Microbial aetiology of acute diarrhoea in children under five years of age in Khartoum, Sudan

Campylobacter at the Human-Food Interface: The African Perspective

The foodborne pathogen Campylobacter is a major cause of human gastroenteritis, accounting for an estimated annual 96 million cases worldwide. Assessment of the true burden of Campylobacter in the African context is handicapped by the under-reporting of diarrhoeal incidents and ineffective monitoring and surveillance programmes of foodborne illnesses, as well as the minimal attention given to Campylobacter as a causative agent of diarrhoea. The present review of the literature highlights the variability in the reported occurrence of Campylobacter in humans and animal food sources across different countries and regions in Africa. Campylobacter infection is particularly prevalent in the paediatric population and has been isolated from farm animals, particularly poultry, and foods of animal origin. The reported prevalence of Campylobacter in children under the age of five years ranges from 2% in Sudan to 21% in South Africa. In poultry, the prevalence ranges from 14.4% in Ghana to 96% in Algeria. This review also highlights the alarming trend of increased Campylobacter resistance to clinically important antimicrobials, such as ciprofloxacin and erythromycin, in humans and food animals in Africa. This review adds to our understanding of the global epidemiology of Campylobacter at the human–food animal interface, with an emphasis from the African perspective. Interinstitutional and intersectoral collaborations, as well as the adoption of the One Health approach, would be useful in bridging the gaps in the epidemiological knowledge of Campylobacter in Africa.

Assessing Students' Knowledge on WASH-Related Diseases

Water-, sanitation-, and hygiene-related diseases are killing many people each year in developing countries, including Rwanda, and children under the age of five are the most vulnerable. This research assessed human waste disposal practices, knowledge on diseases caused by contact with human faeces, and knowledge on causes and prevention of selected WASH-related diseases. One thousand one hundred and seventy-three students were interviewed out of 2900 students. The results showed, regarding students’ waste disposal practices, that 96.3% use latrines, 20.5% practice open defecation in bushes, and 3.2% defecate in water bodies. Regarding knowledge on diseases caused by contact with human faeces, 56.9% responded that they were aware of cholera, 26.5% of diarrhoea, 2.2% of dysentery, 0.3% of malaria, 0.1% of shigellosis, and 3.8% of typhoid. The majority of the respondents, between 50–99%, could not identify the main causes of the WASH-related diseases. This paper also showed that students lack health knowledge in regard to WASH-related diseases’ causes and prevention. Therefore, the provision of water and sanitation infrastructures should go with the provision of health education on how to avoid these diseases and possible ways to improve the well-being of the students both at home and in their various schools.

Acute gastroenteritis associated with Rotavirus A among children less than 5 years of age in Nepal

BACKGROUND

Rotavirus gastroenteritis is a major public health problem in Nepal. This study was conducted to obtain information associated with Rotavirus gastroenteritis and to perform genotyping of Rotavirus A.

METHODS

Hospital based cross sectional study was conducted from January to December 2017 among children less than 5 years of age attending Kanti Children's Hospital and Tribhuvan University Teaching Hospital. Rotavirus A antigen detection was performed by Enzyme Linked Immunosorbent Assay (ELISA) using ProSpecT Rotavirus Microplate Assay. Rotavirus A positive strains were further confirmed by genotyping using Reverse-Transcription Polymerase Chain Reaction (RT-PCR).

RESULTS

A total of 1074 stool samples were collected, of them 770 were hospitalized, and 304 were non-hospitalized cases. Rotavirus A infection was found in 28% of children with infection rate higher in hospitalized (34%) than in non-hospitalized (14%) children. Rotavirus A detection was higher in male (31%) than in female (24%), but this was statistically not significant (p > 0.05). Rotavirus A positivity was higher in children of age group 0-23 months, this result was statistically not significant (p > 0.05) with higher frequency found in the months of November, December, January, February and March (p < 0.05). On the basis of molecular analysis of Rotavirus A genotyping, G12P[6] (46.39%) was found to be the predominant followed by G1P[8] (35.05%), G3P[8] (7.21%) and G1P[6] (5.15%) while 4.12% was mixed infection and 1.03% was partially typed (p < 0.05).

CONCLUSION

Rotavirus A infection occurred throughout the year, but the infection was significantly higher during the month of March. The higher frequency of rotavirus infection was observed among children of age group 0-23 months; however this was not found to be statistically significant. In this study, G12P[6] is predominant genotype observed. The results of genotyping are essential for the introduction of Rotavirus vaccine in Nepal.

Systematic review of the rotavirus infection burden in the WHO-EMRO region

Rotavirus gastroenteritis imposes a heavy burden on low- and middle-income countries. The World Health Organization defines the Eastern Mediterranean region (WHO-EMRO) as a diverse area in terms of socioeconomic status and health indicators. Rotavirus vaccination has been introduced, at least partially, in 19 out of the 22 EM countries; however, vaccine coverage remains low, and data on rotavirus disease burden is scarce.Available data on rotavirus prevalence, seasonality, vaccination status, and genotype evolution was systematically compiled following a literature review that identified 165 relevant WHO-EMRO epidemiology studies published between 1990 and 2017.Although the infectious agents responsible for acute gastroenteritis vary over time, rotavirus remained the leading cause of acute gastroenteritis in children, as seen in 76.3% of reviewed publications. Younger children (<2 years old) were at higher risk and thus increased vaccination coverage and surveillance systems are required to reduce the rotavirus gastroenteritis burden in WHO-EMRO countries.

Childhood Diarrhoea in the Eastern Mediterranean Region with Special Emphasis on Non-Typhoidal Salmonella at the Human⁻Food Interface

Diarrhoeal disease is still one of the most challenging issues for health in many countries across the Eastern Mediterranean region (EMR), with infectious diarrhoea being an important cause of morbidity and mortality, especially in children under five years of age. However, the understanding of the aetiological spectrum and the burden of enteric pathogens involved in diarrhoeal disease in the EMR is incomplete. Non-typhoidal Salmonella (NTS), the focus of this review, is one of the most frequently reported bacterial aetiologies in diarrhoeal disease in the EMR. Strains of NTS with resistance to antimicrobial drugs are increasingly reported in both developed and developing countries. In the EMR, it is now widely accepted that many such resistant strains are zoonotic in origin and acquire their resistance in the food-animal host before onward transmission to humans through the food chain. Here, we review epidemiological and microbiological aspects of diarrhoeal diseases among children in the EMR, with emphasis on the implication and burden of NTS. We collate evidence from studies across the EMR on the zoonotic exposure and antimicrobial resistance in NTS at the interface between human and foods of animal origin. This review adds to our understanding of the global epidemiology of Salmonella with emphasis on the current situation in the EMR.

Real-time multiplex polymerase chain reaction with high-resolution melting-curve analysis for the diagnosis of enteric infections associated with diarrheagenic Escherichia coli

Introduction

Although diarrheagenic Escherichia coli (DEC) strains are important bacterial causative agents of diarrhoea, they are not routinely sought as stool pathogens in clinical laboratories as conventional microbiological testing are unable to distinguish between normal flora and pathogenic strains of E. coli. This study was undertaken to determine the prevalence of DEC pathotypes amongst children with and without diarrhoea and to detect specific virulent genes present in different DEC pathotypes, using real-time multiplex polymerase chain reaction (PCR) with high-resolution melting (HRM) technology.

Materials and Methods

Stool samples were obtained from cases and controls. Using a set of conventional biochemical tests, E. coli strains were identified. Further, these isolates were subjected to multiplex PCR system for the detection of virulence genes of different pathotypes of DEC. Real-time multiplex PCR was performed for the detection of specific virulent genes of DEC pathotypes, using Rotor-Gene Q instrument (Qiagen) having High-resolution Melt analyser using Type-it HRM PCR kit (Qiagen) containing EvaGreen fluorescent intercalating dye.

Results

In this study, we had successfully standardised two multiplex PCR assays which were found to be effective for direct detection of enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), enterotoxigenic E. coli (ETEC) and enteroinvasive E. coli (EIEC). A total of 42 DEC strains were detected at an overall rate of 19.3% (n = 42), from the total 217 E. coli isolates recovered from the cases (n = 39, 17.9%) and control (n = 3, 3.8%) groups. Amongst the 42 DEC pathotypes (39 from cases and 3 from controls), EPEC (10%), EAEC (8.82%), ETEC (2.94%) and EIEC (1.18%) were found in children with diarrhoea (cases) and in children without diarrhoea (control) only EAEC (2.13%) and EPEC (4.26%) were detected. Age distribution, gender variation, seasonal variation and clinical features were also analysed.

Conclusion

This study helped evaluate the prevalence of DEC amongst children (<18 years of age) with and without diarrhoea using multiplex real-time PCR with HRM analysis.

Probiotics, mechanisms of action, and clinical perspectives for diarrhea management in children

Infectious diarrhea is the second most common cause of morbidity and mortality in children under 5 years of age in the underdeveloped areas of the world. Conventional treatment consists of rehydration, which may be coupled with antimicrobial agents in more severe bacterial infections or with antiprotozoal agents. In the last few decades, research on the use of probiotic strains, such as Lactobacillus rhamnosus GG ATCC 53013 (LGG), Lactobacillus reuteri DSM 17938 and Saccharomyces boulardii, has gained much attention to prevent and treat diarrheal diseases. However, they are rarely used in the clinical routine, perhaps because there are still gaps in the knowledge about the effective benefit to the patient in terms of the reduction of the duration of diarrhea and its prevention. Furthermore, only a few probiotic strains are safely indicated for usage in pediatric practice. This review summarizes the current knowledge on the antimicrobial mechanisms of probiotics on distinct enteropathogens and their role in stimulating host defense mechanisms against intestinal infections. In addition, we highlight the potential of probiotics for the treatment and prevention of diarrhea in children. We conclude that the use of probiotics is beneficial for both the treatment and prevention of diarrhea in children and that the identification of other candidate probiotics might represent an important advance to a greater reduction in hospital stays and to prevent infectious diarrhea in a larger portion of this population.

Serum zinc levels of hospitalized children with acute diarrhea differ by the isolated viruses

BACKGROUND

Acute diarrhea constitutes a major global burden to morbidity and mortality in under-five children. Research has shown that micronutrient zinc plays a pivotal role in childhood diarrhea; however, there are contradictory reports of its therapeutic benefit across the various causative enteropathogens.

OBJECTIVES

The aim of the study was to determine the prevalence of viral etiology (rotavirus, adenovirus, and norovirus) and compare the serum zinc levels of children with acute diarrhea.

METHODS

A comparative cross-sectional study in which 100 hospitalized children with acute diarrhea aged one-59 months and 100 controls were recruited. Viruses were investigated from stool specimens using the immunochromatographic technique, while serum zinc was determined through the colorimetric method. Data analysis was with SPSS 20 software package.

RESULTS

The prevalence of viruses in the subjects was 62.0% with rotavirus isolated in 30 (30.0%) of the patients, while adenovirus and norovirus were detected in 21 (21.0%) and 11 (11.0%) patients, respectively. Rotavirus was the only virus detected in 2 (2.0%) of the controls. The mean serum zinc level of 65.3 ± 7.4 µg/dl in the subjects was significantly lower than 69.0 ± 6.5µg/dl in the controls (P < 0.001). The prevalence of zinc deficiency in the subjects (47.0%) was significantly higher than 32.0% in the controls (P = 0.030). The mean serum zinc levels differed significantly among the viruses isolated in the subjects (P < 0.001).

CONCLUSIONS

Viruses contribute largely to etiology of acute diarrhea in Nigerian under-five children. Zinc deficiency was also highly prevalent in the study population. The serum zinc levels varied significantly across the different viruses isolated.

Characterization of Pathogenic Bacteria Isolated from Sudanese Banknotes and Determination of Their Resistance Profile

Background

Banknotes are one of the most exchangeable items in communities and always subject to contamination by pathogenic bacteria and hence could serve as vehicle for transmission of infectious diseases. This study was conducted to assess the prevalence of contamination by pathogenic bacteria in Sudanese banknotes, determine the susceptibility of the isolated organisms towards commonly used antibiotics, and detect some antibiotic resistance genes.

Methods

This study was carried out using 135 samples of Sudanese banknotes of five different denominations (2, 5, 10, 20, and 50 Sudanese pounds), which were collected randomly from hospitals, food sellers, and transporters in all three districts of Khartoum, Bahri, and Omdurman. Bacterial prevalence was determined using culture-based techniques, and their sensitivity patterns were determined using the Kirby–Bauer disk diffusion method. Genotypic identification was carried out using PCR and 16S rDNA sequencing. Antibiotic resistance genes of some isolates were detected using PCR technique.

Results

All Sudanese banknotes were found to be contaminated with pathogenic bacteria. Klebsiella pneumoniae was found to be the most frequent isolate (23%), whereas Bacillus mycoides (15%) was the most abundant Gram-positive isolate. There was a significant relationship between the number of isolates and the banknote denomination with p value <0.05 (the lower denomination showed higher contamination level). Our study has isolated bacteria that are resistant to penicillins and cephalosporins. Multidrug-resistant strains harboring resistant genes (mecA, blaCTX-M, and blaTEM) were also detected.

Conclusion

All studied Sudanese banknotes were contaminated with pathogenic bacteria, including multidrug-resistant strains, and may play a significant role in the transmission of bacterial infections.

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

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

Molecular Characterization and Antimicrobial Resistance Pattern of Escherichia coli Recovered from Wastewater Treatment Plants in Eastern Cape South Africa

Wastewater treatment plants (WWTPs) are designed to eliminate organic matter and pathogens but most WWTPs discharges antimicrobial resistance pathogens into aquatic milieu. The study aimed to examine the antibiotics resistant patterns and the presence of some resistance genes among E. coli isolates from WWTPs effluents. Water were collected from WWTPs final effluents, filtered through nitrocellulose membrane and the filter papers were placed on chromogenic agar plates, incubated for 24 h at 37 °C. Presumptive E. coli isolates (173) were obtained from the culture method. From the presumptive E. coli isolates screened by polymerase chain reaction (PCR), 111 isolates were positive and the positive isolates were further screened for six diarrheagenic E. coli pathotypes (EPEC, ETEC, EHEC, DAEC, EIEC, and EAEC) and from the pathotypes screened, nine isolates harboured daaE gene. The phenotypic susceptibility patterns of the 111 isolates to 12 antibiotics were determined by Kirby-Bauer disk diffusion technique. All the isolates were resistant to erythromycin and clindamycin. From the resistance genes screened, 31 isolates harboured mcr-1 gene and nine isolates harboured ermA gene. The study reveals that water samples recovered from the final effluents of WWTPs may likely be one of the major sources of antibiotic-resistant in Escherichia coli.

Characteristics of diarrheagenic Escherichia coli among children under 5 years of age with acute diarrhea: a hospital based study

BACKGROUND

Diarrhea is the leading infectious cause of childhood morbidity and mortality. Among bacterial agents, diarrheagenic Escherichia coli (DEC) is the major causal agent of childhood diarrhea in developing countries, particularly in children under the age of 5 years. Here, we performed a hospital-based prospective study to explore the pathotype distribution, epidemiological characteristics and antibiotic resistance patterns of DEC from < 5-year-old diarrheal children.

METHODS

Between August 2015 and September 2016, 684 stool samples were collected from children (< 5 years old) with acute diarrhea. All samples were cultured and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and biochemical tests. PCR was used for subtyping, and enteropathogenic E. coli (EPEC) isolates were identified simultaneously with serology. Furthermore, antimicrobial sensitivity tests and sequencing of antibiotic resistance-related genes were conducted.

RESULTS

DEC strains were identified in 7.9% of the 684 stool samples. Among them, the most commonly detected pathotype was EPEC (50.0% of DEC), of which 77.8% were classified as atypical EPEC (aEPEC). Age and seasonal distribution revealed that DEC tended to infect younger children and to occur in summer/autumn periods. Multidrug-resistant DEC isolates were 66.7%; resistance rates to ampicillin, co-trimoxazole, cefazolin, cefuroxime, cefotaxime, and ciprofloxacin were ≥ 50%. Among 5 carbapenem-resistant DEC, 60.0% were positive for carbapenemase genes (2 blaNDM-1 and 1 blaKPC-2). Among 30 cephalosporin-resistant DEC, 93.3% were positive for extended-spectrum β-lactamase (ESBL) genes, with blaTEM-1 and blaCTX-M-55 being the most common types. However, no gyrA or gyrB genes were detected in 16 quinolone-resistant isolates. Notably, aEPEC, which has not received much attention before, also exhibited high rates of drug resistance (81.0%, 66.7%, and 14.3% for ampicillin, co-trimoxazole , and carbapenem resistance, respectively).

CONCLUSIONS

EPEC was the most frequent DEC pathotype in acute diarrheal children, with aEPEC emerging as a dominant diarrheal agent in central China. Most DEC strains were multidrug-resistant, making even ciprofloxacin unsuitable for empiric treatment against DEC infection. Among carbapenem-resistant DEC strains, those harboring blaNDM-1 and blaKPC-2 were the main causal agents. blaTEM-1 and blaCTX-M-55 were the major genetic determinants associated with high levels of cephalosporin resistance.

Molecular characterization of diarrheagenic Escherichia coli pathotypes: Association of virulent genes, serogroups, and antibiotic resistance among moderate-to-severe diarrhea patients

BACKGROUND

Diarrheagenic Escherichia coli (DEC) signifies as an important etiological agent of moderate-to-severe diarrhea. This study was primarily focused on molecular identification of DEC pathotypes; their association with serogroups and estimates of resistance profiles against different antibiotics regime.

METHODS

Five hundred seventy-two stool specimens from diarrhea patients were investigated for DEC pathotypes. Molecular pathotypes were identified by amplification of virulence genes associated with distinct pathotypes followed by sequencing. Diarrhea is a self-limiting disease, however, severity and persistence of infection suggest antibiotic use. Therefore, AST and MIC were determined against common antibiotic regimen. Correlations between molecular pathotypes and serogroups were analyzed by somatic "O" antigen serotyping.

RESULTS

The present findings reveal incidence of DEC as an etiological agent up to a level of 21% among all diarrheal age groups. DEC infection rate was higher in children. Enteropathogenic E. coliEPEC, a molecular pathotype of DEC, was found as a predominant pathotype with highest frequency of 13.7%. Two other molecular pathotypes enterotoxigenic E. coli (ETEC) and enteroaggregative E. coli (EAEC) accounted for 5.7% and 1.3%, respectively for all diarrhea incidences. Serological analysis deciphered somatic antigens O26, O2, and O3 as major serogroups identified among EPEC, ETEC, and EAEC pathotypes, respectively. All DEC pathotypes exhibited high levels of antibiotic resistance except for cotrimoxazole and norfloxacin.

CONCLUSION

Comprehensive molecular characterization of DEC pathotypes, their incidence estimates, and antibiogram patterns will help in ascertaining better diagnostic and therapeutic measures in management of diarrheal diseases.

Update on the epidemiology of rotavirus in the Middle East and North Africa

Rotavirus (RV) is the leading cause of severe acute gastroenteritis (AGE) worldwide. Consequently, we conducted a systematic literature review on articles studying RV in the 25 countries of the MENA region during the past 15years (2000-2015). The methods and reporting were set according to the 2015 preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) and based on the elements from the international prospective register of systematic reviews (PROSPERO). Our literature search identified 169 studies meeting our predefined inclusion criteria. Studies reporting on RV were conducted in 19 out of the 24 countries of the MENA region. The largest number of studies was reported in Turkey (n=32), Iran (n=31), Saudi Arabia (n=19) and Egypt (n=17). The majority of studies reporting on RV gastroenteritis rates were clinical observational studies. In 115 studies out of 169, RV was reported among in-patients whereas 35 studies reported RV among outpatients. The predominantly reported RV genotype in the region was G1[P8] followed by G2[P4] and G9[P8]. The majority of studies (n=108) were conducted among children less than 5years of age whereas the remaining studies reported on AGE among other age groups and rarely adults. In MENA countries, RV infection was reported all year round with peaks described in cold as well as hot months. This systematic review provides a current update on the epidemiology of RV-associated gastroenteritis in countries of the MENA region and draws attention to the major gaps existing in the continuous monitoring of RV.

Correlates of multi-drug non-susceptibility in enteric bacteria isolated from Kenyan children with acute diarrhea

BACKGROUND

Reduced antimicrobial susceptibility threatens treatment efficacy in sub-Saharan Africa, where data on the burden and correlates of antibiotic resistance among enteric pathogens are limited.

METHODS

Fecal samples from children aged 6 mos-15 yrs presenting with acute diarrhea in western Kenya were cultured for bacterial pathogens. HIV-uninfected children with identified Shigella or Salmonella species or pathogenic Escherichia coli (EPEC, ETEC, EAEC or EIEC) were included in this cross-sectional sub-study. Non-susceptibility to ampicillin, ceftriaxone, ciprofloxacin, cotrimoxazole, and tetracycline was determined using MicroScan Walkaway40 Plus. Multivariable log-binomial regression was used to identify correlates of multi-drug non-susceptibility (MDNS, non-susceptibility to ≥ 3 of these antibiotics).

RESULTS

Of 292 included children, median age was 22.5 mos. MDNS was identified in 62.5% of 318 isolates. Non-susceptibility to cotrimoxazole (92.8%), ampicillin (81.3%), and tetracycline (75.0%) was common. Young age (6-24 mos vs. 24-59 mos adjusted prevalence ratio [aPR] = 1.519 [95% confidence interval: 1.19, 1.91]), maternal HIV (aPR = 1.29 [1.01, 1.66]); and acute malnutrition (aPR = 1.28 [1.06, 1.55]) were associated with higher prevalence of MDNS, as were open defecation (aPR = 2.25 [1.13, 4.50]), household crowding (aPR = 1.29 [1.08, 1.53]) and infrequent caregiver hand-washing (aPR = 1.50 [1.15, 1.95]).

CONCLUSIONS

Young age, HIV exposure, acute malnutrition and poor sanitation may increase risk of antibiotic non-susceptible enteric pathogen infections among children in Kenya.

Detection and sequencing of rotavirus among sudanese children

INTRODUCTION

Diarrheal diseases are a big public health problem worldwide, particularly among developing countries. The current study was conducted to detect and characterize group A rotavirus among admitted children with gastroenteritis to the pediatric hospitals, Sudan.

METHODS

A total of 755 stool samples were collected from Sudanese children with less than 5 years of age presenting with acute gastroenteritis during the period from April to September 2010. Enzyme-linked immunosorbent assay (ELISA) was used to Detection of Rotavirus antigens. Ribonucleic acid (RNAs) were extracted from rotavirus-positive stool samples using (QIAamp® Viral RNA Mini Kit). (Omniscript® Reverse Transcription kit) was used to convert RNA to complementary Deoxyribonucleic acid (cDNA). The cDNAs were used as template for detection of VP4-P (P for Protease-sensitive) and VP7-G (G for Glycoprotein) genotyping of Rotavirus using nested PCR and sequencing.

RESULTS

Out of the 755 stool samples from children with acute gastroenteritis, 121 were positive for rotavirus A. Among 24 samples that were sequenced; the VP7 predominant G type was G1 (83.3%), followed by G9 (16.7%). Out of these samples, only one VP4 P[8] genotype was detected.

CONCLUSION

As a conclusion the VP7 predominant G type was G1, followed by G9 whereas only one VP4 genotype was detected and showed similarity to P[8] GenBank strain. It appears that the recently approved rotavirus vaccines in Sudan are well matched to the rotavirus genotypes identified in this study, though more studies are needed.

Antimicrobial resistance in Africa: a systematic review

BACKGROUND

Antimicrobial resistance (AMR) is widely acknowledged as a global problem, yet in many parts of the world its magnitude is still not well understood. This review, using a public health focused approach, aimed to understand and describe the current status of AMR in Africa in relation to common causes of infections and drugs recommended in WHO treatment guidelines.

METHODS

PubMed, EMBASE and other relevant databases were searched for recent articles (2013-2016) in accordance with the PRISMA guidelines. Article retrieval and screening were done using a structured search string and strict inclusion/exclusion criteria. Median and interquartile ranges of percent resistance were calculated for each antibiotic-bacterium combination.

RESULTS

AMR data was not available for 42.6% of the countries in the African continent. A total of 144 articles were included in the final analysis. 13 Gram negative and 5 Gram positive bacteria were tested against 37 different antibiotics. Penicillin resistance in Streptococcus pneumoniae was reported in 14/144studies (median resistance (MR): 26.7%). Further 18/53 (34.0%) of Haemophilus influenza isolates were resistant to amoxicillin. MR of Escherichia coli to amoxicillin, trimethoprim and gentamicin was 88.1%, 80.7% and 29.8% respectively. Ciprofloxacin resistance in Salmonella Typhi was rare. No documented ceftriaxone resistance in Neisseria gonorrhoeae was reported, while the MR for quinolone was 37.5%. Carbapenem resistance was common in Acinetobacter spp. and Pseudomonas aeruginosa but uncommon in Enterobacteriaceae.

CONCLUSION

Our review highlights three important findings. First, recent AMR data is not available for more than 40% of the countries. Second, the level of resistance to commonly prescribed antibiotics was significant. Third, the quality of microbiological data is of serious concern. Our findings underline that to conserve our current arsenal of antibiotics it is imperative to address the gaps in AMR diagnostic standardization and reporting and use available information to optimize treatment guidelines.

Cryptosporidium and Giardia in Africa: current and future challenges

Cryptosporidium and Giardia are important causes of diarrhoeal illness. Adequate knowledge of the molecular diversity and geographical distribution of these parasites and the environmental and climatic variables that influence their prevalence is important for effective control of infection in at-risk populations, yet relatively little is known about the epidemiology of these parasites in Africa. Cryptosporidium is associated with moderate to severe diarrhoea and increased mortality in African countries and both parasites negatively affect child growth and development. Malnutrition and HIV status are also important contributors to the prevalence of Cryptosporidium and Giardia in African countries. Molecular typing of both parasites in humans, domestic animals and wildlife to date indicates a complex picture of both anthroponotic, zoonotic and spill-back transmission cycles that requires further investigation. For Cryptosporidium, the only available drug (nitazoxanide) is ineffective in HIV and malnourished individuals and therefore more effective drugs are a high priority. Several classes of drugs with good efficacy exist for Giardia, but dosing regimens are suboptimal and emerging resistance threatens clinical utility. Climate change and population growth are also predicted to increase both malnutrition and the prevalence of these parasites in water sources. Dedicated and co-ordinated commitments from African governments involving "One Health" initiatives with multidisciplinary teams of veterinarians, medical workers, relevant government authorities, and public health specialists working together are essential to control and prevent the burden of disease caused by these parasites.

Viral and Bacterial Etiology of Acute Diarrhea among Children under 5 Years of Age in Wuhan, China

BACKGROUND

Acute diarrhea remains the serious problem in developing countries, especially among children under 5 years of age. Currently, only two or three common diarrhea pathogens were screened at most hospitals in China. The aim of this study was to provide a wide variety of diarrhea pathogens and their antimicrobial resistance patterns in children under 5 years of age.

METHODS

Totally 381 stool samples collected from Tongji Hospital between July 1, 2014 and June 30, 2015 were tested by culture and/or polymerase chain reaction for eight kinds of bacteria and five kinds of viruses. An antimicrobial sensitivity test was performed using dilution method recommended by the Clinical and Laboratory Standards Institute.

RESULTS

Viral infections were mainly identified in infants (0-11 months), whereas bacterial infections were more prevalent in the age of 24-59 months. About 69.8% of samples were positive for at least one pathogen, 51.7% of samples were virus positive, followed by bacteria positive cases (19.4%), and 12.6% of cases displayed co-infections with two viruses or a virus and a bacterium. Rotavirus was the most prevalent pathogen, followed closely by norovirus, while Salmonella was the most commonly isolated bacteria, followed by diarrheagenic Escherichia coli (DEC) and Campylobacter. More than 40% of Salmonella spp. and DEC isolates were resistant to first-line antibiotics (ampicillin, trimethoprim-sulfamethoxazole, and tetracycline). Around 10% of Salmonella spp. isolates were resistant to ceftriaxone and ciprofloxacin simultaneously. Campylobacter spp. displayed high resistance to ciprofloxacin but kept low resistance to azithromycin and doxycycline.

CONCLUSIONS

The etiology of acute diarrhea varies in children of different age groups. The high frequency of infection with viruses suggests the urgent demand for new viral vaccine development. Proper use of antibiotics in the treatment of acute diarrhea is crucial due to the high level of antibiotic resistance.

Prevalence and antibiotic resistance of bacterial pathogens isolated from childhood diarrhea in Beijing, China (2010-2014)

BACKGROUND

Diarrhea is one of the main causes of morbidity and mortality among children less than 5 years of age worldwide, and its causes vary by region. This study aimed to determine the etiologic spectrum, prevalent characteristics and antimicrobial resistance patterns of common enteropathogenic bacteria from diarrheagenic children in Beijing, the capital of China.

METHODS

Stool samples were collected from 2524 outpatients who were aged 0-5 years in Beijing, China during 2010-2014. Microbiological methods, real-time PCR and antimicrobial susceptibility test were used to identify the bacterial causes and antimicrobial resistance patterns in the isolates.

RESULTS

Of the 2524 patients screened, we identified the causes of 269 cases (10.7 %) as follows: diarrheagenic Escherichia coli (4.6 %), Salmonella (4.3 %), Shigella (1.4 %) and Vibrio parahaemolyticus (0.4 %). Atypical EPEC, Salmonella enteritidis, Shigella sonnei and serotype O3:K6 were the most common serogroups or serotypes of the four etiological bacteria. The prevalence of pathogens was correlated with age, season and clinical symptoms. The highest proportion of all causative bacteria was found in children aged 3-5 years and in summer. The clinical symptoms associated with specific bacterial infection, such as fever; abdominal pain; vomiting; and watery, mucus, and bloody stool, were observed frequently in diarrheal patients. Salmonella showed moderate rates of resistance (40-60 %) to ampicillin, nalidixic acid, streptomycin and sulfisoxazole. Resistance to at least three antimicrobials was found in 50 % of isolates. Of the top three serotypes in Salmonella, high-level antimicrobial resistance to single and multiple antibiotics was more common among Salmonella typhimurium and Salmonella 1, 4, [5], 12:i:- than among S. enteritidis. More than 90 % of Shigella isolates showed more alarming resistance to most antibiotics, with a widened spectrum compared to Salmonella.

CONCLUSION

Constant antibiotic surveillance is warranted because the bacteria were highly resistant to various antimicrobials. Our study contributes to the strengthening of the existing surveillance system and provides aid for effective prevention and control strategies for childhood diarrhea.

Characteristics of bacterial pathogens associated with acute diarrhea in children under 5 years of age: a hospital-based cross-sectional study

Background

Acute diarrhea is a leading cause of morbidity and mortality in children, particularly in those under the age of 5 years. Rotavirus is recognized as the leading cause of acute diarrhea in children, however, the contribution of bacterial pathogens as causative agents varies throughout the world. Here we report a hospital-based prospective study to analyze the characteristics of bacterial pathogens associated with acute diarrhea in children under 5 years of age.

Methods

Stool samples were collected from 508 patients with acute diarrhea under 5 years of age who presented at our hospital. Nine pathogens were isolated and identified by culturing, serology or PCR, these included Salmonella spp., Shigella spp., Vibrio cholerae, diarrheagenic Escherichia coli (DEC), Aeromonas spp., Plesiomonas spp., Vibrio parahaemolyticus, Campylobacter spp. and Yersinia enterocolitica. Antimicrobial sensitivity tests of these pathogens were conducted. The most commonly detected pathogen, Salmonella spp., was further investigated by PCR and sequencing of antibiotic resistance-related genes.

Results

Pathogens were identified in 20.1 % of the 508 samples. The most commonly detected pathogens were Salmonella spp. (8.5 %), followed by DEC (4.7 %), Campylobacter jejuni (3.0 %) and Aeromonas spp. (2.0 %). The resistance rates to ampicillin and tetracycline in Salmonella spp. were >60 %, but were <30 % to cephalosporins and quinolones. More than 50 % of DEC strains displayed resistance to ampicillin, cefotaxime and tetracycline, and 60 % of C. jejuni strains were resistant to ciprofloxacin but highly sensitive to the other antibiotics. Among 12 cephalosporin-resistant Salmonella isolates, TEM-1 and CTX-M-14 determinants were present in two (16.7 %) isolates. PCR screening for plasmid-mediated quinolone resistance genes revealed gyrA mutations in one of three highly quinolone resistant isolates.

Conclusions

Salmonella spp., DEC, Campylobacter spp. and Aeromonas spp. were the most commonly detected bacterial pathogens in children under the age of 5 years with acute diarrhea. Our findings indicate that ampicillin and tetracycline are not suitable as first line therapeutic drugs against Salmonella spp. Resistance to third generation cephalosporins and quinolones was also detected. TEM-1 and CTX-M-14 genetic determinants, and gyrA mutations, were the major mechanisms associated with high levels of cephalosporin and quinolone resistance, respectively, in Salmonella isolates.