Prevalence of gastrointestinal pathogens in developed and developing countries: systematic review and meta-analysis

Prevalence of Blastocystis sp. and other gastrointestinal pathogens among diarrheic COVID-19 patients in Italy

Background

Gastrointestinal pathogens (GPs) contribute significantly to the burden of illness worldwide with diarrhoea being the most common among gastrointestinal symptoms (GSs). In the COVID-19 disease, diarrhoea, could be one of the initial presenting symptoms. However, no data on the potential correlation between diarrhoea-causing pathogens and SARS-CoV-2 infection are available. Therefore, we carried out a 2-years retrospective study aimed to evaluate the prevalence of "classic" GPs among SARS-CoV-2 infected and non-infected patients with diarrhoea in Italy.

Methods

Results of SARS-CoV-2 research from nasopharyngeal and detection of GPs from stool swab samples by Allplex™ SARS-CoV-2 and GI Virus, Bacteria and Parasite Assay were analysed for all patients with diarrhoea referring to Policlinico Ospedaliero Universitario, Foggia, (Italy) from February 2022 to October 2023.

Results

Out of the 833 involved patients, 81 (3.9%) were COVID-19 positive, while 752 (90.3%) were COVID-19 negative. Among COVID-19-positive patients, 37% (n = 30/81) were found positive for one or more GPs with a higher prevalence of protozoan parasites (18.5%) (Blastocystis ST1-ST4 subtypes, Dientamoeba fragilis genotype I), followed by bacteria (7.4%) (Campylobacter sp., Salmonella sp.). Viral pathogens were more frequent among COVID-19 negative patients (Adenovirus, Norovirus). Among GPs, Blastocystis ST3 subtype was the most prevalent registered in the 16% of patients (p = 0.0001).

Conclusions

Based on obtained results, a likely interaction between the classic GPs and SARS-CoV-2 infection can be speculated, driven by protozoan parasites. Moreover, these results also provide baseline data to understand more deeply Blastocystis sp. role in this scenario of dysbiosis, particularly in those cases of SARS-CoV-2 co-infection.

Promising clinical and immunological efficacy of Bacillus clausii spore probiotics for supportive treatment of persistent diarrhea in children

Persistent diarrhea is a severe gastroenteric disease with relatively high risk of pediatric mortality in developing countries. We conducted a randomized, double-blind, controlled clinical trial to evaluate the efficacy of liquid-form Bacillus clausii spore probiotics (LiveSpo CLAUSY; 2 billion CFU/5 mL ampoule) at high dosages of 4-6 ampoules a day in supporting treatment of children with persistent diarrhea. Our findings showed that B. clausii spores significantly improved treatment outcomes, resulting in a 2-day shorter recovery period (p < 0.05) and a 1.5-1.6 folds greater efficacy in reducing diarrhea symptoms, such as high frequency of bowel movement of ≥ 3 stools a day, presence of fecal mucus, and diapered infant stool scale types 4-5B. LiveSpo CLAUSY supportive treatment achieved 3 days (p < 0.0001) faster recovery from diarrhea disease, with 1.6-fold improved treatment efficacy. At day 5 of treatment, a significant decrease in blood levels of pro-inflammatory cytokines TNF-α, IL-17, and IL-23 by 3.24% (p = 0.0409), 29.76% (p = 0.0001), and 10.87% (p = 0.0036), respectively, was observed in the Clausy group. Simultaneously, there was a significant 37.97% decrease (p = 0.0326) in the excreted IgA in stool at day 5 in the Clausy group. Overall, the clinical study demonstrates the efficacy of B. clausii spores (LiveSpo CLAUSY) as an effective symptomatic treatment and immunomodulatory agent for persistent diarrhea in children.Trial registration: NCT05812820.

Multicenter evaluation of BioCode GPP for syndromic molecular detection of gastrointestinal pathogens from stool specimens

Acute gastroenteritis (AGE) is a leading cause of morbidity and mortality worldwide across all age groups that disproportionally affects young children in low- and middle-income countries and immunocompromised patients in high-income countries. Regional outbreaks of AGE are typically detected by traditional microbiological detection methods that target limited organisms and are associated with low sensitivity and lengthy time-to-results. Combined, these may result in repeat testing, imprecise or delayed treatment, and delayed recognition of outbreaks. We conducted a multi-site prospective study comparing the BioCode Gastrointestinal Pathogen Panel (BioCode GPP) for the detection of 17 common bacterial, viral, and protozoan causes of gastroenteritis with reference methods, including stool culture, enzyme immunoassays, pathogen-specific PCR assays, and sequencing. One thousand five hundred fifty-eight residual, de-identified stool samples (unpreserved stool and stool in Cary-Blair transport medium) were enrolled and tested for 11 bacterial, 3 viral, and 3 protozoan pathogens. BioCode GPP and reference methods were positive for 392 (25.2%) and 283 (18.2%) samples, respectively (P < 0.0001). In this study, the BioCode GPP and reference methods detected 69 and 65 specimens positive for Clostridioides difficile, 51 and 48 for enteroaggregative Escherichia coli, 33 and 27 for enterotoxigenic E. coli, 50 and 47 for norovirus GI/GII, and 30 and 22 for rotavirus A, respectively. The BioCode GPP showed good positive and negative agreements for each pathogen ranging from 89.5% to 100%, with overall sensitivity and specificity of 96.1% and 99.7%, post adjudication. The BioCode GPP detected >1 pathogens in 49 samples, representing 12.5% of the total 392 positive specimens.

IMPORTANCE

This study highlights performance of a novel technology for timely and accurate detection and differentiation of 17 common bacterial, viral, and protozoan causes of gastroenteritis. Utilizing molecular tests such as the BioCode Gastrointestinal Pathogen Panel may improve the detection of gastrointestinal pathogens and provide actionable results, particularly for patient populations at most risk.

Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance

BACKGROUND

Syndromic surveillance of acute gastroenteritis plays a significant role in the diagnosis and management of gastrointestinal infections that are responsible for a substantial number of deaths globally, especially in developing countries. In Lebanon, there is a lack of national surveillance for acute gastroenteritis, and limited data exists regarding the prevalence of pathogens causing diarrhea. The one-year study aims to investigate the epidemiology of common gastrointestinal pathogens and compare our findings with causative agents of diarrhea reported by our study collaborative centers.

METHODS

A multicenter, cross-sectional study was conducted over a one-year period. A total of 271 samples were obtained from outpatients and inpatients presenting with symptoms of acute gastroenteritis at various healthcare facilities. The samples were then analyzed using Allplex gastrointestinal assay that identifies a panel of enteric pathogens.

RESULTS

Overall, enteropathogens were detected in 71% of the enrolled cases, 46% of those were identified in patients as single and 54% as mixed infections. Bacteria were observed in 48%, parasites in 12% and viruses in 11%. Bacterial infections were the most prevalent in all age groups. Enteroaggregative E. coli (26.5%), Enterotoxigenic E. coli (23.2%) and Enteropathogenic E. coli (20.3%) were the most frequently identified followed by Blastocystis hominis (15.5%) and Rotavirus (7.7%). Highest hospitalization rate occurred with rotavirus (63%), Enterotoxigenic E. coli (50%), Blastocystis hominis (45%) and Enteropathogenic E. coli (43%). Enteric pathogens were prevalent during summer, fall and winter seasons.

CONCLUSIONS

The adoption of multiplex real-time PCR assays in the diagnosis of gastrointestinal infections has identified gaps and improved the rates of detection for multiple pathogens. Our findings highlight the importance of conducting comprehensive surveillance to monitor enteric infections. The implementation of a syndromic testing panel can therefore provide healthcare professionals with timely and accurate information for more effective treatment and public health interventions.

Knowledge and Behavioral Practice of Mothers About Childhood Diarrhea in Arar City, Saudi Arabia

BACKGROUND

Diarrhea is the second most significant cause of child morbidity and mortality, especially in developing countries. The World Health Organization (WHO) advises that mothers and other caregivers be able to recognize the symptoms of dehydration. Therefore, this study aimed to assess the knowledge and behavioral practices regarding diarrhea among mothers in Arar City, Saudi Arabia.

METHODS

This cross-sectional survey used an anonymous online questionnaire distributed among mothers of children aged one to five years in Arar City. The snowball convenient sampling method was used to recruit the participants. Information on knowledge and behavioral practices regarding diarrhea was obtained from the mothers of children through an electronic questionnaire. The Chi-square test and Fisher's exact test were used to evaluate the relationship between studied variables, as appropriate with statistical significance at P<0.05.

RESULTS

A total of 479 mothers participated in this survey. Of these, 421 were included in the analysis. Most mothers fall within the age range of 20-40 years (71.1%). A large sector of the studied mothers had high education (72.4%) and was a housewife (40.4%). Most children were above one year old (77.7%). Most participants (69.6%) fell into the moderate knowledge category and 56.3% had moderate behavioral practice scores. Maternal education was significantly associated with knowledge. Furthermore, maternal education and behavioral practice levels were significantly correlated (P < 0.01).

CONCLUSION

The findings highlight the importance of targeted education programs and community-based interventions to improve mothers' knowledge and promote appropriate behavioral practices related to childhood diarrhea that ultimately will lead to improved health outcomes for children globally.

Knowledge, Attitude, and Practices on Food Safety among Food Handlers Working in Public Food Service Establishments in Lemi Kura Subcity, Addis Ababa, Ethiopia

Foodborne diseases, resulting from poor food handling and sanitation practices, are common public health problems globally. The primary contributing factors to potential foodborne disease outbreaks are often attributed to the poor perception and practices of food handlers regarding food safety. This study is aimed at assessing the knowledge, attitude, and practices of food handlers working in public food service establishments in Lemi Kura subcity, Addis Ababa, Ethiopia. A cross-sectional study was conducted from December 2022 to September 2023, involving 400 food handlers from 20 randomly selected public food service establishments. Data were collected using a structured interview-administered questionnaire and an observational checklist. The collected data were entered into Microsoft Excel and then transferred to SPSS version 20 for analysis. Descriptive statistics were employed to summarize the data, and Pearson's chi-square test was used to evaluate the association of sociodemographic factors with the knowledge, attitude, and practices of food handlers towards food safety. Of the 400 food handlers, 65.5% had good knowledge about food safety. All food handlers were knowledgeable that washing hand before handling food will reduce risk of poisoning, bacteria are the main cause of food poisoning, and temperature plays a big role in bacterial growth. This study also revealed that 65.3% of the food handlers had good attitude towards food safety and 55.3% of food handlers had good food handling practice. Based on the observation, 38.5% of food handlers had good food handling practice. Taking training, age, and work experience of food handlers have statistically significant (P < 0.05) association with good attitude towards food safety. Additionally, taking training, educational level, employment, and work experience of food handlers have statistically significant (P < 0.05) association with good practice towards food safety. However, there was no statistically significant association between all sociodemographic factors and knowledge about food safety. Good knowledge and attitude were also associated with good food handling practices of the respondents. Based on the observation, there was a statistically significant association between employment status and good food handling practice. In conclusion, the findings suggest the necessity for implementing formal educational and training programs aimed at positively influencing the knowledge and attitude of food handlers, subsequently improving their food handling practices.

Fecal prevalence of Campylobacter spp. in house dogs in Lebanon: A pilot study

Background and Aim

Campylobacter spp. are Gram-negative bacilli that are widely recognized as a primary cause of bacterial gastroenteritis worldwide. Campylobacteriosis is the disease caused by this pathogen. Recently, greater attention has been given to the prevalence of campylobacteriosis in different animals, including pets. These animals are considered to be significant reservoirs for this zoonosis. In Lebanon, the occurrence of Campylobacter infection is high. Our first-of-its-kind pilot study in Lebanon aimed to estimate the fecal prevalence of Campylobacter species in house dogs.

Materials and Methods

Thirty-five rectal swabs were collected from male and female house dogs of different ages, both with or without diarrhea. Samples obtained from the dogs were subjected to qualitative microbiological culture testing and molecular diagnosis by polymerase chain reaction assays after bacterial DNA extraction.

Results

Fecal prevalence of Campylobacter spp. in house dogs in this study was 17%. There was a relatively higher prevalence among young females and a significant difference between healthy dogs and those suffering from diarrhea.

Conclusion

Campylobacteriosis was found to be prevalent among house dogs in Lebanon, making them potential carriers of Campylobacter species.

A pilot study of dietary fibres on pathogen growth in an ex vivo colonic model reveals their potential ability to limit vancomycin-resistant Enterococcus expansion

Aim: Dietary fibre is important for shaping gut microbiota. The aim of this pilot study was to investigate the impact of dietary fibres on pathogen performance in the presence of gut microbiota. Methods: In an ex vivo gut model, pooled faecal samples were spiked with a cocktail of representative gastrointestinal pathogens and fermented with yeast β-glucan for 24 hours, after which 16S rRNA amplicon sequencing and short-chain and branched-chain fatty acid (SCFA and BCFA) analyses were performed. In addition, oat β-glucan, arabinoxylan, yeast β-glucan, and galactooligosaccharides were each tested against individual representative pathogens and pathogen growth was assessed via qPCR. Glucose served as a control carbon source. Results: Based on 16S rRNA amplicon sequencing, yeast β-glucan selected for higher proportions of Bacteroides (P = 0.0005, ~6 fold) and Clostridia (P = 0.005, ~3.6 fold) while species of Escherichia/Shigella (P = 0.021, ~2.8 fold) and Lactobacillus (P = 0.007, ~ 15.7-fold) were higher in glucose. Pathogen relative abundance did not differ between glucose and yeast β-glucan. In the absence of pathogens, higher production of BCFAs (P = 0.002) and SCFAs (P = 0.002) fatty acids was observed for fibre group(s). For individual pathogens, yeast β-glucan increased growth of Escherichia coli, Salmonella typhimurium, and Listeria monocytogenes (P < 0.05), arabinoxylan increased S. typhimurium (P < 0.05). Tested fibres decreased vancomycin-resistant Enterococcus faecium (P < 0.05), with yeast β-glucan causing a 1-log reduction (P < 0.01), while galactooligosaccharides decreased L. monocytogenes (P < 0.05). Conclusion: Tested fibres differentially influenced the growth of pathogens, but yeast β-glucan could represent a dietary strategy to help limit vancomycin-resistant enterococci (VRE) expansion in the gut.

Impact of COVID-19 Restrictions on Acute Gastroenteritis in Children: A Regional, Danish, Register-Based Study

This study aimed to evaluate the impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) restrictions such as social distancing on the occurrence of acute gastroenteritis (AGE) among children. This study is a register-based study, including every child seen in the departments of paediatrics with the initial diagnosis of AGE in three neighbouring hospitals in Denmark, from March 2018 through February 2021. The study also included every positive stool sample for AGE-causing pathogens analysed in these three hospitals from children during the same period. The Wilcoxon rank-sum test was used to determine differences between the period during the SARS-CoV-2 restrictions and before. In all, 222,157 children were seen in the three paediatric departments during this period. Of these, 3917 children were diagnosed with AGE. We found a decrease of 46.6% in AGE-related visits per month after the SARS-CoV-2 restrictions were introduced compared to before (p-value < 0.001). Positive stool samples decreased by 38.2% (p-value = 0.008) during the restrictions. This study found that cases of paediatric AGE decreased significantly the during COVID-19 restrictions, suggesting that studies should be conducted to determine whether this reduction was a result of good hand hygiene and social distancing or just a result of altered health-seeking behaviour among children.

Selection of G-rich ssDNA aptamers for the detection of enterotoxins of the cholera toxin family

Cholera and milder diarrheal disease are caused by Vibrio cholerae and enterotoxigenic Escherichia coli and are still a prominent public health concern. Evaluation of suspicious isolates is essential for the rapid containment of acute diarrhea outbreaks or prevention of epidemic cholera. Existing detection techniques require expensive equipment, trained personnel and are time-consuming. Antibody-based methods are also available, but cost and stability issues can limit their applications for point-of-care testing. This study focused on the selection of single stranded DNA aptamers as simpler, more stable and more cost-effective alternatives to antibodies for the co-detection of AB₅ toxins secreted by enterobacteria causing acute diarrheal infections. Cholera toxin and Escherichia coli heat-labile enterotoxin, the key toxigenicity biomarkers of these bacteria, were immobilized on magnetic beads and were used in a SELEX-based selection strategy. This led to the enrichment of sequences with a high % GC content and a dominant G-rich motif as revealed by Next Generation Sequencing. Enriched sequences were confirmed to fold into G-quadruplex structures and the binding of one of the most abundant candidates to the two enterotoxins was confirmed. Ongoing work is focused on the development of monitoring tools for potential environmental surveillance of epidemic choleraand milder diarrheal disease.

Orally Ingested Probiotic, Prebiotic, and Synbiotic Interventions as Countermeasures for Gastrointestinal Tract Infections in Nonelderly Adults: A Systematic Review and Meta-Analysis

Meta-analyses have not examined the prophylactic use of orally ingested probiotics, prebiotics, and synbiotics for preventing gastrointestinal tract infections (GTIs) of various etiologies in adult populations, despite evidence that these gut microbiota-targeted interventions can be effective in treating certain GTIs. This systematic review and meta-analysis aimed to estimate the effects of prophylactic use of orally ingested probiotics, prebiotics, and synbiotics on GTI incidence, duration, and severity in nonelderly, nonhospitalized adults. CENTRAL, PubMed, Scopus, and Web of Science were searched through January 2022. English-language, peer-reviewed publications of randomized, placebo-controlled studies testing an orally ingested probiotic, prebiotic, or synbiotic intervention of any dose for ≥1 wk in adults who were not hospitalized, immunosuppressed, or taking antibiotics were included. Results were analyzed using random-effects meta-analyses of intention-to-treat (ITT) and complete case (CC) cohorts. Heterogeneity was explored by subgroup meta-analysis and meta-regression. The risk of bias was assessed using the Cochrane risk-of-bias 2 tool. Seventeen publications reporting 20 studies of probiotics (n = 16), prebiotics (n = 3), and synbiotics (n = 1) were identified (n > 6994 subjects). In CC and ITT analyses, risk of experiencing ≥1 GTI was reduced with probiotics (CC analysis-risk ratio: 0.86; 95% CI: 0.73, 1.01) and prebiotics (risk ratio: 0.80; 95% CI: 0.66, 0.98). No effects on GTI duration or severity were observed. Sources of heterogeneity included the study population and number of probiotic strains administered but were often unexplained, and a high risk of bias was observed for most studies. The specific effects of individual probiotic strains and prebiotic types could not be assessed owing to a lack of confirmatory studies. Findings indicated that both orally ingested probiotics and prebiotics, relative to placebo, demonstrated modest benefit for reducing GTI risk in nonelderly adults. However, results should be interpreted cautiously owing to the low number of studies, high risk of bias, and unexplained heterogeneity that may include probiotic strain-specific or prebiotic-specific effects. This review was registered at PROSPERO as CRD42020200670.

Prevalence of Campylobacter spp. in broilers in North Lebanon

Background and Aim: Great attention has been given recently to the prevalence of different Campylobacter spp. in poultry since the latter are considered the major contributing reservoir of human campylobacteriosis. In Lebanon, the occurrence of campylobacteriosis in humans is high. The aim of our first-of-its-kind study in the country was to estimate the prevalence of Campylobacter spp. in broilers from a convenient sample of farms in North Lebanon. Materials and Methods: One hundred twenty-five fecal samples were collected from 25 broiler farms, which were selected, examined, and classified according to their biosecurity level and rearing system. All samples were subjected to qualitative microbiological culture testing and polymerase chain reaction (PCR) assays to detect Campylobacter spp. Results: Despite the reported use of antibiotics, cell culture and PCR were positive for 44% and 88%, respectively. This implies that this bacterium is resistant to antibiotics used on the farms. Furthermore, Campylobacter infection rate was higher in open (92%) than in closed (85%) system farms. All farms with poor biosecurity measures, and 82% of farms with good biosecurity measures had Campylobacter infections, and the difference was significant (p < 0.05). Conclusion: Our results show that campylobacteriosis was found prevalent among broilers in North Lebanon, making them potential carriers of Campylobacter spp. Future studies should include antibiotic susceptibility testing to check the susceptibility pattern of isolates.

Prevalence of Intestinal Parasitosis in Guinea: Systematic Review of the Literature and Meta-Analysis

BACKGROUND

Intestinal parasitosis constitute a major public health issue, particularly in sub-tropical and tropical areas. Even though they are classified as neglected tropical diseases, no national study has been carried out recently in Guinea to estimate the prevalence of intestinal parasitosis.

OBJECTIVE

A systematic review and meta-analysis aimed to determine the overall prevalence of intestinal parasitosis in Guinea.

METHOD

The PRISMA method was used to perform a systematic review and meta-analysis. The studies carried out in order to study intestinal parasitosis in Guinea and published between 2010 and 2020 were searched in online public databases. The prevalence of parasitosis was calculated by a random-effects meta-analysis. Subgroup comparisons were performed using Q-tests. Statistical analyses were performed with the R software. This review was registered with PROSPERO under the identification number CRD42022349743.

RESULTS

69 studies were selected out of 1230 studies identified in online public databases. The meta-analysis involved 44,186 people with an overall prevalence of intestinal parasitic infections of 52%.

CONCLUSIONS

This is the first study in Guinea to assess the prevalence of intestinal parasitic infections in different regions of the country. It was found that intestinal parasitosis are a real health problem in Guinea, hence, the need to put in place national strategies for regular control.

Contrasting Hygiene-Related Gastrointestinal Infections and Stress-Related Diseases at a Primary Health Care Facility within a Sub-Saharan African City: Before and during the COVID-19 Pandemic

BACKGROUND

With the advent of the COVID-19 pandemic caused by SARS-CoV-2, protocols such as social distancing and upscaling of hygiene practices were implemented to limit the spread of the disease. Meanwhile, along with COVID-19 came stress due to restrictions on movement, trade and transport, and closure of schools, among others.

AIM

This study compared the prevalence of hygiene-related gastrointestinal infections and stress-related diseases before (March 2019-February 2020) and during (March 2020-February 2021) the COVID-19 pandemic.

METHODOLOGY

This was a retrospective single-center review of deidentified patient data from the Korle Bu Polyclinic, Accra, Ghana.

RESULTS

Comparing the pre-COVID-19 era to the COVID-19 era, there was a statistically nonsignificant change in the number of cases and prevalence of gastroenteritis and enteric fever (p = 0.084 and 0.081, respectively), although for gastroenteritis, the prevalence was higher for the pre-COVID-19 era compared to during COVID-19 by 1.8 per 1000 cases, while that of enteric fever was higher during the COVID-19 era compared to the pre-COVID-19 era by 1.0 per 1000 cases. Of the stress-related diseases, statistically significant increases in the prevalence of anxiety disorders (p = 0.028), insomnia (p = 0.001), and headache (p = 0.010), were noted, with 2.3, 5.5, and 2.4 per 1000 cases, respectively. There were more female cases than male cases recorded for depression (p = 0.001), headache (p = 0.010), and hypertension (p = 0.001) during the pandemic, and these were statistically significant.

CONCLUSION

During the pandemic, a significant increase in the prevalence of stress-related diseases was observed. However, a statistically nonsignificant change was recorded for gastrointestinal infections, with females reporting more of these disorders. Consequently, it is important to strengthen the capacity for managing stress-related conditions alongside diseases that cause pandemics when they arise.

Molecular epidemiology, genetic diversity, and vaccine availability of viral acute gastroenteritis in the middle East and North Africa (MENA) region

Acute gastroenteritis is the cause of considerable mortality and morbidity worldwide, particularly among children under five years in underdeveloped countries. Most acute gastroenteritis (AGE) cases are attributed to viral etiologies, including rotavirus, norovirus, adenovirus, astrovirus, and sapovirus. This paper aimed to determine the prevalence rate of different viral etiologies of AGE in the Middle East and North Africa (MENA) region. Moreover, this paper explored rotavirus phylogenetic relatedness, compared VP7 and VP4 antigenic regions of rotavirus with vaccine strains, and explored the availability of vaccines in the MENA region. The literature search identified 160 studies from 18 countries from 1980 to 2019. The overall prevalence of rotavirus, norovirus, adenovirus, astrovirus, and sapovirus were 29.8 %, 13.9 %, 6.3 %, 3.5 %, and 3.2 % of tested samples, respectively. The most common rotavirus genotype combinations in the MENA region were G1P[8], G9P[9], and G2P[4], whereas GII.4 was the predominant norovirus genotype all of which were reported in almost all the studies with genotyping data. The comparison of VP7 and VP4 between circulating rotavirus in the MENA region and vaccine strains has revealed discrete divergent regions, including the neutralizing epitopes. Rotavirus vaccine was introduced to most of the countries of the MENA region; however, only a few studies have assessed the effectiveness of vaccine introduction. This paper provides a comprehensive update on the prevalence of the different viral agents of AGE in the MENA region.

Isolation and Genotyping of Adenoviruses from Wastewater and Diarrheal Samples in Egypt from 2016 to 2020

Human adenoviruses (HAdV) are a prevalent cause of diarrhea in children all over the world. Adenoviral infections are responsible for 2% to 10% of diarrheic cases. A long-term investigation was required to gain better knowledge about the incidence of HAdV in Egypt. Herein, we conducted 5 years of detection, isolation, and genotyping of HAdV in fecal and sewage samples from 2016 to 2020, in Cairo, Egypt using molecular and cell culture assays. Human adenoviruses were identified in 35 of 447 fecal samples (7.8%), but only 53.3% (64/120) of the sewage samples. Children under the age of two had the highest positive rate for HAdV infection (77.1%). Species F of HAdV was the most common prevalent genotype in fecal and sewage samples, at 88.5% and 85.9%, respectively. The most prevalent genotypes detected in fecal samples were HAdV-41 (71.2%), HAdV-40 (17.2%), HAdV-6 (5.7%), and HAdV-1 (5.7%). In contrast, the most common genotypes in sewage samples were HAdV-41 (64%), HAdVs-40 (21.8%), HAdV-6 (7.8%), HAdV-1 (4.7%), and HAdV-2 (1.6%). HAdV was detected in all months of the year, with a peak period for clinical samples from December to February (p < 0.001), which matched Egypt’s rainy season, while the monthly distribution of HAdV in sewage samples remained consistent throughout the year, with no statistically significant peak period. Interestingly, the HAdV-type 41 genotype was the most common genotype during all of the years of this study. Throughout a 5-year period, our work revealed the infection rate, seasonal distribution, virus isolates, and genetic diversity of HAdV infections in environmental and clinical samples in Cairo, Egypt. Non-enteric adenovirus types (1, 2 and 6), as well as enteric adenovirus (41 and 40), may play a key role in gastroenteritis in Egypt.

Recent Advances in Early Diagnosis of Viruses Associated with Gastroenteritis by Biosensors

Gastroenteritis, as one of the main worldwide health challenges, especially in children, leads to 3–6 million deaths annually and causes nearly 20% of the total deaths of children aged ˂5 years, of which ~1.5 million gastroenteritis deaths occur in developing nations. Viruses are the main causative agent (~70%) of gastroenteritis episodes and their specific and early diagnosis via laboratory assays is very helpful for having successful antiviral therapy and reduction in infection burden. Regarding this importance, the present literature is the first review of updated improvements in the employing of different types of biosensors such as electrochemical, optical, and piezoelectric for sensitive, simple, cheap, rapid, and specific diagnosis of human gastroenteritis viruses. The Introduction section is a general discussion about the importance of viral gastroenteritis, types of viruses that cause gastroenteritis, and reasons for the combination of conventional diagnostic tests with biosensors for fast detection of viruses associated with gastroenteritis. Following the current laboratory detection tests for human gastroenteritis viruses and their limitations (with subsections: Electron Microscope (EM), Cell Culture, Immunoassay, and Molecular Techniques), structural features and significant aspects of various biosensing methods are discussed in the Biosensor section. In the next sections, basic information on viruses causing gastroenteritis and recent developments for fabrication and testing of different biosensors for each virus detection are covered, and the prospect of future developments in designing different biosensing platforms for gastroenteritis virus detection is discussed in the Conclusion and Future Directions section as well.

Prevalence and drug resistance patterns of Gram-negative enteric bacterial pathogens from diarrheic patients in Ethiopia: A systematic review and meta-analysis

Background

Diarrhoea is the leading cause of morbidity and mortality in the world particularly in developing countries and among vulnerable groups of the population. Gram-negative enteric bacterial pathogens (GNEBPs) are a group of organisms that reside mainly in the intestine and induce diarrhoea. Antimicrobial agents are usually the part of their treatment regimen. The therapeutic effect of antimicrobials is hindered by the emergence and spread of drug-resistant strains. The information regarding the prevalence and antimicrobial resistance patterns of GNEBPs in Ethiopia is limited and found in a scattered form.

Objectives

This study was designed to determine the pooled prevalence and drug resistance patterns of GNEBPs by meta-analysis of data from diarrhoeic patients in Ethiopia.

Method

A comprehensive literature search was conducted through internet searches using Google Scholar, PubMed, Science Direct, HINARI databases, and reference lists of previous studies. Published articles were included in the study based on priorly set inclusion and exclusion criteria. Results were presented in the forest plot, tables, and figures with a 95% confidence interval (CI). The inconsistency index (I²) test statistics was used to assess heterogeneity across studies. The pooled prevalence estimate of GNEBPs and their drug resistance patterns were computed by a random-effects model. Software for Statistics and Data Science (STATA) version 14 statistical software was used for the analysis.

Result

After removing those articles which did not fulfil the inclusion criteria, 43 studies were included in the analysis. Studies were conducted in 8 regions of the country and most of the published articles were from the Amhara region (30.23%) followed by Oromia (18.60%) and Southern Nations, Nationalities, and Peoples’ region (SNNP) (18.60%). The pooled prevalence of GNEBPs was 15.81% (CI = 13.33–18.29). The funnel plot indicated the presence of publication bias. The pooled prevalence of GNEBPs in Addis Ababa, Amhara, SNNP, and Oromia regions were 20.08, 16.67, 12.12, and 11.61%, respectively. The pooled prevalence was 14.91, 18.03, and 13.46% among studies conducted from 2006–2010, 2011–2015, and 2016–2021, respectively and it was the highest (20.35%) in children having age less than or equal to 15 years. The pooled prevalence of Escherichia coli, Campylobacter spp., Shigella spp., and Salmonella enterica were 19.79, 10.76, 6.24, and 5.06%, respectively. Large proportions (60–90%) of the isolates were resistant to ampicillin, amoxicillin, tetracycline, and trimethoprim-sulphamethoxazole. The pooled prevalence of multidrug resistance (MDR) was 70.56% (CI = 64.56–76.77%) and MDR in Campylobacter spp., Shigella spp., E. coli, and S. enterica. were 80.78, 79.08, 78.20, and 59.46%, respectively.

Conclusion

The pooled estimate showed a high burden of GNEBPs infections and a high proportion of drug resistance characters to commonly used antimicrobial agents in Ethiopia. Therefore, performing drug susceptibility tests, establishing an antimicrobial surveillance system and confirmation by molecular techniques are needed.

Travellers' diarrhoea - prevention, trends and role of microbiome

OBJECTIVES

In this review, we present a contemporary look at the management of travellers' diarrhoea (TD), and we discuss the potential role of a microbiome as well as the administration of live microorganisms in order to prevent TD.

METHODS

We performed a comprehensive search using the PubMed and Web of Science databases for the period 2014-2021, looking for original and review articles on travellers' diarrhoea.

RESULTS

TD belongs among the most frequent illnesses experienced by travellers. For the most part, it is manifested as an acute yet self limiting condition, and only in a few cases proceeds to a prolonged form. Epidemiological analyses have shown that the majority of TD cases are caused by bacterial infections. In practice, pharmacological therapy is often used in the prevention and treatment of TD, since patients naturally seek preventive measures against the development of its severe course and its impact on planned activities. Bismuth salicylate is a strongly recommended TD prophylaxis but is not available on all European Union markets. Although the antibiotic prophylaxis is not generally recommended in guidelines, some antibiotic or chemotherapeutic agents are accessible over-the-counter in certain countries, and travellers are routinely encouraged to use them preventively. This routine can alter the microbiome of the traveller and promote the spread of drug resistant bacteria in their place of residence. Probiotic administration is considered safe, although the quality of evidence in favour of its prophylactic use in TD is currently low.

CONCLUSIONS

The challenge for public health authorities is to educate personnel that can directly influence the behaviour of travellers through safe and effective pharmacological alternatives to antibiotics. Manipulation of the gut microbiome using specific probiotic strains can represent a safe and promising intervention.

Effect of diet on pathogen performance in the microbiome

Intricate interactions among commensal bacteria, dietary substrates and immune responses are central to defining microbiome community composition, which plays a key role in preventing enteric pathogen infection, a dynamic phenomenon referred to as colonisation resistance. However, the impact of diet on sculpting microbiota membership, and ultimately colonisation resistance has been overlooked. Furthermore, pathogens have evolved strategies to evade colonisation resistance and outcompete commensal microbiota by using unique nutrient utilisation pathways, by exploiting microbial metabolites as nutrient sources or by environmental cues to induce virulence gene expression. In this review, we will discuss the interplay between diet, microbiota and their associated metabolites, and how these can contribute to or preclude pathogen survival.

Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome

Mobile genetic elements (MGEs) carrying antibiotic resistance genes (ARGs) disseminate ARGs when they mobilise into new bacterial hosts. The nature of such horizontal gene transfer (HGT) events between human gut commensals and pathogens remain poorly characterised. Here, we compare 1354 cultured commensal strains (540 species) to 45,403 pathogen strains (12 species) and find 64,188 MGE-mediated ARG transfer events between the two groups using established methods. Among the 5931 MGEs, we find 15 broad host range elements predicted to have crossed different bacterial phyla while also occurring in animal and environmental microbiomes. We experimentally demonstrate that predicted broad host range MGEs can mobilise from commensals Dorea longicatena and Hungatella hathewayi to pathogen Klebsiella oxytoca, crossing phyla simultaneously. Our work establishes the MGE-mediated ARG dissemination network between human gut commensals and pathogens and highlights broad host range MGEs as targets for future ARG dissemination management.

The controversies surrounding Giardia intestinalis assemblages A and B

Giardia intestinalis continues to be one of the most encountered parasitic diseases around the world. Although more frequently detected in developing countries, Giardia infections nonetheless pose significant public health problems in developed countries as well. Molecular characterisation of Giardia isolates from humans and animals reveals that there are two genetically different assemblages (known as assemblage A and B) that cause human infections. However, the current molecular assays used to genotype G. intestinalis isolates are quite controversial. This is in part due to a complex phenomenon where assemblages are incorrectly typed and underreported depending on which targeted locus is sequenced. In this review, we outline current knowledge based on molecular epidemiological studies and raise questions as to the reliability of current genotyping assays and a lack of a globally accepted method. Additionally, we discuss the clinical symptoms caused by G. intestinalis infection and how these symptoms vary depending on the assemblage infecting an individual. We also introduce the host-parasite factors that play a role in the subsequent clinical presentation of an infected person, and explore which assemblages are most seen globally.

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

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

Molecular diagnostics of Salmonella and Campylobacter in human/animal fecal samples remain feasible after long-term sample storage without specific requirements

Rapid advances in the development of sequencing technologies, numbers of commercial providers and diminishing costs have made DNA-based identification and diagnostics increasingly accessible to doctors and laboratories, eliminating the need for local investments in expensive technology and training or hiring of skilled technicians. However, reliable and comparable molecular analyses of bacteria in stool samples are dependent on storage and workflow conditions that do not introduce post-sampling bias, the most important factor being the need to keep the DNA at a stable detectable level. For that reason, there may remain other prohibitively costly requirements for cooling or freezing equipment or special chemical additives.

This study investigates the diagnostic detectability of Salmonella and Campylobacter DNA in human, pig and chicken stool samples, stored at different temperatures and with different preservation methods. Stool samples were spiked with 10⁶ CFU/mL of both Salmonella and Campylobacter strains stored at −20 °C, 5 °C and 20 °C (Room temperature, RT) and treated with either RNAlater, EDTA or Silica/ethanol. DNA was extracted at 9 different time points within 30 days and quantified by Qubit (total DNA) and qPCR (Salmonella and Campylobacter DNA). We found no statistically significant differences among the different preservation methods, and DNA from both species was easily detected at all time points and at all temperatures, both with and without preservation. This suggests that infections by these bacteria can be diagnosed and possibly also analysed in further detail simply by taking a stool sample in any suitable sealed container that can be transported to laboratory analysis without special storage or preservation requirements. We briefly discuss how this finding can benefit infection control in both developed and developing countries.

Resistome and microbial profiling of pediatric patient's gut infected with multidrug-resistant diarrhoeagenic Enterobacteriaceae using next-generation sequencing; the first study from Pakistan

A high prevalence of multidrug-resistant (MDR) pathogens has been reported in adult and pediatric populations of Pakistan. However, data describing the effect of MDR microbes on the gut microbiota is scarce. We designed a cross-sectional pediatric study to investigate the effect of MDR microbes' infection on the gut microbiome and its resistome of children using high-throughput next-generation sequencing (NGS). A cross-sectional study was conducted at a tertiary health care hospital in Peshawar Pakistan, between 5 September 2019 to 15 February 2020. Pediatric patients with acute gastroenteritis (n = 200) were enrolled. All the enrolled pediatric patients underwent initial antimicrobial resistance (AMR) screening using the disk diffusion method. Children with MDR infections were identified and selected for gut microbiome and its resistome profiling using NGS. Out of 200 enrolled pediatric patients, 80 (40%) were found infected with MDR diarrheagenic Enterobacteriaceae consisting of 50 (62.5%) infections caused by extended-spectrum beta-lactamase (ESBL) producing E. coli while 30 (37.5%) by MDR Enterobacter specie. A total of 63 and 17 antibiotic-resistant genes (ARGs) conferring resistance to 7 and 5 classes of antibiotics were identified in the resistomes of MDR diarrheagenic Enterobacteriaceae infected and healthy children, respectively. NGS-based gut microbial profiling of MDR Enterobacter spp., ESBL producing E. coli infected pediatric patients and healthy controls revealed the predominance of Proteobacteria and Actinobacteria, respectively. An increased abundance of several pathogenic gram-negative bacteria namely E. coli, Enterobacter cloacae, and Salmonella enterica was observed in the gut microbiota of children infected with MDR bacterial infections than that of the healthy controls. This work indicates that children with MDR infections have reduced microbial diversity and enriched ARGs than healthy controls. The emergence of MDR bacterial strains and their association with gut dysbiosis needs immediate attention to regulate antibiotics usage in Pakistani children.

Commercial Simplex and Multiplex PCR Assays for the Detection of Intestinal Parasites Giardia intestinalis, Entamoeba spp., and Cryptosporidium spp.: Comparative Evaluation of Seven Commercial PCR Kits with Routine In-House Simplex PCR Assays

Nowadays, many commercial kits allowing the detection of digestive parasites by DNA amplification methods have been developed, including simplex PCR assays (SimpPCRa) allowing the identification of a single parasite, and multiplex PCR assays (MultPCRa) allowing the identification of several parasites at once. Thus, aimed at improving the diagnosis of intestinal protozoal infections, it is essential to evaluate the performances of these new tools. A total of 174 DNA samples collected between 2007 and 2017 were retrospectively included in this study. Performances of four commercial SimpPCRa (i.e., CerTest-VIASURE^TM) and three MultPCRa (i.e., CerTest-VIASURE^TM, FAST-TRACK-Diagnostics-FTD-Stool-Parasite^TM and DIAGENODE-Gastroenteritis/Parasite-panel-I^TM) were evaluated for the detection of Cryptosporidium spp., Entamoeba spp., and Giardia intestinalis in stool samples compared to our routinely used in-house SimpPCRa. Globally, the SimpPCRa showed better sensitivity/specificity for the detection of G. intestinalis, E. histolytica, E. dispar, and Cryptosporidium spp. (i.e., 96.9/93.6%; 100/100%; 95.5/100%; and 100/99.3%, respectively), compared to the three commercial MultPCRa tested. All in all, we showed that MultPCRa offer an interesting alternative for the detection of protozoans in stool samples depending on the clinical context.

Molecular and epidemiological characterization of human adenoviruses infection among children with acute diarrhea in Shandong Province, China

Background

Human adenovirus (HAdV) had been recognized as one of the most common enteric viruses associated with acute diarrhea in children. The present study was carried out to demonstrate the molecular and epidemiological characterization of HAdV Infections among children in Shandong province in China between July 2017 and June 2018.

Methods

Fecal specimens were collected from children under 5 years old with acute diarrhea. DNA was extracted from the stool specimens and adenovirus DNA was detected by PCR amplification with specific primers. The amplification products were subjected to electrophoresis and visualized on a UV transilluminator. All positive RT-PCR amplification products were sequenced and the obtained sequences analyzed by MEGA (version 7.0). Demographic information and clinical manifestation data were also analyzed.

Results

In total, 656 fecal specimens were collected and the overall positive rate of HAdV was 7.47%. HAdV infections were detected in all age groups, in which children aged 13–24 months presented the highest positive rate. Seasonal pattern could be observed with a peak in December, January and February. Diarrhea, vomiting, dehydration and fever were the main clinical manifestations, in which vomiting was the most common accompanied symptom. By phylogenetic analysis, four species (A, B, C, and F) were detected and seven different serotypes were identified. HAdV-41 (48.98%, 24/49) was the most common serotype followed by HAdV-3 (18.37%, 9/49), HAdV-31 (14.29%, 7/49), HAdV-7 (8.16%, 4/49), HAdV-40 (4.08%, 2/49), HAdV-1 (4.08%, 2/49) and HAdV-2 (2.04%, 1/49).

Conclusion

This study indicated that HAdV infection was an important cause of acute diarrhea among children under 5 years old in Shandong province. The results will contribute to (a) increase understanding of the role of HAdV in diarrheal children and enhance identification of the predominant diarrhea pathogen for diagnosis; (b) avoid abuse of antibiotics; (c) monitor the change of prevalent HAdV serotypes and promote vaccine development and vaccination.

Aetiology and risk factors of bacterial gastroenteritis among febrile outpatients at the Dschang District Hospital, West Region of Cameroon: a cross-sectional study

OBJECTIVES

To investigate the bacterial aetiologies and associated risk factors of gastroenteritis among typhoid suspected cases.

DESIGN

Cross-sectional study.

SETTING

This study was conducted at Dschang District Hospital of the Menoua Division, West Region of Cameroon, between April-November 2019 and June 2020.

PARTICIPANTS

Participants aged ≥2 years (mean 34±18.77 years) and of both sex suspected of having typhoid fever were included, while non-suspected typhoid cases were excluded. Self-reported sociodemographic and health information at recruitment was obtained from 556 participants.

METHODS

Collected stool samples were examined macroscopically and microscopically and subjected to culture. After culture, Gram staining was performed, followed by biochemical testing and characterisation using the Analytical Profile Index (API-20E) test kit.

INTERVENTIONS'

No intervention was done during the period of study.

OUTCOME MEASURES

We identified bacterial causing gastroenteritis, and associated risk factors calculated using binary regression, adjusting for sociodemographic and health variables.

RESULTS

Of 556 patients, 74.28% tested positive for gastroenteritis. Among pathogens responsible for gastroenteritis, Escherichia coli was found to be the main cause (21.1%), followed by Salmonella typhi (10.4%), Citrobacter diversus (8.2%), and Proteus mirabilis (8.2%), Proteus vulgaris (7.3%), whereas Citrobacter spp and Yersinia enterocolitica were less represented among pathogens causing the disease among patients. A significant difference (p=0.002) was observed between abdominal pain and all the micro-organisms isolated from the patients. Patients having primary level of education were significantly associated (p=0.017; 3.163 (95% CI 1.228 to 8.147)) with the prevalence of gastroenteritis. Consumption of beverages (Wald statistic: 4.823; OR: 2.471; 95% CI (1.102 to 5.539); p=0.028), use of modern toilet (Wald statistic: 4.471; OR: 1.723; 95% CI (1.041 to 2.852); p=0.034) were strongly associated with gastroenteritis and rearing of bird (Wald statistic: 4.880; OR: 0.560; 95% CI (0.335 to 0.937); p=0.027), was found to be protective.

CONCLUSION

Acute bacterial gastroenteritis is a significant cause of morbidity in Dschang, with the prevalence of 74.28%. Many pathogens accounted for gastroenteritis, and E. coli (21.1%) could be a major cause, followed by S. typhi (10.4%), C. diversus (8.2%), P. mirabilis (8.2%), P. vulgaris (7.3%), whereas Citrobacter spp and Y. enterocolitica were less represented. Gastroenteritis was highly associated with primary level of education, consumption of beverages, use of modern toilet while rearing of birds was unexpectedly found to be protective against Gastroenteritis. Further characterisation is planned.

The Ecology and Antibiotic Resistance Patterns of Gastrointestinal Tract Infections in A Tertiary Care Hospital in Oman

A wide range of gastrointestinal (GI) illnesses is caused by foodborne bacteria that can arise from either a direct bacterial infection or bacterial toxin ingestion. The treatment of these infections has been hampered by the appearance of resistant strains. This current study aims to investigate the prevalence of Gastrointestinal tract (GIT) infections in Omani patients and their resistance pattern against commonly used antibiotics. Seven hundred and ninety fresh stool samples were obtained from Omani patients attending Sultan Qaboos University Hospital with GI manifestation from the 1st of June to the 30th of November 2019. Bacterial identification in stool samples was carried out by inoculation in culture media, microscopical examination and biochemical tests confirmed by MALDI. BD PhoenixTM. The antibiotics sensitivity testing was carried out by the Manual disk diffusion method and by MALDI. BD PhoenixTM. Out of 790 stool samples, 49 samples were positive for GIT bacterial infections. Salmonella spp. was the most prevalent isolate and more associated with children less than ten years old. Out of the 49 bacterial isolates, 3 (6.1%) were Clostridium difficili, 4 (8.2%) were Shigella flexneri, 5 (10.2%) were Campylobacter jejuni, and different Salmonella spp. serotypes were detected such as Salmonella Kentucky (8.2%), Salmonella enteritidis (6.1%), Salmonella infantis (4.1%), Salmonella welteverden (4.1%), Salmonella typhimurium (4.1%), Salmonella anatum (2.0%), Salmonella tesvia (2.0%), Salmonella Uganda (2.0%), Salmonella Arizona (2.0%) and (40.8%) of other Salmonella spp. serotypes. Eighty percent of isolated Campylobacter jejuni were resistant to Ciprofloxacin and Tetracycline. Salmonella spp. and Shigella flexneri were highly resistant to Amikacin, Gentamicin, and Cefuroxime. The low level of bacterial infection detected among screened patients in the present study indicates the excellent hand washing hygiene practice in reducing GIT infections among patients in Oman. This good hand washing hygiene practice is of great help in the efforts of controlling the spread of other severe diseases like COVID-19. However, detecting the emerging of antibiotic-resistant of GIT bacterial pathogens among patients in Oman, such as Salmonella and Shigella to a commonly used antibiotic such as Gentamicin, is alarming.

Assessing the microbial risk of faecal sludge use in Ugandan agriculture by comparing field and theoretical model output

Reuse of faecal sludge in agriculture has many potential benefits, but also poses risks to human health. To better understand the potential risks, Quantitative Microbial Risk Assessment (QMRA) was performed for three population groups in Kampala, Uganda: wastewater and faecal sludge treatment plant workers; farmers using faecal sludge; and consumers of faecal sludge-fertilised vegetables. Two models were applied for farmers and consumers, one based on pathogen concentrations from field sampling of sludge, soils and vegetables, and one based on theoretical pathogen contribution from the last sludge application, including decay and soil to crop transfer of pathogens. The risk was evaluated for two pathogens (enterohaemorrhagic E. coli (EHEC) and Ascaris lumbricoides). The field data on sludge, soil and vegetables indicated that the last application of faecal sludge was not the sole pathogen source. Correspondingly, the model using field data resulted in higher risks for farmers and consumers than the theoretical model assuming risk from sludge only, except when negligible for both. For farmers, the yearly risk of illness, based on measured concentrations, was 26% from EHEC and 70% from Ascaris, compared with 1.2% and 1.4%, respectively, considering the theoretically assumed contribution from the sludge. For consumers, the risk of illness based on field samples was higher from consumption of leafy vegetables (100% from EHEC, 99% from Ascaris) than from consumption of cabbages (negligible for EHEC, 26% from Ascaris). With the theoretical model, the risk of illness from EHEC was negligible for both crops, whereas the risk of illness from Ascaris was 64% and 16% for leafy vegetables and cabbage, respectively. For treatment plant workers, yearly risk of illness was 100% from EHEC and 99.4% from Ascaris. Mitigation practices evaluated could reduce the relative risk by 30-70%. These results can help guide treatment and use of faecal sludge in Kampala, to protect plant workers, farmers and consumers.

Gastrointestinal infection in Italy during the Roman Imperial and Longobard periods: A paleoparasitological analysis of sediment from skeletal remains and sewer drains

OBJECTIVE

This study aims to investigate parasitic infection in Italy during the Roman period (27 BCE-476 CE) and subsequent Longobard (Lombard) period (6th-8th CE).

MATERIALS

Sediment samples from drains and burials from Roman Imperial-period sites in Italy (Lucus Feroniae, Oplontis, Vacone, and Vagnari), Late Antique and Longobard-period burials at Selvicciola (ca. 4th-8th CE), and Longobard-period burials at Vacone and Povegliano Veronese.

METHODS

Microscopy was used to identify helminth eggs and enzyme-linked immunosorbent assay (ELISA) to detect protozoan antigens.

RESULTS

Roundworm and whipworm were found in pelvic sediment from Roman-period burials, while roundworm and the protozoan Giardia duodenalis were identified in Roman-period drains. In pelvic sediment from the Late Antique through Longobard periods, roundworm and Taenia tapeworm eggs were identified.

CONCLUSIONS

Fecal-oral parasites were found throughout Imperial Roman Italy, suggesting that gastrointestinal infections caused a significant disease burden. In the Longobard period we see continuity in transmission of fecal-oral parasites, and the appearance of zoonotic parasites acquired from eating undercooked meat.

SIGNIFICANCE

A wealth of information exists about certain diseases in the Roman period, but relatively little is known about intestinal parasites in Italy during the Roman and Longobard periods. This is the first evidence for Giardia in Roman period Italy, and for any parasites in the Longobard period in Italy.

LIMITATIONS

Low egg concentrations and lack of controls for some samples makes it difficult to differentiate true infections from environmental contamination in some cases.

SUGGESTIONS FOR FUTURE RESEARCH

Continual study of samples from Roman and Longobard period Italy.

Prevalence of intestinal parasitic infections and Campylobacter spp. among children with gastrointestinal disorders in Tehran, Iran

Co-infection of intestinal parasitic infections (IPIs) and Campylobacter spp. are public health problem in both developing and developed countries. This study was conducted to determine prevalence of IPIs and Campylobacter spp. among children with gastrointestinal disorders in Tehran. In this descriptive cross-sectional survey, 283 fresh stool samples were collected from all individuals and examined by standard parasitological methods including direct slide smear, formalin-ether concentration, trichrome staining, modified Ziehl-Neelsen staining, and chromotrope 2R staining techniques were used for detection of intestinal protozoa and helminths. Furthermore, culture and multiplex-PCR were also used to identify the species of Campylobacter. Data analysis was performed using SPSS version 16. IPIs were detected microscopically in 22.26% of the total study population, with a higher prevalence in Giardia duodenalis (7.06%) and Blastocystis hominis (7.06%). Campylobacter were detected molecularly in 14.8% (95.2% of C. jejuni vs. 4.8% of C. coli) of the total study populations; of these, 3.5% had co-existence with IPIs colonized patients. Our results showed a relatively high prevalence of IPIs and Campylobacter in children with diarrhea. Further research is needed to better understand their co-infection and ensure future advances in clinical trials, testing, and development of therapeutic approaches for these pathogens.

A 21-year retrospective analysis of environmental impacts on paediatric acute gastroenteritis in an affluent setting

BACKGROUND

Extreme weather events happen more frequently along with global warming and they constitute a challenge for public health preparedness. For example, many investigations showed heavy rainfall was associated with an increased risk of acute gastroenteritis. In this study, we examined the associations between different meteorological factors and paediatric acute gastroenteritis in an affluent setting in China controlling for pollutant effects.

METHODS

Aggregated total weekly number of intestinal infection-related hospital admissions, and meteorological and air pollution data during 1998-2018 in Hong Kong were collected and analysed by a combination of quasi-Poisson generalized additive model and distributed lag nonlinear model. Study population was restricted to children under 5 years of age at the time of admission.

RESULTS

While heavy rainfall did not exhibit a statistically significant association with the risk of paediatric admission due to intestinal infections, low temperature and humidity extremes (both relative humidity and vapour pressure) did. Compared with the temperature at which the lowest risk was detected (i.e. 22.5 °C), the risk was 6.4% higher (95% confidence interval: 0.0% to 13.0% at 15.1 °C (i.e. the 5th percentile)). We also found the risk of paediatric admission was statistically significantly associated with an increase in the number of extreme cold days in a week over the study period.

CONCLUSION

Cold condition may have greater impact on disease transmission through increased stability and infectivity of enteric viruses in affluent settings like Hong Kong and thus resulted in an increased risk for paediatric acute gastroenteritis. On the contrary, an insignificant impact from heavy rainfall and high temperature may indicate a minor effect on disease transmission through bacterial growth in contaminated food and water. With the identified impacts of weather factors, extreme weather events are likely to distort the prevalence and seasonal pattern of diarrhoeal diseases in the future.

The clinical path to deliver encapsulated phages and lysins

The global emergence of multidrug-resistant pathogens is shaping the current dogma regarding the use of antibiotherapy. Many bacteria have evolved to become resistant to conventional antibiotherapy, representing a health and economic burden for those afflicted. The search for alternative and complementary therapeutic approaches has intensified and revived phage therapy. In recent decades, the exogenous use of lysins, encoded in phage genomes, has shown encouraging effectiveness. These two antimicrobial agents reduce bacterial populations; however, many barriers challenge their prompt delivery at the infection site. Encapsulation in delivery vehicles provides targeted therapy with a controlled compound delivery, surpassing chemical, physical and immunological barriers that can inactivate and eliminate them. This review explores phages and lysins' current use to resolve bacterial infections in the respiratory, digestive, and integumentary systems. We also highlight the different challenges they face in each of the three systems and discuss the advances towards a more expansive use of delivery vehicles.

Zakażenia przewodu pokarmowego w XXI wieku w Polsce i na świecie

Na początku XXI wieku wciąż istnieje ogólnoświatowy problem zakażeń przewodu pokarmowego we wszystkich grupach wiekowych ludności. Za najpowszechniejszy czynnik etiologiczny chorób biegunkowych na świecie przenoszony przez skażoną żywność uważany jest Norovirus oraz bakterie z rodzaju Salmonella i Campylobacter, jednak za największą liczbę nieżytów żołądkowo-jelitowych odpowiadają rotawirusy. Ciągle terenami endemicznymi ciężkich zakażeń pokarmowych jest Afryka, Azja Południowo-Wschodnia, Ameryka Łacińska oraz wschodnia część Basenu Morza Śródziemnego. Na tych terenach utrzymują się „stare” czynniki etiologiczne biegunek, takie jak np.: Vibrio cholerae, Salmonella Typhi, Salmonella Paratyphi. Grupą szczególnie narażoną na infekcje pokarmowe pozostają dzieci <5. roku życia. Głównym czynnikiem etiologicznym biegunek w tej grupie wiekowej – zarówno w krajach rozwiniętych, jak i rozwijających się – są rotawirusy. Odpowiadają one za 500 tys. zgonów rocznie. Polska ze względu na ograniczone standardy diagnostyczne, epidemiologicznie różni się częstotliwością występowania poszczególnych patogenów biegunkowych od pozostałych krajów. Dotyczy to niższej zapadalności na zakażenia o etiologiach: Campylobacter, Norovirus, Shigella. Dominującym czynnikiem zakażeń pokarmowych o podłożu bakteryjnym w kraju są pałeczki Salmonella, natomiast wirusowym rotawirusy. Wiedza na temat chorób infekcyjnych układu pokarmowego może być w XXI w. na nowo sformułowana, a lista czynników etiologicznych poszerzona, sprzyjają temu zaś badania mikrobioty jelit oraz powszechne stosowanie nowych technik diagnostycznych m.in. spektometrii mas i real-time PCR.

Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium

The change of dietary habits in Western societies, including reduced consumption of fiber, is linked to alterations in gut microbial ecology. Nevertheless, mechanistic connections between diet-induced microbiota changes that affect colonization resistance and enteric pathogen susceptibility are still emerging. We sought to investigate how a diet devoid of soluble plant fibers impacts the structure and function of a conventional gut microbiota in specific-pathogen-free (SPF) mice and how such changes alter susceptibility to a rodent enteric pathogen. We show that absence of dietary fiber intake leads to shifts in the abundances of specific taxa, microbiome-mediated erosion of the colonic mucus barrier, a reduction of intestinal barrier-promoting short-chain fatty acids, and increases in markers of mucosal barrier integrity disruption. Importantly, our results highlight that these low-fiber diet-induced changes in the gut microbial ecology collectively contribute to a lethal colitis by the mucosal pathogen Citrobacter rodentium, which is used as a mouse model for enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC, respectively). Our study indicates that modern, low-fiber Western-style diets might make individuals more prone to infection by enteric pathogens via the disruption of mucosal barrier integrity by diet-driven changes in the gut microbiota, illustrating possible implications for EPEC and EHEC infections.

Quantitative analysis and virulence phenotypes of atypical enteropathogenic Escherichia coli (EPEC) acquired from diarrheal stool samples from a Midwest US hospital

Infectious diarrhea causes approximately 179 million illnesses annually in the US. Multiplex PCR assays for enteric pathogens detect enteropathogenic Escherichia coli (EPEC) in 12-29% of diarrheal stool samples from all age groups in developed nations. The aim of this study was to isolate and characterize EPEC from diarrhea samples identified as EPEC positive by BioFire Gastrointestinal Panel (GIP). EPEC is the second most common GIP-detected pathogen, equally present in sole and mixed infections peaking during summer months. EPEC bacterial load is higher in samples with additional pathogens. EPEC-GIP-positive stool samples were cultured on MacConkey II agar and analyzed by colony PCR for eaeA and bfpA to identify and classify EPEC isolates as typical (tEPEC) or atypical (aEPEC). EPEC were not recovered from the majority of stool samples with only 61 isolates obtained from 277 samples; most were aEPEC from adults. bfpA-mRNA was severely diminished in 3 of 4 bfpA-positive isolates. HeLa and SKCO-15 epithelial cells were infected with EPEC isolates and virulence-associated phenotypes, including adherence pattern, attachment level, pedestal formation, and tight junction disruption, were assessed. All aEPEC adherence patterns were represented with diffuse adherence predominating. Attachment rates of isolates adhering with defined adherence patterns were higher than tEPEC lacking bfpA (ΔbfpA). The majority of isolates formpedestals. All but one isolate initially increases but ultimately decreases transepithelial electrical resistance of SKCO-15 monolayers, similar to ΔbfpA. Most isolates severely disrupt occludin; ZO-1 disruption is variable. Most aEPEC isolates induce more robust virulence-phenotypes in vitro than ΔbfpA, but less than tEPEC-E2348/69.

The phenomenon of summer diarrhea and its waning, 1910-1930

During the first two decades of the 20th century, diarrheal deaths among American infants and children surged every summer. Although we still do not know what pathogen (or pathogens) caused this phenomenon, the consensus view is that it was eventually controlled through public health efforts at the municipal level. Using data from 26 major American cities for the period 1910-1930, we document the phenomenon of summer diarrhea and explore its dissipation. We find that water filtration is associated with a 15 percent reduction in diarrheal mortality among children under the age of two during the non-summer months, but does not seem to have had an effect on diarrheal mortality during the summer. In general, we find little evidence to suggest that public health interventions undertaken at the municipal level contributed to the dissipation of summer diarrhea.

Risk assessment of waterborne infections in Enugu State, Nigeria: Implications of household water choices, knowledge, and practices

This research investigated the prevalence of waterborne infections (WBIs) and the risks associated with household drinking water choices, knowledge, and practices. A cross-sectional multi-stage sampling research design was employed. A well-structured questionnaire was used to sample 403 individuals representing 115 household; and stool samples collected and subjected to standard parasitic and bacterial diagnostic methods. From the 403 samples, 344 (85.4%) were positive for at least one waterborne pathogen of nine isolates: E. coli (38.0%), Giardialamblia (35.2%), E. histolytica (33.0%), Salmonellatyphi (19.9%), Proteus spp. (13.2%), Shigelladysentery (9.4%), Klebsiella spp. (7.4%), Enterobacter spp. (5.5%), and Cryptosporidium spp. (5.2%). Prevalence of WBIs was >75% in all age groups, but decreased with age. Prevalence of WBIs was >80% in all communities. Risk was not biased by gender. Odds of infection from public well (OR = 2.487; CI₉₅: 1.296–4.774) and borehole/vendor (OR = 2.175; CI₉₅: 1.231–3.843) users was over two times greater than non-users. Risk of WBDs was significantly reduced by 60% in sachet water drinkers (OR = 0.392; CI₉₅: 0.217–0.709; p < 0.05). Surprisingly, river/stream water users had a significant reduced risk of WBDs than non-users (OR = 0.335; CI₉₅: 0.150–0.749; p < 0.05). Poor hygiene was the most important determinant of WBIs; poor sanitary practice increased odds of WBIs by 400% (OR = 4.945; CI₉₅: 2.358–10.371; p < 0.05). This study shows that most household water choices are vulnerable to contamination at many points in their journey from source to mouth; and advocates adequate provision of safe water, “point of use” household water treatment, and good storage methods to effectively curb WBIs.

Acute Infectious Gastroenteritis in Infancy and Childhood

BACKGROUND

Despite the introduction of vaccination against rotavirus, and even though it can often be treated on an outpatient basis, acute infectious gastroenteritis is nevertheless the second most common non-traumatic cause of emergency hospitaliza - tion in children aged 1 to 5 years, accounting for approximately 9% of cases (39 410 cases in 2017). The most common path - ogens are viruses (47% rotavirus, 29% norovirus, and 14% adenovirus).

METHODS

This review is based on publications retrieved by a selective search in PubMed employing the terms "acute gastro - enteritis children" AND "dehydration" OR "rehydration" OR "prevention," and by manual searching (based, for example, on reference lists and expert knowledge), with subsequent evaluation including consideration of the relevant guidelines.

RESULTS

The degree of dehydration can be judged from weight loss and other clinical findings. In 17 randomized controlled trials conducted on a total of 1811 children with mild or moderate dehydration, oral rehydration with oral rehydration solution was just as effective as intravenous rehydration with respect to weight gain, duration of diarrhea, and fluid administration, and was associated with shorter hospital stays (weighted mean difference, -1.2 days; 95% confidence interval [-2.38; -0.02]). Oral rehydration therapy failed in 4% of patients [1; 7]. In children who are vomiting or who refuse oral rehydration solution, continuous nasogastric application is just as effective as intravenous rehydration and is the treatment of first choice.

CONCLUSION

In Germany, children with mild or moderate dehydration are often hospitalized for intravenous rehydration therapy, despite the good evidence supporting ambulatory oral rehydration. Obstacles to intersectoral care, the nursing shortage, and inadequate reimbursement must all be overcome in order to reduce unnecessary hospitalizations and thereby lessen the risk of nosocomial infection.

Accuracy and Cross-Reactivity of Rapid Diagnostic Tests for Norovirus and Rotavirus in a Real Clinical Setting

Background

Rapid diagnostic test (RDT) of norovirus and rotavirus is commonly used for outbreak screening and patient management. Varying accuracy of the test and cross-reactivity has been reported and could affect the outcome of management. The primary purpose of this study is to provide the accuracy of norovirus and rotavirus rapid diagnostic tests and to analyze the cross-reactivity of both tests.

Materials and Methods

Stool samples collected from every acute diarrhea patient aged <15 years old who was admitted at Bhumibol Adulyadej Hospital, Bangkok, Thailand, from November 2014 to September 2016 underwent the following test: QuickNaviTM – Norovirus2 for norovirus, VIKIA^® Rota-Adeno for rotavirus, and aerobic bacterial culture. Real-time reverse transcription polymerase chain reaction was used as a gold standard for virus detection. False-positive results determined cross-reactivity.

Results

From 358 stool specimens, the sensitivity of RDTs for norovirus and rotavirus was 27.5% and 44.8%, respectively. The specificity of RDTs for norovirus and rotavirus was 97.7% and 91.6%, respectively. False positive results of RDT for norovirus occurred in 6 samples (1.7%) and 22 samples (6.1%) in RDT for rotavirus. Rotavirus RDT was found to have cross-reactivity with 11 norovirus infection and 3 bacterial infected stools.

Conclusion

We found that the RDTs for both rotavirus and norovirus have high specificity but low sensitivity. Cross-reactivity was observed in positive rotavirus RDT with half of it being norovirus.

Antibacterial Activity of Bacteriocinogenic Commensal Escherichia coli against Zoonotic Strains Resistant and Sensitive to Antibiotics

Antibiotic resistance concerns various areas with high consumption of antibiotics, including husbandry. Resistant strains are transmitted to humans from livestock and agricultural products via the food chain and may pose a health risk. The commensal microbiota protects against the invasion of environmental strains by secretion of bacteriocins, among other mechanisms. The present study aims to characterize the bactericidal potential of bacteriocinogenic Escherichia coli from healthy humans against multidrug-resistant and antibiotic-sensitive strains from pigs and cattle. Bacteriocin production was tested by the double-layer plate method, and bacteriocin genes were identified by the PCR method. At least one bacteriocinogenic E. coli was detected in the fecal samples of 55% of tested individuals, adults and children. Among all isolates (n = 210), 37.1% were bacteriocinogenic and contained genes of colicin (Col) Ib, ColE1, microcin (Mcc) H47, ColIa, ColM, MccV, ColK, ColB, and single ColE2 and ColE7. Twenty-five E. coli carrying various sets of bacteriocin genes were further characterized and tested for their activity against zoonotic strains (n = 60). Strains with ColE7 (88%), ColE1-ColIa-ColK-MccH47 (85%), MccH47-MccV (85%), ColE1-ColIa-ColM (82%), ColE1 (75%), ColM (67%), and ColK (65%) were most active against zoonotic strains. Statistically significant differences in activity toward antibiotic-resistant strains were shown by commensal E. coli carrying MccV, ColK-MccV, and ColIb-ColK. The study demonstrates that bacteriocinogenic commensal E. coli exerts antagonistic activity against zoonotic strains and may constitute a defense line against multidrug-resistant strains.

Novel multiplex real-time PCR assays reveal a high prevalence of diarrhoeagenic Escherichia coli pathotypes in healthy and diarrhoeal children in the south of Vietnam

Background

Diarrhoeagenic Escherichia coli (DEC) infections are common in children in low-middle income countries (LMICs). However, detecting the various DEC pathotypes is complex as they cannot be differentiated by classical microbiology. We developed four multiplex real-time PCR assays were to detect virulence markers of six DEC pathotypes; specificity was tested using DEC controls and other enteric pathogens. PCR amplicons from the six E. coli pathotypes were purified and amplified to be used to optimize PCR reactions and to calculate reproducibility. After validation, these assays were applied to clinical samples from healthy and diarrhoeal Vietnamese children and associated with clinical data.

Results

The multiplex real-time PCRs were found to be reproducible, and specific. At least one DEC variant was detected in 34.7% (978/2815) of the faecal samples from diarrhoeal children; EAEC, EIEC and atypical EPEC were most frequent Notably, 41.2% (205/498) of samples from non-diarrhoeal children was positive with a DEC pathotype. In this population, only EIEC, which was detected in 34.3% (99/289) of diarrhoeal samples vs. 0.8% (4/498) non-diarrhoeal samples (p < 0.001), was significantly associated with diarrhoea. Multiplex real-time PCR when applied to clinical samples is an efficient and high-throughput approach to DEC pathotypes.

Conclusions

This approach revealed high carriage rates of DEC pathotypes among Vietnamese children. We describe a novel diagnostic approach for DEC, which provides baseline data for future surveillance studies assessing DEC burden in LMICs.

Viral gastroenteritis in hospitalized patients: Evaluation of immunochromatographic methods for rapid detection in stool samples

BACKGROUND

. Viral infections are recognized as the most common cause of acute gastroenteritis (AGE). Virus detection by immune analytical methods is recommended for diagnosis because of its simplicity and low cost.

OBJECTIVES

. Two commercial immunochromatographic (ICG) techniques (Materlab) for rapid detection of rotavirus/adenovirus and norovirus respectively, were evaluated by comparison to the results obtained using PCR methods. In addition, clinical and epidemiologic characteristics of AGE infections have been described.

STUDY DESIGN

. A total of 100 faecal samples collected from patients with AGE (84% children) admitted into a Spanish Hospital between February and July 2018, were studied for rotavirus-A, adenovirus and norovirus GI/GII by the ICG tests as well as by PCR and sequencing. Other enteric viruses (enterovirus and astrovirus) were investigated by PCR methods. Gastrointestinal bacteria and parasites were also tested.

RESULTS

. Evaluated ICG tests yielded high specificity (>97%). Sensitivity values were high for rotavirus/adenovirus (>80%) but lower for norovirus (57%). Overall, and taking into account coinfections, viruses (32%), bacteria (14%) and parasites (1%) could be detected. Rotavirus-A were the most frequently identified viruses (16%), followed by enterovirus (12%), norovirus (4%), adenovirus 41 (4%) and astrovirus (1%). In five vaccinated children, a rotavirus was detected.

CONCLUSIONS

. ICG technique is a useful tool for the routine diagnosis of AGE infections at hospital, but for surveillance and epidemiological studies, it is needed the use of amplification and sequencing methods, which also allow monitoring of new strains or variants emergence. In this study, an etiological pathogen was determined only in 44% of samples.

The knowledge, attitude, and practices of food handlers in central South African hospices

The escalating number of foodborne diseases and food poisoning outbreaks demand a better call for improved food-handling practices. Hospices are typically described as nongovernmental organizations that offer palliative care to terminally ill patients. The majority of hospice food handlers are not trained in food safety aspects, and services are offered on a voluntary basis. In this study, a descriptive survey design comprising of semistructured questionnaire was utilized to assess the knowledge, attitudes, and practices of the hospice food handlers (n = 100) in hospices around Central South Africa. More than half of the participants (68%) had not taken basic food safety training. The average percentage of the correct answers on the knowledge questionnaire was 66.8%. The participants had a mean age of 35 years (SD = 9.27). Attendance of food safety course had a significant effect on both the practices of using gloves to touch or distribute unwrapped foods (χ 2 = 8.411, p-value = .012), and washing hands after using gloves (χ 2 = 12.560, p-value = .001). The overall KAP mean score was 78.38. A statistically significant difference was found between the trained and untrained food handlers regarding food safety knowledge (p < .001). There was substantial lack of knowledge regarding the correct temperature for a refrigerator including hot ready-to-eat food.

Performance of the QIAstat-Dx Gastrointestinal Panel for Diagnosing Infectious Gastroenteritis

Detection and identification of enteropathogens that cause infectious gastroenteritis are essential steps for appropriate patient treatment and effective isolation precautions. Several syndrome-based tests have recently become available, with the gastrointestinal panel (GIP) assay on the QIAstat-Dx as the most recent addition to the syndromic testing landscape.

Detection and identification of enteropathogens that cause infectious gastroenteritis are essential steps for appropriate patient treatment and effective isolation precautions. Several syndrome-based tests have recently become available, with the gastrointestinal panel (GIP) assay on the QIAstat-Dx as the most recent addition to the syndromic testing landscape. The QIAstat-Dx GIP assay offers simultaneous testing for 24 bacterial, viral, and parasitic enteropathogens using a single test that reports the results in 70 min. In this study, we compared the performance of the GIP assay to laboratory-developed real-time PCR assays (LDTs), using 172 prospectively and retrospectively collected fecal samples from patients suspected to have infectious gastroenteritis. The GIP assay detected 97/107 enteropathogens (91%) that were detected by LDTs, and the overall agreement of results increased to 95% when excluding discrepant results with cycle threshold (C_T) values of >35. Further, the GIP assay detected 42 additional enteropathogens that were not detected, or tested, by LDTs. These included 35 diarrheagenic Escherichia coli targets for which the clinical relevance is unclear for most. The main advantage of the QIAstat-Dx system compared to other syndromic testing systems is the ability to generate C_T values that could help with the interpretation of results. However, compared to LDTs, the GIP assay is limited by flexibility and high-throughput testing. In conclusion, the GIP assay offers an easy, sample-to-answer workflow with a rapid detection of the most common enteropathogens and therefore has the potential to direct appropriate therapy and infection control precautions.

High-dimensional analysis of intestinal immune cells during helminth infection

Single cell isolation from helminth-infected murine intestines has been notoriously difficult, due to the strong anti-parasite type 2 immune responses that drive mucus production, tissue remodeling and immune cell infiltration. Through the systematic optimization of a standard intestinal digestion protocol, we were able to successfully isolate millions of immune cells from the heavily infected duodenum. To validate that these cells gave an accurate representation of intestinal immune responses, we analyzed them using a high-dimensional spectral flow cytometry panel and confirmed our findings by confocal microscopy. Our cell isolation protocol and high-dimensional analysis allowed us to identify many known hallmarks of anti-parasite immune responses throughout the entire course of helminth infection and has the potential to accelerate single-cell discoveries of local helminth immune responses that have previously been unfeasible.