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

Human adenoviruses in children with gastroenteritis: a systematic review and meta-analysis

PURPOSE

Human adenoviruses (HAdVs) have always been suggested as one of the main causes of gastroenteritis in children. However, no comprehensive report on the global epidemiology of these viruses in pediatric gastroenteritis is available.

METHODS

A systematic search was conducted to obtain published papers from 2003 to 2023 in three main databases PubMed, Scopus, and Web of Science.

RESULTS

The estimated global pooled prevalence of HAdV infection in children with gastroenteritis was 10% (95% CI: 9-11%), with a growing trend after 2010. The highest prevalence was observed in Africa (20%, 95% CI: 14-26%). The prevalence was higher in inpatients (11%; 95% CI: 8-13%) and patients aged 5 years old and younger (9%; 95% CI: 7-10%). However, no significant difference was observed between male and female patients (P = 0.63). The most prevalent species was found to be the species F (57%; 95% CI: 41-72%). The most common HAdVs observed in children with gastroenteritis were types 40/41, 38, and 2. Analysis of case-control studies showed an association between HAdV and gastroenteritis in children (OR: 2.28, 95% CI; 1.51-3.44).

CONCLUSION

This study provided valuable insights into the importance of HAdVs in children with gastroenteritis, especially in hospitalized and younger children. The results can be used in future preventive measurements and the development of effective vaccines.

Semi-quantitative assessment of gastrointestinal viruses in stool samples with Seegene Allplex gastrointestinal panel assays: a solution to the interpretation problem of multiple pathogen detection?

PURPOSE

The aim of the study was to determine and evaluate the clinical usefulness of pathogen specific semi-quantitative cut-offs in stool samples with multiple pathogen detections.

METHODS

The PCR (Seegene Allplex Gastrointestinal Virus Assay) data from 4527 positive samples received over 16 months were retrospectively analyzed to investigate the distribution of the Ct values of each individual viral pathogen. By using interquartile ranges for each viral pathogen, pathogen specific semi-quantitative cut-offs were determined.

RESULTS

After a thorough analysis of the Ct values, a well-founded decision to exclude all results with a Ct value higher than 35 was made. This approach made it possible to generate a more nuanced report and to facilitate clinical interpretation in case of mixed infections by linking a lower Ct value of a pathogen to a greater likelihood of being a relevant causative pathogen. Moreover, not reporting viral pathogens with a Ct value higher than 35 led to a significant reduction (p < 0.0001) of reported mixed infections compared to oversimplified qualitative or qualitative reporting.

CONCLUSION

By omitting very high Ct values and reporting semi-quantitatively, value was added to the syndromic reports, leading to an easier to read lab report, especially in mixed infections.

Worldwide prevalence and genotype distribution of human astrovirus in gastroenteritis patients: A systematic review and meta-analysis

AIM

Human astrovirus (HAstV) is an important causative agent of gastroenteritis in humans, which mainly infects young children and the elderly. The goal of this study was to conduct a meta-analytic review of the prevalence of HAstV amongst patients with gastroenteritis, and to shed light on the connection between HAstV infection and gastroenteritis.

METHODS

Systematic literature searches were conducted to identify all potentially relevant studies recorded up to April 8th, 2022. For study weighting, the inverse variance method was employed and the random-effects model was applied to evaluate data. For case-control studies, the pooled odds ratio (OR) and 95% confidence interval (CI) were calculated to establish the relationship between HAstV infection and gastroenteritis.

RESULTS

Among 302423 gastroenteritis patients from 69 different countries, the overall pooled prevalence of HAstV infection was 3.48% (95% CI: 3.11%-3.89%). Case-control approach was used in 39 investigations, and the overall prevalence of HAstV infection among the 11342 healthy controls was 2.01% (95% CI: 1.40%-2.89%). Gastroenteritis and HAstV infection were associated with a pooled OR of 2.16 (95% CI: 1.72-2.71; P < 0.0001; I² = 33.7%). The most commonly found HAstV genotypes in gastroenteritis patients were HAstV1 (62.18%), HAstV7 (33.33%), and HAstV-MLB1 (17.43%).

CONCLUSION

The frequency of HAstV infection was the highest in children under the age of five, and in developing countries. The prevalence rate of HAstV was not influenced by gender. Semi-nested and nested RT-PCR were highly sensitive assays for detecting HAstV infections.

Rotavirus infections and their genotype distribution in Rwanda before and after the introduction of rotavirus vaccination

Rotavirus vaccination has reduced mortality and hospital admissions due to rotavirus diarrhoea, but its effect on rotavirus infections and the impact of rotavirus genotypes are still unclear. Real-time PCR was used to detect rotavirus and other pathogens in faeces samples from children below five years of age with acute diarrhoea, collected before (n = 827) and after (n = 807, 92% vaccinated) the introduction of vaccination in Rwanda in 2012. Rotavirus was genotyped by targeting VP7 to identify G1, G2, G3, G4, G9 and G12 and VP4 to identify P[4], P[6] and P[8]. In vaccinated children, rotavirus infections were rarer (34% vs. 47%) below 12 months of age, severe dehydration was less frequent, and rotavirus was more often found as a co-infecting agent. (79% vs 67%, p = 0.004). Norovirus genogroup II, astrovirus, and sapovirus were significantly more often detected in vaccinated children. The predominant rotavirus genotypes were G2P[4] and G12P[6] in 2009-2010 (50% and 12%), G9P[8] and G1P[8] in 2011-2012 (51% and 22%), and G12P[8] in 2014-2015 (63%). Rotavirus vaccination in Rwanda has reduced the severity of rotavirus gastroenteritis and rotavirus infection frequency during the first year of life. Rotavirus infections were frequent in vaccinated children with diarrhoea, often as co-pathogen. Rotavirus genotype changes might be unrelated to vaccination because shifts were observed also before its introduction.

The prevalence, risk factors analysis and evaluation of two diagnostic techniques for the detection of Cryptosporidium infection in diarrheic sheep from Pakistan

Background

Cryptosporidium spp. is recognized as an opportunistic zoonotic parasite that infects humans as well as wild and domestic animals. This enteric protozoan is a major cause of diarrhea in humans and animals and often result in death due to severe dehydration. The present study was designed to investigate the prevalence, identification of various risk factors and evaluation of sensitivity of the two diagnostic techniques for rapid and correct detection of Cryptosporidium infection in diarrheic sheep in Pakistan.

Methods

A total of 360 fecal samples were collected and processed for detection of Cryptosporidium infection after proper preservation. These samples were properly stained with modified Ziehl-Neelsen acid staining and then examined under simple microscope at 100x magnification for confirmation of Cryptosporidium oocysts. The same samples were again processed through simple PCR for confirmation of the Cryptosporidium spp.

Results

The age wise prevalence was detected through simple microscopy and PCR. We found highest prevalence at the age of ≤1 year followed by 1–2 years of age while the lowest prevalence was recorded at the age of ≥ 2–3 years of sheep and found significant difference between different ages (P<0.05). The sex wise prevalence showed the highest prevalence in male (♂) animals detected compared to female (♀). The overall prevalence was detected 27.08% and 18.80% through PCR and simple microscopy, respectively, and significant difference between two diagnostic techniques were observed (P<0.05). Considering the seasonality, the highest prevalence was recorded through simple microscopy in autumn, summer, and spring, while the lowest in winter. These results were confirmed through PCR.

Conclusion

It was concluded that molecular detection is the most efficient, specific and sensitive technique for detection of Cryptosporidium infection than simple microscopy. Moreover sheep is the major potential source of infection to other wild and domestic animals including humans.

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.

Prevalence, determinants, and antimicrobial susceptibility patterns of Campylobacter infection among under-five children with diarrhea at Governmental Hospitals in Hawassa city, Sidama, Ethiopia. A cross-sectional study

Background

Campylobacteriosis, is a zoonotic bacterial disease observed with a rising worldwide. It is becoming the most commonly recognized cause of bacterial gastroenteritis in under-five mortality in recent years. This study was done to determine the prevalence and determinants of Campylobacter infection among under-fives with acute watery diarrhea.

Methods

This institutional-based cross-sectional study was conducted at governmental and private health institutions in Hawassa city. All outpatient under-five children who met the inclusion criteria from April 2021 to August 2021 were enrolled in this study. Demographic and clinical data were obtained using a standardized data collection tool. Stool samples were collected from each participant with a sterile container and inoculated on a campylobacter agar media. The isolates were identified by using biochemical tests and a disc diffusion technique was performed to determine the antimicrobial sensitivity patterns of the isolates. Data were entered and analyzed using SPSS version 21. Descriptive and Logistic regression analysis was applied to determine the determinants of Campylobacter infection. P-value < 0.05 was considered statistically significant.

Results

A total of 235 under-five children were enrolled in this study with a 100% response rate. Of these 130 (55.3%) and 105(44.7%) were males and females respectively with the age range of 2 months to 60 months with the mean age of 25 months. The majority of the 150 (63.2%) were rural residents. Of 235 under-fives with acute watery diarrhea, 16 (6.8%) patients were found to have Campylobacter infection with (95% CI, 3.8–10.2%). Consumption of pasteurized milk (AOR: 0.12; 95% CI 0.02–0.75, P<0.05), presence of domestic animals like cats, hens, and cows (AOR: 0.09: 95% CI 0.01–0.67, P<0.05), absence of handwashing practice before food preparation (AOR: 3.63, 95% CI 1.15–11.46, P<0.05) showed significant association with campylobacter infection.

The antimicrobial susceptibility patterns of the isolated bacteria were 100% sensitivity to Azithromycin, Chloramphenicol, and Gentamicin, however; it was 100% resistant to Cephalothin. The associations of socio-demographic, environmental, and behavioral factors were compared and consumption of unpasteurized milk, the presence of domestic animal like the cat was significantly associated.

Conclusion

Campylobacter infection showed a comparatively low prevalence in under-fives with acute watery diarrhea. In this study contact with cats, consumption of unpasteurized milk were associated with Campylobacter infection. The treatment approach of Campylobacter infection must consider the sensitivity profile of antibiotics as indicated in the study. We, therefore, recommend further studies to determine the species responsible for Campylobacter infection with other co-morbidities and the susceptibility pattern for each species to indicate appropriate antibiotic therapy.

Global molecular prevalence and genotype distribution of Sapovirus in children with gastrointestinal complications: A systematic review and meta-analysis

Sapovirus (SaV) is an emerging cause of children gastrointestinal complications such as acute gastroenteritis (AGE). The aim of the present systematic review and meta-analysis was to estimate the global prevalence of the SaV in children and association of infection with SaVs and AGE in children based on case-control studies. Four international databases (PubMed, Scopus, Web of Sciences and Google Scholar) were used to retrieve English-language studies published between January 2000 and December 2020. Comprehensive Meta-Analysis software was applied to estimate the overall prevalence, publication bias and heterogeneity index. The pooled prevalence of SaV infection among children with gastroenteritis was 3.4% [95% confidence interval (CI): 2.9%-3.9%] based on a random-effects meta-analysis. Genogroup I was the dominant genogroup of SaV in children with gastroenteritis [2.2% (95% CI: 1.6%-3.0%)], association analysis showed that SaV was associated with gastroenteritis [OR: 1.843 (95% CI: 1.27-2.66)]. Given the significant prevalence of the virus in children, it is necessary to pay more attention to this situation. Therefore, preventive health measures in children should be a priority.

Prevalence of diarrhoeal pathogens among children under five years of age with and without diarrhoea in Guinea-Bissau

BACKGROUND

Childhood diarrhoea, a major cause of morbidity and mortality in low-income regions, remains scarcely studied in many countries, such as Guinea-Bissau. Stool sample drying enables later qPCR analyses of pathogens without concern about electricity shortages.

METHODS

Dried stool samples of children under five years treated at the Bandim Health Centre in Bissau, Guinea-Bissau were screened by qPCR for nine enteric bacteria, five viruses, and four parasites. The findings of children having and not having diarrhoea were compared in age groups 0-11 and 12-59 months.

RESULTS

Of the 429 children- 228 with and 201 without diarrhoea- 96.9% and 93.5% had bacterial, 62.7% and 44.3% viral, and 52.6% and 48.3% parasitic pathogen findings, respectively. Enteroaggregarive Escherichia coli (EAEC; 60.5% versus 66.7%), enteropathogenic E. coli (EPEC; 61.4% versus 62.7%), Campylobacter (53.2% versus 51.8%), and enterotoxigenic E. coli (ETEC; 54.4% versus 44.3%) were the most common bacterial pathogens. Diarrhoea was associated with enteroinvasive E. coli (EIEC)/Shigella (63.3%), ETEC (54.4%), astrovirus (75.0%), norovirus GII (72.6%) and Cryptosporidium (71.2%). The only pathogen associated with severe diarrhoea was EIEC/Shigella (p<0.001). EAEC was found more frequent among the infants, and EIEC/Shigella, Giardia duodenalis and Dientamoeba fragilis among the older children.

CONCLUSIONS

Stool pathogens proved common among all the children regardless of them having diarrhoea or not.

Systematic Review on the Correlation of Quantitative PCR Cycle Threshold Values of Gastrointestinal Pathogens With Patient Clinical Presentation and Outcomes

Background: Quantitative (q) polymerase chain reaction (PCR) cycle threshold (Ct) values represent the number of amplification cycles required for a positive PCR result and are a proxy of pathogen quantity in the tested sample. The clinical utility of Ct values remains unclear for gastrointestinal infections. Objectives: This systematic review assesses the global medical literature for associations between Ct values of gastrointestinal pathogens and patient presentation and clinical outcomes. Data Sources: MEDLINE, EMBASE, Cochrane library databases: searched January 14-17, 2020. Study Eligibility Criteria: Studies reporting on the presence or absence of an association between Ct values and clinical outcomes in adult and pediatric populations were included. Animal studies, reviews, meta-analyses, and non-English language studies were excluded. Participants: Humans infected with gastrointestinal pathogens, detected with qPCR. Interventions: Diagnostics assessing Ct values. Extracted data were reported narratively. Results: Thirty-three eligible studies were identified; the most commonly studied pathogens were Clostridioides difficile (n = 15), norovirus (n = 10), and rotavirus (n = 9). Statistically significant associations between low C. difficile Ct values and increased symptom severity or poor outcome were reported in 4/8 (50%) studies, and increased risk of death in 1/2 (50%) studies; no significant associations were found between Ct value and duration of symptoms or length of hospital stay. Among studies of norovirus, 5/7 (71%), mainly genogroup II, reported symptomatic cases with significantly lower median Ct values than controls. Significantly lower rotavirus Ct values were also observed in symptomatic cases vs. controls in 3/7 (43%) studies, and associated with more severe symptoms in 2/2 studies. Contradictory associations were identified for non-C. difficile bacterial and parasitic pathogens. Conclusions: In conclusion, some studies reported clinically useful associations between Ct values and patient or healthcare outcomes; additional, well-designed, large-scale trials are warranted based on these findings. Systematic Review Registration: [PROSPERO], identifier [CRD42020167239].

Polymicrobial gastroenteritis in children

AIM

Co-infections with viral and bacterial enteropathogens often augment severity of diarrhoea, however, there is limited evidence on the clinical importance of bacterial enteric co-infections. We investigated the rate, type and impact of bacterial enteropathogens and their associations in children with gastroenteritis.

METHODS

Retrospective cohort study that included children 0-18 years old with acute bacterial diarrhoea during a 27-year period (1993-2019), in Crete, Greece. Differences in clinical characteristics and pathogen associations were investigated between single and multiple infections.

RESULTS

Two or more bacteria were isolated in stool culture in 53 out of 1932 children (2.74%). Patients with co-infections were younger (p 0.0001) and had higher hospitalisation rates (p 0.03). Escherichia coli (E. coli) was the most prevalent pathogen associated with co-infections, in particular the E. coli enteropathogenic strains O127 and O111 (p 0.001), and Salmonella spp the least (p 0.001). Co-occurrence analysis revealed two positively associated pathogen pairs, E. coli with Campylobacter spp and E. coli (p 0.001) with Salmonella spp (p 0.04).

CONCLUSION

Bacterial enteropathogen co-infection was most common with E. coli strains and related to higher hospitalisation rates and younger age.

Prevalence of cryptosporidiosis among children with diarrhoea under five years admitted to Kosti teaching hospital, Kosti City, Sudan

Background

Cryptosporidiosis is a disease caused by infection with an intestinal coccidian parasite Cryptosporidium. Cryptosporidium species are the second leading cause of diarrheal disease and death in children in developing countries. Until now, no data have been available or published on its prevalence among children with diarrhea in Sudan. Therefore, this paper was designed to determine the prevalence rate of Cryptosporidium among children with diarrhea under 5 years who were admitted to Kosti Teaching Hospital.

Methods

A hospital-based cross-sectional study including children under 5 years old admitted to the pediatric section of the hospital between September 2020 and December 2020. A total of one-hundred and fifty stool samples were collected. All stool samples were examined using the modified Ziehl Neelsen (mZN) staining technique and then examined microscopically for Cryptosporidium infection.

Results

A total of 150 children were examined out of which 70 presented with diarrhea. A greater prevalence of 19/70 (27.1%) of Cryptosporidium was observed in children with diarrhea than children without diarrhea 7/80 (8.8%). There was a significant relationship between the prevalence of Cryptosporidium and the presence of diarrhea in children under 5 years in the Kosti Teaching Hospital(P < 0.05). It was found that a higher prevalence was registered among children using piped-water sources for drinking.

Conclusions

The overall prevalence of parasite detected was 17.3% among children admitted to Kosti Teaching Hospital. The prevalence rate of the infection among Children with diarrhoea was 27.1%. Studying the prevalence rate of cryptosporidiosis among diarrheic children may predict their health status, leading to a better diagnosis, treatment, and, therefore, patients’ status improvement.

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.

A systematic review and meta-analysis reveal that Campylobacter spp. and antibiotic resistance are widespread in humans in sub-Saharan Africa

INTRODUCTION

Campylobacter spp. are zoonotic bacteria that cause gastroenteritis in humans worldwide, whose main symptom is diarrhea. In certain cases, extra intestinal manifestations may occur, such as Guillain Barré syndrome. The bacteria cause severe diarrhea mostly in children and in immunocompromised individuals. This review aims to address the prevalence of Campylobacter spp. in humans in sub-Saharan Africa. It also aims to understand the impact of HIV in the prevalence, as well as to report data on antibiotic resistance and propose research priorities.

METHODS

We followed PRISMA guidelines to find studies on the occurrence of Campylobacter spp. in humans in all countries from sub-Saharan Africa. Studies published between 2000 and 2020 were searched in PubMed, Cochrane Library, CINAHL, African Index Medicus, African Journals Online, Google Scholar and Science Direct. We have conducted a random-effect meta-analysis and calculated the proportion of resistant isolates to different antibiotics.

RESULTS AND DISCUSSION

We found 77 studies that described such occurrence in humans in 20 out of 53 sub-Saharan African countries. Campylobacter jejuni was the most prevalent species. Pooled prevalence was 9.9% (CI: 8.4%-11.6%). No major variations within the different sub-regions were found. Most studies reported Campylobacter spp. as the cause of diarrhea, mainly in children. Some studies reported the bacteria as a possible etiologic agent of acute flaccid paralysis and urinary tract infection. Campylobacter spp. presented a higher pooled prevalence in HIV infected patients, although not statistically significant. High proportions of resistant strains were reported for many antibiotics, including erythromycin and tetracycline.

CONCLUSION

Campylobacter spp. occur in sub-Saharan Africa, although information is scarce or inexistent for many countries. Research priorities should include investigation of the understudied species; extra intestinal manifestations; the impact of HIV infection and associated risk factors. Control strategies should be reinforced to contain the spread of this pathogen and drug resistance.

Association of genetic polymorphism at tumor necrosis factor-α gene promoter - 1031T/C and parasitic infections among children in Northern South Africa

Intestinal parasitic diseases are common in developing countries including South Africa and have been documented to be the most common in children under the age of five. The present study aimed to identify any potential association that may exist between TNF-α promoter gene polymorphism and parasitic infections. A total of 199 blood samples were evaluated from children who were part of the MAL-ED study cohort. The DNA was used to investigate polymorphism in the promoter region of the TNF-α gene at position -1031T/C. The polymorphisms were detected by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) assay. The TC genotype at position -1031 was significantly higher in healthy controls children than in children who were infected with Entamoeba species (59.9% vs 29.4%, P = 0.015) and Entamoeba coli (59.1% vs 30.8%, P = 0.046), indicating that TC genotype may be protective against Entamoeba infections and Entamoeba coli infections. The CC genotype at position -1031 was more common among children with parasite and diarrhea and the results was statistically significant (P = 0.04). This study has revealed that the CC genotype may be is a risk factor for symptomatic parasitic infections while the TC genotype might be protective of Entamoeba infections among children in Dzimauli community.

Prevalence, Risk Factors, and Antimicrobial Resistance Profiles of Thermophilic Campylobacter Species in Humans and Animals in Sub-Saharan Africa: A Systematic Review

Thermophilic Campylobacter species are clinically important aetiologies of gastroenteritis in humans throughout the world. The colonization of different animal reservoirs by Campylobacter poses an important risk for humans through shedding of the pathogen in livestock waste and contamination of water sources, environment, and food. A review of published articles was conducted to obtain information on the prevalence and antimicrobial resistance (AMR) profiles of thermophilic Campylobacter species in humans and animals in sub-Saharan Africa (SSA). Electronic databases, namely, PubMed, Google Scholar, Research4life-HINARI Health, and Researchgate.net, were searched using the following search terms “thermophilic Campylobacter,” “Campylobacter jejuni,” “Campylobacter coli,” “diarrhea/diarrhoea,” “antimicrobial resistance,” “antibiotic resistance,” “humans,” “animals,” “Sub-Saharan Africa,” and “a specific country name.” Initially, a total of 614 articles were identified, and the lists of references were screened in which 22 more articles were identified. After screening, 33 articles on humans and 34 on animals and animal products were included in this review. In humans, Nigeria reported the highest prevalence (62.7%), followed by Malawi (21%) and South Africa (20.3%). For Campylobacter infections in under-five children, Kenya reported 16.4%, followed by Rwanda (15.5%) and Ethiopia (14.5%). The country-level mean prevalence in all ages and under-five children was 18.6% and 9.4%, respectively. The prevalence ranged from 1.7%–62.7% in humans and 1.2%–80% in animals. The most reported species were C. jejuni and C. coli. The AMR to commonly used antimicrobials ranged from 0–100% in both humans and animals. Poultry consumption and drinking surface water were the main risk factors for campylobacteriosis. The present review provides evidence of thermophilic Campylobacter occurrence in humans and animals and high levels of AMR in SSA, emphasizing the need for strengthening both national and regional multisectoral antimicrobial resistance standard surveillance protocols to curb both the campylobacteriosis burden and increase of antimicrobial resistance in the region.

Prevalence and risk factors associated with cryptosporidiosis among children within the ages 0-5 years attending the Limbe regional hospital, southwest region, Cameroon

Background

Cryptosporidiosis is a pathological condition caused by infection with coccidian protozoan parasites Cryptosporidium. Cryptosporidium is one of the most common causes of childhood diarrhea in developing countries. So far, no data has been published on its prevalence among children with diarrhea in Cameroon. This study was therefore, designed to assess the prevalence and risk factors associated with Cryptosporidiosis among children within the ages 0–5 years suffering from diarrhea and being attended to at the Limbe Regional Hospital.

Methods

The study was a hospital based analytical cross-sectional study involving children within the ages 0–5 years (n = 112) hospitalized or consulted in the pediatric departments of the hospital between April 2018 and May 2018. Stool specimens were processed using the modified acid-fast staining method, and microscopically examined for Cryptosporidium infection.

Results

A total of 112 participants were recruited out of which 67 presented with diarrhea. A high prevalence 9/67 (13.40%) of Cryptosporidium was noticed in children with diarrhea than children without diarrhea 1/45 (2.2%). There was a significant relationship (p = 0.041) between prevalence of Cryptosporidium and the presence of diarrhea in children within the ages 0–5 years in the Limbe Regional Hospital. It was realized that children from parents with primary level of education, children whose parents did not respect exclusive breastfeeding and those whose parents were giving them pipe borne water for drinking recorded a higher prevalence.

Conclusions

This study revealed an overall prevalence of 8.9% for Cryptosporidium among children of ages 0–5 years that attended the Limbe Regional Hospital. The prevalence among children that presented with diarrhea was 13.4%. The study clearly demonstrated that Cryptosporidium is an important protozoal etiologic agent for children with diarrhea in Limbe.

Electronic supplementary material

The online version of this article (10.1186/s12889-019-7484-8) contains supplementary material, which is available to authorized users.

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.

Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia

Water borne diarrheal pathogens might accumulate in river water and cause contamination of drinking and irrigation water. The La Paz River basin, including the Choqueyapu River, flows through La Paz city in Bolivia where it is receiving sewage, and residues from inhabitants, hospitals, and industry. Using quantitative real-time PCR (qPCR), we determined the quantity and occurrence of diarrheagenic Escherichia coli (DEC), Salmonella enterica, Klebsiella pneumoniae, Shigella spp. and total enterobacteria in river water, downstream agricultural soil, and irrigated crops, during one year of sampling. The most abundant and frequently detected genes were gapA and eltB, indicating presence of enterobacteria and enterotoxigenic E. coli (ETEC) carrying the heat labile toxin, respectively. Pathogen levels in the samples were significantly positively associated with high water conductivity and low water temperature. In addition, a set of bacterial isolates from water, soil and crops were analyzed by PCR for presence of the genes blaCTX-M, blaKPC, blaNDM, blaVIM and blaOXA-48. Four isolates were found to be positive for blaCTX-M genes and whole genome sequencing identified them as E. coli and one Enterobacter cloacae. The E. coli isolates belonged to the emerging, globally disseminated, multi-resistant E. coli lineages ST648, ST410 and ST162. The results indicate not only a high potential risk of transmission of diarrheal diseases by the consumption of contaminated water and vegetables but also the possibility of antibiotic resistance transfer from the environment to the community.

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.

Potential Diarrheal Pathogens Common Also in Healthy Children in Angola

BACKGROUND

Globally, diarrhea kills almost 1500 children daily. In diagnostics, molecular methods are replacing traditional assays. We aimed to investigate enteropathogens in children with and without diarrhea in Luanda, the capital of Angola.

METHODS

One hundred and ninety-four stool samples from 98 children with acute diarrhea and 96 children without diarrhea were investigated for 17 enteropathogens with multiplex real-time polymerase chain reaction.

RESULTS

The median age of children was 10.5 months. Enteropathogens, bacteria, viruses and parasites were detected in 91%, 78%, 50% and 25%, respectively. A positive finding was significantly (P = 0.003) more common in diarrhea when testing for all pathogens combined, for bacteria alone and for viruses alone. More than one pathogen was found more frequently in diarrhea than in non-diarrhea stool samples, in 87% and in 59% (P < 0.0001), respectively. The median number (interquartile range) of pathogens detected was 3 (2) versus 1.5 (2; P < 0.0001), respectively. When age was taken into account, diarrhea was found to be associated with enterotoxigenic and enteroaggregative Escherichia coli, Shigella, Campylobacter, rotavirus, sapovirus and Cryptosporidium.

CONCLUSIONS

Multiplex polymerase chain reaction detected enteropathogens in almost all stool samples of children in Luanda, albeit this occurred more often in diarrhea. Children with diarrhea showed more mixed infections than children without diarrhea.

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.

Ondansetron treatment reduces rotavirus symptoms-A randomized double-blinded placebo-controlled trial

Background

Rotavirus and norovirus cause acute gastroenteritis with severe diarrhoea and vomiting, symptoms that may lead to severe dehydration and death. The objective of this randomized double-blinded placebo-controlled study was to investigate whether ondansetron, a serotonin receptor antagonist could attenuate rotavirus- and norovirus-induced vomiting and diarrhoea, which would facilitate oral rehydration and possibly accelerate recovery and reduce need for hospitalization.

Methods

Children with acute gastroenteritis, aged 6 months to 16 years where enrolled (n = 104) and randomized to one single oral dose (0.15mg/kg) of ondansetron (n = 52) or placebo (n = 52). The number of diarrhoea and vomiting episodes during the 24 hours following treatment was reported as well as the number of days with symptoms. Pathogens in faeces were diagnosed by real-time PCR. Outcome parameters were analyzed for rotavirus- and norovirus-positive children.

Results

One dose of oral ondansetron reduced duration of rotavirus clinical symptoms (p = 0.014), with a median of two days. Furthermore, ondansetron reduced diarrhea episodes, most pronounced in children that had been sick for more than 3 days before treatment (p = 0.028).

Conclusion

Ondansetron may be a beneficial treatment for children with rotavirus gastroenteritis.

Trial registration

European Clinical Trial Database EudraCT 2011-005700-15.

Can Use of Viral Load Improve Norovirus Clinical Diagnosis and Disease Attribution?

BACKGROUND

Real-time reverse-transcriptase polymerase chain reaction (RT-PCR) is the state-of-the-art diagnostic for norovirus. Cycle threshold (Ct), an indicator of viral load, may be associated with symptomatic disease as well as demographic and outbreak characteristics.

METHODS

Data on (1) outbreak and sporadic cases and (2) asymptomatic controls in the United States and Latin America were analyzed. With multivariate regression models, we assessed relationships between various factors and Ct values, and we calculated odds ratios (ORs) for the presence of symptoms and attributable fractions of norovirus. Receiver-operating characteristic analysis was performed to define an optimal Ct cutoff to identify disease-causing infections.

RESULTS

Cycle threshold values were lower (ie, higher viral loads) among symptomatic cases (model-adjusted mean ± standard error: 25.3 ± 1.2) compared with asymptomatic controls (28.5 ± 1.4). Cycle threshold values were significantly different across age groups, norovirus genogroups, timing of specimen collection, outbreak settings, and transmission modes. Genogroup II (GII) Ct values were associated with presence of symptoms (OR = 1.1), allowing us to estimate that 16% of diarrheal disease was attributable to norovirus. The optimized Ct cutoff led to poor sensitivity and specificity for genogroup I and GII.

CONCLUSIONS

Cycle threshold values were associated with host, pathogen, and outbreak factors. Cycle threshold values may not effectively distinguish disease-causing infection for individual patients, but they are useful for epidemiological studies aiming to attribute disease.

Group A rotavirus gastroenteritis: post-vaccine era, genotypes and zoonotic transmission

This article provides a review of immunity, diagnosis, and clinical aspects of rotavirus disease. It also informs about the changes in epidemiology of diarrheal disease and genetic diversity of circulating group A rotavirus strains following the introduction of vaccines. Group A rotavirus is the major pathogen causing gastroenteritis in animals. Its segmented RNA genome can lead to the emergence of new or unusual strains in human populations via interspecies transmission and/or reassortment events.

Norovirus infections in young children in Lusaka Province, Zambia: clinical characteristics and molecular epidemiology

Background

The burden, clinical features, and molecular epidemiology of norovirus infection in young children in southern Africa are not well defined.

Methods

Using data from a health facility-based surveillance study of children <5 years in Lusaka Province, Zambia presenting with diarrhea, we assessed the burden of norovirus infection. A convenience sample of 454 stool specimens was tested for norovirus using reverse-transcriptase polymerase chain reaction (RT-PCR). RT-PCR positive samples underwent additional nucleotide sequencing for genogroup and genotype identification. Clinical features and severity of diarrheal illnesses were compared between norovirus-positive and -negative subjects using Chi-squared and t-tests.

Results

Norovirus was detected in 52/454 (11.5%) specimens tested. Abdominal pain, fever, and vomiting were the most common presenting features in norovirus-associated illnesses. However, there were no significant differences in the clinical features of norovirus-positive compared to norovirus-negative illnesses. Of 43 isolates that were available for sequencing, 31 (72.1%) were genogroup II (GII) and 12 (27.9%) were genogroup I (GI). The distribution of genotypes was diverse.

Conclusions

Noroviruses were detected in approximately 10% of young children with diarrhea in the Lusaka Province of Zambia, with GII representing the majority of infections. These findings support the role of norovirus in symptomatic diarrhea disease in Africa. Further studies are needed to confirm these observations and to evaluate prevention strategies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-017-2206-2) contains supplementary material, which is available to authorized users.

Correlation of Clinical Outcomes With Multiplex Molecular Testing of Stool From Children Admitted to Hospital With Gastroenteritis in Botswana

BACKGROUND

Diarrheal disease is a leading cause of death for young children. Most pediatric gastroenteritis is caused by viral pathogens; consequently, current recommendations advocate against routine antibacterial therapy if children present without bloody stools.

METHODS

In this prospective cohort study, we enrolled children with severe acute gastroenteritis admitted to hospital in Botswana. Details of presenting history, physical examination, and course in the hospital were recorded. Stool samples were characterized using a 15 pathogen polymerase chain reaction assay.

RESULTS

There were 671 participants with a median age of 8.3 months; 77 (11%) had severe acute malnutrition. Only 74 children had bloody stools, of whom 48 (65%) had a detectable bacterial pathogen, compared to 195 of 592 (33%) of those without. There were 26 deaths (3.9%). Covariates associated with death in multivariable logistic regression were the detection of any of Campylobacter/Shigella/enterotoxigenic Escherichia coli (odds ratio [OR] 2.57, 95% confidence interval [CI] 1.07-6.17), severe acute malnutrition (OR 4.34, 95% CI 1.79-10.5), and antibiotic therapy (OR 8.82, 95% CI 2.03-38.2). There was no significant association between bloody stools and death, and the effect of Campylobacter/Shigella/enterotoxigenic E. coli infection on death was not modified by the presence of bloody stools.

CONCLUSIONS

Detection of bacterial enteropathogens is associated with increased mortality in children in sub-Saharan Africa. Unfortunately, most children with these infections do not have bloody stools, and bloody dysentery was not found to be associated with worse outcomes. Clinical trials evaluating outcomes associated with more aggressive diagnostic strategies in children presenting with severe acute gastroenteritis in sub-Saharan Africa should be undertaken.

Reassuringly low carriage of enteropathogens among healthy Swedish children in day care centres

OBJECTIVES

Infectious gastroenteritis is one of the most common diseases among children and has a considerable impact on health and socio-economy. Day care centres are high-risk environments for infections. The aim of this study was to investigate if asymptomatic preschool children constitute a reservoir for potential enteropathogens.

STUDY DESIGN

In total, 438 individual diapers were collected from day care centres in Uppsala, Sweden, during spring and autumn, and molecular techniques were used to estimate the prevalence of asymptomatic carriage of multiple enteropathogens.

METHODS

Faecal samples were analysed with multiplex polymerase chain reaction (PCR) (xTAG^® Gastrointestinal Pathogen Panel; Luminex Corporation, Toronto, Canada) targeting 21 different pathogens. Samples with a median fluorescence intensity above threshold were re-analysed with a second PCR assay.

RESULTS

Sixteen of the 438 samples were positive for enteropathogens, 1.6% for enteric adenovirus, 0.7% for Campylobacter spp., and 0.7% for norovirus.

CONCLUSIONS

Preschool children in Uppsala constitute a limited reservoir for potential enteropathogens.

Prevalence and molecular characterization of human noroviruses and sapoviruses in Ethiopia

Viral gastroenteritis is a major public health problem worldwide. In Ethiopia, very limited studies have been done on the epidemiology of enteropathogenic viruses. The aim of this study was to detect and characterize noroviruses (NoVs) and sapoviruses (SaVs) from acute gastroenteritis patients of all ages. Fecal samples were collected from diarrheic patients (n = 213) in five different health centers in Addis Ababa during June-September 2013. The samples were screened for caliciviruses by reverse transcription polymerase chain reaction (RT-PCR) using universal and genogroup-specific primer pairs. Phylogenetic analyses were conducted using the sequences of the PCR products. Of the clinical samples, 25.3 % and 4.2 % were positive for NoV and SaV RNA, respectively. Among the norovirus positives, 22 were sequenced further, and diverse norovirus strains were identified: GI (n = 4), GII (n = 17) and GIV (n = 1). Most strains were GII (n = 17/22: 77.2 %), which were further divided into three different genotypes (GII.4, GII.12/GII.g recombinant-like and GII.17), with GII.17 being the dominant (7/17) strain detected. GI noroviruses, in particular GI.4 (n = 1), GI.5 (n = 2) and GI.8 (n = 1), were also detected and characterized. The GIV strain detected is the first from East Africa. The sapoviruses sequenced were also the first reported from Ethiopia. Collectively, this study showed the high burden and diversity of noroviruses and circulation of sapoviruses in diarrheic patients in Ethiopia. Continued surveillance to assess their association with diarrhea is needed to define their epidemiology, disease burden, and impact on public health.

Aetiology of diarrhoeal disease and evaluation of viral-bacterial coinfection in children under 5 years old in China: a matched case-control study

Globally, diarrhoeal diseases are the second leading cause of death among children under 5 years old. Few case-control studies on the aetiology of diarrhoea have been conducted in China. A case-control study on 922 children under 5 years old who presented with diarrhoea and individually matched controls was conducted in China between May 2011 and January 2013. Quantitative PCR was used to analyze stool samples for 10 diarrhoeal pathogens. Potential enteric pathogens were detected in 377 (81.8%) of 461 children with diarrhoea and 215 controls (46.6%, p <0.001). Rotavirus, norovirus GII, Shigella and adenovirus were qualitatively associated with diarrhoea. Using receiver operating characteristic curves, the optimal cutoff threshold for defining a symptomatic individual was 72, 5840, and 10(4) copies per reaction for rotavirus (odds ratio 259), norovirus GII (odds ratio 10.6) and Shigella (odds ratio 5.1). The attributable fractions were 0.18 for rotavirus, 0.08 for norovirus GII, 0.01 for Shigella and 0.04 for adenovirus. Coinfections between pathogens were common. Two pairs, rotavirus and adenovirus, and norovirus GII and Salmonella were positively associated. The co-occurrence of rotavirus and sapovirus, astrovirus, enterotoxigenic Escherichia coli or Campylobacter jejuni only occurred in children with disease. Coinfection was not correlated with clinical symptoms. Quantitative data are critical. Our results indicate that increased pathogen loads increase the OR between diarrhoea and rotavirus, norovirus GII and Shigella. Coinfections with rotavirus and norovirus GII are common and occur in a nonrandom distribution. Despite testing for ten diarrhoeal pathogens, over two-thirds of cases do not have a recognized attributable cause.

Noroviruses: epidemiology, immunity and prospects for prevention

In recent years, noroviruses have become recognized as an important cause of both sporadic and epidemic acute gastroenteritis (AGE), largely due to the improved availability of broadly reactive real-time RT-PCR (TaqMan-based RT-PCR) assays. While there is substantial diversity among noroviruses, one specific genotype, GII.4, is the most common etiology in sporadic and epidemic AGE. Outbreaks of norovirus AGE most commonly occur in healthcare facilities and restaurants and result in significant morbidity and mortality and substantial healthcare costs. Norovirus vaccine development is progressing, and Phase I and II human trials have shown proof-of-principle that norovirus vaccines can reduce illness and infection.

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.

Detection of major diarrheagenic bacterial pathogens by multiplex PCR panels

Diarrheal diseases remain a major threat to the youngest population in low- and middle-income countries. The main bacterial pathogens causing diarrhea are diarrheagenic Escherichia coli (DEC) that consists of enteroaggregative (EAEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), enterohemorrhagic EHEC and enteroinvasive E. coli (EIEC), Salmonella, Shigella spp. (S. dysenteria, S. sonnei, S. flexneri) Campylobacter (C. coli, C. jejuni), Vibrio (V. vulnificus, V. parahaemolyticusm, V. cholerae), Yersinia enterocolitica and Aeromonas hydrophila. The aim of this study was to set up rapid multiplex PCR (mPCR) panels to identify these diarrheagenic pathogens based on their specific virulence genes. Primers against specific target genes were combined into three mPCR panels: one for diarrheal E. coli, one for pathogens causing mainly bloody diarrhea, and the third for the remaining pathogens. The panels were tested against a set of stool samples from Swedish children with diarrhea and controls and the analysis identified bacterial pathogens in 14/54 (26%) of the samples. These results show that our three developed mPCR panels can detect main bacterial diarrheagenic pathogens in clinical samples.