Molecular Characterization of Diarrheagenic Escherichia Coli in Children Less Than 5 Years of Age with Diarrhea in Ouagadougou, Burkina Faso

Diarrheagenic Escherichia coli in Stool Specimens Collected from Patients Attending Primary Healthcare Facilities in Ethiopia: Whole-Genome Sequencing-Based Molecular Characterization

The diarrheagenic Escherichia coli (DEC) is the major cause of diarrheal diseases in Africa, including Ethiopia. However, the genetic diversity of E. coli pathotypes found in Ethiopia has not been studied well. This study aimed to characterize potential DEC belonging to enteropathogenic (EPEC), Shiga toxin-producing (STEC), enteroaggregative (EAEC), enterotoxigenic (ETEC), and enteroinvasive (EIEC) E. coli pathotypes from stool specimens of patients attending primary healthcare units (n = 260) in Addis Ababa and Hossana using whole-genome sequencing. Real-time PCR assays were used to identify DEC isolates belonging to EPEC, STEC, EAEC, ETEC, and EIEC pathotypes, which were then subjected to whole-genome sequencing on the Illumina platform. Twenty-four whole-genome nucleotide sequences of DEC strains with good enough quality were analyzed for virulence-associated genes (VAGs), antibiotic resistance genes (ARGs), phylogenetic groups, serogroups, and sequence types. The majority (62.5%) of DEC isolates belonged to the phylogenetic group B1. The identified DEC isolates belonged to 21 different serogroups and 17 different sequence types. All tested DEC isolates carried multiple VAGs and ARGs. The findings highlight the high diversity in the population structure of the studied DEC isolates, which is important for designing targeted interventions to reduce the diarrheal burden in Ethiopia.

Comparative prevalence of diarrheagenic Escherichia coli between children below five years with close contact to food animals in Kisumu County, Kenya

Introduction

diarrheal infections in young children below five years and food animals are caused by diarrheagenic Escherichia coli strains. The study focused on understanding the association between DEC pathotypes in children below five years and food animals to establish the possibility of zoonotic transmission.

Methods

samples from 150 children who presented with diarrhea at the Kisumu County Hospital and 100 stool samples from food animals were collected and processed using culture methods. Molecular identification of the pathotypes was assayed using a primer-specific polymerase chain reaction that targeted the six virulence genes related to the diarrheagenic Escherichia coli pathotypes.

Results

one hundred and fifty-six study subjects (100 children samples and 56 food animals) samples were positive for E. coli polymerase chain reaction detection revealed a prevalence of (23%) among children below five years and a prevalence of (20%) among the food animals. Children samples showed Enteroaggregative Escherichia coli, having high phenotypic frequency of (12%) followed by Enterotoxigenic Escherichia coli, (5.3%) and Enteropathogenic Escherichia (3.3%) the least being mixed infections Enteroaggregative/Enterotoxigenic Escherichia coli and Enteroaggregative/Enteropathogenic Escherichia coli with (1.3%) respectively. The food animals found in children homesteads were detected to harbor pathogenic strains of E. coli. Enteropathogenic Escherichia coli was the most prevalent pathotypes detected in cattle (13%) followed by Enterotoxigenic Escherichia coli detected in goats at (4%) and poultry at (3%).

Conclusion

presence of diarrheagenic Escherichia coli in food animals could serve as reservoirs of transmitting these bacteria to children below five years.

Epidemiology of Cefotaxime-Hydrolysing β-Lactamase-Producing Escherichia coli in Children with Diarrhoea Reported Globally between 2012 and 2022

The global spread of cefotaxime-hydrolysing β-lactamase (CTX-M)-producing Escherichia coli (E. coli) and its associated impact on paediatric diarrhoeal treatment and management has become a public health concern. This review assessed surveillance studies on CTX-M-producing E. coli associated with diarrhoea in children published between 2012 and 2022 globally. A total of thirty-eight studies were included for data analysis, categorised into continental regions, and tabulated. The majority (68%) of studies were conducted in Asian countries while few studies were conducted in Europe (11%) and Africa (18%), respectively. On the African continent, the majority (11%) of studies were conducted in Northern Africa while no studies were reported in East Africa. On the American continent, 3% of the studies were reported from South America. The studies included were classified into diarrheagenic E. coli (74%; 28/38) and faecal carriage (26%; 10/38). Of all the E. coli pathotypes associated with CTX-M production, EPEC was frequently reported. The prevalence of CTX-M-producing E. coli including the CTX-M-15-producing variants ranged between 1% and 94%. About 37% of the studies generalised the report as blaCTX-M-positive E. coli. The use of sequencing in characterising the CTX-M-producing E. coli was reported in only 32% of all the studies. This review provides information on the epidemiology of CTX-M-15-producing E. coli in paediatric diarrhoea and the extent to which surveillance is being performed. This is relevant in informing clinical practice for the management of diarrhoea as well as the design of future surveillance studies.

Shiga toxin-producing Escherichia coli O157:H7 among diarrheic patients and their cattle in Amhara National Regional State, Ethiopia

BACKGROUND

Shiga toxin-producing Escherichia coli O157:H7 (STEC O157:H7) is a zoonotic pathogen that causes diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome worldwide. This study aimed to determine the prevalence, antibiotic susceptibility, and associated risk factors of STEC O157:H7 among diarrheic patients and their cattle.

METHODS

A cross-sectional study was conducted among diarrheic patients and their cattle in Amhara National Regional State, Ethiopia from December- 2020 to June- 2022. A total of 1,149 diarrheic patients and 229 cattle were included in the study. STEC O157:H7 detection was done using culture, latex agglutination test, and polymerase chain reaction on diarrheic stool samples and recto-anal mucosal swabs of cattle. Antibiotic susceptibility tests were performed using disk diffusion techniques. Risk factors association were identified using binary and multivariable logistic regression analysis.

RESULTS

The overall prevalence of STEC O157:H7 in diarrheic patients and their cattle was 11.1% (128/1149) and 14.4% (33/229) respectively. High percentage of the study subjects were found in under-five children (34.5%). Age less than 5 (AOR: 4.02, 95%CI:1.608-10.058,P = 0.003), and greater than 64 years old (AOR:3.36, 95% CI:1.254-8.986, P = 0.016), presence of diarrheic patient in the house (AOR:2.11, 95%CI:1.309-3.390, P = 0.002), availability of cattle in the house (AOR:2.52, 95%CI:1.261-5.049, P = 0.009), and habit of consuming raw foods (AOR:4.35, 95%CI:2.645-7.148, P = 0.000) were risk factors. Antibiotic resistance was shown in 109(85.2%), and 31(93.9%) isolates from diarrheic patients and their cattle respectively. The highest levels of antibiotic resistance were found to tetracycline (54.7%, 69.7%) in diarrheic patients and their cattle respectively. Multiple drug resistance was also observed among 56(43.8%) and 11(33.3%) isolates in diarrheic patients and their cattle respectively.

CONCLUSION

Our study showed high prevalence of STEC O157:H7 in diarrheic patients and their cattle. Therefore, health education should be given to the community on how to care for animals, proper sanitation, and the impact of raw food consumption.

Epidemiology and Risk Factors for Diarrheagenic Escherichia coli Carriage among Children in Northern Ibadan, Nigeria

Diarrhea is a leading cause of childhood morbidity in Africa, but few studies, focus on bacterial diarrheal etiology including multicountry studies that typically excluded Nigeria. We collected stool specimens from 477 children under 5 years of age, 120 with diarrhea, who were enrolled in our prospective case-control study between November 2015 and August 2019. All were attending primary health clinics on the northern outskirts of Ibadan. Up to 10 Escherichia coli isolates were obtained per specimen, and at least three of them were sequenced using Illumina whole-genome sequence technology. Genomes were assembled using SPAdes and evaluated for quality using QUAST. VirulenceFinder was used to identify virulence genes. The microbiological quality of water from 14 wells within the study area was assessed using total and coliform counts. Diarrheagenic E. coli (DEC) were isolated from 79 (65.8%) cases and 217 (60.8%) control children. A number of hybrid DEC pathotypes, Salmonella spp., Yersinia spp., and all DEC pathotypes except Shiga toxin-producing E. coli were detected, but no pathogen showed association with disease (P > 0.05). Enterotoxigenic E. coli were more commonly recovered from children without diarrhea aged below 6 months but exclusively detected in children with diarrhea aged over 9 months. Temporally linked, genetically similar enteroaggregative E. coli were isolated from children in different households in eight instances. No well water sample drawn in the study was potable. Children in northern Ibadan were commonly colonized with DEC. Access to water, proper sanitation, and vaccination against the prevailing pathogens may be critical for protecting children from the less overt consequences of enteric pathogen carriage.

Contribution of the Rapid LAMP-Based Diagnostic Test (RLDT) to the Evaluation of Enterotoxigenic Escherichia coli (ETEC) and Shigella in Childhood Diarrhea in the Peri-Urban Area of Ouagadougou, Burkina Faso

The estimates of enterotoxigenic Escherichia coli (ETEC) and Shigella burden in developing countries are limited by the lack of rapid, accessible, and sensitive diagnostics and surveillance tools. We used a "Rapid LAMP based Diagnostic Test (RLDT)" to detect ETEC and Shigella in diarrheal and non-diarrheal stool samples from a 12-month longitudinal cohort of children under five years of age in a peri-urban area of Ouagadougou in Burkina Faso (West Africa). To allow comparison with the RLDT-Shigella results, conventional culture methods were used to identify Shigella strains in the stool samples. As conventional culture alone cannot detect ETEC cases, a subset of E. coli-like colonies was tested using conventional PCR to detect ETEC toxins genes. Of the 165 stool samples analyzed for ETEC, 24.9% were positive when using RLDT against 4.2% when using culture followed by PCR. ETEC toxin distribution when using RLDT was STp 17.6% (29/165), LT 11.5% (19/165), and STh 8.5% (14/165). Of the 263 specimens tested for Shigella, 44.8% were positive when using RLDT against 23.2% when using culture. The sensitivity and specificity of the RLDT compared to culture (followed by PCR for ETEC) were 93.44% and 69.8% for Shigella and 83.7% and 77.9% for ETEC, respectively. This study indicates that both Shigella and ETEC are substantially underdiagnosed when using conventional culture and highlights the potential contribution of the new RLDT method to improve enteric disease burden estimation and to guide future efforts to prevent and control bacterial enteric infection and disease.

Molecular Characterization of Hetero-Pathogenic and Diarrheagenic Escherichia coli Pathotypes in Diarrheic Children under Five Years and Exposure Environment in Ogun State, South-West Nigeria

BACKGROUND

Diarrheagenic Escherichia coli (DEC) is one of the most common etiological agents of moderate-to-severe diarrhea in Low- and Middle-Income Countries (LMICs). Therefore, determining the source(s) of DEC in index cases and exposure environment is important for developing a prevention strategy. The current study aims to investigate the prevalence of DEC among children under 5 years and their exposure environment in Ogun State, Nigeria.

METHODS

Samples from 228 diarrheic children and their exposure environment were collected and screened for E. coli. Bio-chemically compatible distinct colonies were molecularly characterized using a 7-virulence-gene multiplex PCR with virulence factors (VFs) indicative of four pathotypes of E. coli: enterotoxigenic (ETEC), verotoxigenic (VTEC), enteropathogenic (EPEC), and enteroinvasive (EIEC). Representative pathotypes were subjected to antimicrobial susceptibility and over-expressed efflux pump assays.

RESULTS

One or more VFs typical of specific pathotypes were detected in 25.9% (59/228) diarrhea cases consisting of ETEC (21.5%) and EPEC (0.4%), while hetero-pathogenic pathotypes were found in 4.0% of cases. Of the food sources, 27.9% (101/362) were positive for DEC, of which ETEC accounted for 21.0%, VTEC 1.9%, EPEC 0.6%, EIEC 0.6%, and hetero-pathogenic pathotypes were 3.9%. Furthermore, ETEC was the only pathotype detected in the wastewater (4/183). Interestingly, the consumption of street-vended foods was the most significant (p = 0.04) risk factor for DEC infection in the study area. A total of 73.3% of selected DEC pathotypes showed resistance to antimicrobials, while 27.5% demonstrated over-expression of efflux pump activity.

CONCLUSION

The high prevalence of ETEC across all sources and the occurrence of hetero-pathogenic DEC in diarrheic children and food sources emphasizes the importance of establishing a better strategy for the control and prevention of diarrhea among children in low- and medium-income households.

Molecular identification of diarrheagenic Escherichia coli pathotypes and their antibiotic resistance patterns among diarrheic children and in contact calves in Bahir Dar city, Northwest Ethiopia

Diarrheagenic Escherichia coli strains are an essential cause of diarrheal infection in younger children and animals. The study was focused on understanding the associated characteristics of various DEC strains among children and calves, establishing the possible zoonotic transmission, and determining their antibiotic resistance patterns. Samples from 144 acute diarrheic children and 50 diarrheic calves were collected and processed using traditional culture methods. The molecular identification of pathotypes was completed using primer-specific polymerase chain reaction (PCR) targeting ten virulence genes (stx1, stx2, eae, aatA, lt, st, ial, hlyA bfpA, and daaE) related to six DEC pathotypes (EPEC, ETEC, EHEC, EAEC EIEC, and DAEC). The antimicrobial susceptibility testing was carried out using the Kirby-Bauer disk diffusion method. Colonies from 74 study subjects (54 diarrheic children and 20 diarrheic calves) were positive for E. coli isolates. Subsequent PCR detection discovered that 77% of children and 85% of calves' isolates were positive for one or more virulence genes typical of particular strains. Among those ETEC [(18%), (26%)] is being the maximum predominant, and [(15%), (15%)] were positive for STEC, [(13%), (8%)] for atypical EPEC, [(6%), (7%)] for EHEC, [(6%), (5%)] for EAEC, and [(6%), (4%)] for EIEC strains in children's and calves, respectively. Of the identified E. coli isolates, about 29% were found to be hybrid isolates. ETEC (66.7%) and STEC (58.9%) strains showed a better detection rate in contact children with diarrheic calves than children with no contacts. Most antibiotic resistances were obtained towards amoxicillin (64.9%), gentamycin (56.8%), and ampicillin (54.1%). Up to sixty-five percent of isolates were resistant to a minimum of three categories of antibiotics. This is the primary report on the wide occurrence of the six-diarrheagenic Escherichia coli strains, and ETEC was found to be the predominant pathotype among children and contact calves in Ethiopia.

Molecular characterization of diarrheagenic Escherichia coli isolates from children with diarrhea: A cross-sectional study in four provinces of Mozambique: Diarrheagenic Escherichia coli in Mozambique

OBJECTIVES

Analyze the frequency of diarrheagenic Escherichia coli (DEC) pathotypes and their antimicrobial resistance profiles among children aged <15 years with diarrhea in four Mozambican provinces.

METHODS

A cross-sectional hospital-based surveillance program of diarrhea was implemented in Maputo, Sofala, Zambézia, and Nampula. A single stool sample was collected from each child from May 2014 to May 2017. Culture methods and biochemical characterization were performed to detect E. coli strains. DEC pathotypes were determined by conventional polymerase chain reaction targeting specific virulence genes. Antimicrobial susceptibility was assessed by the Kirby-Bauer method.

RESULTS

From 723 specimens analyzed by culture, 262 were positive for E. coli. A total of 208 samples were tested by polymerase chain reaction for DEC identification, of which 101 (48.6%) were positive for a DEC pathotype. The predominant pathotypes were enteroaggregative (66.3%, 67/101), enteropathogenic (15.8%, 16/101), enterotoxigenic (13.9%, 14/101), and enteroinvasive E. coli (4.0%, 4/101). No Shiga toxin-producing E. coli was identified. Regardless of the province, the most frequent pathotype was enteroaggregative E. coli. Isolated DEC presented high frequency of resistance to ampicillin (97.8%), tetracycline (68.3%), chloramphenicol (28.4%), nalidixic acid (19.5%), and gentamicin (14.4%).

CONCLUSION

Children with diarrhea in Mozambique had DEC and higher resistance to ampicillin and tetracycline.

Characteristics of diarrheagenic Escherichia coli among patients with acute diarrhea in China, 2009‒2018

Objectives To investigate the epidemiological features of diarrheagenic Escherichia coli (DEC) in patients with acute diarrhea in China. Methods An active sentinel surveillance was performed in all-age patients with acute diarrhea in China, 2009‒2018. DEC was isolated and identified by serological assay and PCR from stool samples. Results DEC was determined in 6.68% (6,119/91,651) of the patients, with higher positive rates among females than among males (6.97% vs. 6.46%) and among 18‒59 years patients (7.88%) than among other age groups. Five pathotypes were identified, the most prevalent was enteroaggregative E. coli (EAEC), followed by enteropathogenic E. coli (EPEC), and enterotoxigenic E. coli (ETEC). Pediatric patients <5 years had higher positive rate of EAEC (2.07%), followed by EPEC (1.81%), and enterohemorrhagic E. coli (EHEC) (0.31%), while the 18‒59 years patients had higher infection of ETEC (2.36%). ETEC and EPEC were more frequently identified in urban than rural areas, with age and gender adjusted positive rate of 1.68% vs. 1.14% respectively, and 1.77% vs. 1.55%, while EIEC and EHEC were more frequently identified in rural areas. Conclusions These findings highlight the epidemiology features of DEC and underscores the need for conducting DEC surveillance.

Characterization and Antibiotic Susceptibility Profiles of Pathogenic Escherichia Coli Isolated from Diarrhea Samples within the Buffalo City Metropolitan Municipality, Eastern Cape, South Africa

Objectives:

Developing countries like South Africa are still faced with numerous challenges such as poor environmental sanitation, lack of clean drinking water and inadequate hygiene which have contributed largely to diarrheal infections and deaths in children. This study was aimed at investigating the prevalence of pathotypes, antimicrobial resistance and drug resistance determinants among Escherichia coli (E. coli) isolates from diarrhea stool samples within Buffalo City Municipality, Eastern Cape, South Africa.

Methods:

Fresh diarrheal stool samples were collected from 140 patients attending public health centres within the Municipality and presumptive E. coli isolates were obtained from the stool samples using E. coli chromogenic agar while PCR amplification methods were used to confirm the presumptive isolates as well as delineate them into pathotypes based on the presence of certain virulence genes. In addition, antimicrobial susceptibility and screening of some of the antimicrobial resistant determinants were performed on all the confirmed isolates.

Results:

A total of 394 presumptive E. coli isolates from 140 diarrhea stool samples were subjected to polymerase chain reaction amplification, of which 265 were confirmed positive as E. coli. Pathotypes delineation of the positive E. coli isolates validated the presence of ETEC 106 (40%), EAEC 48 (18%), DAEC 37 (14%), and EPEC 31 (11%) while no EIEC pathotype was detected. All E. coli isolates exhibited maximum susceptibility to gentamicin (95%), amikacin (91%), nitrofurantoin (91%), meropenem (90%), chloramphenicol (91%) norfloxacin (84%) and imipenem (83%). However, the isolates showed multidrug resistance to penicillin G, ampicillin, trimethoprim, tetracycline, doxycycline, and erythromycin, with over 71% of the isolates resistant to the drugs. The prevalence and distribution of the five resistance determinants assessed were as follow; sulphonamides; sulII (12%), beta lactams; [ampC (22%); blaTEM, (25%)], and tetracyclines (tetA (35%).

Conclusion:

The results from this study suggest the probable involvement of E. coli pathotypes as an etiologic agent of diarrhea in the study area and revealed high levels of multidrug resistance among the isolates, which could be a major health burden.

DETECTION OF DIARRHEAGENIC ESCHERICHIA COLI IN HUMAN DIARRHEIC STOOL AND DRINKING WATER SAMPLES IN OUAGADOUGOU, BURKINA FASO

Background:

The presence of diarrheagenic Escherichia coli (DEC) in drinking water, is a grave public health problem. This study was aimed at characterization of diarrheagenic Escherichia coli isolated from drinking water and faecal samples from diarrheic patients in Ouagadougou, Burkina Faso.

Materials and Methods:

A total of 242 water samples consisting of 182 potable sachets and 60 from boreholes were collected in the period between October 2018 and April 2019 in the city of Ouagadougou. Faecal samples were also collected from 201 diarrheic patients visiting National Public Health Laboratory for a biological diagnosis by coproculture. The presence of virulence genes associated with DEC was determined by 16-plex polymerase chain reaction from bacteria culture.

Results:

From drinking water, we found 17% (42/242) Escherichia coli isolates in which 1% (2/242) DEC were detected. Among analyzed samples (182 sachet water versus 60 borehole water), the two DEC (01 ETEC and 01 EPEC) were detected in sachet water. DEC were detected in 20% (40/201) of patients. Enteroaggregative Escherichia coli (EAEC) were mostly detected in 10% followed by Enteropathogenic Escherichia coli (EPEC) in 4%, Enteroinvasive Escherichia coli (EIEC) in 2%, and Shiga toxin-producing Escherichia coli (STEC) 0.5%. However, Enterotoxigenic Escherichia coli (ETEC) was not detected alone, but in co-infections with EAEC.

Conclusion:

The present study documented the prevalence of Escherichia coli pathovars associated in patients with diarrhea, and shows that drinking water might be a source of DEC transmission in human.

Prevalence, phylogeny, and antimicrobial resistance of Escherichia coli pathotypes isolated from children less than 5 years old with community acquired- diarrhea in Upper Egypt

Background

Diarrhoea, affecting children in developing countries, is mainly caused by diarrheagenic Escherichia coli (DEC). This study principally aimed to determine the prevalence of DEC pathotypes and Extended-spectrum β-lactamase (ESBL) genes isolated from children under 5 years old with diarrhea.

Methods

A total of 320 diarrhoea stool samples were investigated. E. coli isolates were investigated for genes specific for enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC) and enterohemorrhagic E. coli (EHEC) using polymerase chain reaction (PCR). Furthermore, antimicrobial susceptibility testing, detection of antibiotic resistance-genes and phylogenetic typing were performed.

Results

Over all, DEC were isolated from 66/320 (20.6%) of the children with diarrhoea. EAEC was the predominant (47%), followed by typical EPEC (28.8%) and atypical EPEC (16.6%). Co-infection by EPEC and EAEC was detected in (7.6%) of isolates. However, ETEC, EIEC and EHEC were not detected. Phylogroup A (47%) and B2 (43.9%) were the predominant types. Multidrug-resistance (MDR) was found in 55% of DEC isolates. Extended-spectrum β-lactamase (ESBL) genes were detected in 24 isolates (24 blaTEM and 15 blaCTX-M-15). Only one isolate harbored AmpC β-lactamase gene (DHA gene).

Conclusion

The study concluded that, EAEC and EPEC are important causative agents of diarrhoea in children under 5 years. MDR among DEC has the potential to be a big concern.

Diarrheagenic Escherichia coli Pathotypes From Children Younger Than 5 Years in Kano State, Nigeria

Diarrheagenic Escherichia coli (DEC) is one of the leading causes of gastrointestinal disorders worldwide and an important public health challenge. DEC infection is often underdiagnosed during routine microbiological analysis, especially in resource constrained settings; the use of molecular tests could however help to determine the distribution of DEC and its clinical significance. Here, a study to assess the prevalence of DEC in clinical samples from patients <5 years attending three hospitals in Kano state, Nigeria, was carried out. Samples from 400 patients and 50 controls were collected and screened for E. coli. Compatible colonies from 248 individuals (215 patients and 33 controls) were characterized using biochemical test, a set of real-time PCRs for detection of nine virulence factors (VF: eae, bfpA, elt, est, stx1, stx2, ehxA, aggR, and invA) associated with five DEC pathotypes (EPEC, ETEC, EHEC, EAEC, and EIEC) and antimicrobial susceptibility tests. One or more VFs typical of specific pathotypes were detected in 73.8% (183/248) of the isolates, with those associated with EAEC (36.3%), ETEC (17.3%), and EPEC (6.0%) being the most common, although proportion of specific pathotypes differed between hospitals. est was the only VF detected in a significantly higher proportion in cases compared to controls (P = 0.034). Up to 86.9% of DEC were resistant to at least one class of antibiotics, with trimethoprim-sulfamethoxazole being the least effective drug (77.6% resistance). Our results demonstrate the widespread circulation of different DEC pathotypes that were highly resistant to trimethoprim-sulfamethoxazole among children in Kano state, and highlight the need of characterizing the causative agents in cases of gastrointestinal disorders.