Companion Animals are Spillover Hosts of the Multidrug-Resistant Human Extraintestinal Escherichia coli Pandemic Clones ST131 and ST1193
This repository provides de novo assemblies of paired-end short-read sequencing data for our phylogenomic study of E. coli sequence type (ST)131 in an accessible format. If you use this data in your publications please cite:
Kidsley AK^, White RT, Beatson SA, Saputra S, Schembri MA, Gordon D, Johnson JR, O'Dea M,
Mollinger JL, Abraham S*,Trott DJ*. Companion animals are spillover hosts of the
multidrug-resistant human extraintestinal Escherichia coli pandemic clones ST131 and ST1193.
Frontiers in Microbiology, 11:1968. (2020).
doi: 10.3389/fmicb.2020.01968
^CORRESPONDING AUTHORS *AUTHORS CONTRIBUTED EQUALLY
AKK performed experiments, data analysis, drafted & prepared the manuscript. RTW performed
whole genome sequencing & built/analysed the phylogenetic tree.
The Illumina sequence read data have been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA627752 (20 paired reads).
Contains:
- Assemblies/ - the assembled contigs from Velvet that have been ordered against E. coli ST131 strain EC958 (GenBank: HG941718.1) described by Forde et al. (2014).
- Contigs from the draft assemblies were ordered against the complete chromosome of EC958 using Mauve by Darling, et al. (2004).
- The assembly statistics are provided.
The following table facilitates this:
| Strain | Alternate ID | SRA Accession | BioSample accession |
|---|---|---|---|
| MS10667 | Q13/1/80 | SRR11608173 | SAMN14686254 |
| MS10669 | W13/1/13 | SRR11608172 | SAMN14686255 |
| MS10670 | N13/1/75 | SRR11608161 | SAMN14686256 |
| MS10671 | N13/1/109 | SRR11608160 | SAMN14686257 |
| MS10672 | N13/4/38 | SRR11608159 | SAMN14686258 |
| MS10673 | N13/1/351 | SRR11608158 | SAMN14686259 |
| MS10674 | S13/1/53 | SRR11608157 | SAMN14686260 |
| MS10675 | N13/4/125 | SRR11608156 | SAMN14686261 |
| MS10677 | N13/4/101 | SRR11608155 | SAMN14686262 |
| MS10678 | N13/1/272 | SRR11608154 | SAMN14686263 |
| MS10893 | 2338849 | SRR11608171 | SAMN14686264 |
| MS10895 | 4209016 | SRR11608170 | SAMN14686265 |
| MS10898 | 2306405 | SRR11608169 | SAMN14686266 |
| MS10899 | 2400728-Feline | SRR11608168 | SAMN14686267 |
| MS10900 | 4180360 | SRR11608167 | SAMN14686268 |
| MS10901 | B08/0924 | SRR11608166 | SAMN14686269 |
| MS10902 | MU1 | SRR11608165 | SAMN14686270 |
| MS10903 | MU4 | SRR11608164 | SAMN14686271 |
| MS10908 | 2435694 | SRR11608163 | SAMN14686272 |
| Q13/1/261 | Q13/1/261 | SRR11608162 | SAMN14686315 |
Note: The data is ~102.4 MB
Option 1) Download the current release as an archive:
$ wget https://github.com/RhysWhite/ST131_19_Pets/archive/master.zip -O ST131_19_Pets_AU_v1.tar.gz
$ unzip ST131_19_Pets_AU_v1.tar.gz
Option 2) Clone the current master branch in this repository:
Please ensure you have git installed. git can be really useful for scientists. See here for some discussion.
With git:
$ git clone --recursive https://github.com/RhysWhite/ST131_19_Pets_AU.git
# The --recursive option is used to pull down all the smaller repositories