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

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.

Clinical and nutritional correlates of bacterial diarrhoea aetiology in young children: a secondary cross-sectional analysis of the ABCD trial

OBJECTIVE

The objective was to assess the association between nutritional and clinical characteristics and quantitative PCR (qPCR)-diagnosis of bacterial diarrhoea in a multicentre cohort of children under 2 years of age with moderate to severe diarrhoea (MSD).

DESIGN

A secondary cross-sectional analysis of baseline data collected from the AntiBiotics for Children with Diarrhoea trial (NCT03130114).

PATIENTS

Children with MSD (defined as >3 loose stools within 24 hours and presenting with at least one of the following: some/severe dehydration, moderate acute malnutrition (MAM) or severe stunting) enrolled in the ABCD trial and collected stool sample.

STUDY PERIOD

June 2017-July 2019.

INTERVENTIONS

None.

MAIN OUTCOME MEASURES

Likely bacterial aetiology of diarrhoea. Secondary outcomes included specific diarrhoea aetiology.

RESULTS

A total of 6692 children with MSD had qPCR results available and 28% had likely bacterial diarrhoea aetiology. Compared with children with severe stunting, children with MAM (adjusted OR (aOR) (95% CI) 1.56 (1.18 to 2.08)), some/severe dehydration (aOR (95% CI) 1.66 (1.25 to 2.22)) or both (aOR (95% CI) 2.21 (1.61 to 3.06)), had higher odds of having likely bacterial diarrhoea aetiology. Similar trends were noted for stable toxin-enterotoxigenic Escherichia coli aetiology. Clinical correlates including fever and prolonged duration of diarrhoea were not associated with likely bacterial aetiology; children with more than six stools in the previous 24 hours had higher odds of likely bacterial diarrhoea (aOR (95% CI) 1.20 (1.05 to 1.36)) compared with those with fewer stools.

CONCLUSION

The presence of MAM, dehydration or high stool frequency may be helpful in identifying children with MSD who might benefit from antibiotics.

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.

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.

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.

IFN-λ4 is associated with increased risk and earlier occurrence of several common infections in African children

Genetic polymorphisms within the IFNL3/IFNL4 genomic region, which encodes type III interferons, have been strongly associated with clearance of hepatitis C virus. We hypothesized that type III interferons might be important for the immune response to other pathogens as well. In a cohort of 914 Malian children, we genotyped functional variants IFNL4-rs368234815, IFNL4-rs117648444, and IFNL3-rs4803217 and analyzed episodes of malaria, gastrointestinal, and respiratory infections recorded at 30,626 clinic visits from birth up to 5 years of age. Compared to children with the rs368234815-TT/TT genotype (IFN-λ4-Null), rs368234815-dG allele was most strongly associated with an earlier time-to-first episode of gastrointestinal infections (p = 0.003). The risk of experiencing an infection episode during the follow-up was also significantly increased with rs368234815-dG allele, with OR = 1.53, 95%CI (1.13-2.07), p = 0.005 for gastrointestinal infections and OR = 1.30, 95%CI (1.02-1.65), p = 0.033 for malaria. All the associations for the moderately linked rs4803217 (r² = 0.78 in this set) were weaker and lost significance after adjusting for rs368234815. We also analyzed all outcomes in relation to IFN-λ4-P70S groups. Our results implicate IFN-λ4 and not IFN-λ3 as the primary functional cause of genetic associations with increased overall risk and younger age at first clinical episodes but not with recurrence or intensity of several common pediatric infections.

Distribution and Genetic Variability of Sapoviruses in Africa

In this review, we describe the distribution and genetic diversity of sapoviruses detected among humans, animals and the environment in African countries. Databases were searched for studies conducted in African countries and published between Jan 2005 and Mar 2019. Only studies where RT- PCR was used for initial detection were included in the systematic review. We identified 27 studies from 14 African countries with 18 focused on human sapoviruses, two on animal sapoviruses and seven on sapoviruses observed in the environment. Samples. The overall estimated pooled prevalence of human sapovirus infections among symptomatic and asymptomatic individuals was similar at 5.0% (95% Confidence Interval (CI): 3.0–7.0) and 2.0% (95% CI: 1.0–3.0), respectively. In environmental samples sapovirus detection rates ranged from 0% to 90% while in animal studies it was 1.7% to 34.8%. Multiple causes of gastroenteritis, sensitivity of detection method used, diversity of sapovirus strains and rotavirus vaccine coverage rate are some of the factors that could have contributed to the wide range of sapovirus detection rates that were reported. The studies reported human genogroups GI, GII, and GIV, with genogroup GI being the most prevalent. Some potential novel strains were detected from animal samples. Most studies genotyped a small portion of either the capsid and/or polymerase region. However, this is a limitation as it does not allow for detection of recombinants that occur frequently in sapoviruses. More studies with harmonized genotyping protocols that cover longer ranges of the sapovirus genome are needed to provide more information on the genomic characterization of sapoviruses circulating in African countries. Further investigations on animal to human transmission for sapoviruses are needed as inter-species transmissions have been documented for other viruses.

Clinical characteristics associated with increased resource utilization of hospitalized children under 5 years with acute gastroenteritis at a tertiary hospital in the northern region of Ghana: a retrospective study

Introduction

Acute gastroenteritis (AGE) is a leading cause of mortality in children in developing countries. Management of AGE consumes medical resources, including antibiotics and intra-venous fluids, but factors affecting resource utilization in the management of AGE are under-studied. We hope to identify clinical predictors of resource utilization in AGE.

Methods

We performed a retrospective chart review of patients 1-60 months of age admitted to a tertiary hospital in Northern Ghana between January 2013 and December 2014 with an admitting diagnosis of AGE. We collected data on patient demographics, presenting symptoms, and subsequent management. Our primary outcome was prolonged hospital length of stay, defined as >4 days. Secondary outcomes included other measures of resource utilization, such as use of antibiotics, antimalarials and intravenous fluids. Demographic and clinical characteristics were compared between groups with Pearson chi square test for categorical variables and ANOVA for continuous variables. Multivariable logistic regression modeling for each outcome included all variables found to be significant in the bivariate analysis.

Results

We reviewed charts for 473 patients admitted for AGE during this timeframe. 264 (56%) were male, median age was 12 months. 448 (95%) received antibiotics, 396 (84%) received antimalarials and 365 (77.2%) received intravenous fluids. 167 (35.3%) had prolonged LOS >4 days. Following multiple logistic regression analysis, clinical features associated with prolonged LOS included fever duration (OR 2.87, 95% CI 2.28-3.61 per 1-day increase), mild (OR 2.39, 95% CI 1.12-5.08) or moderate (OR 3.13, 95% CI 1.57-6.21) dehydration (compared to none) and symptom duration (OR 1.13, 95% CI 1.01-1.27 per 1-day increase).

Conclusion

Dehydration and duration of symptoms prior to presentation predict prolonged hospital LOS in young children with AGE in Northern Ghana.

Methods for the detection of Cryptosporidium and Giardia: From microscopy to nucleic acid based tools in clinical and environmental regimes

The detection and characterization of genotypes and sub genotypes of Cryptosporidium and Giardia is essential for their enumeration, surveillance, prevention, and control. Different diagnostic methods are available for the analysis of Cryptosporidium and Giardia including conventional phenotypic tools that face major limitations in the specific diagnosis of these protozoan parasites. The substantial advancement in the development of genetic signature based molecular tools for the quantification, diagnosis and genetic variation analysis has increased the understanding of the epidemiology and preventive measures of related infections. The conventional methods such as microscopy, antibody and enzyme based approaches, offer better detection results when combined with advanced molecular methods. Gene based approaches increase the precision of identification, for example, many signatures detected in environmental matrices represent species/genotype that are not infectious to humans. This review summarizes the available methods and the advantages and limitations of advance detection techniques like nucleic acid-based approaches for the detection of viable oocysts and cysts of Cryptosporidium and Giardia along with the conventional and widely accepted detection techniques like microscopy, antibody and enzyme based ones. This technical article also encourages the wide application of molecular methods in genetic characterization of distinct species of Cryptosporidium and Giardia, to adopt necessary preventive measures with reliable identification and mapping the source of contamination.

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.

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.

Rapid and Accurate Diagnosis Based on Real-Time PCR Cycle Threshold Value for the Identification of Campylobacter jejuni, astA Gene-Positive Escherichia coli, and eae Gene-Positive E. coli

We previously developed a multiplex real-time PCR assay (Rapid Foodborne Bacterial Screening 24 ver.5, [RFBS24 ver.5]) for simultaneous detection of 24 foodborne bacterial targets. Here, to overcome the discrepancy of the results from RFBS24 ver.5 and bacterial culture methods (BC), we analyzed 246 human clinical samples from 49 gastroenteritis outbreaks using RFBS24 ver.5 and evaluated the correlation between the cycle threshold (CT) value of RFBS24 ver.5 and the BC results. The results showed that the RFBS24 ver.5 was more sensitive than BC for Campylobacter jejuni and Escherichia coli harboring astA or eae, with positive predictive values (PPV) of 45.5-87.0% and a kappa coefficient (KC) of 0.60-0.92, respectively. The CTs were significantly different between BC-positive and -negative samples (p ＜ 0.01). All RFBS24 ver.5-positive samples were BC-positive under the lower confidence interval (CI) limit of 95% or 99% for the CT of the BC-negative samples. We set the 95% or 99% CI lower limit to the determination CT (d-CT) to discriminate for assured BC-positive results (d-CTs: 27.42-30.86), and subsequently the PPVs (94.7%-100.0%) and KCs (0.89-0.95) of the 3 targets were increased. Together, we concluded that the implication of a d-CT-based approach would be a valuable tool for rapid and accurate diagnoses using the RFBS24 ver.5 system.

Etiology of Diarrhea, Nutritional Outcomes, and Novel Intestinal Biomarkers in Tanzanian Infants

OBJECTIVE

Diarrheal diseases are a leading cause of morbidity and mortality worldwide, but the etiology of diarrhea and its relation to nutritional outcomes in resource-limited settings is poorly defined. We sought to determine the etiology of community-acquired diarrhea in Tanzanian infants and to assess the association with anthropometrics and novel intestinal biomarkers.

METHODS

A convenience sample of infants in a trial of zinc and/or multivitamin supplementation in Tanzania was selected. Subjects were enrolled at age 6 weeks and studied for 18 months. Stool samples were obtained from children with acute diarrhea. A novel, polymerase chain reaction-based TaqMan array was used to screen stool for 15 enteropathogens. A subset of subjects had serum gastrointestinal biomarkers measured.

RESULTS

One hundred twenty-three subjects with diarrhea were enrolled. The mean ± SD age at stool sample collection was 12.4 ± 3.9 months. Thirty-five enteropathogens were identified in 34 (27.6%) subjects: 11 rotavirus, 9 Cryptosporidium spp, 7 Shigella spp, 3 Campylobacter jejuni/coli, 3 heat stable-enterotoxigenic Escherichia coli, and 2 enteropathogenic E coli. Subjects with any identified enteropathogen had significantly lower weight-for-length z scores (-0.55 ± 1.10 vs 0.03 ± 1.30, P = 0.03) at the final clinic visit than those without an identified pathogen. Fifty of the 123 subjects (40.7%) had serum analyzed for antibodies to lipopolysaccharide (LPS) and flagellin. Subjects with any identified enteropathogen had lower immunoglobulin (IgA) antibodies to LPS (0.75 ± 0.27 vs 1.13 ± 0.77, P = 0.01) and flagellin (0.52 ± 0.16 vs 0.73 ± 0.47, P = 0.02) than those without an identified pathogen.

CONCLUSIONS

This quantitative polymerase chain reaction method may allow identification of enteropathogens that place children at higher risk for suboptimal growth. IgA anti-LPS and flagellin antibodies hold promise as emerging intestinal biomarkers.

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.

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.