Clinical features, risk factors, and impact of antibiotic treatment of diarrhea caused by Shigella in children less than 5 years in Manhiça District, rural Mozambique

Prevalence, antimicrobial susceptibility pattern and associated factors of Salmonella and Shigella among under five children with diarrhea attending Bule Hora University Teaching Hospital, Bule Hora, West Guji, Ethiopia

BACKGROUND

Salmonella and Shigella are a critical concern of the developing world and responsible for the high rate of diarrhea-related deaths. The treatment of these infections remains a challenge, due to the global rise in broad-spectrum resistance to many antibiotics. The aim of this study to determine the prevalence, antimicrobial susceptibility patterns, and associated factors of Salmonella and Shigella among under five children with diarrhea attending Bule Hora University Teaching Hospital, Bule Hora, West Guji, Ethiopia.

METHODS

A hospital-based cross-sectional study was conducted from July 01 to October 30, 2023. Three hundred sixty-five under five children with diarrhea were enrolled consecutively using convenient sampling technique. Data about patient socio-demographics, signs, and symptoms was obtained from the parents/guardians of each child using a questionnaire. Stool specimens from diarrheic children were collected and processed for isolation of Salmonella and Shigella using standard bacteriological methods. Antibiotic susceptibility patterns were determined by using the Kirby Bauer disc diffusion method. Data analysis was performed by using SPSS version 25. A p-value < 0.05 at 95% CI was considered statistically significant.

RESULTS

The prevalence of salmonella and Shigella isolates were 6.3% (23/365) and 4.9% (18/365) respectively. The isolates were 95.1% susceptible to ciprofloxacin and 73.2% to ceftriaxone. The isolates were 39.02% multidrug resistance to classes of drug choice for susceptibility tests. Presence of vomiting (AOR = 2.36), contact with diarrhoeal patient (AOR = 3.38), untrimmed fingernail (AOR = 5.20), storing cooked food in open containers (AOR = 6.5), unimproved source of drinking water from well and river (AOR = 3.86 & 3.2) showed statistically significant association with Salmonella and Shigella infections.

CONCLUSION

The prevalence of Salmonella and Shigella isolates were relatively high in the study area. The isolates were found to be sensitive to Ceftriaxone, ciprofloxacin, and cotrimoxazole; and could be possible antimicrobial choices of infection. Contact with diarrhoeal patients, untrimmed fingernails, storing cooked food in open containers and unimproved sources of drinking water were the main sources of infection. Therefore, to alleviate this infection, culture based bacterial species identification and promoting antibiotics sensitivity-based treatment are strongly recommended to avoid empirical treatment in the study area.

Whole genome sequencing and antimicrobial resistance among clinical isolates of Shigella sonnei in Addis Ababa, Ethiopia

BACKGROUND

Shigellosis is an acute gastroenteritis infection and one of Ethiopia's most common causes of morbidity and mortality, especially in children under five. Antimicrobial resistance (AMR) has spread quickly among Shigella species due to inappropriate antibiotic use, inadequacies of diagnostic facilities, and unhygienic conditions. This study aimed to characterize Shigella sonnei (S. sonnei) using whole genome sequence (WGS) analysis in Addis Ababa, Ethiopia.

METHODS

The raw reads were quality-filtered and trimmed, and a minimum length of 50bp was retained and taxonomically classified using MiniKraken version 1. The whole genome data were aligned with Antibiotic Resistance Gene (ARG) sequences of the Comprehensive Antibiotic Resistance Database (CARD) by Resistance Gene Identifier (RGI). Plasmids were analyzed using the PlasmidFinder tool version 2.1. Additionally, AMR and virulence genes were screened at the Centre for Genomic Epidemiology (CGE) web-based server.

RESULTS

All isolates in our investigation contained genes encoding blaEC-8 and blaZEG-1. Here, 60.7% of the isolates were phenotypically sensitive to cefoxitin among the blaEC-8 genes detected in the genotyping analysis, whereas all isolates were completely resistant to amoxicillin and erythromycin phenotypically. The study also identified genes that conferred resistance to trimethoprim (dfrA). Plasmid Col156 and Col (BS512) types were found in all isolates, while IncFII and Col (MG828) plasmids were only identified in one isolate.

CONCLUSION

This study found that many resistant genes were present, confirming the high variety in S. sonnei strains and hence a divergence in phylogenetic relationships. Thus, combining WGS methods for AMR prediction and strain identification into active surveillance may be beneficial for monitoring the spread of AMR in S. sonnei and detecting the potential emergence of novel variations.

Prevalence of Shigella species and antimicrobial resistance patterns in Africa: systematic review and meta-analysis

BACKGROUND

Shigellosis continues to pose a significant public health problem in Africa; however, there is a lack of comprehensive knowledge regarding its prevalence, serogroup distribution, and antimicrobial resistance profiles. Therefore, the objective of this systematic review and meta-analysis was to determine the overall prevalence of Shigella, the distribution of species, and the patterns of antimicrobial resistance across Africa.

METHODS

Following PRISMA guidelines, a systematic search strategy was conducted using the PubMed, Web of Science and Scopus databases from January 31, 2024 to February 10, 2024. The study quality was assessed using the Joanna Briggs Institute checklist, and data were analyzed using the R statistical language and the R package 'meta'. The random effects model was employed to estimate the pooled prevalence, while heterogeneity was assessed using the I2 statistic and prediction interval.

RESULTS

A total of 116 studies from 29 African countries were included in this meta-analysis, involving the examination of 99,510 samples. The overall pooled estimate of Shigella prevalence was determined to be 5.9% (95% CI: 4.9 - 7.0%). Regional prevalence showed prevalences of Southern Africa (6.9 [95% CI: 3.0 - 12.2%]), Northern Africa (6.7% [95% CI: 4.1 - 9.8%]), Eastern Africa (6.2% [95% CI: 4.9 - 7.6%]), Central Africa (4.5% [95% CI: 2.6 - 6.8%]) and Western Africa (4.0% [95% CI: 2.5 - 5.9%]). Shigella prevalence was found to be higher in children (6.6%, 95% CI: 3.2 - 11.1%) than in adults (3.6%, 95% CI: 1.6 - 6.3%). The most prevalent species was S. flexneri (53.6%, 95% CI: 46.1%-61.0%), followed by S. sonnei (11.5%, 95% CI: 7.7%-15.7%), S. dysenteriae (10.1%, 95% CI: 6.2 - 14.5%) and S. boydii (7.7%, 95% CI: 4.7 - 11.1%). Among the currently recommended first-line antibiotics, ciprofloxacin and ceftriaxone showed resistance prevalences of 10.0% (95% CI: 4.5%-16.9%) and 8.5% (95% CI: 2.4-16.9%) respectively.

CONCLUSION

This review highlights the burden of shigellosis in Africa. S. flexneri remains the most prevalent species associated with shigellosis cases with S. sonnei being the second most dominant. The antimicrobial resistance patterns observed in the study suggest local antimicrobial patterns in choosing antibiotics for the treatment of Shigellosis.

RECOMMENDATION

There is the need to explore alternative treatments for shigellosis with particular focus on vaccine development. There is also the need for more genomic epidemiology studies exploring the dissemination and risk of drug-resistant S. sonnei clones in Africa.

Risk Factors of Seizure in Childhood Shigellosis

Objectives

Shigellosis is one of the common causes of bacterial diarrhea in children. Seizures are common in shigellosis. It is essential to identify the risk factors of seizure in this disease.

Materials & Methods

This study was conducted on 224 children with shigellosis. The patients were divided into: With (case groups = 63 cases) and without seizures (control group = 161 cases). Groups were compared regarding different variables such as age, gender, clinical symptoms, and laboratory findings. Data analysis was done using statistical tests and SPSS software. Logistic regression analysis was used to determine the risk factors of seizures.

Results

Out of 224 cases of children with shigellosis, 107 (47.8%) were male and 117 (52.2%) female. Significant differences were observed between the two groups in terms of age, history of febrile convulsions, frequency of bloody diarrhea, frequency of fever, duration of diarrhea before hospitalization, abdominal pain, increase in BUN, hyponatremia, hypocalcemia, and red blood cell count in stool (P<0.05). Logistic regression analysis showed that a history of febrile seizure, fever, and hyponatremia are the risk factors for seizures in shigellosis.

Conclusion

This study concluded that a history of febrile seizure, fever, and hyponatremia are risk factors for seizure in childhood shigellosis, thus rapid diagnosis and treatment of childhood shigellosis with risk factors is very important.

Comparative study on epidemiological and etiological characteristics of patients with acute diarrhea with febrile or non-febrile symptoms in China

BACKGROUND

Acute diarrhea with fever can potentially represent a more severe form of the disease compared to non-febrile diarrhea. This study was to investigate the epidemiological characteristics and enteric pathogen composition of febrile-diarrheal patients, and to explore factors including pathogens associated with fever by age group.

METHODS

A nationwide surveillance study of acute diarrheal patients of all ages was conducted in 217 sentinel hospitals from 31 provinces (autonomous regions or municipalities) in China between 2011 and 2020. Seventeen diarrhea-related pathogens, including seven viruses and ten bacteria, were investigated and their association with occurrence of fever symptoms was assessed using multivariate logistic analysis.

RESULTS

A total of 146,296 patients with acute diarrhea (18.6% with fever) were tested. Th diarrheal children below 5 years had the highest frequency of fever (24.2%), and related to significantly higher prevalence of viral enteropathogens (40.2%) as compared with other age groups (P < 0.001). Within each age group, the febrile-diarrheal patients were associated with a significantly higher prevalence of bacterial pathogens than afebrile-diarrheal patients (all P < 0.01). There was discrepancy when each pathogen was compared, i.e., nontyphoidal Salmonella (NTS) was overrepresented in febrile vs non-febrile patients of all age groups, while the febrile vs non-febrile difference for diarrheagenic Escherichia coli (DEC) was only significant for adult groups. The multivariate analysis revealed significant association between fever and infection with rotavirus A among children [odds ratio (OR) = 1.60], for DEC in adult groups (OR = 1.64), for NTS in both children (OR = 2.95) and adults (OR = 3.59).

CONCLUSIONS

There are significant discrepancy of the infected enteric pathogens in patients with acute diarrhea with fever between age groups, and it is valuable for priority detection of NTS and rotavirus A in patients with children < 5 years old and NTS and DEC in adult patients. The results may be useful in identifying dominant pathogen candidates for the application of diagnostic assays and prevention control.

Microbiological assessment reveals that Salmonella, Shigella and Campylobacter infections are widespread in HIV infected and uninfected patients with diarrhea in Mozambique

Diarrhea is an important cause of hospitalizations in Mozambique. However, little attention has been paid to the impact HIV infection on the prevalence or clinical manifestations of enteric bacterial infections. This study aimed to determine the prevalence of Salmonella spp., Shigella spp. and Campylobacter spp. in HIV-infected and HIV-uninfected patients with diarrhea, identify risk factors for infection, and explore the association between HIV status, viral load, and bacterial prevalence. We conducted a case-control study at the Centro de Saúde de Mavalane and Centro de Saúde 1° de Maio in Maputo, Mozambique, from November 2021 to May 2022. We recruited 300 patients, including 150 HIV-infected (cases) and 150 HIV-uninfected patients (controls), aged between 0-88 years, presenting with diarrhea. Stool samples were collected for bacterial isolation through culture, and for each HIV-infected patient, 4 ml of venous blood were obtained for viral load detection through PCR. A total of 129 patients (43.0%) had at least one bacterial infection. The prevalence of Salmonella spp., Shigella spp. and Campylobacter spp. was 33.0% (n = 99), 15.0% (n = 45) and 4.3% (n = 13), respectively. The prevalence of any bacterial infection did not differ significantly between HIV-infected (45.3%, n = 68) and HIV-uninfected patients (40.7%, = 61) (p = 0.414). Overall, having 2-3 symptoms of enteric disease (p = 0.008) and a basic education (p = 0.030) were factors associated with bacterial infection. Of the 148 patients for whom HIV-1 RNA levels were available, 115 had copy numbers ≤ 75. Another 13 had levels between 76 and 1,000 and the remaining 20 had an average of 327,218.45 copies/ml. Bivariate logistic regression found that Shigella spp. were associated with HIV (p = 0.038), although no association was found in the multivariate analysis. Enteric infections are common in both HIV-infected and -uninfected patients. Low schooling influences the occurrence of enteric infections, which highlights the need to raise awareness about their prevention.

Clinical characteristics and influencing factors of infectious diarrhea in preschool children: An observational study

Infectious diarrhea is a common disease in preschool children, but the pathogenic species, origins, and influencing factors remain debatable. Therefore, more studies are required to solve these debatable topics. A number of 260 eligible preschool children diagnosed with infectious diarrhea in our hospital were enrolled in the infection group. Meanwhile, a number of 260 matched healthy children from the health center were enrolled in the control group. The pathogenic species and origins, the time of onset of infectious diarrhea in the infection group, demographic data, exposure history, hygiene habits, dietary habits, and other variables in both groups were initially collected from medical documents. In addition, a questionnaire was used to complete and confirm study variables through face-to-face or telephone interviews. Then, the univariate and multivariate regression analyses were used to screen the influencing factors of infectious diarrhea. Among 260 infected children, salmonella (15.77%), rotavirus (13.85%), shigella (11.54%), vibrio (10.38%), and norovirus (8.85%) were the top 5 common pathogens; January (13.85%), December (12.69%), August (12.31%), February (11.92%), and July (8.46%) were the top 5 frequent times of infectious diarrhea. The distribution of onset time for infectious diarrhea was commonly found in winter and summer, and the pathogens always originated from foods. The results of multivariate regression analysis showed that recent exposure to diarrhea, flies, and/or cockroaches indoors were the 2 risk factors for infectious diarrhea; Meanwhile, rotavirus vaccination, regular hand-washing, tableware disinfection, separate preparation of cooked and raw foods, and regular intake of lactobacillus products were the 5 protective factors for infectious diarrhea in preschool children. Infectious diarrhea has a diversity of pathogenic species, origins, and influencing factors in preschool children. Activities focusing on these influencing factors such as rotavirus vaccination, consumption of lactobacillus products, and other conventional factors would be beneficial to preschool children's health.

Spatiotemporal variation in risk of Shigella infection in childhood: a global risk mapping and prediction model using individual participant data

BACKGROUND

Diarrhoeal disease is a leading cause of childhood illness and death globally, and Shigella is a major aetiological contributor for which a vaccine might soon be available. The primary objective of this study was to model the spatiotemporal variation in paediatric Shigella infection and map its predicted prevalence across low-income and middle-income countries (LMICs).

METHODS

Individual participant data for Shigella positivity in stool samples were sourced from multiple LMIC-based studies of children aged 59 months or younger. Covariates included household-level and participant-level factors ascertained by study investigators and environmental and hydrometeorological variables extracted from various data products at georeferenced child locations. Multivariate models were fitted and prevalence predictions obtained by syndrome and age stratum.

FINDINGS

20 studies from 23 countries (including locations in Central America and South America, sub-Saharan Africa, and south and southeast Asia) contributed 66 563 sample results. Age, symptom status, and study design contributed most to model performance followed by temperature, wind speed, relative humidity, and soil moisture. Probability of Shigella infection exceeded 20% when both precipitation and soil moisture were above average and had a 43% peak in uncomplicated diarrhoea cases at 33°C temperatures, above which it decreased. Compared with unimproved sanitation, improved sanitation decreased the odds of Shigella infection by 19% (odds ratio [OR]=0·81 [95% CI 0·76-0·86]) and open defecation decreased them by 18% (OR=0·82 [0·76-0·88]).

INTERPRETATION

The distribution of Shigella is more sensitive to climatological factors, such as temperature, than previously recognised. Conditions in much of sub-Saharan Africa are particularly propitious for Shigella transmission, although hotspots also occur in South America and Central America, the Ganges-Brahmaputra Delta, and the island of New Guinea. These findings can inform prioritisation of populations for future vaccine trials and campaigns.

FUNDING

NASA, National Institutes of Health-The National Institute of Allergy and Infectious Diseases, and Bill & Melinda Gates Foundation.

Shigellosis in young children in low-income and middle-income countries: insights from molecular diagnostics

PURPOSE OF REVIEW

To describe the impact of molecular diagnostics on our understanding of the burden and epidemiology of shigellosis in children in low-income and middle-income countries.

RECENT FINDINGS

The incorporation of molecular diagnostics has led to a substantial increase in estimates of the burden of shigellosis and have allowed for further resolution of other aspects of Shigella epidemiology, including the clinical characteristics of shigellosis, the association between clinical and subclinical Shigella infection and linear growth shortfalls, protection after natural infection, duration of convalescent shedding, and host determinants of susceptibility.

SUMMARY

The increased sensitivity and precision afforded by molecular approaches has represented a major advance in our understanding of the epidemiology and burden of shigellosis in the settings of highest importance.

Associated factors, post infection child growth, and household cost of invasive enteritis among under 5 children in Bangladesh

Both Campylobacter- and Shigella-induced invasive enteritis are common in under-5 Bangladeshi children. Our study aimed to determine the factors associated with Campylobacter and Shigella enteritis among under-5 children, the post-infection worsening growth, and the household cost of invasive enteritis. Data of children having Shigella (591/803) and Campylobacter (246/1148) isolated from the fecal specimen in Bangladesh were extracted from the Global Enteric Multicenter Study (GEMS) for the period December 2007 to March 2011. In multiple logistic regression analysis, fever was observed more frequently among shigellosis cases [adjusted OR 2.21; (95% CI 1.58, 3.09)]. Breastfeeding [aOR 0.55; (95% CI 0.37, 0.81)] was found to be protective against Shigella. The generalized estimating equations multivariable model identified a negative association between Shigella and weight-for-height z score [aOR − 0.11; (95% CI − 0.21, − 0.001)]; a positive association between symptomatic Campylobacter and weight-for-age z score [aOR 0.22; (95% CI 0.06, 0.37)] and weight-for-height z score [aOR 0.22; (95% CI 0.08, 0.37)]. Total costs incurred by households were more in shigellosis children than Campylobacter-induced enteritis ($4.27 vs. $3.49). Households with low-level maternal education tended to incur less cost in case of their shigellosis children. Our findings underscore the need for preventive strategies targeting Shigella infection, which could potentially reduce the disease burden, associated household costs, and child growth faltering.

Emergence of multidrug-resistant Shigella species harboring extended-spectrum beta-lactamase genes in pediatric patients with diarrhea from southwest of Iran

Owing to the scarce evidence about the multidrug-resistant (MDR) beta-lactamase-producing Shigella isolates in Iran, this study aimed to evaluate the occurrence of extended-spectrum beta-lactamases (ESBL) and AmpC β-lactamases in Shigella species collected in the southwest of Iran. This study was conducted on Shigella species isolated from stool samples of pediatric patients aged less than 15 years suffering from diarrhea. These isolates were identified by bacteriology tests, serotyping, and polymerase chain reaction (PCR). The antibiotic resistance was determined by disc diffusion. The production of ESBLs and AmpC was investigated by phenotypic confirmatory tests and PCR. In total, 79 Shigella isolates, including 46.8% (n = 37) of S. flexneri and 53.2% (n = 42) of S. sonnei, were isolated, respectively. The most effective antibiotic was imipenem with 93.7% of susceptibility followed by ampicillin (29.1%), and cotrimoxazole (30.4%).The resistance rates of ceftriaxone, ceftazidime, and cefotaxime were 41.8%, 34.2%, and 41.8%, respectively. Also, a total of 57 (72.2%) isolates showed MDR profiles. The phenotypic tests showed that 43.0% (34/79) of isolates can produce ESBLs, and no one was positive for ApmC. The frequency of bla_TEM and bla_CTX-M were 30.4% and 32.9%, respectively, while the bla_PER, bla_SHV, and AmpC genes were not detected. The ESBL-producing isolates had a significant (p-value ˂ 0.05) resistance rate against ceftriaxone, ceftazidime, cefotaxime, cefepime, erythromycin, and amikacin. The significant prevalence of MDR Shigella isolates harboring ESBL genes highlights the need for effective surveillance measures to prevent the more spread of drug resistance among species.

Epidemiology of Shigella infections and diarrhea in the first two years of life using culture-independent diagnostics in 8 low-resource settings

Culture-independent diagnostics have revealed a larger burden of Shigella among children in low-resource settings than previously recognized. We further characterized the epidemiology of Shigella in the first two years of life in a multisite birth cohort. We tested 41,405 diarrheal and monthly non-diarrheal stools from 1,715 children for Shigella by quantitative PCR. To assess risk factors, clinical factors related to age and culture positivity, and associations with inflammatory biomarkers, we used log-binomial regression with generalized estimating equations. The prevalence of Shigella varied from 4.9%-17.8% in non-diarrheal stools across sites, and the incidence of Shigella-attributable diarrhea was 31.8 cases (95% CI: 29.6, 34.2) per 100 child-years. The sensitivity of culture compared to qPCR was 6.6% and increased to 27.8% in Shigella-attributable dysentery. Shigella diarrhea episodes were more likely to be severe and less likely to be culture positive in younger children. Older age (RR: 1.75, 95% CI: 1.70, 1.81 per 6-month increase in age), unimproved sanitation (RR: 1.15, 95% CI: 1.03, 1.29), low maternal education (<10 years, RR: 1.14, 95% CI: 1.03, 1.26), initiating complementary foods before 3 months (RR: 1.10, 95% CI: 1.01, 1.20), and malnutrition (RR: 0.91, 95% CI: 0.88, 0.95 per unit increase in weight-for-age z-score) were risk factors for Shigella. There was a linear dose-response between Shigella quantity and myeloperoxidase concentrations. The burden of Shigella varied widely across sites, but uniformly increased through the second year of life and was associated with intestinal inflammation. Culture missed most clinically relevant cases of severe diarrhea and dysentery.

The effect of acute malnutrition on enteric pathogens, moderate-to-severe diarrhoea, and associated mortality in the Global Enteric Multicenter Study cohort: a post-hoc analysis

Background

Host vulnerabilities associated with acute malnutrition could facilitate the ability of specific enteric pathogens to cause diarrhoea and associated mortality. Using data from the Global Enteric Multicenter Study, we assessed whether acute malnutrition modifies the association between common enteric pathogens and moderate-to-severe diarrhoea, and whether associations between enteric pathogens and death were modified by acute malnutrition.

Methods

Children with moderate-to-severe diarrhoea and age-matched and community-matched controls were included in this post-hoc analysis if their mid-upper arm circumference had been measured and if they were older than 6 months of age. Acute malnutrition was defined as mid-upper arm circumference below 12·5 cm, capturing both severe acute malnutrition (<11·5 cm) and moderate acute malnutrition (≥11·5 cm and <12·5 cm). We tested whether acute malnutrition modified associations between enteric pathogens and moderate-to-severe diarrhoea in conditional logistic regression models. Among children with moderate-to-severe diarrhoea, Cox proportional hazards regression evaluated the modifying effect of acute malnutrition on the relationship between pathogens and 60-day fatality rate.

Findings

The age, site, and co-infection adjusted odds ratios (aORs) for moderate-to-severe diarrhoea associated with typical enteropathogenic Escherichia coli among children aged 6–11 months was 2·08 (95% CI 1·14–3·79) in children with acute malnutrition, and 0·97 (0·77–1·23) in children with better nutritional status, compared with healthy controls. Enterotoxigenic E coli producing heat-stable toxin among children aged 12–23 months also had a stronger association with moderate-to-severe diarrhoea in children with acute malnutrition (aOR 7·60 [2·63–21·95]) than among similarly aged children with better nutritional status (aOR 2·39 [1·76–3·25]). Results for Shigella spp, norovirus, and sapovirus suggested they had a stronger association with moderate-to-severe diarrhoea than other pathogens among children with better nutritional status, although Shigella spp remained associated with moderate-to-severe diarrhoea in both nutritional groups. 92 (64%) of 144 children with moderate-to-severe diarrhoea who died had acute malnutrition. Pathogen-specific 60-day fatality rates for all pathogens were higher among children with acute malnutrition, but no individual pathogen had a significantly larger increase in its relative association with mortality.

Interpretation

Acute malnutrition might strengthen associations between specific pathogens and moderate-to-severe diarrhoea. However, the strong link between acute malnutrition and mortality during moderate-to-severe diarrhoea in children is not limited to specific infections, and affects a broad spectrum of enteric pathogens. Interventions addressing acute malnutrition could be an effective way to lower the mortality of both childhood malnutrition and diarrhoea.

Funding

The Bill & Melinda Gates Foundation.

Childhood diarrhoeal diseases in developing countries

Diarrhoeal diseases collectively constitute a serious public health challenge globally, especially as the leading cause of death in children (after respiratory diseases). Childhood diarrhoea affecting children under the age of five accounts for approximately 63% of the global burden. Accurate and timely detection of the aetiology of these diseases is very crucial; but conventional methods, apart from being laborious and time-consuming, often fail to identify difficult-to-culture pathogens. The aetiological agent of an average of up to 40% of cases of diarrhoea cannot be identified. This review gives an overview of the recent trends in the epidemiology and treatment of diarrhoea and aims at highlighting the potentials of metagenomics technique as a diagnostic method for enteric infections.