examine the association between the derived biomarker scores (based on mRNA and protein levels) and stool pathogen gene counts to determine pathogen specific effects on gut physiology and immune responses. Inflammation scores were positively associated with Shigella and enteropathogenic E.Coli (EPEC) infection, while gut integrity scores were negatively associated with Shigella, EPEC and, shigatoxigenic E.coli (STEC) infection. Our expanded panel of biomarkers hold promise as tools to measure systemic outcomes of enteric pathogen infection. mRNA biomarkers complement established protein biomarkers by providing important cell-specific physiological and immunological consequences of pathogen carriage that can lead to chronic end states such as EED.

High prevalence of small intestine bacteria overgrowth and asymptomatic carriage of enteric pathogens in stunted children in Antananarivo, Madagascar

Environmental Enteric Dysfunction (EED) refers to an incompletely defined syndrome of inflammation, reduced absorptive capacity, and reduced barrier function in the small intestine. It is widespread among children and adults in low- and middle-income countries and is also associated with poor sanitation and certain gut infections possibly resulting in an abnormal gut microbiota, small intestinal bacterial overgrowth (SIBO) and stunting.

We investigated bacterial pathogen exposure in stunted and non-stunted children in Antananarivo, Madagascar by collecting fecal samples from 464 children (96 severely stunted, 104 moderately stunted and 264 non-stunted) and the prevalence of SIBO in 109 duodenal aspirates from stunted children (61 from severely stunted and 48 from moderately stunted children). SIBO assessed by both aerobic and anaerobic plating techniques was very high: 85.3% when selecting a threshold of ≥10⁵ CFU/ml of bacteria in the upper intestinal aspirates. Moreover, 58.7% of the children showed more than 10⁶ bacteria/ml in these aspirates. The most prevalent cultivated genera recovered were Streptococcus, Neisseria, Staphylococcus, Rothia, Haemophilus, Pantoea and Branhamella. Feces screening by qPCR showed a high prevalence of bacterial enteropathogens, especially those categorized as being enteroinvasive or causing mucosal disruption, such as Shigella spp., enterotoxigenic Escherichia coli, enteropathogenic E. coli and enteroaggregative E. coli. These pathogens were detected at a similar rate in stunted children and controls, all showing no sign of severe diarrhea the day of inclusion but both living in a highly contaminated environment (slum-dwelling). Interestingly Shigella spp. was the most prevalent enteropathogen found in this study (83.3%) without overrepresentation in stunted children.

About 2 million children under the age of 5 suffer from stunted growth in Madagascar. Although deficient diet is the major cause of undernutrition, impaired absorption or assimilation caused by Environmental Enteric dysfunction (EED) has been proposed to play an important role in stunting. EED is widespread among children and adults in low- and middle-income countries (LMIC) and is also associated with undernutrition, poor sanitation, certain gut infections resulting in an abnormal gut microbiota and small intestinal bacterial overgrowth (SIBO) although the role of SIBO in EED remains unclear. The current study highlights the presence at high concentrations of bacterial taxa usually found in the oro-pharyngeal sphere in a high number of duodenal fluids of stunted children. This uncommon presence suggests a decompartmentalization of the gastrointestinal tract and a possible pro-inflammatory effect due to the ectopic presence of some of these bacteria in the duodenum.

The study also points to a high prevalence of enteropathogens (especially Shigella spp.) in the feces of both stunted and control children, hence preventing from proposing a direct association with stunting. This suggests that, beside combatting poverty and improving diet, environmental sanitation, quality of water sources, hygiene promotion and health education are key points to mitigate stunting and restore nutritional benefits.

A Pilot Study Investigating the Expression Levels of Pluripotency-Associated Genes in Rectal Swab Samples for Colorectal Polyp and Cancer Diagnosis and Prognosis

Change in gene expression is inevitable in cancer development. With more studies demonstrating the contributions of cancer stem cells (CSCs) in colorectal cancer (CRC) development, this study is aimed at investigating whether rectal swab specimen serves as a tool for detection of dysregulation of CSC or stem cell (SC) markers and at evaluating its potential as a new promising screening method for high-risk patients. Expression levels of 15 pluripotency-associated genes were assessed by quantitative PCR in 53 rectal swab specimens referred for endoscopic screening. Dysregulated genes and joint panels based on such genes were examined for their diagnostic potentials for both polyp and CRC. Out of 15 genes, Oct4, CD26, c-MYC, and CXCR4 showed significantly differential expression among normal, polyp, and CRC patients. A panel of Oct4 and CD26 showed an AUC value of 0.80 (p = 0.003) in identifying CRC patients from polyp/normal subjects, with sensitivity and specificity of 84.6% and 69.2%. A panel of c-MYC and CXCR4 achieved CRC/polyp identification with an AUC value of 0.79 (p = 0.002), with a sensitivity of 82.8% and specificity of 80.0%. The sensitivity for polyp and CRC was 80.0% and 85.7%, respectively. Further analysis showed that higher c-MYC and CXCR4 level was detected in normal subjects who developed polyps after 5-6 years, in comparison with subjects with no lesion developed, and the AUC of the c-MYC and CXCR4 panel increased to 0.88 (p < 0.001), with sensitivity and specificity of 84.4% and 92.3%, respectively, when these patients were included in the polyp group. This study suggests that the Oct4 and CD26 panel is a promising biomarker for distinguishing CRC from normal and polyp patients, whereas the c-MYC and CXCR4 panel may identify polyp and CRC from normal individuals.

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.

Polymicrobial enteric infections in African infants with diarrhoea-results from a longitudinal prospective case-control study

OBJECTIVES

This longitudinal case-control study aimed to determine the frequency of polymicrobial enteric detections in Ghanaian infants with and without diarrhoea.

METHODS

Infants aged 1-12 months with and without diarrhoea attending the outpatient department of a peri-urban Ghanaian hospital were prospectively assessed and stool samples were collected on days 0, 6 and 28 and analysed for 18 enteric pathogens with PCR.

RESULTS

At least one enteric pathogen was detected in 100 of 107 cases with diarrhoea (93%) and in 82 of 97 controls (85%). The number of pathogens was higher in cases than in controls (median three versus two pathogens, p 0.001). The adjusted attributable fraction (AF) for diarrhoea was highest for enterotoxigenic Escherichia coli (7.2%, 95% CI -2.0% to 16.3%), rotavirus (4.1%, 95% CI 0.6%-7.5%), Giardia lamblia (2.3%, 95% CI -0.7 to 5.3%) and astrovirus (2.3%, 95% CI -2.9 to 7.5%). In cases, a higher pathogen number was significantly associated with watery stool consistency (median 3, interquartile range (IQR) 2-5 versus median 2.5, IQR 1-4, p 0.014), stool frequency five or more per day (median 4, IQR 3-5 versus median 3, IQR 2-4, p 0.048) and vomiting (median 4, IQR 3-5 versus median 3, IQR 2-4, p 0.025). During follow-up, 94% (78/83) of cases and 85% (67/79) of controls had acquired at least one new pathogen without developing a new episode of diarrhoea.

CONCLUSION

Enteric pathogens could be identified in the stool of the vast majority of Ghanaian infants, whereby pathogens were very frequently acquired without resulting in new episodes of diarrhoea during follow-up. A higher number of co-occurring pathogens may increase the risk of diarrhoea and disease severity.

Comparison of two commercial and one in-house real-time PCR assays for the diagnosis of bacterial gastroenteritis

Introduction

The aim of the study was a comparative evaluation of in-house real-time PCR and commercial real-time PCR (Fast Track Diagnostics (FTD), ampliCube/Mikrogen) targeting enteropathogenic bacteria from stool in preparation of Regulation (EU) 2017/746 on in vitro diagnostic medical devices.

Methods

Both 241 stool samples from patients and 100 samples from German laboratory control schemes (“Ringversuche”) were used to comparatively assess in-house real-time PCR, the FTD bacterial gastroenteritis kit, and the ampliCube gastrointestinal bacterial panels 1&2 either with the in-house PCRs as gold standard and as a test comparison without gold standard applying latent class analysis. Sensitivity, specificity, intra- and inter-assay variation and Cohen’s kappa were assessed.

Results

In comparison with the gold standard, sensitivity was 75–100% for strongly positive samples, 20–100% for weakly positive samples, and specificity ranged from 96 to 100%. Latent class analysis suggested that sensitivity ranges from 81.2 to 100% and specificity from 58.5 to 100%. Cohen’s kappa varied between moderate and nearly perfect agreement, intra- and inter-assay variation was 1–3 to 1–4 Ct values.

Conclusion

Acceptable agreement and performance characteristics suggested replaceability of the in-house PCR assays by the commercial approaches.

Prevalence and diversity of enteric pathogens among cholera treatment centre patients with acute diarrhea in Uvira, Democratic Republic of Congo

BACKGROUND

Cholera remains a major global health challenge. Uvira, in the Democratic Republic of the Congo (DRC), has had endemic cholera since the 1970's and has been implicated as a possible point of origin for national outbreaks. A previous study among this population, reported a case confirmation rate of 40% by rapid diagnostic test (RDT) among patients at the Uvira Cholera Treatment Centre (CTC). This study considers the prevalence and diversity of 15 enteric pathogens in suspected cholera cases seeking treatment at the Uvira CTC.

METHODS

We used the Luminex xTAG® multiplex PCR to test for 15 enteric pathogens, including toxigenic strains of V. cholerae in rectal swabs preserved on Whatman FTA Elute cards. Results were interpreted on MAGPIX® and analyzed on the xTAG® Data Analysis Software. Prevalence of enteric pathogens were calculated and pathogen diversity was modelled with a Poisson regression.

RESULTS

Among 269 enrolled CTC patients, PCR detected the presence of toxigenic Vibrio cholerae in 38% (103/269) of the patients, which were considered to be cholera cases. These strains were detected as the sole pathogen in 36% (37/103) of these cases. Almost half (45%) of all study participants carried multiple enteric pathogens (two or more). Enterotoxigenic Escherichia coli (36%) and Cryptosporidium (28%) were the other most common pathogens identified amongst all participants. No pathogen was detected in 16.4% of study participants. Mean number of pathogens was highest amongst boys and girls aged 1-15 years and lowest in women aged 16-81 years. Ninety-three percent of toxigenic V. cholerae strains detected by PCR were found in patients having tested positive for V. cholerae O1 by RDT.

CONCLUSIONS

Our study supports previous results from DRC and other cholera endemic areas in sub-Sahara Africa with less than half of CTC admissions positive for cholera by PCR. More research is required to determine the causes of severe acute diarrhea in these low-resource, endemic areas to optimize treatment measures.

TRIAL REGISTRATION

This study is part of the impact evaluation study entitled: "Impact Evaluation of Urban Water Supply Improvements on Cholera and Other Diarrheal Diseases in Uvira, Democratic Republic of Congo" registered on 10 October 2016 at clinicaltrials.gov Identification number: NCT02928341 .

Rectal Swabs as an Alternative Sample Collection Method to Bulk Stool for the Real-Time PCR Detection of Giardia duodenalis

Though bulk stool remains the gold standard specimen type for enteropathogen diagnosis, rectal swabs may offer comparable sensitivity with greater ease of collection for select pathogens. This study sought to evaluate the validity and reproducibility of rectal swabs as a sample collection method for the molecular diagnosis of Giardia duodenalis. Paired rectal swab and bulk stool samples were collected from 86 children ages 0-4 years living in southwest Niger, with duplicate samples collected among a subset of 50 children. Infection was detected using a previously validated real-time PCR diagnostic targeting the small subunit ribosomal RNA gene. Giardia duodenalis was detected in 65.5% (55/84) of bulk stool samples and 44.0% (37/84) of swab samples. The kappa evaluating test agreement was 0.81 (95% CI: 0.54-1.00) among duplicate stool samples (N = 49) and 0.75 (95% CI: 0.47-1.00) among duplicate rectal swabs (N = 48). Diagnostic sensitivity was 93% (95% CI: 84-98) by bulk stool and 63% (95% CI: 49-75) by rectal swabs. When restricting to the lowest three quartiles of bulk stool quantitation cycle values (an indication of relatively high parasite load), sensitivity by rectal swabs increased to 78.0% (95% CI: 64-89, P < 0.0001). These findings suggest that rectal swabs provide less sensitive and reproducible results than bulk stool for the real-time PCR diagnosis of G. duodenalis. However, their fair sensitivity for higher parasite loads suggests that swabs may be a useful tool for detecting higher burden infections when stool collection is excessively expensive or logistically challenging.

Evaluation of the FecalSwab for Stool Specimen Storage and Molecular Detection of Enteropathogens on the BD Max System

The FecalSwab system (Copan Italia, Brescia, Italy) is a convenient alternative to bulk stool for the diagnosis of enteric pathogens. Although the U.S. Food and Drug Administration (FDA) approved for transport and culture of enteric bacterial pathogens, the FecalSwab has not been well assessed for its suitability with molecular platforms. In this study, we evaluated the FecalSwab as a specimen type for the BD Max system using the viral and bacterial enteric panels (BD Diagnostics, Baltimore, MD, USA). A total of 186 unpreserved stool specimens were collected and used to prepare matched bulk stool and FecalSwab samples. Performance was equivalent (P > 0.48) to bulk stool for all targets when 50 μl of FecalSwab specimen was loaded onto the BD Max assays. As stool specimens are often collected off-site from the clinical microbiology laboratory and require transport, we assessed the stability of stool specimens stored for up to 14 days at 4°C, 22°C, or 35°C to account for varying transportation conditions. Molecular detection for the majority of viral targets (excluding astrovirus) was unaffected (change in cycle threshold [ΔC_T ] ≤ 1) by sample storage temperature over the 2-week period; however, detection of enteric bacteria was variable if specimens were not refrigerated (22°C or 35°C). By demonstrating equivalent performance to matched bulk stool and maintaining molecular detection sensitivity when stored at 4°C, we suggest that the FecalSwab is a suitable specimen type for enteropathogen diagnostics on the BD Max system.

Evaluation of Anatomically Designed Flocked Rectal Swabs for Use with the BioFire FilmArray Gastrointestinal Panel for Detection of Enteric Pathogens in Children Admitted to Hospital with Severe Gastroenteritis

Diagnosing diarrheal disease is difficult in part due to challenges in obtaining and transporting a bulk stool specimen, particularly in resource-limited settings. We compared the performance of flocked rectal swabs to that of traditional bulk stool samples for enteric pathogen detection using the BioFire FilmArray gastrointestinal panel in children admitted to four hospitals in Botswana with community onset severe gastroenteritis. Of the 117-matched flocked rectal swab/stool pairs, we found no significant difference in pathogen detection rates between the flocked rectal swab samples and traditional bulk stool sampling methods for any bacterial (168 versus 167, respectively), viral (94 versus 92, respectively), or protozoan (18 versus 18, respectively) targets. The combination of flocked rectal swab samples with FilmArray testing allows for the rapid diagnosis of infectious gastroenteritis, facilitating a test-and-treat approach for infections that are life-threatening in many resource-limited settings. The culture recovery rates for bacterial pathogens utilizing this approach need to be assessed.

New Tools to Test Stool: Managing Travelers' Diarrhea in the Era of Molecular Diagnostics

Travelers' diarrhea affects up to 60% of visitors to tropical and subtropical regions. Although symptoms are generally self-limited, some infections are associated with significant morbidity and occasional mortality. Newer molecular diagnostic techniques allow for highly sensitive, specific, and expeditious testing of a wide range of potential pathogens. Identification of the causative pathogen of travelers' diarrhea allows for targeted therapy and management and a reduction in empiric broad-spectrum coverage.

Pigment Visibility on Rectal Swabs Used To Detect Enteropathogens: a Prospective Cohort Study

Data are lacking regarding the impact of visible pigment on rectal swab diagnostic accuracy. We describe the test characteristics of rectal swabs with and without pigment in children with gastroenteritis. Between December 2014 and September 2017, children (age, <18 years) with ≥3 episodes of vomiting and/or diarrhea in a 24-h period and symptoms for <7 days were enrolled through two pediatric emergency departments and from a province-wide nursing telephone advice line in Alberta, Canada. Specimens were analyzed by employing nucleic acid amplification panels. The primary outcomes were the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the rectal swabs, with stool specimen results being used as the reference standard. An enteropathogen was detected in 76.0% (1,399/1,841) of the paired specimens. A total of 54.4% (1,001/1841) of the swabs had visible pigment. The respective enteropathogen detection characteristics of swabs with and without visible pigment were as follows: 92.2% (95% confidence interval [CI], 90.0%, 94.0%) versus 83.7% (95% CI, 80.5%, 86.4%) for sensitivity, 94.3% (95% CI, 90.5%, 96.6%) versus 91.2% (95% CI, 86.3%, 94.5%) for specificity, 97.9% (95% CI, 96.4%, 98.8%) versus 96.5% (95% CI, 94.5%, 97.8%) for PPV, and 80.9% (95% CI, 76.0%, 85.1%) versus 65.8% (95% CI, 60.0%, 71.1%) for NPV. Processing of swabs without visible pigment would increase the rate of identification of positive swabs from 50.0% (682/1,365) to 88.3% (1,205/1,365). There is a modest decrease in the reliability of a negative test on swabs without evidence of pigment, but the overall yield is significantly greater when they are not excluded from testing. Hence, rectal swabs without visible feces should not be routinely rejected from testing.

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.

Evaluation of rectal swab use for the determination of enteric pathogens: a prospective study of diarrhoea in adults

OBJECTIVES

A stool sample is the sample of choice for microbiological testing of enteric pathogens causing diarrhoea, but a rectal swab can be a more practical alternative. A prospective observational study was performed to evaluate the diagnostic performance of flocked rectal swab specimens using the syndromic molecular approach to determine the aetiology of diarrhoea in adults.

METHODS

We compared the performance of rectal swabs with stool samples as the reference standard in determining viral, bacterial and protozoal pathogens using real-time multiplex PCR as well as standard stool culture. Paired samples of stool and rectal swab specimens were collected from 304 adult patients with diarrhoea, presented at the Department of Infectious Diseases, University Medical Centre Ljubljana, between June 2016 and August 2017.

RESULTS

Overall sensitivity of rectal swab samples in the syndromic molecular approach was 83.2% (95% CI 77.2%-88.1%). Pathogen group-specific analysis of rectal swabs showed sensitivity of 65.6% (95% CI 52.7%-77.1%) for viruses and 57.1% (95% CI 28.9%-82.3%) for parasites. For bacteria, sensitivity was 86.5% (95% CI 79.5%-91.8%) when PCR was performed and 61.4% (95% CI 52.4%-69.9%) when culture for bacteria was performed. Mean threshold cycle (Ct) values for most pathogens were higher in rectal swab specimens than in stool specimens.

CONCLUSIONS

Our results indicate that rectal swabs can be used in the diagnosis of diarrhoea in adults when stool specimens are not available or when rapid aetiological determination is needed. However, rectal swabs should be analysed using a molecular approach. The mean Ct value for most pathogens is higher in rectal swab specimens than in stool specimens.

Comparison of stool collection and storage on Whatman FTA Elute cards versus frozen stool for enteropathogen detection using the TaqMan Array Card PCR assay

The use of Polymerase Chain Reaction (PCR) assays for pathogen detection in travelers' diarrhea (TD) field studies is limited by the on-site processing and storage requirements for fecal specimens. The objectives of this investigation were to i) characterize the pathogen distribution in deployed military personnel with TD using the TaqMan® Array Card PCR (TAC) on frozen stool and diarrheal smears on Whatman FTA Elute cards (FTA cards), and to ii) compare TAC detection of enteropathogen targets using smeared FTA cards and frozen stool, using TAC on frozen stool as the 'reference standard'. Stool samples, obtained from active duty personnel with acute TD enrolled in a field trial, were smeared onto FTA cards and stored at room temperature. A corresponding aliquot of stool was frozen in a cryovial. FTA cards and frozen stool samples were tested at a central lab, using a customized TAC for detection of TD pathogens. 187 paired frozen stool samples and smeared FTA cards were stored for a median of 712 days (IQR 396-750) before testing. Overall detection rates were 78.6% for frozen stool and 73.2% for FTA cards. Diarrheagenic Escherichia coli were the most common bacteria identified. Using the TAC results on frozen stool as the reference, the overall sensitivity and specificity of TAC on FTA cards was 72.9% and 98.0% respectively. TAC on FTA cards demonstrated a decrease in sensitivity with increasing frozen stool quantification cycle (Cq) (90.0% in FTA cards with a corresponding frozen stool Cq < 30, and 72.9% in samples with a corresponding frozen stool Cq < 35). Our findings support the use and further development of FTA cards in combination with a quantitative PCR assay for enteropathogen detection in TD field studies.

Coinfection with Enteric Pathogens in East African Children with Acute Gastroenteritis-Associations and Interpretations

Enteric coinfections among children in low-income countries are very common, but it is not well known if specific pathogen combinations are associated or have clinical importance. In this analysis, feces samples from children in Rwanda and Zanzibar less than 5 years of age, with (N = 994) or without (N = 324) acute diarrhea, were analyzed by real-time polymerase chain reaction targeting a wide range of pathogens. Associations were investigated by comparing co-detection and mono-detection frequencies for all pairwise pathogen combinations. More than one pathogen was detected in 840 samples (65%). A negative association (coinfections being less common than expected from probability) was observed for rotavirus in combination with Shigella, Campylobacter, or norovirus genogroup II, but only in patients, which is statistically expected for agents that independently cause diarrhea. A positive correlation was observed, in both patients and controls, between Ct (threshold cycle) values for certain virulence factor genes in enteropathogenic Escherichia coli (EPEC) (eae and bfpA) and toxin genes in enterotoxigenic E. coli (eltB and estA), allowing estimation of how often these genes were present in the same bacteria. A significant positive association in patients only was observed for Shigella and EPEC-eae, suggesting that this coinfection might interact in a manner that enhances symptoms. Although interaction between pathogens that affect symptoms is rare, this work emphasizes the importance and difference in interpretation of coinfections depending on whether they are positively or negatively associated.

Clinical Relevance of Gastrointestinal Microbiota During Pregnancy: A Primer for Nurses

Emerging evidence about the human microbiome, a collective term for all the microorganisms living in and on the human body, consistently demonstrates the critical influence it has on host physiology and disease risk. The microbiota in the gastrointestinal (GI) tract has the most significant and far-reaching effect on human physiology. The maternal GI microbiota can decrease the risk of adverse pregnancy outcomes by modulating energy extraction, glucose metabolism, vitamin production, and host immunity essential for optimal maternal and neonatal health. Moreover, the maternal GI microbiota is thought to influence colonization of the fetus and neonate that may predispose them to different health trajectories. This article provides a basic understanding about the influence of the structure of the maternal GI microbiota, the fundamental role it plays during pregnancy, and the factors that influence the structure, and subsequently function, of the GI microbiota in the general and pregnant population. While only a small number of studies have examined this topic during pregnancy, the preponderance of the evidence supports the need to clarify baseline structure and function of GI microbiota and its associations with pregnancy outcomes. In addition, the results from the studies conducted in the general population can be extrapolated to pregnancy in many cases. This knowledge is essential for clinicians who need to understand the implications of the microbiota for disease and wellness in order to address the care factors that may adversely influence the GI microbiota during pregnancy.

A Novel Protocol Obviates Endoscope Sampling for Carbapenem-Resistant Enterobacteriaceae: Experience of a Center with a Prior Outbreak

BACKGROUND

Numerous published outbreaks, including one from our institution, have described endoscope-associated transmission of multidrug-resistant organisms (MDROs). Individual centers have adopted their own protocols to address this issue, including endoscope culture and sequestration. Endoscope culturing has drawbacks and may allow residual bacteria, including MDROs, to go undetected after high-level disinfection.

AIM

To report the outcome of our novel protocol, which does not utilize endoscope culturing, to address our outbreak.

METHODS

All patients undergoing procedures with elevator-containing endoscopes were asked to permit performance of a rectal swab. All endoscopes underwent high-level disinfection according to updated manufacturer's guidance. Additionally, ethylene oxide (EtO) sterilization was done in the high-risk settings of (1) positive response to a pre-procedure risk stratification questionnaire, (2) positive or indeterminate CRE polymerase chain reaction (PCR) from rectal swab, (3) refusal to consent for PCR or questionnaire, (4) purulent cholangitis or infected pancreatic fluid collections. Two endoscopes per weekend were sterilized on a rotational basis.

RESULTS

From September 1, 2015 to April 30, 2016, 556 endoscopy sessions were performed using elevator-containing endoscopes. Prompted EtO sterilization was done on 46 (8.3%) instances, 3 from positive/indeterminate PCR tests out of 530 samples (0.6%). No CRE transmission was observed during the study period. Damage or altered performance of endoscopes related to EtO was not observed.

CONCLUSION

In this pilot study, prompted EtO sterilization in high-risk patients has thus far eliminated endoscope-associated MDRO transmission, although no CRE infections were noted throughout the institution during the study period. Further studies and a larger patient sample will be required to validate these findings.

Rectal swab screening assays of public health importance in molecular diagnostics: Sample adequacy control

Rectal swabs are routinely used by public health authorities to screen for multi-drug resistant enteric bacteria including vancomycin-resistant enterococci (VRE) and carbapenem-resistant enterobacteriaceae (CRE). Screening sensitivity can be influenced by the quality of the swabbing, whether performed by the patient (self-swabbing) or a healthcare practitioner. One common exclusion criterion for rectal swabs is absence of "visible soiling" from fecal matter. In our institution, this criterion excludes almost 10% of rectal swabs received in the microbiology laboratory. Furthermore, over 30% of patients in whom rectal swabs are cancelled will not be re-screened within the next 48h, resulting in delays in removing infection prevention measures. We describe two quantitative polymerase chain reaction (qPCR)-based assays, human RNAse P and eubacterial 16S rDNA, which might serve as suitable controls for sampling adequacy. However, lower amounts of amplifiable human DNA make the 16s rDNA assay a better candidate for sample adequacy control.

Enteropathogen detection in children with diarrhoea, or vomiting, or both, comparing rectal flocked swabs with stool specimens: an outpatient cohort study

BACKGROUND

Enteropathogen detection traditionally relies on diarrhoeal stool samples, but these are inconvenient to collect if they are not immediately available, leading to suboptimum return rates of samples and delayed or missed diagnostic opportunities. We sought to compare the enteropathogen yields of rectal swabs and stool specimens in children with diarrhoea or vomiting, or both.

METHODS

The Alberta Provincial Pediatric EnTeric Infection TEam (APPETITE) did a study in three outpatient cohorts in Calgary and Edmonton (AB, Canada)-children enrolled in the Pediatric Emergency Research Canada emergency departments, children receiving routine vaccinations at a Calgary health clinic, and symptomatic children who met criteria for treatment at home. Eligible participants were children younger than 18 years, with at least three episodes of vomiting or diarrhoea in the preceding 24 h and fewer than 7 days of symptoms. After excluding those enrolled within the previous fortnight, unable to follow-up, or having psychiatric illness, neutropenia, or requiring emergent care, we attempted to collect rectal swabs and stool from all participants. Specimens were tested with the multianalyte assay Luminex xTAG Gastrointestinal Pathogen Panel, an in-house five-virus panel and bacterial culture. Primary outcomes were comparative yield (calculated as the proportion of submitted paired specimens only in which at least one pathogen was identified) and overall yield (which calculated the proportion of study participants in whom at least one pathogen was identified in all specimens, where unsubmitted specimens were analysed as negative). We used McNemar's test to do pathogen-specific analyses, and generalised estimating equations (GEE) for the global (ie, any) pathogen analyses, with adjustments made for the presence of diarrhoea, location, and their interactions with specimen type.

FINDINGS

Between Dec 12, 2014, and Aug 31, 2016, we studied 1519 eligible participants, 1147 (76%) of whom provided stool specimens and 1514 (>99%) provided swab specimens. 871 (76%) of 1147 stool specimens and 1024 (68%) of 1514 swabs were positive for any pathogen (p<0·0001). Comparative yield adjusted odds ratios (ORs) for stool specimens relative to swabs were 1·24 (95% CI 1·11-1·38) in children with diarrhoea at presentation and 1·76 (1·47-2·11) in children without diarrhoea. GEE analysis identified an interaction between the presence of diarrhoea and specimen type (p=0·0011) and collection location (p=0·0078). In an overall yield analysis, pathogen yield was 57% (871 of 1519 children) for stool specimens and 67% (1024 of 1519 children) for rectal swabs, with an unadjusted OR of 0·65 (95% CI 0·59-0·72) for stool relative to swab.

INTERPRETATION

Rectal swabs should be done when enteropathogen identification and rapid detection are needed, appropriate molecular diagnostic technology is available, and a stool specimen is not immediately available. In view of their high yield, we urge that the recommendation against the use of rectal swabs as diagnostic specimens be reconsidered.

FUNDING

Alberta Innovates-Health Solutions Team Collaborative Research Innovation Opportunity.

Maternal-Child Microbiome: Specimen Collection, Storage, and Implications for Research and Practice

BACKGROUND

The maternal microbiome is a key contributor to the development and outcomes of pregnancy and the health status of both mother and infant. Significant advances are occurring in the science of the maternal and child microbiome and hold promise in improving outcomes related to pregnancy complications, child development, and chronic health conditions of mother and child.

OBJECTIVES

The purpose of this study was to review site-specific considerations in the collection and storage of maternal and child microbiome samples and its implications for nursing research and practice.

APPROACH

Microbiome sampling protocols were reviewed and synthesized. Precautions across sampling protocols were also noted.

RESULTS

Oral, vaginal, gut, placental, and breast milk are viable sources for sampling the maternal and/or child microbiome. Prior to sampling, special considerations need to be addressed related to various factors including current medications, health status, and hygiene practices. Proper storage of samples will avoid degradation of cellular and DNA structures vital for analysis.

DISCUSSION

Changes in the microbiome throughout the perinatal, postpartum, and childhood periods are dramatic and significant to outcomes of the pregnancy and the long-term health of mother and child. Proper sampling techniques are required to produce reliable results from which evidence-based practice recommendations will be built. Ethical and practical issues surrounding study design and protocol development must also be considered when researching vulnerable groups such as pregnant women and infants. Nurses hold the responsibility to both perform the research and to translate findings from microbiome investigations for clinical use.

Slow Clearance of Norovirus following Infection with Emerging Variants of Genotype GII.4 Strains

The emergence of new norovirus genotype GII.4 strains is associated with widespread norovirus epidemics. Extended periods of viral shedding can contribute to the epidemic potential of norovirus. To describe the duration of viral shedding in infections with novel emerging GII.4 strains versus infections with previously circulating strains, we performed a prospective cohort study of patients hospitalized with norovirus gastroenteritis during separate winter seasons. Rectal swab samples were obtained at the time of inclusion and weekly during follow-ups. The subgenotype strain was determined from capsid sequences. The outcome was defined by the detection of virus for >14 days (slow clearance) or by the detection of negative samples within 14 days (rapid clearance). Two major epidemic GII.4 strains emerged during the study period, GII.4 New Orleans 2009, in 2010, and GII.4 Sydney 2012, in 2012. From these two seasons, sequences were available from 24 cases where the duration of shedding could be determined. The median age of the patients was 83 years and 50% were women. The majority of patients were infected with virus that clustered with the respective season's epidemic strain (n = 19), whereas 5 patients had previously circulating strains (3 were Den Haag 2006b, in 2010, and 2 were New Orleans 2009, in 2012). Among the patients infected with an epidemic strain, the proportion who shed virus for >14 days was significantly higher (16/19 [84%] versus 1/5 [20%], P = 0.01). In summary, a slow clearance of norovirus from stool was more common in infections with novel epidemic GII.4 strains. This suggests that the average duration of shedding may be longer during seasons when new GII.4 strains have emerged.

Tropheryma whipplei associated with diarrhoea in young children

Tropheryma whipplei was detected in preliminary studies in faeces of young children with diarrhoea and also in faeces of asymptomatic persons, not only in Europe but also in Africa. In this study, the link between this bacterium and the presence of acute diarrhoea was evaluated in a large group of children. From December 2009 to January 2013, rectal swabs collected from 3796 children in the emergency departments of university hospitals in Marseille, France, were analysed: 555 children (245 female and 310 male, from 6 days to 6 years old) with acute diarrhoea defined as at least three loose stools per day for <1 week and 3241 children (1444 female and 1797 male, from 22 days to 6 years old) without diarrhoea. Specific quantitative real-time PCR was performed to detect the presence of T. whipplei and of two enteric pathogens Clostridium difficile and Giardia duodenalis. Tropheryma whipplei was significantly more common in children with diarrhoea (22/555, 4%) than without (56/3241, 1.7%; p 0.001). Neither C. difficile nor G. duodenalis showed this association. For C. difficile, 39 of 531 (7.3%) children with diarrhoea were positive versus 184 of 3119 (5.9%) of children without diarrhoea (p 0.25). For G. duodenalis, 2 of 529 (0.37%) children with diarrhoea were positive versus 5 of 3119 (0.16%) children without diarrhoea (p 0.26). Tropheryma whipplei was found more commonly in autumn. Tropheryma whipplei is significantly associated with diarrhoea in children, suggesting that the bacterium may be a cause of acute diarrhoea.

B7-H4 expression in human infiltrating ductal carcinoma‑associated macrophages

B7-H4 is a co‑inhibitory molecule of the B7 family, which is expressed on antigen‑presenting cells (APCs) and is able to limit the T‑cell immune response. Macrophages act as professional APCs and are important for immunoregulation of the tumor microenvironment in breast cancer. In order to identify the association between the presence of B7‑H4 on macrophages and infiltrating ductal carcinoma (IDC), the present study investigated the expression of B7‑H4 on macrophages with different polarizations. The expression levels of B7‑H4 in IDC tissues were determined using immunohistochemistry, and the expression of B7‑H4 on macrophages in the breast IDC microenvironment were determined using western blot analysis and reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR). The expression levels of interleukin (IL)‑6 and IL‑10 were detected in IDC tissues and the supernatants of polarized macrophages using an enzyme‑linked immunosorbent assay and RT‑qPCR. The present study demonstrated that B7‑H4 was overexpressed in IDC tissues and macrophages. In vitro, M1 and M2 macrophages exhibited different expression levels of B7‑H4. IL‑6 and ‑10 exhibited higher expression in the IDC tissues compared with in distal pericarcinomatous tissues. In conclusion, B7‑H4 exhibited overexpression in IDC tissues and cultured macrophage cells. Furthermore, M2 macrophages exhibited higher expression levels of B7‑H4 compared with the M1 subtype. In addition, IL‑6 and ‑10 may be associated with B7‑H4 expression on macrophages of different polarizations in the IDC microenvironment.

A comparison of flocked swabs and traditional swabs, using multiplex real-time PCR for detection of common gastroenteritis pathogens in Botswana

We compared the performance of flocked and matched traditional rectal swabs collected from 236 children admitted with gastroenteritis in Botswana. All samples were tested using real time multiplex-PCR assays for nine enteric pathogens. There was a 20% higher detection of Shigella from flocked swabs, but most other pathogens had similar detection rates.

Optimization of Quantitative PCR Methods for Enteropathogen Detection

Detection and quantification of enteropathogens in stool specimens is useful for diagnosing the cause of diarrhea but is technically challenging. Here we evaluate several important determinants of quantification: specimen collection, nucleic acid extraction, and extraction and amplification efficiency. First, we evaluate the molecular detection and quantification of pathogens in rectal swabs versus stool, using paired flocked rectal swabs and whole stool collected from 129 children hospitalized with diarrhea in Tanzania. Swabs generally yielded a higher quantification cycle (Cq) (average 29.7, standard deviation 3.5 vs. 25.3 ± 2.9 from stool, P<0.001) but were still able to detect 80% of pathogens with a Cq < 30 in stool. Second, a simplified total nucleic acid (TNA) extraction procedure was compared to separate DNA and RNA extractions and showed 92% (318/344) sensitivity and 98% (951/968) specificity, with no difference in Cq value for the positive results (ΔCq(DNA+RNA-TNA) = -0.01 ± 1.17, P = 0.972, N = 318). Third, we devised a quantification scheme that adjusts pathogen quantity to the specimen's extraction and amplification efficiency, and show that this better estimates the quantity of spiked specimens than the raw target Cq. In sum, these methods for enteropathogen quantification, stool sample collection, and nucleic acid extraction will be useful for laboratories studying enteric disease.

Norovirus vaccines: Correlates of protection, challenges and limitations

Norovirus (NoV) is responsible for at least 50% of all gastroenteritis outbreaks worldwide. NoVs are classified into 6 different genogroups (GGI- GGVI) based on the viral capsid protein with NoV genogroup II genotype 4 (GII.4) being the predominant strain causing human diseases. Supportive therapy involving reversal of dehydration and electrolyte deficiency is the main treatment of NoV gastroenteritis. However, the worldwide increased recognition of NoV as an important agent of diarrheal gastroenteritis prompted researchers to focus on establishing preventive strategies conferring long-lasting immunity. This review describes the current status of animal and human vaccine models/studies targeting NoV and addresses the factors hampering the development of a broadly effective vaccine.

Human Norovirus prevalence in Africa: a review of studies from 1990 to 2013

OBJECTIVES

To assess the contribution of Human Norovirus to diarrhoeal diseases in Africa.

METHODS

We conducted a systematic review of the PubMed and EMBASE databases for published articles of Human Norovirus in Africa between 1990 and 2013. Data were extracted from selected studies and analysed.

RESULTS

A total of 208 eligible studies were identified, of which 55 (from 19 countries) met the inclusion criteria. Many cases were of sporadic gastroenteritis (70.9%) in children (82%), 65.4% of which were seen in an outpatient setting. Over half (59.4%) of the affected children were under 5 years of age. The pooled prevalence rate of Human NoV was 11% (95% CI 8-14%), and the meta-analysis indicated significant heterogeneity between the studies. However, the conditional negative binomial regression could not clearly find the factors affecting the Human NoV prevalence rates reported. A close relationship was found between Human Norovirus strains from environmental and clinical samples.

CONCLUSION

Unreported sporadic gastroenteritis cases of Human Norovirus are common in Africa. Most are community-associated infections. Possible environmental transmission routes have been documented. Combined environmental and clinical studies are required for targeted actions to control transmission of Human Norovirus in Africa. Systematic surveillance of Human Norovirus is needed to measure the burden of Norovirus-induced gastroenteritis in Africa and support any requirements for vaccine development.

Norovirus prevention and the prevalence of asymptomatic norovirus infection in kindergartens and primary schools in Changzhou, China: Status of the knowledge, attitudes, behaviors, and requirements

BACKGROUND

We estimated the status of norovirus infection and prevention in kindergartens and primary schools and identified poor areas for which future education is needed. We evaluated the knowledge, attitude, behavior, requirements of outbreak prevention, and rate of asymptomatic carriers.

METHODS

Two self-administered questionnaires were conducted for data collection. Five hundred seventy-four teachers from kindergartens and primary schools and 3,114 students from primary schools in Changzhou city were sampled for questionnaire investigation. In addition, 511 rectal swabs from healthy children were taken for norovirus detection.

RESULTS

Twenty-one of 511 children were asymptomatically infected with norovirus. The rate of asymptomatic norovirus infection children in kindergartens was 2.7% and 4.7% in primary schools. Nineteen of 21 positive samples were GII strains, the other 2 were GI strains. In addition, we found that primary schools were less prepared to prevent norovirus outbreaks than kindergartens. Settings in the suburban counties needed more education on norovirus prevention.

CONCLUSIONS

The results of this study emphasize the need for training of primary schools and suburban schools about norovirus prevention. Asymptomatic norovirus infection should receive more attention.

Low serum levels of CCL5 are associated with longer duration of viral shedding in norovirus infection

BACKGROUND

The mechanisms that determine the duration of fecal shedding of norovirus in humans have not been described in detail.

OBJECTIVES

We investigated serum inflammatory mediator levels in relation to the duration of viral shedding in norovirus infection.

STUDY DESIGN

A prospective cohort study of patients hospitalized with acute norovirus genogroup II infection. Rectal swab samples were obtained at inclusion and day 7, 14, 21 and 28. Serum levels of 42 inflammatory mediators were determined with a Luminex-based cytokine assay. Sera from 20 healthy blood donors served as controls.

RESULTS

Altogether, 28 patients (54% women, median age 83 years, median duration of symptoms 3 days) were included. Twelve subjects cleared the virus within 14 days and 16 were norovirus-RNA positive for >21 days, constituting the two study groups ("rapid" vs. "slow" clearance). Individuals with norovirus infection had higher levels of IL-18, CXCL9, CXCL10, soluble IL-2 receptor and macrophage migration inhibitory factor (MIF), compared to controls (p<0.05), with the highest median concentrations in the slow clearance group. In contrast, CCL5 levels were lower in the slow compared to the rapid clearance group (median 54 vs. 134 ng/mL, p<0.05), and lower in norovirus-infected patients than in controls.

CONCLUSION

Low levels of CCL5 were associated with longer duration of viral shedding, suggesting that CCL5 may influence the clearance of norovirus.

Role of noroviruses as aetiological agents of diarrhoea in developing countries

Diarrhoea is considered to be the second leading cause of death due to infections among children  < 5 years of age worldwide that may be caused by bacteria, parasites, viruses and non-infectious agents. The major causative agents of diarrhoea in developing countries may vary from those in developed countries. Noroviruses are considered to be the most common cause of acute diarrhoea in both children and adults in industrialized countries. On the other hand, there is a lack of comprehensive epidemiological evidence from developing countries that norovirus is a major cause of diarrhoea. In these regions, asymptomatic norovirus infections are very common, and similar detection rates have been observed in patients with diarrhoea and asymptomatic persons. This review summarizes the current knowledge of norovirus infection in developing countries and seeks to position infections with noroviruses among those of other enteropathogens in terms of disease burden in these regions.

Pattern of circulation of norovirus GII strains during natural infection

Norovirus (NoV) is considered a major cause of nonbacterial gastroenteritis among people of all ages worldwide, but the natural course of infection is incompletely known. In this study, the pattern of circulation of NoVs was studied among 146 children and 137 adults in a small community in southwestern Cameroon. The participants provided monthly fecal samples during a year. NoV RNA was detected in at least one sample from 82 (29%) of the participants. The partial VP1 region could be sequenced in 36 NoV GII-positive samples. Three different genotypes were identified (GII.1, GII.4, and GII.17), with each genotype circulating within 2 to 3 months and reappearing after a relapse period of 2 to 3 months. Most infections occurred once, and 2 episodes at most within a year were detected. No difference in the frequency of NoV infection between children and adults was recorded. The same genotype was detected for a maximum of 2 consecutive months in 3 children only, suggesting that a less than 30-day duration of viral shedding in natural infection was common. Reinfection within a year with the same genotype was not observed, consistent with short-term homotypic immune protection. The study revealed that NoV strains are circulating with a limited duration of viral shedding both in the individuals and the population as part of their natural infection. The results also provide evidence of cross-protective immunity of limited duration between genotypes of the same genogroup.

Real-time PCR identification of agents causing diarrhea in Rwandan children less than 5 years of age

BACKGROUND

Knowledge about causes of acute diarrhea among children in developing countries is insufficient. Molecular methods might improve diagnostics of infectious gastroenteritis, but due to the high sensitivity, findings may be difficult to interpret.

METHODS

Feces samples from Rwandan children 0.5-5.0 years of age, with diarrhea for <96 hours (patients, n = 544) or without diarrhea for 14 days (controls, n = 162), were analyzed by real-time polymerase chain reaction targeting 17 pathogens.

RESULTS

At least 1 agent was detected in 94% of patients and in 79% of controls, with higher rates in sick children for rotavirus (42% vs. 2%, P < 0.0001) and enterotoxigenic Escherichia coli (ETEC)-estA (21% vs. 9%, P = 0.0006). Detection rates did not differ significantly for adenovirus (39% vs. 36%), ETEC-eltB (29% vs. 30%), Campylobacter (14% vs. 17%) or Shigella (13% vs. 10%), but for Shigella the threshold cycle (Ct) values were lower (pathogen loads were higher) in sick children than in controls. By multivariate analysis, including gender and age, detection of rotavirus (P < 0.0001), ETEC-estA (P = 0.001), Shigella (P = 0.004) and norovirus genogroup II (P = 0.009) was associated with symptomatic infection, and a Ct value below a cutoff (in the range 28-29) improved identification of ETEC-estA, Shigella and norovirus genogroup II.

CONCLUSION

Real-time polymerase chain reaction can detect essentially all diarrheagenic agents, and provides Ct values that improve identification of clinically relevant infections.

Recent advances in clinical parasitology diagnostics

Microscopy has several limitations in the diagnosis of parasitic infection. New technologies have emerged to address some of these limitations. We review recent advances in three key areas. The detection of enteric protozoa is a commonly requested test, particularly with increasing travel to and migration from endemic countries. Microscopy is slow and labor intensive and requires a high level of technical expertise. It also lacks both sensitivity and specificity. Recently developed nucleic acid amplification tests are automated and rapid and show superior accuracy. Proteomics shows promise for both the diagnosis of infections where parasite detection is difficult and the potential for accurate assessment of cure in these cases. Finally, rapid and simple diagnostic tests suitable for use in low-resource settings are now allowing for improved study and control of infection in endemic regions.

Detection of pathogenic viruses in sewage provided early warnings of hepatitis A virus and norovirus outbreaks

Most persons infected with enterically transmitted viruses shed large amounts of virus in feces for days or weeks, both before and after onset of symptoms. Therefore, viruses causing gastroenteritis may be detected in wastewater, even if only a few persons are infected. In this study, the presence of eight pathogenic viruses (norovirus, astrovirus, rotavirus, adenovirus, Aichi virus, parechovirus, hepatitis A virus [HAV], and hepatitis E virus) was investigated in sewage to explore whether their identification could be used as an early warning of outbreaks. Samples of the untreated sewage were collected in proportion to flow at Ryaverket, Gothenburg, Sweden. Daily samples collected during every second week between January and May 2013 were pooled and analyzed for detection of viruses by concentration through adsorption to milk proteins and PCR. The largest amount of noroviruses was detected in sewage 2 to 3 weeks before most patients were diagnosed with this infection in Gothenburg. The other viruses were detected at lower levels. HAV was detected between weeks 5 and 13, and partial sequencing of the structural VP1protein identified three different strains. Two strains were involved in an ongoing outbreak in Scandinavia and were also identified in samples from patients with acute hepatitis A in Gothenburg during spring of 2013. The third strain was unique and was not detected in any patient sample. The method used may thus be a tool to detect incipient outbreaks of these viruses and provide early warning before the causative pathogens have been recognized in health care.

Evaluation of anatomically designed flocked rectal swabs for molecular detection of enteric pathogens in children admitted to hospital with severe gastroenteritis in Botswana

Two-hundred eighty matched bulk stool and anatomically designed flocked rectal swab samples were collected from children admitted to the hospital with acute diarrhea in Botswana. Their parents were asked about the acceptability of the swab collection method compared with bulk stool sampling. All samples underwent identical testing with a validated 15-target (9 bacterial, 3 viral, and 3 parasite) commercial multiplex PCR assay. The flocked swabs had a 12% higher yield for bacterial pathogen targets (241 versus 212; P = 0.003) compared with that of stool samples, as well as similar yields for viral targets (110 versus 113; P = 0.701) and parasite targets (59 versus 65; P = 0.345). One hundred sixty-four of the flocked swab-stool pairs were also tested with separate laboratory-developed bacterial and viral multiplex assays, and the flocked rectal swabs had a performance that was similar to that seen with commercial assay testing. Almost all parents/guardians found the swabs acceptable. Flocked rectal swabs significantly facilitate the molecular diagnosis of diarrheal disease in children.

Diarrhoeagenic microbes by real-time PCR in Rwandan children under 5 years of age with acute gastroenteritis

Acute gastroenteritis is a main cause of disease and death among children in low-income countries. The causality rates and pathogenic characteristics of putative aetiological agents remain insufficiently known. We used real-time PCR targeting 16 diarrhoeagenic agents to analyse stool samples from children ≤5.0 years old with acute diarrhoea in Rwanda. Among the 880 children (median age 14.2 months; 41% female) at least one pathogen was detected in 92% and two or more agents in 63% of cases. Rotavirus was detected in 36.9%, adenovirus in 39.7%, enterotoxigenic Escherichia coli (ETEC) with genes for labile (eltB) or stable (estA) toxin in 31.3% and 19.0%, E. coli with eae or bfpA genes in 25.2% and 14.2%, Shigella in 17.5% and Cryptosporidium in 7.8%. Rotavirus and ETEC-estA were associated with more severe dehydration than diarrhoea due to other causes. Shigella was associated with bloody stools and higher CRP. Microbial loads (Ct values) of rotavirus, ETEC-estA and Shigella were associated with severity of symptoms. Rotavirus, ETEC-estA and E. coli with bfpA were associated with younger age, Shigella with older age. Antibiotic treatment was given to 42% and was associated with dehydration, fever and CRP, but not with pathogen. We conclude that rotavirus and ETEC-estA were the most important causes of diarrhoea with dehydration, that Shigella caused bloody diarrhoea but less severe dehydration, that microbial loads of rotavirus, ETEC-estA and Shigella were associated with severity of symptoms, and that antibiotic use was frequent and in poor agreement with microbiological findings.

Rectal swab for detection of norovirus by real-time PCR: similar sensitivity compared to faecal specimens

Rapid diagnosis and immediate infection control precautions are cornerstones in the prevention of norovirus outbreaks. However, faecal sampling for norovirus PCR--the standard of care--is time consuming. From 2009 to 2011, parallel faecal and rectal swab samples were consecutively obtained from patients with acute gastroenteritis presenting at our emergency department. In total, 109 complete sample pairs of 108 patients were analysed by specific norovirus real-time PCR. The sensitivity of real-time PCR was 97.3% (36/37) for both sampling methods. A rectal swab is a reasonable option for detection of norovirus by real-time PCR, if a stool specimen is not readily available.

Evaluation of anamnestic criteria for the identification of patients with acute community onset viral gastroenteritis in the emergency department--A prospective observational study

BACKGROUND

To our knowledge no clinical criteria for the identification of community onset viral gastroenteritis in individual patients have been evaluated systematically with modern PCR-based diagnostic assays as gold standard.

OBJECTIVE

The aim of this study was to identify factors independently associated with the detection of virus by PCR in rectal swab samples from patients with acute community onset gastroenteritis.

METHODS

A prospective observational study was conducted from December 2010 through March 2011 at the emergency department (ED) of a large teaching hospital. All patients who reported vomiting and/or diarrhoea up to 48 h prior to their visit to the ED were asked to participate. A rectal swab sample was obtained from each patient. Symptoms, date of onset, and epidemiological data were recorded. Samples were analysed with a multiple real-time PCR targeting 6 viral agents (astrovirus, adenovirus, rotavirus, sapovirus, and norovirus GI and GII).

RESULTS

Two hundred and five patients fulfilled the inclusion criteria, of whom 66 agreed to participate; their median (IQR) age was 65 (38-84) y and 43 (65%) were females. Thirty-one (47%) were positive by PCR for at least 1 of the agents examined (26 norovirus, 2 sapovirus, 2 rotavirus, and 1 adenovirus). Diarrhoea and a short duration of symptoms (≤ 2 days) were independently associated with a positive rectal swab sample, with odds ratios of 7.5 (95% confidence interval (CI) 2.0-28) and 10.4 (95% CI 1.9-56), respectively (p < 0.01 for both). A multivariate model including these 2 variables had a sensitivity of 81% (25/31) and a specificity of 69% (24/35).

CONCLUSIONS

Diarrhoea and a short duration of symptoms were the only anamnestic criteria independently associated with acute community onset viral gastroenteritis confirmed by PCR.

Real-time PCR threshold cycle cutoffs help to identify agents causing acute childhood diarrhea in Zanzibar

Molecular assays might improve the identification of causes of acute diarrheal disease but might lead to more frequent detection of asymptomatic infections. In the present study, real-time PCR targeting 14 pathogens was applied to rectal swabs from 330 children aged 2 to 59 months in Zanzibar, including 165 patients with acute diarrhea and 165 asymptomatic control subjects. At least one pathogen was detected for 94% of the patients and 84% of the controls, with higher rates among patients for norovirus genogroup II (20% versus 2.4%; P<0.0001), rotavirus (10% versus 1.8%; P=0.003), and Cryptosporidium (30% versus 11%; P<0.0001). Detection rates did not differ significantly for enterotoxigenic Escherichia coli (ETEC)-estA (33% versus 24%), ETEC-eltB (44% versus 46%), Shigella (35% versus 33%), and Campylobacter (35% versus 33%), but for these agents threshold cycle (CT) values were lower (pathogen loads were higher) in sick children than in controls. In a multivariate analysis, CT values for norovirus genogroup II, rotavirus, Cryptosporidium, ETEC-estA, and Shigella were independently associated with diarrhea. We conclude that this real-time PCR allows convenient detection of essentially all diarrheagenic agents and provides CT values that may be critical for the interpretation of results for pathogens with similar detection rates in patients and controls. The results indicate that the assessment of pathogen loads may improve the identification of agents causing gastroenteritis in children.