Temporal Variability of <italic toggle="yes">Escherichia coli</italic> Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics

ABSTRACT The stability of the Escherichia coli populations in the human gastrointestinal tract is not fully appreciated, and represents a significant knowledge gap regarding gastrointestinal community structure, as well as resistance to incoming pathogenic bacterial species and antibiotic treatment....

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Autores principales:	Taylor K. S. Richter, Tracy H. Hazen, Diana Lam, Christian L. Coles, Jessica C. Seidman, Yaqi You, Ellen K. Silbergeld, Claire M. Fraser, David A. Rasko
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	Escherichia coli diversity microbial genomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/d0f6525f5813414f9f2278c21e27b30d
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spelling	oai:doaj.org-article:d0f6525f5813414f9f2278c21e27b30d2021-11-15T15:22:21ZTemporal Variability of <italic toggle="yes">Escherichia coli</italic> Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics10.1128/mSphere.00558-182379-5042https://doaj.org/article/d0f6525f5813414f9f2278c21e27b30d2018-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00558-18https://doaj.org/toc/2379-5042ABSTRACT The stability of the Escherichia coli populations in the human gastrointestinal tract is not fully appreciated, and represents a significant knowledge gap regarding gastrointestinal community structure, as well as resistance to incoming pathogenic bacterial species and antibiotic treatment. The current study examines the genomic content of 240 Escherichia coli isolates from 30 children, aged 2 to 35 months old, in Tanzania. The E. coli strains were isolated from three time points spanning a six-month time period, with and without antibiotic treatment. The resulting isolates were sequenced, and the genomes compared. The findings in this study highlight the transient nature of E. coli strains in the gastrointestinal tract of these children, as during a six-month interval, no one individual contained phylogenomically related isolates at all three time points. While the majority of the isolates at any one time point were phylogenomically similar, most individuals did not contain phylogenomically similar isolates at more than two time points. Examination of global genome content, canonical E. coli virulence factors, multilocus sequence type, serotype, and antimicrobial resistance genes identified diversity even among phylogenomically similar strains. There was no apparent increase in the antimicrobial resistance gene content after antibiotic treatment. The examination of the E. coli from longitudinal samples from multiple children in Tanzania provides insight into the genomic diversity and population variability of resident E. coli within the rapidly changing environment of the gastrointestinal tract of these children. IMPORTANCE This study increases the number of resident Escherichia coli genome sequences, and explores E. coli diversity through longitudinal sampling. We investigate the genomes of E. coli isolated from human gastrointestinal tracts as part of an antibiotic treatment program among rural Tanzanian children. Phylogenomics demonstrates that resident E. coli are diverse, even within a single host. Though the E. coli isolates of the gastrointestinal community tend to be phylogenomically similar at a given time, they differed across the interrogated time points, demonstrating the variability of the members of the E. coli community in these subjects. Exposure to antibiotic treatment did not have an apparent impact on the E. coli community or the presence of resistance and virulence genes within E. coli genomes. The findings of this study highlight the variable nature of specific bacterial members of the human gastrointestinal tract.Taylor K. S. RichterTracy H. HazenDiana LamChristian L. ColesJessica C. SeidmanYaqi YouEllen K. SilbergeldClaire M. FraserDavid A. RaskoAmerican Society for MicrobiologyarticleEscherichia colidiversitymicrobial genomicsMicrobiologyQR1-502ENmSphere, Vol 3, Iss 6 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Escherichia coli diversity microbial genomics Microbiology QR1-502
spellingShingle	Escherichia coli diversity microbial genomics Microbiology QR1-502 Taylor K. S. Richter Tracy H. Hazen Diana Lam Christian L. Coles Jessica C. Seidman Yaqi You Ellen K. Silbergeld Claire M. Fraser David A. Rasko Temporal Variability of <italic toggle="yes">Escherichia coli</italic> Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics
description	ABSTRACT The stability of the Escherichia coli populations in the human gastrointestinal tract is not fully appreciated, and represents a significant knowledge gap regarding gastrointestinal community structure, as well as resistance to incoming pathogenic bacterial species and antibiotic treatment. The current study examines the genomic content of 240 Escherichia coli isolates from 30 children, aged 2 to 35 months old, in Tanzania. The E. coli strains were isolated from three time points spanning a six-month time period, with and without antibiotic treatment. The resulting isolates were sequenced, and the genomes compared. The findings in this study highlight the transient nature of E. coli strains in the gastrointestinal tract of these children, as during a six-month interval, no one individual contained phylogenomically related isolates at all three time points. While the majority of the isolates at any one time point were phylogenomically similar, most individuals did not contain phylogenomically similar isolates at more than two time points. Examination of global genome content, canonical E. coli virulence factors, multilocus sequence type, serotype, and antimicrobial resistance genes identified diversity even among phylogenomically similar strains. There was no apparent increase in the antimicrobial resistance gene content after antibiotic treatment. The examination of the E. coli from longitudinal samples from multiple children in Tanzania provides insight into the genomic diversity and population variability of resident E. coli within the rapidly changing environment of the gastrointestinal tract of these children. IMPORTANCE This study increases the number of resident Escherichia coli genome sequences, and explores E. coli diversity through longitudinal sampling. We investigate the genomes of E. coli isolated from human gastrointestinal tracts as part of an antibiotic treatment program among rural Tanzanian children. Phylogenomics demonstrates that resident E. coli are diverse, even within a single host. Though the E. coli isolates of the gastrointestinal community tend to be phylogenomically similar at a given time, they differed across the interrogated time points, demonstrating the variability of the members of the E. coli community in these subjects. Exposure to antibiotic treatment did not have an apparent impact on the E. coli community or the presence of resistance and virulence genes within E. coli genomes. The findings of this study highlight the variable nature of specific bacterial members of the human gastrointestinal tract.
format	article
author	Taylor K. S. Richter Tracy H. Hazen Diana Lam Christian L. Coles Jessica C. Seidman Yaqi You Ellen K. Silbergeld Claire M. Fraser David A. Rasko
author_facet	Taylor K. S. Richter Tracy H. Hazen Diana Lam Christian L. Coles Jessica C. Seidman Yaqi You Ellen K. Silbergeld Claire M. Fraser David A. Rasko
author_sort	Taylor K. S. Richter
title	Temporal Variability of <italic toggle="yes">Escherichia coli</italic> Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics
title_short	Temporal Variability of <italic toggle="yes">Escherichia coli</italic> Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics
title_full	Temporal Variability of <italic toggle="yes">Escherichia coli</italic> Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics
title_fullStr	Temporal Variability of <italic toggle="yes">Escherichia coli</italic> Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics
title_full_unstemmed	Temporal Variability of <italic toggle="yes">Escherichia coli</italic> Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics
title_sort	temporal variability of <italic toggle="yes">escherichia coli</italic> diversity in the gastrointestinal tracts of tanzanian children with and without exposure to antibiotics
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/d0f6525f5813414f9f2278c21e27b30d
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Temporal Variability of <italic toggle="yes">Escherichia coli</italic> Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics

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