scholarly journals Diarrheagenic Escherichia coli in sub-Saharan Africa: Status, Uncertainties and Necessities

2009 ◽  
Vol 3 (11) ◽  
pp. 817-842 ◽  
Author(s):  
Iruka N Okeke
Keyword(s):  
Escherichia Coli ◽  
Diarrheal Disease ◽  
Sub Saharan Africa ◽  
Considerable Proportion ◽  
E Coli ◽  
Epidemiological Surveys ◽  
Local Reference ◽  
Uremic Syndrome ◽  
Diagnostic Capacity ◽  
Sub Saharan

Diarrhea is a leading cause of illness and death, particularly in developing countries.  Enteropathogenic Escherichia coli, enterotoxigenic E. coli (ETEC), enteroinvasive E. coli, enterohemorrhaghic E. coli (EHEC), enteroaggregative E. coli (EAEC) and diffusely adherent E. coli (DAEC) have been associated with diarrheal disease in different parts of Africa, particularly among young children, HIV-positive individuals, and visitors from abroad.  Each of these E. coli pathotypes uses distinct mechanisms, which are only partially understood, to colonize infected hosts and produce diarrhea.  All known diarrheagenic E. coli pathotypes have been reported from diverse locations within Africa but the true burden from these pathogens is unknown because very few studies seeking these organisms with discriminatory methodology have been performed.  Recent reports implicate ETEC and EAEC in a considerable proportion of childhood and travellers' diarrheas and suggest that some sub-types of these categories may have greater epidemiological significance than others.  The significant contribution of EHEC to bloody diarrhea and hemolytic uremic syndrome is underappreciated because diagnostic capacity for this pathotype is generally inferior to that for confounders such as Shigella and Entamoeba.   Recent studies in Africa have revealed the worrisome emergence of antimicrobial resistance and high asymptomatic carriage rates for diarrheagenic E. coli but bacterial and host factors that predispose to disease, as well as non-human reservoirs, are largely unknown.  Future diarrheal disease research needs to focus on broadening the repertoire of pathogens sought in epidemiological surveys to include multiple categories of diarrheagenic E. coli while building capacity to detect these pathogens in local reference laboratories.

scholarly journals Gambian poultry isolates from hyperendemic group of AMR Escherichia coli strains in sub-Saharan Africa

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Ebenezer Foster-Nyarko ◽  
Nabil-Fareed Alikhan ◽  
Anuradha Ravi ◽  
Nicholas Thomson ◽  
Sheikh Jarju ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Guinea Fowl ◽  
Sub Saharan Africa ◽  
Pathogenic Potential ◽  
E Coli ◽  
Antimicrobial Resistance Gene ◽  
Microbiological Techniques ◽  
Sub Saharan ◽  
Genomic Cluster ◽  
Sequence Types

Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from ten chickens and nine guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (four of them novel), of which ST155 was the most common (22/68, 32%). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64%) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates sit within a tight genomic cluster (100 alleles difference) of strains from poultry and livestock in sub-Saharan Africa (the Gambia, Uganda and Kenya). Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.

scholarly journals The Isolation Rate ofEscherichia coli0157:H7 in Toronto and Surrounding Communities

1990 ◽  
Vol 1 (1) ◽  
pp. 23-27 ◽  
Author(s):  
Andrew E Simor ◽  
Christine Watt ◽  
Donald E Low
Keyword(s):  
Escherichia Coli ◽  
Hemolytic Uremic Syndrome ◽  
Diarrheal Disease ◽  
Hemorrhagic Colitis ◽  
Isolation Rate ◽  
E Coli ◽  
History Of ◽  
Uremic Syndrome ◽  
Stool Specimens ◽  
Differential Medium

Verocytotoxin-producing strains ofEscherichia coli,most often serotype 0157:H7, have been associated with both sporadic and epidemic diarrheal disease in Canada. In order to determine the isolation rate ofE coli0157:H7 in outpatients with diarrhea, all stool specimens submitted for culture to Med-Chem Laboratories in Metropolitan Toronto between June 1988 and September 1989 were cultured on MacConkey-Sorbitol agar in addition to standard enteric media. A total of 46 (0.3%) of 16,125 stool specimens yieldedE coli0157:H7 or verotoxin-producingE coli0157:H−. These isolates came from 31 patients with diarrhea; only 16 (52%) had a history of hemorrhagic colitis and one patient developed hemolytic uremic syndrome. Although MacConkey-Sorbitol agar was useful as a differential medium for detectingE coli0157:H7, 14.5% of all specimens yielded nonsorbitol-fermenting isolates. It is not certain whether the routine use of MacConkey-Sorbitol agar is justified when isolation rates ofE coli0157:117 are very low.

scholarly journals Genomic diversity of Escherichia coli from healthy children in rural Gambia

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10572
Author(s):  
Ebenezer Foster-Nyarko ◽  
Nabil-Fareed Alikhan ◽  
Usman N. Ikumapayi ◽  
Golam Sarwar ◽  
Catherine Okoi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genomic Diversity ◽  
Sub Saharan Africa ◽  
Minor Role ◽  
Healthy Children ◽  
E Coli ◽  
Asymptomatic Children ◽  
Study Population ◽  
Sub Saharan ◽  
Host Evolution

Little is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). We identified 56 genotypes, with an average of 2.7 genotypes per host. These were spread over 37 seven-allele sequence types and the E. coli phylogroups A, B1, B2, C, D, E, F and Escherichia cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. Several isolates encode putative virulence factors commonly found in Enteropathogenic and Enteroaggregative E. coli, and 53% of the isolates encode resistance to three or more classes of antimicrobials. Thus, resident E. coli in these children may constitute reservoirs of virulence- and resistance-associated genes. Moreover, several study strains were closely related to isolates that caused disease in humans or originated from livestock. Our results suggest that within-host evolution plays a minor role in the generation of diversity compared to independent immigration and the establishment of strains among our study population. Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species.

scholarly journals Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

2020 ◽  
Author(s):  
Ebenezer Foster-Nyarko ◽  
Nabil-Fareed Alikhan ◽  
Anuradha Ravi ◽  
Nicholas M. Thomson ◽  
Sheikh Jarju ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Guinea Fowl ◽  
Genomic Diversity ◽  
Sub Saharan Africa ◽  
Human Society ◽  
E Coli ◽  
Backyard Poultry ◽  
Link Type ◽  
Sub Saharan

AbstractChickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from ten chickens and nine guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (four of them novel), of which ST155 was the most common (22/68, 32%). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64%) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates belong to a unique cgMLST cluster comprised of closely related (38-39 alleles differences) isolates from poultry and livestock from sub-Saharan Africa—suggesting that strains can be exchanged between poultry and livestock in this setting. Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.Author notesAll supporting data and protocols have been provided within the article or as supplementary data files. Eleven supplementary figures and eight supplementary files are available with the online version of this article.Data summaryThe genomic assemblies for the isolates reported here are available for download from EnteroBase (http://enterobase.warwick.ac.uk/species/index/ecoli) and the EnteroBase assembly barcodes are provided in File S2.Sequences have been deposited in the NCBI SRA, under the BioProject ID: PRJNA616250 and accession numbers SAMN14485281 to SAMN14485348 (File S2). Assemblies have been deposited in GenBank under the BioProject ID: PRJNA616250 and accession numbers CP053258 and CP053259.Impact statementDomestic birds play a crucial role in human society, in particular contributing to food security in low-income countries. Many households in Sub-Saharan Africa rear free-range chickens and guinea fowl, which are often left to scavenge for feed in and around the family compound, where they are frequently exposed to humans, other animals and the environment. Such proximity between backyard poultry and humans is likely to facilitate transmission of pathogens such as Escherichia coli or antimicrobial resistance between the two host species. Little is known about the population structure of E. coli in rural chickens and guinea fowl, although this information is needed to contextualise the potential risks of transmission of bacterial strains between humans and rural backyard poultry. Thus, we sought to investigate the genomic diversity of E. coli in backyard poultry from rural Gambia.

scholarly journals Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

2020 ◽  
Author(s):  
Ebenezer Foster-Nyarko ◽  
Nabil-Fareed Alikhan ◽  
Anuradha Ravi ◽  
Nicholas M. Thomson ◽  
Sheikh Jarju ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Type Species ◽  
Guinea Fowl ◽  
Genomic Diversity ◽  
Sub Saharan Africa ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Antimicrobial Resistance Gene ◽  
Sub Saharan

Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (4 of them novel), of which ST155 was the most common (22/68, 32 %). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64 %) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates belong to a unique cgMLST cluster comprising closely related (38–39 alleles differences) isolates from poultry and livestock from sub-Saharan Africa – suggesting that strains can be exchanged between poultry and livestock in this setting. Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.

scholarly journals Genomic diversity of Escherichia coli isolates from healthy children in rural Gambia

2020 ◽  
Author(s):  
Ebenezer Foster-Nyarko ◽  
Nabil-Fareed Alikhan ◽  
Usman Nurudeen Ikumapayi ◽  
Sarwar Golam ◽  
M Jahangir Hossain ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genomic Diversity ◽  
Sub Saharan Africa ◽  
Minor Role ◽  
Healthy Children ◽  
E Coli ◽  
Asymptomatic Children ◽  
Study Population ◽  
Sub Saharan ◽  
Host Evolution

AbstractLittle is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n=88 isolates from 21 positive stools). We identified 56 genotypes, with an average of 2.7 genotypes per host. These were spread over 37 seven-allele sequence types and the E. coli phylogroups A, B1, B2, C, D, E, F and Escherichia cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. Several study strains were closely related to isolates that caused disease in humans or originated from livestock. Our results suggest that within-host evolution plays a minor role in the generation of diversity than independent immigration and the establishment of strains among our study population. Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species.

Prevalence of Pathogens in Young Children Presenting to Hospital with Diarrhea from Lambaréné, Gabon

2021 ◽  
Vol 105 (1) ◽  
pp. 254-260
Author(s):  
Gédéon Prince Manouana ◽  
Natalie Byrne ◽  
Mirabeau Mbong Ngwese ◽  
Alvyn Nguema Moure ◽  
Philipp Hofmann ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Diarrheal Disease ◽  
Demographic Data ◽  
Infectious Agent ◽  
Diagnostic Tools ◽  
African Countries ◽  
Sub Saharan ◽  
Preventative Interventions ◽  
Pathogenic Agents ◽  
Multiple Pathogens

Abstract.Diarrheal disease is the second most frequent cause of mortality in children younger than 5 years worldwide, causing more than half a million deaths each year. Our knowledge of the epidemiology of potentially pathogenic agents found in children suffering from diarrhea in sub-Saharan African countries is still patchy, and thereby hinders implementation of effective preventative interventions. The lack of cheap, easy-to-use diagnostic tools leads to mostly symptomatic and empirical case management. An observational study with a total of 241 participants was conducted from February 2017 to August 2018 among children younger than 5 years with diarrhea in Lambaréné, Gabon. Clinical and demographic data were recorded, and a stool sample was collected. The samples were examined using a commercial rapid immunoassay to detect Rotavirus/adenovirus, conventional bacterial culture for Salmonella spp., and multiplex real-time PCR for Cryptosporidium spp., Giardia lamblia, Cyclospora cayetanensis, enterotoxigenic Escherichia coli (ETEC), and enteroinvasive Escherichia coli (EIEC)/Shigella. At least one infectious agent was present in 121 of 241 (50%) samples. The most frequently isolated pathogens were EIEC/Shigella and ETEC (54/179; 30.2% and 44/179; 24.6%, respectively), followed by G. lamblia (33/241; 13.7%), Cryptosporidium spp. (31/241; 12.9%), and Rotavirus (23/241; 9.5%). Coinfection with multiple pathogens was observed in 33% (40/121) of the positive cases with EIEC/Shigella, ETEC, and Cryptosporidium spp. most frequently identified. Our results provide new insight into the possible causes of diarrheal disease in the Moyen-Ogooué region of Gabon and motivate further research on possible modes of infection and targeted preventive measures.

Potential Public Health Significance of Non-Escherichia coli Coliforms in Food

1979 ◽  
Vol 42 (2) ◽  
pp. 161-163 ◽  
Author(s):  
ROBERT M. TWEDT ◽  
BRENDA K. BOUTIN
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Diarrheal Disease ◽  
Health Hazard ◽  
High Yield ◽  
Potential Health ◽  
E Coli ◽  
Potential Health Hazard ◽  
Health Significance

Several coliform species other than Escherichia coli are often associated with and possibly responsible for acute and chronic diarrheal disease. Recent evidence suggests that non-Escherichia coli coliforms may be capable of colonizing the human intestine and producing enterotoxin(s) in high-yield. Whether these organisms are newly capable of causing disease because of infestation with extrachromosomal factors mediating pathogenicity or simply because of inherent pathogenic capabilities that have gone unrecognized, they pose a potential health hazard. Food, medical, and public health microbiologists should be aware that the non-E. coli coliforms contaminating foods may be potential enteropathogens. This possibility may make determination of their pathogenic capabilities even more important than identification of their taxonomic characteristics.

scholarly journals Prevalence and molecular detection of shiga toxin producing Escherichia coli from diarrheic cattle

2016 ◽  
Vol 14 (1) ◽  
pp. 63-68 ◽  
Author(s):  
MM Akter ◽  
S Majumder ◽  
KH MNH Nazir ◽  
M Rahman
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Molecular Detection ◽  
Chain Reaction ◽  
Specific Primers ◽  
Fecal Samples ◽  
E Coli ◽  
Uremic Syndrome ◽  
Polymerase Chain ◽  
Positive Isolate

Shiga toxin-producing Escherichia coli (STEC) are zoonotically important pathogen which causes hemorrhagic colitis, diarrhea, and hemolytic uremic syndrome in animals and humans. The present study was designed to isolate and identify the STEC from fecal samples of diarrheic cattle. A total of 35 diarrheic fecal samples were collected from Bangladesh Agricultural University (BAU) Veterinary Teaching Hospital. The samples were primarily examined for the detection of E. coli by cultural, morphological and biochemical characteristics, followed by confirmation of the isolates by Polymerase Chain Reaction (PCR) using gene specific primers. Later, the STEC were identified among the isolated E. coli through detection of Stx-1 and Stx-2 genes using duplex PCR. Out of 35 samples, 25 (71.43%) isolates were confirmed to be associated with E. coli, of which only 7 (28%) isolates were shiga toxin producers, and all of them were positive for Stx-1. However, no Stx-2 positive isolate could be detected. From this study, it may be concluded that cattle can act as a reservoir of STEC which may transmit to human or other animals.J. Bangladesh Agril. Univ. 14(1): 63-68, June 2016

scholarly journals Prevalence and antibiotic resistance of bacterial pathogens isolated from childhood diarrhoea in four provinces of Kenya

2012 ◽  
Vol 6 (07) ◽  
pp. 572-578 ◽  
Author(s):  
Willie Kipkemboi Sang ◽  
Valerie Oundo ◽  
David Schnabel
Keyword(s):  
Antimicrobial Resistance ◽  
Rural Areas ◽  
Hospital Admissions ◽  
Sub Saharan Africa ◽  
Vibrio Cholera ◽  
Antimicrobial Drug Resistance ◽  
E Coli ◽  
Shigella Isolate ◽  
Stool Samples ◽  
Sub Saharan

Introduction: Diarrhoea is one of the main causes of morbidity and mortality among children in sub-Saharan Africa, and one of the main causes of hospital admissions in rural areas of Kenya. In Kenya, antimicrobial resistance surveillance has been conducted only at the institutional levels, with limited sharing of information and analysis of data. As a result, the actual scale of regional or national antimicrobial drug resistance is not well defined. Methodology: Stool samples were collected between 1 October 2007 and 30 September 2008 from a total of 651 outpatients with diarrhoea who were under five years of age in four provinces of Kenya.  Conventional, biochemical methods, multiplex PCR and antimicrobial susceptibility were conducted to identify the bacterial causes and virulence factors in the isolates, respectively.  Results: Of the 651 patients screened, we identified the causes of 115 cases (17.7%) as follows: Pathogenic E. coli (11.2%) [enteroaggregative (8.9%), enterotoxigenic (1.2%), enteroinvasive (0.6%), shigatoxigenic (0.5%)], Salmonella (3.5%), Shigella (2%) and Vibrio cholera O1 (0.7%). The highest levels of resistance among the E. coli isolates were observed in ampicillin and trimethoprim/sulphamethoxazole each at 95% followed by tetracycline at 81%. Shigella isolate levels of resistance ranged from 80% to 100% for ampicillin, tetracycline and trimethoprim/sulphamethoxazole. Conclusion: The highest prevalence of antimicrobial resistance was to ampicillin followed by trimethoprim/sulphamethoxazole and tetracycline. Though still at low levels, the major concern from our findings is the emerging resistance of enteric pathogens that was observed to quinolones (ciprofloxacin, nalidixic acid, norfloxacin) and gentamycin.

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