Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Capsule type-specific rabbit polyclonal antisera | Tollersrud et al.1 | N/A |
| Bacterial and virus strains | ||
| S. aureus isolates | This paper | N/A |
| Biological samples | ||
| Skin samples from children with atopic dermatitis | This paper | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Blood agar | BBL™ Blood Agar Base (Infusion Agar) | 90000–048 |
| PCRClean-DX SPRI beads | Aline Biosciences | C-1003–250 |
| Polyethylene glycol (PEG) 8000 | Hampton Research | HR2–535 |
| ReadyLyse Lysozyme Solution | EpiCentre | R1810M |
| KAPA HiFi HotStart ReadyMix | Roche | 7958927001 |
| Tryptic soy agar plates | Hardy Diagnostics | A10 |
| Nitrocellulose BA85 filters | Whatman, Inc. | Cat#09301102 |
| Trypsin, bovine pancreas | Fisher Scientific | Cat#AAJ6368803 |
| Skim milk | BD BBL™/Difco™ |
Cat#DF0032173 |
| Tween 20 | Millipore Sigma | Cat#P1379 |
| KPL 1-Component TMB Membrane Peroxidase Substrate | ThermoFisher Scientific | Cat#002019 |
| Fusidic acid | Sigma-Aldrich | CAS: 6990–06-3 |
| ChromAgar Colorex S. aureus | DRG international inc | Cat # TA672 |
| Critical commercial assays | ||
| Wizard Genomic DNA purification kit | Promega | A1120 |
| Illumina Tagment DNA TDE1 Enzyme and Buffer Kits | Illumina | 20034198 |
| PlexWell library prep system | seqWell | plexWell 384 |
| Puritan™ Opti- Tranz™ Liquid Amies Media Transport Tube with Rayon Tip Swab, Polysterne Handle | Puritan | LA-61PR |
| Puritan™ Opti- Tranz™ Liquid Amies Media Transport Tube with Miniature Rayon Tip Swab, Aluminum Handle | Puritan | LA61SAR |
| Experimental models: Organisms/strains | ||
| C57BL/6 female mice | Jackson Laboratories | Strain #:000664 |
| Deposited data | ||
| Raw sequencing data | This paper | Genbank: PRJNA715375, PRJNA715649, PRJNA816913 |
| Software and algorithms | ||
| All original code | This paper | https://github.com/keyfm/aureus_ad |
| Python (v3.7.3) | N/A | https://www.python.org/ |
| Snakemake (v5.4.2) | Mölder et al.2 | https://snakemake.github.io/ |
| Matlab (v2015b, v2018a) | Mathworks | https://www.mathworks.com/products/matlab.html |
| Cutadapt (v1.18) | Martin3 | https://cutadapt.readthedocs.io/en/stable/ |
| Sickle (v1.33) | Joshi & Fass4 | https://github.com/najoshi/sickle |
| Bowtie 2 (v2.2.6) | Langmead & Salzburg5 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| SAMtools (v1.5) and BCFtools (v1.2) | Danecek et al.6 | https://github.com/samtools/ |
| Kraken 2 (v2.0.8) | Wood et al.7 | https://github.com/DerrickWood/kraken2 |
| BLAST (v2.7.1) | NCBI | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| PHYLIP (v3.69) | Felsenstein8 | https://evolution.genetics.washington.edu/phylip.html |
| FigTree (v1.4.4) | N/A | https://github.com/rambaut/figtree |
| SPAdes (v3.13) | Bankevich et al.9 | https://github.com/ablab/spades |
| Prokka (v4.8.1) | Seeman10 | https://github.com/tseemann/prokka |
| CD-HIT (v4.8) | Fu et al.11 | http://weizhong-lab.ucsd.edu/cd-hit/ |
| treeTime | Sagulenko et al.12 | http://https//github.com/neherlab/treetime |
| lolipop | N/A | https://github.com/cdeitrick/Lolipop |
| ggmueller | N/A | https://cran.r-project.org/package=ggmuller |
| growthrater | N/A | https://github.com/vedomics/growthrateR |
| SRST2 | Inouye et al.13 | https://github.com/katholt/srst2 |
| MLST | N/A | https://github.com/tseemann/mlst |
| treeWAS | Collins & Didelot 14 | https://github.com/caitiecollins/treeWAS |
| Other | ||
| Public S. aureus annotations used in annotation of assemblies | NCBI Genbank | NC_002745, NC_003140, NC_002758, NC_002774, NC_009641, NC_003923, NC_002952, NC_002953, NC_005951, NC_002951, NC_006629, NC_007795, NC_007793, NC_007790, NC_007791, NC_007792 |
| 276 public S. aureus genomes analyzed |
Edslev et al., Young et al., Harkins et al., Harkins et al. 15–18 | See Table S10 |
| Tegaderm (bio-occlusive film) | 3M | 1624W |