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

Adrian L Cookson; David W Lacher; Flemming Scheutz; David A Wilkinson; Patrick J Biggs; Jonathan C Marshall; Gale Brightwell

doi:10.1128/MRA.00476-19

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

Microbiol Resour Announc. 2019 Aug 15;8(33):e00476-19. doi: 10.1128/MRA.00476-19.

Authors

Adrian L Cookson^{1

2}, David W Lacher³, Flemming Scheutz⁴, David A Wilkinson^{2

5}, Patrick J Biggs^{2

6

5}, Jonathan C Marshall^{2

6}, Gale Brightwell^{7

5}

Affiliations

¹ AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand adrian.cookson@agresearch.co.nz.
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.
⁷ AgResearch Limited, Hopkirk Research Institute, 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.