gndDb, a Database of Partial gnd Sequences To Assist with Analysis of Escherichia coli Communities Using High-Throughput Sequencing-Reference-Cited by-同舟云学术

gndDb, a Database of Partial gnd Sequences To Assist with Analysis of Escherichia coli Communities Using High-Throughput Sequencing

Published:2019-08-15 Issue:33 Volume:8 Page:
ISSN:2576-098X
Container-title:Microbiology Resource Announcements
language:en
Short-container-title:Microbiol Resour Announc

Author:

Cookson Adrian L.¹²^ORCID,Lacher David W.³,Scheutz Flemming⁴,Wilkinson David A.²⁵^ORCID,Biggs Patrick J.²⁶⁵,Marshall Jonathan C.²⁶,Brightwell Gale¹⁵

Affiliation:

1. AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand

2. mEpiLab, Hopkirk Research Institute, School of Veterinary Science, Massey University, Palmerston North, New Zealand

3. Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA

4. Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark

5. New Zealand Food Science and Safety Research Centre, Massey University, Palmerston North, New Zealand

6. School of Fundamental Sciences, Massey University, Palmerston North, New Zealand

Abstract

The use of culture methods to detect Escherichia coli diversity does not provide sufficient resolution to identify strains present at low levels. Here, we target the hypervariable gnd gene and describe a database containing 534 distinct partial gnd sequences and associated O groups for use with culture-independent E. coli community analysis.

Publisher

American Society for Microbiology

Subject

Genetics,Immunology and Microbiology (miscellaneous),Molecular Biology

Link

https://journals.asm.org/doi/pdf/10.1128/MRA.00476-19

Reference11 articles.

1. Culture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure

2. Genetic Diversity and Structure in Escherichia coli Populations

3. Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus

4. Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria.

5. A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster

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