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

Absence of measurable quantities of Candida auris and Cryptococcus spp. in the gut microbiota of Ghanaian individuals with and without HIV infection as confirmed by applying multiple real-time PCR assays

Introduction. Fungal infections are relevant health risks for individuals with acquired immunodeficiency in the resource-limited tropics, but available surveillance data are scarce. For Candida auris and Cryptococcus spp., the evolution from environmental reservoirs to human pathogens causing life-threatening diseases is currently discussed as a public health concern in the context of climate change and limited treatment options.Gap statement. Uncovering the gastrointestinal tract as an epidemiological niche of fungi emerging from the environment into individuals for whom fungal infections are not diagnosed.Aim. To contribute to data on the local epidemiology of C. auris and Cryptococcus spp. in Western African Ghana by analysing gastrointestinal samples of Ghanaian individuals.Methodology. Four real-time PCR assays targeting C. auris and five real-time PCR assays targeting Cryptococcus spp. were applied with stool samples of 875 non-age-stratified Ghanaian HIV patients and 30 Ghanaian control individuals without known HIV infection. Also, 664 samples from Ghanaian children under 2 years of age were investigated. The true abundance of the target micro-organism was considered as unlikely in the case of one or fewer positive signals, likely in the case of two to three positive signals and highly likely in the case of four or more positive signals per sample in the real-time PCR assays.Results. The combined application of sensitive, target-specific real-time PCR assays indicates that neither C. auris, Cryptococcus neoformans complex nor Cryptococcus gattii complex were part of the gut microbiota of Ghanaian individuals with or without HIV infection.Conclusion. Despite the significant disease burden from these pathogens in immunosuppressed Ghanaian individuals, detection from gastrointestinal samples was unlikely, which should be taken into account when discussing screening strategies for these fungi of public health concern. In contrast, the detection of these fungi from such samples should not routinely be considered as commensal colonization flora.

Clustering of Gastrointestinal Microorganisms in Human Stool Samples from Ghana

The study was conducted to identify cluster patterns of enteric microorganisms with potential etiological relevance for infectious gastroenteritis in stool samples of individuals from Ghana, which is a known high-endemicity setting for infectious gastroenteritis. These patterns were compared to previous observations with specimens from Colombian indigenous people in order to assess potentially stable clustering for temporally and spatially distinct populations from high-endemicity regions. By doing so, the study aimed to identify stable clusters as markers of microbial interaction with potential importance for etiological relevance assignment in cases of multiple enteric pathogen detections. Stool samples from 1569 Ghanaian individuals (875 from HIV patients, 30 from HIV-negative control adult patients, and 644 from children < 2 years of age) were assessed for enteric microorganisms by applying real-time PCR. As a result, nucleic acids of bacterial microorganisms were most frequently detected, followed by protozoa, microsporidia, and helminths. Interestingly, the cluster assessment confirmed interaction patterns known from the previous analysis with Colombian indigenous people, demonstrating a high likelihood of Blastocystis hominis for clustering with other microorganisms and a prominent, potentially mediating role of Dientamoeba fragilis for microbial interactions within the clusters. In conclusion, the assessment confirmed conserved clustering of enteric microorganisms with potential etiological relevance for human infectious gastroenteritis over geographically distinct high-endemicity settings. Furthermore, the composition of abundant microorganisms is more important than regional factors for the determination of the interplay of enteric microorganisms in the human gut. Thereby, some microbial pathogens and commensals seem more susceptible to a changing microbial composition in the human gut than others.

Gastrointestinal Panel Performance for the Diagnosis of Acute Gastroenteritis in Pediatric Patients

BACKGROUND

Various methods are used to identify the causative organisms of acute gastroenteritis (AGE) in children. The gastrointestinal (GI) panel has the potential to detect up to 22 pathogens rapidly through the multiplex real-time PCR test. We studied the impact of the GI panel on clinical management in the pediatric population.

METHODS

A retrospective study was conducted to collect data on GI panel results and clinical details of inpatient children presenting with AGE at King Hamad University Hospital, Kingdom of Bahrain, over the course of one year.

RESULTS

One hundred nine samples were collected. The GI panel was positive in 96 samples (88.1%), with the majority detected in the toddler age group. Forty-one (42.7%) samples were positive for at least one organism. Salmonella was the most frequently encountered bacteria as a single isolate, 10/55 (18.2%), while enteropathogenic Escherichia coli was the most common co-infected organism, 16/41 (39%). Norovirus was the most common virus among the viruses. Bacterial detection peaked from July to October, while viral detection plateaued throughout the year. The GI panel and stool culture were positive for the same organism in 17 samples, versus one sample with a different organism. Sixty-two (56.9%) samples had a positive GI panel but negative stool cultures and stool analysis, and half of those detected viruses. The GI panel was positive in 86.2% of severely ill patients; the majority were bacteria. Bacterial detection was associated with a higher CRP compared to viruses.

CONCLUSION

The GI panel is an informative tool for detecting the causative pathogen of AGE in children. However, it can detect multiple organisms, indicating a possible carrier status, which points toward future studies.

Collider Bias Assessment in Colombian Indigenous Wiwa and Kogui Populations with Chronic Gastroenteric Disorder of Likely Infectious Etiology Suggests Complex Microbial Interactions Rather Than Clear Assignments of Etiological Relevance

Multiple microbial detections in stool samples of indigenous individuals suffering from chronic gastroenteric disorder of a likely infectious origin, characterized by recurring diarrhea of variable intensity, in the rural north-east of Colombia are common findings, making the assignment of etiological relevance to individual pathogens challenging. In a population of 773 indigenous people from either the tribe Wiwa or Kogui, collider bias analysis was conducted comprising 32 assessed microorganisms including 10 bacteria (Aeromonas spp., Campylobacter spp., enteroaggregative Escherichia coli (EAEC), enteropathogenic Escherichia coli (EPEC), enterotoxigenic Escherichia coli (ETEC), Salmonella spp., Shiga toxin-producing Escherichia coli (STEC), Shigella spp./enteroinvasive Escherichia coli (EIEC), Tropheryma whipplei and Yersinia spp.), 11 protozoa (Blastocystis spp., Cryptosporidium spp., Cyclospora spp., Dientamoeba fragilis, Entamoeba coli, Entamoeba bangladeshi/dispar/histolytica/moshkovskii complex, Entamoeba histolytica, Endolimax nana, Giardia duodenalis, Iodamoeba buetschlii and Pentatrichomonas hominis), 8 helminths (Ascaris spp., Enterobius vermicularis, Hymenolepis spp., Necator americanus, Schistosoma spp., Strongyloides spp., Taenia spp. and Trichuris spp.), microsporidia (Encephalocytozoon spp.) and fungal elements (microscopically observed conidia and pseudoconidia). The main results indicated that negative associations potentially pointing towards collider bias were infrequent events (n = 14), while positive associations indicating increased likelihood of co-occurrence of microorganisms quantitatively dominated (n = 88). Microorganisms showing the most frequent negative associations were EPEC (n = 6) and Blastocystis spp. (n = 3), while positive associations were most common for Trichuris spp. (n = 16), Dientamoeba fragilis (n = 15), Shigella spp./EIEC (n = 12), Ascaris spp. (n = 11) and Blastocystis spp. (n = 10). Of note, positive associations quantitively dominated for Blastocystis spp. In conclusion, collider bias assessment did not allow clear-cut assignment of etiological relevance for detected enteric microorganisms within the assessed Colombian indigenous population. Instead, the results suggested complex microbial interactions with potential summative effects. Future studies applying alternative biostatistical approaches should be considered to further delineate respective interactions.

Comparison of the Diagnostic Accuracy of Three Real-Time PCR Assays for the Detection of Arcobacter butzleri in Human Stool Samples Targeting Different Genes in a Test Comparison without a Reference Standard

Potential etiological relevance for gastroenteric disorders including diarrhea has been assigned to Arcobacter butzleri. However, standard routine diagnostic algorithms for stool samples of patients with diarrhea are rarely adapted to the detection of this pathogen and so, A. butzleri is likely to go undetected unless it is specifically addressed, e.g., by applying pathogen-specific molecular diagnostic approaches. In the study presented here, we compared three real-time PCR assays targeting the genes hsp60, rpoB/C (both hybridization probe assays) and gyrA (fluorescence resonance energy transfer assay) of A. butzleri in a test comparison without a reference standard using a stool sample collection with a high pretest probability from the Ghanaian endemicity setting. Latent class analysis was applied with the PCR results obtained with a collection of 1495 stool samples showing no signs of PCR inhibition to assess the real-time PCR assays' diagnostic accuracy. Calculated sensitivity and specificity were 93.0% and 96.9% for the hsp60-PCR, 100% and 98.2% for the rpoB/C-PCR, as well as 12.7% and 99.8% for the gyrA-PCR, respectively. The calculated A. butzleri prevalence within the assessed Ghanaian population was 14.7%. As indicated by test results obtained with high-titer spiked samples, cross-reactions of the hsp60-assay and rpoB/C-assay with phylogenetically related species such as A. cryaerophilus can occur but are less likely with phylogenetically more distant species like, e.g., A. lanthieri. In conclusion, the rpoB/C-assay showed the most promising performance characteristics as the only assay with sensitivity >95%, albeit associated with a broad 95%-confidence interval. In addition, this assay showed still-acceptable specificity of >98% in spite of the known cross-reactivity with phylogenetically closely related species such as A. cryaerophilus. If higher certainty is desired, the gyrA-assay with specificity close to 100% can be applied for confirmation testing with samples showing positive rpoB/C-PCR results. However, in case of a negative result in the gyrA-assay, this cannot reliably exclude the detection of A. butzleri in the rpoB/C-assay due to the gyrA-assay's very low sensitivity.

The Gut Microbiome of an Indigenous Agropastoralist Population in a Remote Area of Colombia with High Rates of Gastrointestinal Infections and Dysbiosis

An Indigenous agropastoralist population called the Wiwa from the Sierra Nevada de Santa Marta, in North-East Colombia, shows high rates of gastrointestinal infections. Chronic gut inflammatory processes and dysbiosis could be a reason, suggesting an influence or predisposing potential of the gut microbiome composition. The latter was analyzed by 16S rRNA gene amplicon next generation sequencing from stool samples. Results of the Wiwa population microbiomes were associated with available epidemiological and morphometric data and compared to control samples from a local urban population. Indeed, locational-, age-, and gender-specific differences in the Firmicutes/Bacteriodetes ratio, core microbiome, and overall genera-level microbiome composition were shown. Alpha- and ß-diversity separated the urban site from the Indigenous locations. Urban microbiomes were dominated by Bacteriodetes, whereas Indigenous samples revealed a four times higher abundance of Proteobacteria. Even differences among the two Indigenous villages were noted. PICRUSt analysis identified several enriched location-specific bacterial pathways. Moreover, on a general comparative scale and with a high predictive accuracy, we found Sutterella associated with the abundance of enterohemorrhagic Escherichia coli (EHEC), Faecalibacteria associated with enteropathogenic Escherichia coli (EPEC) and helminth species Hymenolepsis nana and Enterobius vermicularis. Parabacteroides, Prevotella, and Butyrivibrio are enriched in cases of salmonellosis, EPEC, and helminth infections. Presence of Dialister was associated with gastrointestinal symptoms, whereas Clostridia were exclusively found in children under the age of 5 years. Odoribacter and Parabacteroides were exclusively identified in the microbiomes of the urban population of Valledupar. In summary, dysbiotic alterations in the gut microbiome in the Indigenous population with frequent episodes of self-reported gastrointestinal infections were confirmed with epidemiological and pathogen-specific associations. Our data provide strong hints of microbiome alterations associated with the clinical conditions of the Indigenous population.

High Burden of Co-Infection with Multiple Enteric Pathogens in Children Suffering with Diarrhoea from Rural and Peri-Urban Communities in South Africa

Infectious diarrhoea contributes to high morbidity and mortality in young children from sub-Saharan Africa. The aim of this study was to assess the prevalence of single and multiple diarrhoeal-causing pathogen combinations in children suffering from diarrhoea from rural and peri-urban communities in South Africa. A total of 275 diarrhoea stool specimens were collected between 2014 and 2016 from Hospitals and Primary Health Care clinics. The BioFire^® FilmArray^® Gastrointestinal panel was used to simultaneously detect 22 diarrhoea pathogens (viruses, bacteria, parasites) known to cause diarrhoea. A total of 82% (226/275) enteric pathogens were detected in the stool specimens. The two most detected bacterial, viral and parasitic pathogens each included: EAEC (42%), EPEC (32%), Adenovirus F40/41 (19%), Norovirus (15%), Giardia (8%) and Cryptosporidium (6%), respectively. Single enteric pathogen infections were recorded in 24% (65/275) specimens with EAEC, and Norovirus was found in 26% (17/65) and 14% (9/65) of the specimens, respectively. Multiple enteric pathogen combinations were recorded in 59% (161/275) of the stool specimens with 53% (85/161) containing two pathogens, 22% (35/161) containing three pathogens and 25% (41/161) containing four or more pathogens. The results from this study demonstrated the complex nature of pathogen co-infections in diarrhoeal episodes which could have an impact on treatment effectiveness.

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

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

Intestinal Helminth Infections in Ghanaian Children from the Ashanti Region between 2007 and 2008—A Retrospective Cross-Sectional Real-Time PCR-Based Assessment

In spite of ongoing eradication programs, helminth infections are still a medical issue in Ghana. For follow-up assessments on the decline of regional helminth infections, historic baseline prevalence values obtained with standardized diagnostic procedures can be helpful. In this retrospective cross-sectional study, real-time PCR targeting the nematodes Ancylostoma spp. (ITS2), Ascaris lumbricoides (ITS1), Enterobius vermicularis (ITS1), Necator americanus (ITS2), Strongyloides stercoralis (18S rRNA) and Trichuris trichiura (18S rRNA), the trematodes Schistosoma spp. (ITS2) as well as the cestodes Hymenolepis nana (ITS1), Taenia saginata (ITS1) and Taenia solium (ITS1) was applied with 2046 DNA eluates from stool samples of Ghanaian children from the Ashanti region collected between 2007 and 2008 in order to retrospectively define prevalence values. The overall prevalence was low with 3.8% (n = 77) and only 0.1% (n = 2) double infections with helminths were recorded. The three most frequently detected enteric helminth species comprised 2% S. stercoralis (n = 41), 0.8% H. nana (n = 16), and 0.7% N. americanus (n = 14), while only sporadic infection events were recorded for other helminth species comprising 0.1% E. vermicularis (n = 2), 0.1% Schistosoma spp. (n = 2), 0.1% T. saginata (n = 1) and 0.1% T. trichiura (n = 1). A. lumbricoides, Ancylostoma spp. and T. solium were not detected at all. In conclusion, the retrospective assessment suggests a low prevalence of enteric helminth infections in Ghanaian children from the Ashanti Region within the assessment period between 2007 and 2008.

Investigation of the use of multiplex PCR in childhood diarrhea with clinical and epidemiological features

INTRODUCTION

Acute gastroenteritis is one of the most common causes of hospital admission in children. Treatment regimens differ depending on the pathogen. In our study, we aimed to evaluate the epidemiological and clinical features of pediatric patients whose gastrointestinal agents were detected by multiplex PCR.

MATERIALS AND METHODS

The study included 131 pediatric patients who were followed up at Eskişehir Osmangazi University, Pediatric Department between January 2018 and December 2021.Gastrointestinal pathogens were detected in stool samples by multiplex PCR. The epidemiological and clinical features were reviewed retrospectively.

RESULTS

A total of 203 gastrointestinal pathogens were detected from the stool samples of 131 cases. Of these cases, 56% were male and 44% were female. The mean age was 66 (2-204) months. The most common symptoms were diarrhea, fever, vomiting and abdominal pain. The pathogen detection rate was 69% by multiplex PCR. A single pathogen was detected in 85 (65%) cases and multiple pathogens were detected in 46 (35%) cases. The most common pathogens were enteropathogenic Escherichia coli (EPEC, 23%), Clostridium difficile (21%), norovirus (17%), rotavirus (15%), salmonella (12%) and enterotoxigenic E. coli (ETEC, 11%). Stool culture was positive in 16 (12%) cases and microscopic examination positive in 17 (13%) cases. Probiotic treatment was given to 119 (92%) cases and antimicrobial treatment (metroinidazole, ceftriaxone, azithromycin and oral vancomycin) to 34 (26%) cases. Of the cases, 56 (42%) had chronic disease, 40 (30%) had a history of previous antibiotic use and 17 (13%) had a history of hospitalization in the intensive care unit.

CONCLUSION

The sensitivity of the multiplex PCR in the detection of acute gastroenteritis agents is higher than stool microscopy, stool culture and stool antigen tests. However, due to the inability to distinguish between colonization, carrier state and pathogenicity, it should be evaluated together with other diagnostic tests and clinical findings in order to determine whether the determined agent is pathogenic or not and in the regulation of antimicrobial therapy.

Comparative Evaluation of Real-Time Screening PCR Assays for Giardia duodenalis and of Assays Discriminating the Assemblages A and B

Due to superior sensitivity compared to traditional microscopy, real-time PCR has been well established for the diagnosis of Giardia duodenalis in human stool samples. In this study, screening real-time PCRs for different target genes of G. duodenalis, i.e., the 18S rRNA gene, the gdh (glutamate dehydrogenase) gene and the bg (beta-giardin) gene, were comparatively assessed next to various real-time PCR assays for the discrimination of the assemblages A and B of G. duodenalis targeting the bg gene with and without locked nucleic acid–containing probes as well as the tpi (triose phosphate isomerase) gene. The screening PCRs were assessed by including 872 non-preselected samples with a high pre-test probability for G. duodenalis in the statistical analysis, while 53 G. duodenalis-positive samples as indicated by at least two screening PCRs were finally included in the assessment of the assemblage-specific PCRs. For the screening PCRs, sensitivity estimated with latent class analysis (LCA) ranged from 17.5% to 100%, specificity from 92.3% to 100% with an accuracy-adjusted prevalence of 7.2% for G. duodenalis within the non-preselected sample collection. In detail, sensitivity and specificity were 100% and 100% for the 18S rRNA gene-specific assay, 17.5% and 92.3% for the gdh gene-specific assay, and 31.7% and 100% for the bg gene-specific assay, respectively. Agreement kappa was slight with only 15.5%. For the assemblage-specific PCRs, estimated sensitivity ranged from 82.1% to 100%, specificity from 84.0% to 100% with nearly perfect agreement kappa of 90.1% for assemblage A and yet substantial agreement of 74.8% for assemblage B. In detail for assemblage A, sensitivity and specificity were 100% and 100% for the bg gene-specific assay without locked nucleic acids (LNA) as well as 100% and 97.8% for both the bg gene-specific assay with LNA and the tri gene-specific assay, respectively. For assemblage B, sensitivity and specificity were 100% and 100% for the bg gene-specific assay without LNA, 96.4% and 84.0% for the bg gene-specific assay with LNA, and 82.1% and 100% for the tri gene-specific assay, respectively. Within the assessed sample collection, the observed proportion comprised 15.1% G. duodenalis assemblage A, 52.8% G. duodenalis assemblage B and 32.1% non-resolved assemblages. Only little differences were observed regarding the cycle threshold (Ct) values when comparing the assays. In conclusion, best diagnostic accuracy was shown for an 18S rRNA gene-specific screening assay for G. duodenalis and for a differentiation assay discriminating the G. duodenalis assemblages A and B by targeting the bg gene with probes not containing locked nucleic acids. By adding additional highly specific competitor assays for confirmation testing, diagnostic specificity can be further increased on the cost of sensitivity if optimized specificity is desired.

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

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

Rotaviruses: From Pathogenesis to Disease Control-A Critical Review

Since their first recognition in human cases about four decades ago, rotaviruses have remained the leading cause of acute severe dehydrating diarrhea among infants and young children worldwide. The WHO prequalification of oral rotavirus vaccines (ORV) a decade ago and its introduction in many countries have yielded a significant decline in the global burden of the disease, although not without challenges to achieving global effectiveness. Poised by the unending malady of rotavirus diarrhea and the attributable death cases in developing countries, we provide detailed insights into rotavirus biology, exposure pathways, cellular receptors and pathogenesis, host immune response, epidemiology, and vaccination. Additionally, recent developments on the various host, viral and environmental associated factors impacting ORV performance in low-and middle-income countries (LMIC) are reviewed and their significance assessed. In addition, we review the advances in nonvaccine strategies (probiotics, candidate anti-rotaviral drugs, breastfeeding) to disease prevention and management.

Multicentric Evaluation of SeeGene Allplex Real-Time PCR Assays Targeting 28 Bacterial, Microsporidal and Parasitic Nucleic Acid Sequences in Human Stool Samples

Prior to the implementation of new diagnostic techniques, a thorough evaluation is mandatory in order to ensure diagnostic reliability. If positive samples are scarcely available, however, such evaluations can be difficult to perform. Here, we evaluated four SeeGene Allplex real-time PCR assays amplifying a total of 28 bacteria, microsporidal and parasitic nucleic acid sequence targets in human stool samples in a multicentric approach. In the assessments with strongly positive samples, sensitivity values ranging between 13% and 100% were recorded for bacteria, between 0% and 100% for protozoa and between 7% and 100% for helminths and microsporidia; for the weakly positive samples, the recorded sensitivity values for bacteria ranged from 0% to 100%; for protozoa, from 0% to 40%; and for helminths and microsporidia, from 0% to 53%. For bacteria, the recorded specificity was in the range between 87% and 100%, while a specificity of 100% was recorded for all assessed PCRs targeting parasites and microsporidia. The intra- and inter-assay variations were generally low. Specifically for some helminth species, the sensitivity could be drastically increased by applying manual nucleic acid extraction instead of the manufacturer-recommended automatic procedure, while such effects were less obvious for the bacteria and protozoa. In summary, the testing with the chosen positive control samples showed varying degrees of discordance between the evaluated Allplex assays and the applied in-house reference assays associated with higher cycle threshold values in the Allplex assays, suggesting that samples with very low pathogen densities might be missed. As the targeted species can occur as harmless colonizers in the gut of individuals in high-endemicity settings as well, future studies should aim at assessing the clinical relevance of the latter hint.

Use of multiplex PCR in diagnosis of childhood acute viral diarrhoea caused by rotavirus, norovirus, astrovirus and adenovirus in Upper Egypt

Background

Diarrhoea is still a major public health issue in developing countries, and it is one of the leading causes of morbidity and mortality in children. We aimed to assess the use of a multiplex reverse transcription polymerase chain reaction (RT-PCR) assay for the detection of five viruses, including rotavirus, norovirus (genogroups 1 and 2), astrovirus, and adenovirus, responsible for gastroenteritis in children under 5 years old in primary care centres in Upper Egypt.

Subjects and methods

A total of 500 stool samples were collected. Fifty samples were randomly selected for viral examination using multiplex RT-PCR for the detection of rotavirus, norovirus (genogroups 1 and 2), astrovirus, and adenovirus, causing diarrhoea.

Results

Viruses were detected in 45 (90%) of the 50 stool samples. The most frequently identified virus was norovirus G2, followed by Group A rotavirus, astrovirus and adenovirus. Mixed infection by two and three viruses was observed in 7/50 cases (14%) and 2/50 cases (4%), respectively. Norovirus G1 was not detected in the samples examined.

Conclusion

Our study reveals that multiplex PCR allows for the detection of multiple viral targets in only one reaction, rendering the assay easier to perform compared to existing testing methodologies (RT-PCR and electron microscopy). Additionally, most of the viruses were detected in summer, and the highest prevalence was in the age group less than 1 year. Norovirus G2 and rotavirus were the most frequent agents and the most common coinfections responsible for gastroenteritis in children.

Associations Between Eight Earth Observation-Derived Climate Variables and Enteropathogen Infection: An Independent Participant Data Meta-Analysis of Surveillance Studies With Broad Spectrum Nucleic Acid Diagnostics

Diarrheal disease, still a major cause of childhood illness, is caused by numerous, diverse infectious microorganisms, which are differentially sensitive to environmental conditions. Enteropathogen-specific impacts of climate remain underexplored. Results from 15 studies that diagnosed enteropathogens in 64,788 stool samples from 20,760 children in 19 countries were combined. Infection status for 10 common enteropathogens-adenovirus, astrovirus, norovirus, rotavirus, sapovirus, Campylobacter, ETEC, Shigella, Cryptosporidium and Giardia-was matched by date with hydrometeorological variables from a global Earth observation dataset-precipitation and runoff volume, humidity, soil moisture, solar radiation, air pressure, temperature, and wind speed. Models were fitted for each pathogen, accounting for lags, nonlinearity, confounders, and threshold effects. Different variables showed complex, non-linear associations with infection risk varying in magnitude and direction depending on pathogen species. Rotavirus infection decreased markedly following increasing 7-day average temperatures-a relative risk of 0.76 (95% confidence interval: 0.69-0.85) above 28°C-while ETEC risk increased by almost half, 1.43 (1.36-1.50), in the 20-35°C range. Risk for all pathogens was highest following soil moistures in the upper range. Humidity was associated with increases in bacterial infections and decreases in most viral infections. Several virus species' risk increased following lower-than-average rainfall, while rotavirus and ETEC increased with heavier runoff. Temperature, soil moisture, and humidity are particularly influential parameters across all enteropathogens, likely impacting pathogen survival outside the host. Precipitation and runoff have divergent associations with different enteric viruses. These effects may engender shifts in the relative burden of diarrhea-causing agents as the global climate changes.

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

Acute and chronic diarrheal illness secondary to gastrointestinal infection is a significant cause of morbidity and mortality around the world. A cornerstone of management includes prompt diagnosis and appropriate treatment of culprit pathogens. Timely diagnosis can improve patient care, assist in infection control, and prevent disease outbreaks. Historical methods of diagnosis include traditional culture methods and stool analysis. These are limited by long turnaround time and inability to simultaneously assess multiple pathogens. The advent of multiplexed nucleic acid amplification tests first began with the Food and Drug Administration-approved respiratory virus multiplex polymerase chain reaction (PCR) panel in 2009, followed by gastrointestinal infections in 2013, and neurological infections in 2014. We conducted a review of current literature pertaining to the clinical utility of a gastrointestinal multiplex PCR in management of acute and chronic diarrhea in patients. To date, seven platforms approved by the US Food and Drug Administration are used in detection of various bacterial, viral, and parasitic causative organisms for diagnosis of gastrointestinal infections. The sensitivity and specificity of each assay vary depending on the tested organism. Interpretation of a positive result has to be tailored to the clinical context. Further studies are required to establish the utility of gastrointestinal multiplex PCR from a cost-based perspective, whether specific enteropathogens such as Clostridioides difficile are better assessed with toxin gene detection and whether new parameters such as cycle threshold values can improve clinical application of test results.

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.

Global prevalence and genotype distribution of norovirus infection in children with gastroenteritis: A meta-analysis on 6 years of research from 2015 to 2020

In the post rotavirus vaccine era, norovirus (NoV) plays an increasingly important role in epidemic and sporadic gastroenteritis among children. This study was designed to provide an updated meta-analytic review of the prevalence of NoV among paediatric patients with gastroenteritis and to clarify the relationship between NoV infection and gastroenteritis. Systematic searches of the literature for potentially relevant studies were carried out from 1 January 2015 to 29 May 2020. The inverse variance method was chosen for weighting of the studies, and the random-effects model was used to analyse data. To determine the association between NoV infection and gastroenteritis in children, pooled odds ratio (OR) and its 95% confidence interval (CI) were computed for case-control studies. The pooled prevalence of NoV infection among 12,0531 children with gastroenteritis from 45 countries across the world was 17.7% (95% CI: 16.3%-19.2%). There were 28 studies with a case-control design, and the pooled prevalence of NoV infection among 11,954 control subjects was 6.7% (95% CI: 5.1%-8.8%). The pooled OR of the association of NoV infection and gastroenteritis was 2.7 (95% CI: 2.2-3.4). The most common NoV genotypes were GII.4 (59.3%) and GII.3 (14.9%). The highest frequency of NoV was found in the age group below 1 year. Our findings indicated a substantial burden of gastroenteritis caused by NoV globally, with GII.4 and GII.3 the major genotypes responsible for the majority of NoV-associated gastroenteritis cases among children. Younger age and male sex can be considered risk factors for NoV-associated gastroenteritis among children.

Study of enteric pathogens among children in the tropics and effects of prolonged storage of stool samples

The study was performed to compare real-time PCR after nucleic acid extraction directly from stool samples as well as from samples stored and transported on Whatman papers or flocked swabs at ambient temperature in the tropics. In addition, the possible suitability for a clear determination of likely aetiological relevance of PCR-based pathogen detections based on cycle threshold (Ct) values was assessed. From 632 Tanzanian children <5 years of age with and without gastrointestinal symptoms, 466 samples were subjected to nucleic acid extraction and real-time PCR for gastrointestinal viral, bacterial and protozoan pathogens. Equal or even higher frequencies of pathogen detections from Whatman papers or flocked swabs were achieved compared with nucleic acid extraction directly from stool samples. Comparison of the Ct values showed no significant difference according to the nucleic acid extraction strategy. Also, the Ct values did not allow a decision whether a detected pathogen was associated with gastrointestinal symptoms.

Etiology of diarrhea by multiplex polymerase chain reaction among young children in the United Arab Emirates: a case-control study

Background

Little is known about the etiology of childhood diarrhea in the United Arab Emirates (UAE) especially after the introduction of rotavirus vaccines. This study aimed to identify gastrointestinal pathogens in children with diarrhea (cases) and the carriage rate of these pathogens in asymptomatic children (controls).

Methods

Stool samples were collected from 203 cases and 73 controls who presented to two major hospitals in Al Ain city, UAE. Samples were analyzed with Allplex™ Gastrointestinal Full Panel Assay for common entero-pathogens. The association between diarrhea and the isolated pathogens was calculated in a multivariate logistic regression model. The adjusted attributable fractions (aAFs) were calculated for all pathogens significantly associated with cases.

Results

At least one pathogen was identified in 87 samples (42.8%) from cases and 17 (23.3%) from controls (P < 0.001). Rotavirus, norovirus GII and adenovirus were significantly more prevalent in cases. Their aAFs with 95% ci are 0.95 (0.64, 1.00) for rotavirus, 0.86 (0.38, 0.97) for norovirus GII and 0.84 (0.29, 0.96) for adenovirus. None of the 13 bacteria tested for were more commonly found in the cases than in controls. Cryptosporidium spp. were more significantly detected in cases than in controls. Co-infections occurred in 27.9% of the children. Viruses and parasites were significantly more likely to occur together only in the cases.

Conclusions

Multiplex PCR revealed high positivity rates in both cases and controls which demand a cautious interpretation. Rotavirus remains the main childhood diarrhea pathogen in UAE. Effective strategies are needed to better control rotavirus and other causative pathogens.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-020-05693-1.

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 .

Enteric pathogens in German police officers after predominantly tropical deployments - A retrospective assessment over 5 years

Introduction

The study was performed to assess the infection risk of German police officers on predominantly tropical deployments, mostly United Nations missions, with gastrointestinal pathogens.

Methods

Police officers were offered PCR-based screening for gastrointestinal pathogens before and after deployment. The screening panel comprised enteroinvasive bacteria (Salmonella spp., Shigella spp./enteroinvasive Escherichia coli, Campylobacter jejuni, and Yersinia spp.), enteropathogenic protozoa (Entamoeba histolytica, Giardia duodenalis, Cryptosporidium spp., and Cyclospora cayetanensis), as well as enteric helminths (Ancyclostoma spp., Ascaris lumbricoides, Enterobius vermicularis, Hymenolepis nana, Necator americanus, African Schistosoma spp., Strongyloides stercoralis, Taenia saginata, Taenia solium, and Trichuris trichiura).

Results

G. duodenalis (n = 3), C. jejuni (n = 2), Salmonella spp. (n = 1), Shigella spp./enteroinvasive E. coli (n = 3), and S. stercoralis (n = 3) were detect in 12 out of 133 (9.0%) police officers. The majority had shown gastrointestinal symptoms on deployment and all were asymptomatic at the time of medical assessment. The major infection sites were Sub-Saharan Africa followed by Northern Africa and the Middle East.

Conclusions

Deployment of police officers to tropical deployment sites on United Nations missions is associated with a considerable acquisition risk of gastrointestinal pathogens in a quantitatively relevant minority. Post-deployment screening is advisable to facilitate therapeutic and hygiene-related consequences.

Enteric Viral Co-Infections: Pathogenesis and Perspective

Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of all ages globally. Despite virus–virus co-infection events in the intestine being increasingly detected, little is known about their impact on disease outcomes or human health. Here, we review what is currently known about the clinical prevalence of virus–virus co-infections and how co-infections may influence vaccine responses. While experimental investigations into enteric virus co-infections have been limited, we highlight in vivo and in vitro models with exciting potential to investigate viral co-infections. Many features of virus–virus co-infection mechanisms in the intestine remain unclear, and further research will be critical.

Identification of Enteropathogens by Multiplex PCR among Rural and Urban Guatemalan Children with Acute Diarrhea

Multiplex polymerase chain reaction (PCR) platforms have enhanced understanding of intestinal pathogens in low- and middle-income countries (LMICs). However, few such studies have been performed in Latin America, where poverty, poor sanitation, and undernutrition persist. Multiplex PCR (BioFire, Salt Lake City, UT) was used to identify viral, bacterial, and parasitic pathogens in stool collected on day 1 and 31 from children aged 6 to 35 months with acute, non-bloody diarrhea in two locations (rural and urban) in Guatemala. We analyzed correlation between pathogens and clinical, demographic, and socioeconomic variables; described patterns of pathogen acquisition, persistence, and clearance over the 30-day period; and calculated population attributable fractions (PAFs) for diarrheal causation for individual pathogens. We analyzed 316 subjects (144 urban; 172 rural) enrolled between March 2015 and January 2016. Rural subjects had significantly more malnutrition, animal exposure, and unimproved water/sanitation infrastructure. The majority of subjects had multiple pathogens/sample (4.8 rural and 2.7 urban). Few meaningful correlates were identified between individual pathogens and clinical, demographic, or environmental variables. Escherichia coli pathotypes, Shigella, Campylobacter, and Giardia had high rates of persistence between initial and 30-day follow-up. Statistically significant adjusted PAFs were identified for Campylobacter (14.9%, 95% CI: 3.2-23.1), norovirus (10.2%, 95% CI: 0.4-17.1), sapovirus (7.6%, 95% CI: 2.3-10.9), and adenovirus 40/41 (5.6%, 95% CI: 0.3-8.7). These observations further characterize the diversity and complexity of enteric pathogens in children in LMICs. Patterns of chronic symptomatic and asymptomatic infection among Latin American children are similar to those observed in other LMIC regions. Findings have direct implications for practitioners treating individuals with acute infectious diarrhea and should inform regional public health strategies.

Etiologic features of diarrheagenic microbes in stool specimens from patients with acute diarrhea in Thailand

Many microbial species have been recognized as enteropathogens for humans. Here, we predicted the causative agents of acute diarrhea using data from multiplex quantitative PCR (qPCR) assays targeting 19 enteropathogens. For this, a case-control study was conducted at eight hospitals in Thailand. Stool samples and clinical data were collected from 370 hospitalized patients with acute diarrhea and 370 non-diarrheal controls. Multiple enteropathogens were detected in 75.7% and 13.0% of diarrheal stool samples using multiplex qPCR and bacterial culture methods, respectively. Asymptomatic carriers of enteropathogens were found among 87.8% and 45.7% of individuals by qPCR and culture methods, respectively. These results suggested the complexity of identifying causative agents of diarrhea. An analysis using the quantification cut-off values for clinical relevance drastically reduced pathogen-positive stool samples in control subjects from 87.8% to 0.5%, whereas 48.9% of the diarrheal stool samples were positive for any of the 11 pathogens. Among others, rotavirus, norovirus GII, Shigella/EIEC, and Campylobacter were strongly associated with acute diarrhea (P-value < 0.001). Characteristic clinical symptoms, epidemic periods, and age-related susceptibility to infection were observed for some enteropathogens. Investigations based on qPCR approaches covering a broad array of enteropathogens might thus improve our understanding of diarrheal disease etiology and epidemiological trends.

Duplex PCR for Detection of Aleutian Disease Virus from Biological and Environmental Samples

Aleutian disease is one of the most serious disease entities affecting mink farms. The disease causes significant economic losses in mink breeding countries. The aim of the study was to optimize a diagnostic test based on duplex PCR to enable detection of Aleutian disease virus in biological and environmental samples.

Blood (n = 40) and spleen (n = 40) samples from animals with suspected infection, and swabs from cages in which infected animals were kept (n = 20) were used for analysis. DNA was isolated from the samples, followed by optimization of the duplex PCR reaction targeting sequences coding NS1 and VP2 proteins. The qPCR method was used to determine the sensitivity of the reaction. The specificity of the analysis was confirmed by the sequencing results.

Optimized duplex PCR enabled detection of Aleutian Mink Disease Virus (AMDV) genetic material in biological and environmental samples. Testing of the sensitivity of the method indicated clear amplification for both primer pairs at 102 copies of viral DNA in a reaction. Sequencing confirmed the specificity of the reaction, which in the case of both primer pairs indicated an over 90% agreement between the isolates and the variants of the virus from the databases.

The use of duplex PCR to detect two regions of the AMDV genome may increase the sensitivity and specificity of the method and significantly expand the possibilities of further analysis based on sequencing.

Impact of diagnostic methods on efficacy estimation - a proof-of-principle based on historical examples

INTRODUCTION

Accurate diagnostic methods are essential for evaluating treatment efficacy in clinical trials, including vaccine trials. Although a plethora of studies assessing novel or modified treatment options is available, clinical trials evaluating the sensitivity and specificity of diagnostic methods in compliance with the demands of drug registration trials are scarce. We assessed the accuracy of diagnostic methods in two vaccine trials conducted in 1995 and 2009 to demonstrate the impact of sensitivity and specificity on efficacy estimations.

METHODS

We applied the sensitivity- and specificity-adjusted vaccine efficacy estimator of Lachenbruch for modelling the impact of test characteristics on the outcome of the two vaccine trials by varying diagnostic specificity.

RESULTS

Because of non-ideal diagnostic sensitivity and specificity, the estimation of vaccine efficacy is compromised. We demonstrate the impact of diagnostic accuracy on efficacy estimations with increasing confidence limits.

CONCLUSIONS

Because sensitivity and specificity less than one have a direct impact on efficacy estimations in clinical trials, evaluation of diagnostic methods should lead to a level of evidence comparable with the efficacy assessment of novel treatment options. Furthermore, statistical methods adjusted for sensitivity and specificity of diagnostic methods should be applied for efficacy estimations, or this lack of confidence has to be taken into account when interpreting the results of trials.

Gut carriage of antimicrobial resistance genes among young children in urban Maputo, Mozambique: Associations with enteric pathogen carriage and environmental risk factors

Because poor sanitation is hypothesized as a major direct and indirect pathway of exposure to antimicrobial resistance genes (ARGs), we sought to determine a) the prevalence of and b) environmental risk factors for gut carriage of key ARGs in a pediatric cohort at high risk of enteric infections due to poor water, sanitation, and hygiene (WASH) conditions. We investigated ARGs in stool from young children in crowded, low-income settlements of Maputo, Mozambique, and explored potential associations with concurrent enteric pathogen carriage, diarrhea, and environmental risk factors, including WASH. We collected stool from 120 children <14 months old and tested specimens via quantal, multiplex molecular assays for common bacterial, viral, and protozoan enteric pathogens and 84 ARGs encoding potential resistance to 7 antibiotic classes. We estimated associations between ARG detection (number and diversity detected) and concurrently-measured enteric pathogen carriage, recently-reported diarrhea, and risk factors in the child's living environment. The most commonly-detected ARGs encoded resistance to macrolides, lincosamides, and streptogramins (100% of children); tetracyclines (98%); β-lactams (94%), aminoglycosides (84%); fluoroquinolones (48%); and vancomycin (38%). Neither concurrent diarrhea nor measured environmental (including WASH) conditions were associated with ARG detection in adjusted models. Enteric pathogen carriage and ARG detection were associated: on average, 18% more ARGs were detected in stool from children carrying bacterial pathogens than those without (adjusted risk ratio (RR): 1.18, 95% confidence interval (CI): 1.02, 1.37), with 16% fewer ARGs detected in children carrying parasitic pathogens (protozoans, adjusted RR: 0.84, 95% CI: 0.71, 0.99). We observed gut ARGs conferring potential resistance to a range of antibiotics in this at-risk cohort that had high rates of enteric infection, even among children <14 months-old. Gut ARGs did not appear closely correlated with WASH, though environmental conditions were generally poor. ARG carriage may be associated with concurrent carriage of bacterial enteric pathogens, suggesting indirect linkages to WASH that merit further investigation.

Malaria Coinfections in Febrile Pediatric Inpatients: A Hospital-Based Study From Ghana

Background

The epidemiology of pediatric febrile illness is shifting in sub-Saharan Africa, but malaria remains a major cause of childhood morbidity and mortality. The present study describes causes of febrile illness in hospitalized children in Ghana and aims to determine the burden of malaria coinfections and their association with parasite densities.

Methods

In a prospective study, children (aged ≥30 days and ≤15 years) with fever ≥38.0°C were recruited after admission to the pediatric ward of a primary hospital in Ghana. Malaria parasitemia was determined and blood, stool, urine, respiratory, and cerebrospinal fluid specimens were screened for parasitic, bacterial, and viral pathogens. Associations of Plasmodium densities with other pathogens were calculated.

Results

From November 2013 to April 2015, 1238 children were enrolled from 4169 admissions. A clinical/microbiological diagnosis could be made in 1109/1238 (90%) patients, with Plasmodium parasitemia (n = 728/1238 [59%]) being predominant. This was followed by lower respiratory tract infections/pneumonia (n = 411/1238 [34%]; among detected pathogens most frequently Streptococcus pneumoniae, n = 192/299 [64%]), urinary tract infections (n = 218/1238 [18%]; Escherichia coli, n = 21/32 [66%]), gastrointestinal infections (n = 210 [17%]; rotavirus, n = 32/97 [33%]), and invasive bloodstream infections (n = 62 [5%]; Salmonella species, n = 47 [76%]). In Plasmodium-infected children the frequency of lower respiratory tract, gastrointestinal, and bloodstream infections increased with decreasing parasite densities.

Conclusions

In a hospital setting, the likelihood of comorbidity with a nonmalarial disease is inversely correlated with increasing blood levels of malaria parasites. Hence, parasite densities provide important information as an indicator for the probability of coinfection, in particular to guide antimicrobial medication.

Accounting for aetiology: can regional surveillance data alongside host biomarker-guided antibiotic therapy improve treatment of febrile illness in remote settings?

Background: Across Southeast Asia, declining malaria incidence poses a challenge for healthcare providers, in how best to manage the vast majority of patients with febrile illnesses who have a negative malaria test. In rural regions, where the majority of the population reside, empirical treatment guidelines derived from central urban hospitals are often of limited relevance. In these settings, health workers with limited training deliver care, often without any laboratory diagnostic support. In this paper, we model the impact of point-of-care C-reactive protein testing to inform the decision to prescribe antibiotics and regional surveillance data to inform antibiotic selection, and then simulate the subsequent impact on mortality from febrile illnesses, rooted in the real-world context of rural Savannakhet province, southern Laos. Methods: Our model simulates 100 scenarios with varying quarterly incidence of six key pathogens known to be prevalent in rural Laos. In the simulations, community health workers either prescribe antibiotics in-line with current practice as documented in health facilities in rural Laos, or with the aid of the two interventions. We provide cost-effectiveness estimates for each strategy alone and then for an integrated approach using both interventions. Results: We find that each strategy is predicted to be highly cost-effective, and that the combined approach is predicted to result in the biggest reduction in mortality (averting a predicted 510 deaths per year in rural Savannakhet, a 28% reduction compared to standard practice) and is highly cost-effective, with an incremental cost-effectiveness ratio of just $66 per disability-adjusted life year averted. Conclusions: Substantial seasonal variation in the predicted optimal empirical antibiotic treatment for febrile illness highlights the benefits of up-to-date information on regional causes of fever. In this modelling analysis, an integrated system incorporating point-of-care host biomarker testing and regional surveillance data appears highly cost-effective, and may warrant piloting in a real-life setting.

Current Understanding of Innate Immune Cell Dysfunction in Childhood Undernutrition

Undernutrition affects millions of children in low- and middle-income countries (LMIC) and underlies almost half of all deaths among children under 5 years old. The growth deficits that characterize childhood undernutrition (stunting and wasting) result from simultaneous underlying defects in multiple physiological processes, and current treatment regimens do not completely normalize these pathways. Most deaths among undernourished children are due to infections, indicating that their anti-pathogen immune responses are impaired. Defects in the body's first-line-of-defense against pathogens, the innate immune system, is a plausible yet understudied pathway that could contribute to this increased infection risk. In this review, we discuss the evidence for innate immune cell dysfunction from cohort studies of childhood undernutrition in LMIC, highlighting knowledge gaps in almost all innate immune cell types. We supplement these gaps with insights from relevant experimental models and make recommendations for how human and animal studies could be improved. A better understanding of innate immune function could inform future tractable immune-targeted interventions for childhood undernutrition to reduce mortality and improve long-term health, growth and development.

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

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

Norovirus Infections and Disease in Lower-MiddleandLow-Income Countries, 1997⁻2018

Noroviruses are a major cause of viral gastroenteritis. The burden of the norovirus in low-resource settings is not well-established due to limited data. This study reviews the norovirus prevalence, epidemiology, and genotype diversity in lower-middle-income countries (LMIC) and in low-income countries (LIC). PubMed was searched up to 14 January 2019 for norovirus studies from all LIC and LMIC (World Bank Classification). Studies that tested gastroenteritis cases and/or asymptomatic controls for norovirus by reverse transcription-polymerase chain reaction (RT-PCR) were included. Sixty-four studies, the majority on children <5 years of age, were identified, and 14% (95% confidence interval; CI 14–15, 5158/36,288) of the gastroenteritis patients and 8% (95% CI 7–9, 423/5310) of healthy controls tested positive for norovirus. In LMIC, norovirus was detected in 15% (95% CI 15–16) of cases and 8% (95% CI 8–10) of healthy controls. In LIC, 11% (95% CI 10–12) of symptomatic cases and 9% (95% CI 8–10) of asymptomatic controls were norovirus positive. Norovirus genogroup II predominated overall. GII.4 was the predominant genotype in all settings, followed by GII.3 and GII.6. The most prevalent GI strain was GI.3. Norovirus causes a significant amount of gastroenteritis in low-resource countries, albeit with high levels of asymptomatic infection in LIC and a high prevalence of coinfections.

Diagnostics and genotyping of Canine parvovirus type 2 (CPV-2) from disease cases in south-eastern Poland

Canine parvovirus type 2 is one of the most common causes of death among puppies. Despite preventive vaccination, the disease continues to be diagnosed. The aim of the study was to provide a molecular characterization of CPV-2 isolates found in southeastern Poland. Genetic CPV-2 material was isolated from the blood (n=10) and feces (n=50) of infected dogs. The presence of CPV-2 was confirmed by amplification of sequences coding both VP1 and VP2 protein. The products of the PCR reaction with primers amplifying VP2 protein were sequenced and used for genotyping. Bioinformatics analysis of the sequenced PCR product was performed to determine the phylogenetic relationships with variants recorded in the public databases. Based on the analysis of polymorphism in the nucleotide sequence 7 nucleotide variants were detected and assigned into four amino acid groups. Representatives of three groups contained asparagine at amino acid position 426 of the VP2 protein, which is characteristic of CPV-2a. The variant from the fourth group belonged to type CPV-2b. CPV-2a is the dominant antigenic type of CPV-2 in Poland. The pathogen’s high degree of polymorphism is manifested not only by the presence of numerous variants within the type, but also by the presence of representatives of type CPV-2b. Further studies of the molecular epidemiology of CPV-2 are necessary to optimize the effectiveness of preventive measures.

Accounting for aetiology: can regional surveillance data alongside host biomarker-guided antibiotic therapy improve treatment of febrile illness in remote settings?

Background: Across Southeast Asia, declining malaria incidence poses a challenge for healthcare providers, in how best to manage the vast majority of patients with febrile illnesses who have a negative malaria test. In rural regions, where the majority of the population reside, empirical treatment guidelines derived from central urban hospitals are often of limited relevance. In these settings, relatively untrained health workers deliver care, often without any laboratory diagnostic support. In this paper, our aim was to model the impact on mortality from febrile illness of using point-of-care C-reactive protein testing to inform the decision to prescribe antibiotics and regional surveillance data to inform antibiotic selection, rooted in the real-world context of rural Savannakhet province, southern Laos. Methods: Our model simulates 100 scenarios with varying quarterly incidence of six key pathogens known to be prevalent in rural Laos. In the simulations, community health workers either prescribe antibiotics in-line with current practice as documented in health facilities in rural Laos, or with the aid of the two interventions. We provide cost-effectiveness estimates for each strategy alone and then for an integrated approach using both interventions. Results: We find that each strategy alone is predicted to be highly cost-effective, and that the combined approach is predicted to result in the biggest reduction in mortality (averting a predicted 510 deaths per year in rural Savannakhet, a 28% reduction compared to standard practice) and is highly cost-effective, with an incremental cost-effectiveness ratio of just $66 per disability-adjusted life year averted. Conclusions: Substantial seasonal variation in the predicted optimal empirical antibiotic treatment for febrile illness highlights the benefits of up-to-date information on regional causes of fever. In this modelling analysis, an integrated system incorporating point-of-care host biomarker testing and regional surveillance data appears highly cost-effective, and may warrant piloting in a real-life setting.

Risk factors for childhood enteric infection in urban Maputo, Mozambique: A cross-sectional study

BACKGROUND

Enteric infections are common where public health infrastructure is lacking. This study assesses risk factors for a range of enteric infections among children living in low-income, unplanned communities of urban Maputo, Mozambique.

METHODS & FINDINGS

We conducted a cross-sectional survey in 17 neighborhoods of Maputo to assess the prevalence of reported diarrheal illness and laboratory-confirmed enteric infections in children. We collected stool from children aged 1-48 months, independent of reported symptoms, for molecular detection of 15 common enteric pathogens by multiplex RT-PCR. We also collected survey and observational data related to water, sanitation, and hygiene (WASH) characteristics; other environmental factors; and social, economic, and demographic covariates. We analyzed stool from 759 children living in 425 household clusters (compounds) representing a range of environmental conditions. We detected ≥1 enteric pathogens in stool from most children (86%, 95% confidence interval (CI): 84-89%) though diarrheal symptoms were only reported for 16% (95% CI: 13-19%) of children with enteric infections and 13% (95% CI: 11-15%) of all children. Prevalence of any enteric infection was positively associated with age and ranged from 71% (95% CI: 64-77%) in children 1-11 months to 96% (95% CI: 93-98%) in children 24-48 months. We found poor sanitary conditions, such as presence of feces or soiled diapers around the compound, to be associated with higher risk of protozoan infections. Certain latrine features, including drop-hole covers and latrine walls, and presence of a water tap on the compound grounds were associated with a lower risk of bacterial and protozoan infections. Any breastfeeding was also associated with reduced risk of infection.

CONCLUSIONS

We found a high prevalence of enteric infections, primarily among children without diarrhea, and weak associations between bacterial and protozoan infections and environmental risk factors including WASH. Findings suggest that environmental health interventions to limit infections would need to be transformative given the high prevalence of enteric pathogen shedding and poor sanitary conditions observed.

TRIAL REGISTRATION

ClinicalTrials.gov NCT02362932.

Rapid Clearance and Frequent Reinfection With Enteric Pathogens Among Children With Acute Diarrhea in Zanzibar

Background

Acute infectious gastroenteritis is an important cause of illness and death among children in low-income countries. In addition to rotavirus vaccination, actions to improve nutrition status, sanitation, and water quality are important to reduce enteric infections, which are frequent also among asymptomatic children. The aim of this study was to investigate if the high prevalence of these infections reflects that they often are not cleared properly by the immune response or rather is due to frequent pathogen exposure.

Methods

Rectal swabs were collected at time of acute diarrhea and 14 days later from 127 children, aged 2-59 months and living in rural Zanzibar, and were analyzed by real-time polymerase chain reaction targeting multiple pathogens.

Results

At baseline, detection rates >20% were found for each of enterotoxigenic Escherichia coli, Shigella, Campylobacter, Cryptosporidium, norovirus GII, and adenovirus. At follow-up, a large proportion of the infections had become cleared (34-100%), or the pathogen load reduced, and this was observed also for agents that were presumably unrelated to diarrhea. Still, the detection frequencies at follow-up were for most agents as high as at baseline, because new infections had been acquired. Neither clearance nor reinfection was associated with moderate malnutrition, which was present in 21% of the children.

Conclusions

Children residing in poor socioeconomic conditions, as in Zanzibar, are heavily exposed to enteric pathogens, but capable of rapidly clearing causative and coinfecting pathogens.

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.

Evaluation of the Influence of Gastrointestinal Coinfections on Rotavirus Vaccine Effectiveness in Botswana

BACKGROUND

Studies have demonstrated reduced rotavirus vaccine effectiveness (VE) in resource-limited settings. Enteropathogen coinfections in rotavirus cases have been hypothesized to contribute to the lower VE in such settings. We sought to determine if coinfections affect rotavirus VE in Botswana.

METHODS

Between June 2013 and April 2015, children <60 months old, presenting with severe gastroenteritis at 4 hospitals as part of a national rotavirus surveillance were enrolled. Rotavirus enzyme immunoassay (EIA)-positive samples were tested with an in-house real-time polymerase chain reaction (PCR) panel that detected 9 pathogens and a commercial 15 multiplex PCR gastrointestinal pathogen panel. Coinfection was defined as detection of rotavirus plus 1 of the 5 pathogens with the highest attributable fractions for diarrhea. Vaccine status was compared between rotavirus case patients and non-rotavirus "test-negative" controls. VE was also calculated restricting cases to those with rotavirus as the only pathogen detected.

RESULTS

Two hundred and forty-two children tested rotavirus EIA positive, and 368 children were negative. Of the 182 rotavirus EIA-positive samples tested with the gastrointestinal pathogen panel assay, coinfections were detected in 60 (33%). The overall adjusted 2-dose VE was 59% (95% confidence interval [CI]: 27-77) in the rotavirus coinfection group and 51% (95% CI: -14 to 79) in the rotavirus monoinfection subgroup. Using in-house multiplex PCR panel, of 213 rotavirus EIA-positive subjects, coinfections were detected in 98 samples (46%). The overall adjusted VEs for 2 doses were 48% (95% CI: -2 to 74) and 62% (95% CI: 25-80) in rotavirus monoinfection subgroup.

CONCLUSIONS

We could not find evidence of an effect of enteric coinfections on the effectiveness of rotavirus vaccine.

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

BACKGROUND

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

OBJECTIVE

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

DATA SOURCES

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

REVIEW METHODS

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

RESULTS

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

LIMITATIONS

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

CONCLUSIONS

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

FUTURE WORK

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

STUDY REGISTRATION

This study is registered as PROSPERO CRD2016033320.

FUNDING

The National Institute for Health Research Health Technology Assessment programme.

Molecular versus culture-based testing for gastrointestinal infection

PURPOSE OF REVIEW

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

RECENT FINDINGS

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

SUMMARY

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

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.

Diagnostic performance of the Luminex xTAG gastrointestinal pathogens panel to detect rotavirus in Ghanaian children with and without diarrhoea

Background

Rotavirus is one of the leading causes of childhood diarrhoea worldwide. The highest disease burden is seen in resource-constrained settings of sub-Saharan Africa. Recently, commercial multiplex PCR panels proved their accuracy to diagnose infectious gastroenteritis in Europe and the USA. However, data on their performance using samples from tropical regions in general and to detect rotavirus in particular remains scant. We aimed to analyse the diagnostic performance of the Luminex xTAG gastrointestinal pathogens panel, a multiplex PCR, to detect rotavirus in stool samples from Ghanaian children.

Methods

A total of 682 stool samples were collected in the Ashanti region of Ghana between 2007 and 2008. Of these, 341 were from cases (children with diarrhoea), and another 341 from controls (children without diarrhoea). All samples were analysed using the Luminex xTAG assay and compared to a rotavirus quantitative reverse-transcription PCR (reference assay). Rotavirus reference assay positive samples were P and G genotyped by sequencing the rotavirus VP4 and VP7 genes.

Results

Overall agreement between the Luminex xTAG and the reference assay was excellent (kappa 0.93). The sensitivity and specificity was 88.2 % (95 % confidence interval [CI] 78.2–94.1) and 100 % (95 % CI 99.2–100), respectively. Of 76 rotavirus reference assay positive samples, 64 were successfully genotyped and the Luminex xTAG assay was able to detect all rotavirus genotypes present in the study.

Conclusion

The Luminex xTAG assay proved a sensitive and highly specific tool to detect rotavirus and may aid clinicians and public health authorities in the diagnosis and surveillance of rotavirus.