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

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.

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

Microbial Genomics ◽

10.1099/mgen.0.000484 ◽

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.

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

10.1101/2020.05.14.096289 ◽

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.

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Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana

Genes ◽

10.3390/genes11121504 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1504

Author(s):

Frederick Adzitey ◽

Jonathan Asante ◽

Hezekiel M. Kumalo ◽

Rene B. Khan ◽

Anou M. Somboro ◽

...

Keyword(s):

Escherichia Coli ◽

Stress Response ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Response Factors ◽

Pathogenic Potential ◽

E Coli ◽

Relationship Of ◽

Sequence Types

Escherichia coli are among the most common foodborne pathogens associated with infections reported from meat sources. This study investigated the virulome, pathogenicity, stress response factors, clonal lineages, and the phylogenomic relationship of E. coli isolated from different meat sources in Ghana using whole-genome sequencing. Isolates were screened from five meat sources (beef, chevon, guinea fowl, local chicken, and mutton) and five areas (Aboabo, Central market, Nyorni, Victory cinema, and Tishegu) based in the Tamale Metropolis, Ghana. Following microbial identification, the E. coli strains were subjected to whole-genome sequencing. Comparative visualisation analyses showed different DNA synteny of the strains. The isolates consisted of diverse sequence types (STs) with the most common being ST155 (n = 3/14). Based Upon Related Sequence Types (eBURST) analyses of the study sequence types identified four similar clones, five single-locus variants, and two satellite clones (more distantly) with global curated E. coli STs. All the isolates possessed at least one restriction-modification (R-M) and CRISPR defence system. Further analysis revealed conserved stress response mechanisms (detoxification, osmotic, oxidative, and periplasmic stress) in the strains. Estimation of pathogenicity predicted a higher average probability score (Pscore ≈ 0.937), supporting their pathogenic potential to humans. Diverse virulence genes that were clonal-specific were identified. Phylogenomic tree analyses coupled with metadata insights depicted the high genetic diversity of the E. coli isolates with no correlation with their meat sources and areas. The findings of this bioinformatic analyses further our understanding of E. coli in meat sources and are broadly relevant to the design of contamination control strategies in meat retail settings in Ghana.

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Genomic diversity of Escherichia coli from healthy children in rural Gambia

PeerJ ◽

10.7717/peerj.10572 ◽

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.

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

10.1101/2020.08.28.271627 ◽

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.

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

The Journal of Infection in Developing Countries ◽

10.3855/jidc.586 ◽

2009 ◽

Vol 3 (11) ◽

pp. 817-842 ◽

Cited By ~ 63

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.

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Circulation of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli of Pandemic Sequence Types 131, 648, and 410 Among Hospitalized Patients, Caregivers, and the Community in Rwanda

Frontiers in Microbiology ◽

10.3389/fmicb.2021.662575 ◽

2021 ◽

Vol 12 ◽

Author(s):

Elias Eger ◽

Stefan E. Heiden ◽

Katja Korolew ◽

Claude Bayingana ◽

Jules M. Ndoli ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Sub Saharan Africa ◽

Type I ◽

Beta Lactamase ◽

Community Members ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Extended Spectrum ◽

Sequence Types

Multi-drug resistant (MDR), gram-negative Enterobacteriaceae, such as Escherichia coli (E. coli) limit therapeutic options and increase morbidity, mortality, and treatment costs worldwide. They pose a serious burden on healthcare systems, especially in developing countries like Rwanda. Several studies have shown the effects caused by the global spread of extended-spectrum beta-lactamase (ESBL)-producing E. coli. However, limited data is available on transmission dynamics of these pathogens and the mobile elements they carry in the context of clinical and community locations in Sub-Saharan Africa. Here, we examined 120 ESBL-producing E. coli strains from patients hospitalized in the University Teaching Hospital of Butare (Rwanda), their attending caregivers as well as associated community members and livestock. Based on whole-genome analysis, the genetic diversification and phylogenetics were assessed. Moreover, the content of carried plasmids was characterized and investigated for putative transmission among strains, and for their potential role as drivers for the spread of antibiotic resistance. We show that among the 30 different sequence types (ST) detected were the pandemic clonal lineages ST131, ST648 and ST410, which combine high-level antimicrobial resistance with virulence. In addition to the frequently found resistance genes blaCTX–M–15, tet(34), and aph(6)-Id, we identified csg genes, which are required for curli fiber synthesis and thus biofilm formation. Numerous strains harbored multiple virulence-associated genes (VAGs) including pap (P fimbriae adhesion cluster), fim (type I fimbriae) and chu (Chu heme uptake system). Furthermore, we found phylogenetic relationships among strains from patients and their caregivers or related community members and animals, which indicates transmission of pathogens. Also, we demonstrated the presence and potential transfer of identical/similar ESBL-plasmids in different strains from the Rwandan setting and when compared to an external plasmid. This study highlights the circulation of clinically relevant, pathogenic ESBL-producing E. coli among patients, caregivers and the community in Rwanda. Combining antimicrobial resistance with virulence in addition to the putative exchange of mobile genetic elements among bacterial pathogens poses a significant risk around the world.

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Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

International Journal of Molecular Sciences ◽

10.3390/ijms22115905 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5905

Author(s):

Olivia M. Grünzweil ◽

Lauren Palmer ◽

Adriana Cabal ◽

Michael P. Szostak ◽

Werner Ruppitsch ◽

...

Keyword(s):

Escherichia Coli ◽

Marine Mammals ◽

Virulence Genes ◽

Multidrug Resistant ◽

Healthcare Sector ◽

Whole Genome ◽

E Coli ◽

High Prevalence ◽

Lactamase Gene ◽

Sequence Types

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

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Virulence Properties of mcr-1-Positive Escherichia coli Isolated from Retail Poultry Meat

Microorganisms ◽

10.3390/microorganisms9020308 ◽

2021 ◽

Vol 9 (2) ◽

pp. 308

Author(s):

Michaela Kubelová ◽

Ivana Koláčková ◽

Tereza Gelbíčová ◽

Martina Florianová ◽

Alžběta Kalová ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Poultry Meat ◽

Human Populations ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Mlst Type ◽

On Line ◽

Sequence Types

The great plasticity and diversity of the Escherichia coli genome, together with the ubiquitous occurrence, make E. coli a bacterium of world-wide concern. Of particular interest are pathogenic strains and strains harboring antimicrobial resistance genes. Overlapping virulence-associated traits between avian-source E. coli and human extraintestinal pathogenic E. coli (ExPEC) suggest zoonotic potential and safety threat of poultry food products. We analyzed whole-genome sequencing (WGS) data of 46 mcr-1-positive E. coli strains isolated from retail raw meat purchased in the Czech Republic. The investigated strains were characterized by their phylogroup—B1 (43%), A (30%), D (11%), E (7%), F (4%), B2 (2%), C (2%), MLST type, and serotype. A total of 30 multilocus sequence types (STs), of which ST744 was the most common (11%), were identified, with O8 and O89 as the most prevalent serogroups. Using the VirulenceFinder tool, 3 to 26 virulence genes were detected in the examined strains and a total of 7 (15%) strains met the pathogenic criteria for ExPEC. Four strains were defined as UPEC (9%) and 18 (39%) E. coli strains could be classified as APEC. The WGS methods and available on-line tools for their evaluation enable a comprehensive approach to the diagnosis of virulent properties of E. coli strains and represent a suitable and comfortable platform for their detection. Our results show that poultry meat may serve as an important reservoir of strains carrying both virulence and antibiotic resistance genes for animal and human populations.

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Multidrug Resistance Dissemination in Escherichia coli Isolated from Wild Animals: Bacterial Clones and Plasmid Complicity

Microbiology Research ◽

10.3390/microbiolres12010009 ◽

2021 ◽

Vol 12 (1) ◽

pp. 123-137

Author(s):

Carolina Sabença ◽

Gilberto Igrejas ◽

Patrícia Poeta ◽

Frédéric Robin ◽

Richard Bonnet ◽

...

Keyword(s):

Escherichia Coli ◽

Epidemiological Data ◽

Generation Cephalosporin ◽

Wild Animals ◽

Variable Regions ◽

E Coli ◽

Wild Fauna ◽

Long Read ◽

Sequence Types ◽

Animal Isolates

Objectives. Epidemiological data concerning third-generation cephalosporin (3GC) resistance in wild fauna are scarce. The aim of this study was to characterize the resistance genes, their genetic context, and clonal relatedness in 17 Escherichia coli resistant to 3GC isolated from wild animals. Methods. The isolates were characterized by short-read whole genome sequencing, and long-read sequencing was used for the hybrid assembly of plasmid sequences. Results. The 3GC resistance gene most identified in the isolates was the extended-spectrum β-lactamases (ESBL)-encoding gene blaCTX-M-1 (82.3%), followed by blaCTX-M-32 (5.9%), blaCTX-M-14 (5.9%), and blaSHV-12 (5.9%). E. coli isolates mainly belonged to the sequence types (STs) rarely reported from humans. The single nucleotide polymorphism (SNP)-based typing showed that most E. coli genomes from wild animals (wild boars, birds of prey, and buzzards) formed clonal clusters (<5 SNPs), showing a clonal dissemination crossing species boundaries. blaCTX-M-1-harboring IncI1-ST3 plasmid was the predominant ESBL-encoding plasmid (76.4%) in wild animal isolates. Plasmid comparison revealed a 110-kb self-transferable plasmid consisting of a conserved backbone and two variable regions involved in antimicrobial resistance and in interaction with recipient cells during conjugation. Conclusion. Our results highlighted the unexpected clonal dissemination of blaCTX-M-1-encoding clones and the complicity of IncI1-ST3 plasmid in the spread of blaCTX-M-1 within wild fauna.

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