| Biological samples |
|
|
| Stool samples from UTI patients |
This paper |
N/A |
| Urine samples from UTI patients |
This paper |
N/A |
| Critical commercial assays |
| Hardy Diagnostic’s ESBL agar |
Hardy Diagnostics |
Catalog #:
G321 |
| Hardy Diagnostic’s MAC agar |
Hardy Diagnostics |
Catalog #:
GA35 |
| Mueller Hinton agar |
Hardy Diagnostics |
Catalog #:
C6421 |
| Kirby Bauer disk diffusion antibiotic disks |
Hardy Diagnostics |
N/A |
| Kirby Bauer disk diffusion antibiotic disks |
Becton Dickinson |
N/A |
| Blood agar plates |
Hardy Diagnostics |
Catalog #:
GA50 |
| QIAamp Bacteremia DNA kit |
Qiagen |
Catalog #:
12240–50 |
| Nextera DNA Library Preparation Kit |
Illumina |
Catalog #:
FC-131–1024 |
| Deposited data |
| Raw sequencing data for isolate whole genomes |
This paper |
NCBI SRA: PRJNA682246 |
| Metadata of E. coli isolates sequenced for this study |
This paper |
See Data S1
|
| Reference E. coli genomes |
See Data S6
|
N/A |
| Software and algorithms |
| Trimmomatic v.36 |
(Bolger et al., 2014) |
https://github.com/usadellab/Trimmomatic
|
| SPAdes v.3.11.0 |
(Bankevich et al., 2012) |
https://github.com/ablab/spades
|
| QUAST v5.0.2 |
(Gurevich et al., 2013) |
http://quast.sourceforge.net
|
| checkM v.1.0.13 |
(Parks et al., 2015) |
https://github.com/Ecogenomics/CheckM
|
| Prokka v.1.12 |
(Seemann, 2014) |
https://github.com/tseemann/prokka
|
| RGI-CARD v.5.1.0 |
(Jia et al., 2017) |
https://github.com/arpcard/rgi
|
| Resfinder v.4.0 |
(Zankari et al., 2012) |
https://bitbucket.org/genomicepidemiology/resfinder/src/master/
|
| mlst v2.11 |
(Joensen et al., 2015) |
https://bitbucket.org/genomicepidemiology/mlst/src/master/
|
| serotypefinder v2.0.1 |
(Larsen et al., 2012) |
https://bitbucket.org/genomicepidemiology/serotypefinder/src/master/
|
| Roary v3.8.0 |
(Page et al., 2015) |
https://sanger-pathogens.github.io/Roary/
|
| iTOL v.4 |
(Letunic and Bork, 2019) |
https://itol.embl.de
|
| FastTree v.2.1.10 |
(Price et al., 2009) |
http://www.microbesonline.org/fasttree/
|
| snp-sites v.2.4.0 |
(Page et al., 2016) |
https://github.com/sanger-pathogens/snp-sites
|
| fastANI v1.3 |
(Jain et al., 2018) |
https://github.com/ParBLiSS/FastANI
|
| Bowtie2 v.2.3.4 |
(Langmead et al., 2019) |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| SAMtools v.1.9 |
(Li et al., 2009) |
https://www.htslib.org/download/
|
| BCFtools v.1.9 |
(Danecek and McCarthy, 2017) |
https://www.htslib.org/download/
|
| Ape package in R v.3.6.3 |
(Paradis and Schliep, 2019) |
https://cran.r-project.org/web/packages/ape/index.html
|
| PHYLIP v3.697 |
(Felsenstein, 1989) |
https://evolution.genetics.washington.edu/phylip.html
|
| Snippy v4.3.8 |
N/A |
https://github.com/tseemann/snippy
|
| Genomegamap v1.0.1 |
(Wilson, 2021) |
https://github.com/danny-wilson/genomegaMap
|
| CD-HIT |
(Fu et al., 2012) |
http://weizhong-lab.ucsd.edu/cd-hit/
|
| VEGAN package in R v.3.6.3 |
(Dixon, 2003) |
https://cran.r-project.org/web/packages/vegan/index.html
|
| blast2go |
(Götz et al., 2008) |
https://www.blast2go.com
|
| REVIGO |
(Supek et al., 2011) |
http://revigo.irb.hr
|
| Cytoscape |
(Shannon et al., 2003) |
https://cytoscape.org
|
| PHASTER |
(Arndt et al., 2016) |
https://phaster.ca
|
| plasmidSPAdes v.3.11.0 |
(Antipov et al., 2016) |
https://github.com/ablab/spades
|
| PlasmidFinder v.4.0 |
(Carattoli et al., 2014) |
https://cge.cbs.dtu.dk/services/PlasmidFinder/
|
| Recycler v.0.6.2 |
(Rozov et al., 2017) |
https://github.com/Shamir-Lab/Recycler
|
| ncbi-blast v.2.6.0+ |
(McGinnis and Madden, 2004) |
https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/
|
| eggnog-mapper v.6.8 |
(Huerta-Cepas et al., 2019) |
https://github.com/eggnogdb/eggnog-mapper
|
| Clustal Omega |
(Madeira et al., 2019) |
https://www.ebi.ac.uk/Tools/msa/
|
| MView |
(Madeira et al., 2019) |
https://www.ebi.ac.uk/Tools/msa/
|
| ISfinder |
(Siguier et al., 2006) |
https://isfinder.biotoul.fr
|
| Other |
| MALDI-TOF MS |
VITEK MS, bioMérieux |
N/A |
| NextSeq 500 HighOutput platform |
Illumina |
N/A |
