Genomic diversity of<i>Escherichia coli</i>isolates from non-human primates in the Gambia

Foster-Nyarko, Ebenezer; Alikhan, Nabil-Fareed; Ray, Anuradha; Thilliez, Gaëtan; Thomson, Nicholas M.; Cramer, Jennifer Danzy; Baker, David; Kay, Gemma L.; O’Grady, Justin; Antonio, Martín; Pallen, Mark J.

doi:10.1101/2020.02.29.971309

Cited by 5 publications

(9 citation statements)

References 76 publications

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“…Co-colonization of single hosts with multiple strains may facilitate the spread of AMR-and virulence-associated genes from resistant strains to other bacteria via both horizontal and vertical gene transfer [75]. A high co-colonization rate of E. coli has been described in humans [76,77] and in non-human primates [32], involving pathogenic strains of E. coli. Recently, Li et al reported three to nine sequence types of colistin-resistant E. coli to co-exist within a single broiler chicken [30].…”

Section: Discussionmentioning

confidence: 99%

“…Genomic DNA was extracted from overnight broth cultures prepared from each single colony sub-culture using an in-house 96-well plate lysate method as described previously [32]. The DNA was eluted in Tris/Cl (pH, 8.0) and quantified using the Qubit high-sensitivity DNA assay kit (Invitrogen, MA, USA).…”

Section: Genomic Dna Extractionmentioning

confidence: 99%

“…Whole-genome shotgun sequencing of the DNA extracts was performed for all the study isolates on the Illumina NextSeq 500 instrument (Illumina, San Diego, CA, USA) using a modified Illumina Nextera library preparation protocol as described previously [32]. We ran the final pooled library at a concentration of 1.8 pM on a mid-output flow cell (NSQ 500 Mid Output KT v2 300 cycles; Illumina catalogue no.…”

Section: Illumina Sequencingmentioning

confidence: 99%

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

et al. 2021

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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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Section: Discussionmentioning

confidence: 99%

Section: Genomic Dna Extractionmentioning

confidence: 99%

Section: Illumina Sequencingmentioning

confidence: 99%

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

et al. 2021

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“…Broth cultures were prepared from pure, fresh cultures of each colony-pick in 1 ml Luria-Bertani broth and incubated overnight to attain between 10 9 -10 10 cfu per ml. Genomic DNA was then extracted from the overnight broth cultures using the lysate method described in (33). The eluted DNA was quantified by the Qubit high sensitivity DNA assay kit (Invitrogen, MA, USA) and sequenced on the Illumina NextSeq 500 instrument (Illumina, San Diego, CA) as described previously (34).…”

Section: Genomic Dna Extraction and Genome Sequencingmentioning

confidence: 99%

Genomic diversity ofEscherichia coliisolates from healthy children in rural Gambia

Foster-Nyarko

Alikhan

Ikumapayi

et al. 2020

Preprint

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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 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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“…Similarly, ST681 strains were found nearly worldwide in animals (wild boars, non-human primates) and among isolates causing human ExPEC infections, including UTI [56][57][58][59] . Furthermore, besides reports on UTI caused by ST569, this lineage could have possible food and…”

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confidence: 99%

The darkest place is under the candlestick - healthy urogenital tract as a source of UTI-relatedEscherichia colilineages

Ksiezarek

Novais

Peixe

2021

Preprint

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Since the discovery of the urinary microbiome, including identification of Escherichia coli in healthy hosts, its involvement in UTI development is a subject of high interest.We explored population diversity and antimicrobial resistance of E. coli from urogenital microbiome of asymptomatic and recurrent UTI (rUTI) women. We also evaluated the genomic relationship between extraintestinal pathogenic E. coli (ExPEC) strains from healthy and diseased hosts, particularly of the ST131 lineage.E. coli was highly prevalent in asymptomatic women (48%) with slightly higher prevalence in vaginal samples comparing to urine, and occasionally with multiclonal population in the same individual. B2 was the most frequent phylogenetic group, with most strains classified as ExPEC. We demonstrated that virulence associated genes profile does not allow to distinguish strains isolated from healthy and rUTI host. We identified E. coli widespread lineages e.g., sequence types (ST) 127, ST131 (asymptomatic cohort) and ST73, ST131 (rUTI), frequently resistant to at least one antibiotic. Phylogenomics of ST131 and other ExPEC lineages revealed close relatedness between healthy and diseased host.These findings demonstrate that healthy urogenital microbiome is a source of potentially pathogenic and antibiotic resistant E. coli strains, including globally spread E. coli lineages causing UTI including ST131.

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Genomic diversity ofEscherichia coliisolates from non-human primates in the Gambia

Cited by 5 publications

References 76 publications

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

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

Genomic diversity ofEscherichia coliisolates from healthy children in rural Gambia

The darkest place is under the candlestick - healthy urogenital tract as a source of UTI-relatedEscherichia colilineages

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