SRX1737465 SJV_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418021 SAMN04901223 SJV_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737466 SJV_2 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418023 SAMN04901224 SJV_2 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737467 SJV_11 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418020 SAMN04901233 SJV_11 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737468 Guerrero_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418022 SAMN04901234 Guerrero_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737469 San_Diego_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418024 SAMN04901235 San_Diego_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737470 Michoacan_2 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418025 SAMN04901236 Michoacan_2 WGS GENOMIC RANDOM Illumina Genome Analyzer IIx SRX1737471 Coahuila_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418026 SAMN04901237 Coahuila_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737472 B0727_Argentina SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418027 SAMN04901238 B0727_Argentina WGS GENOMIC RANDOM Illumina MiSeq SRX1737473 Tucson_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418028 SAMN04901239 Tucson_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737474 Tucson_2 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418029 SAMN04901240 Tucson_2 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737475 Tucson_3 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418030 SAMN04901241 Tucson_3 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737476 Tucson_4 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418031 SAMN04901242 Tucson_4 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737477 SJV_3 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418032 SAMN04901225 SJV_3 WGS GENOMIC RANDOM Illumina Genome Analyzer IIx SRX1737478 Tucson_5 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418033 SAMN04901243 Tucson_5 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737479 Tucson_6 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418034 SAMN04901244 Tucson_6 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737480 Tucson_7 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418035 SAMN04901245 Tucson_7 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737481 Tucson_8 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418036 SAMN04901246 Tucson_8 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737482 Tucson_9 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418040 SAMN04901247 Tucson_9 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737483 Tucson_10 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418037 SAMN04901248 Tucson_10 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737484 Tucson_11 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418038 SAMN04901249 Tucson_11 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737485 Tucson_12 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418039 SAMN04901250 Tucson_12 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737486 Tucson_13 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418041 SAMN04901251 Tucson_13 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737487 Tucson_14 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418042 SAMN04901252 Tucson_14 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737488 SJV_4 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418043 SAMN04901226 SJV_4 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737489 Tucson_15 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418044 SAMN04901253 Tucson_15 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737490 Tucson_16 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418045 SAMN04901254 Tucson_16 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737491 Tucson_17 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418046 SAMN04901255 Tucson_17 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737492 Tucson_18 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418047 SAMN04901256 Tucson_18 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737493 Tucson_19 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418048 SAMN04901257 Tucson_19 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737494 Tucson_20 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418049 SAMN04901258 Tucson_20 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737495 Tucson_21 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418050 SAMN04901259 Tucson_21 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737496 Tucson_22 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418051 SAMN04901260 Tucson_22 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737497 Tucson_23 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418052 SAMN04901261 Tucson_23 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737498 San_Antonio_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418053 SAMN04901262 San_Antonio_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737499 SJV_5 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418054 SAMN04901227 SJV_5 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737500 Colorado_Springs_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418055 SAMN04901263 Colorado_Springs_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737501 Sonora_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418056 SAMN04901264 Sonora_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737502 Sonora_2 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418057 SAMN04901265 Sonora_2 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737503 Coahuila_2 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418062 SAMN04901266 Coahuila_2 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737504 Phoenix_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418058 SAMN04901267 Phoenix_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737505 Phoenix_2 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418059 SAMN04901268 Phoenix_2 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737506 Phoenix_3 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418060 SAMN04901269 Phoenix_3 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737507 Phoenix_4 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418061 SAMN04901270 Phoenix_4 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737508 Phoenix_5 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418064 SAMN04901271 Phoenix_5 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737509 Phoenix_6 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418063 SAMN04901272 Phoenix_6 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737510 SJV_6 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418065 SAMN04901228 SJV_6 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737511 Phoenix_7 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418066 SAMN04901273 Phoenix_7 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737512 Phoenix_8 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418067 SAMN04901274 Phoenix_8 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737513 Phoenix_9 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418068 SAMN04901275 Phoenix_9 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737514 Nuevo_Leon_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418069 SAMN04901276 Nuevo_Leon_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737515 Nuevo_Leon_2 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418070 SAMN04901277 Nuevo_Leon_2 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737516 Michoacan_1 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418071 SAMN04901278 Michoacan_1 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737517 B0858_Guatemala SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418072 SAMN04901279 B0858_Guatemala WGS GENOMIC RANDOM Illumina MiSeq SRX1737518 B10757_Nevada SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418073 SAMN04901280 B10757_Nevada WGS GENOMIC RANDOM Illumina MiSeq SRX1737519 B10813_Texas SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418075 SAMN04901281 B10813_Texas WGS GENOMIC RANDOM Illumina MiSeq SRX1737520 B1249_Guatemala SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418074 SAMN04901282 B1249_Guatemala WGS GENOMIC RANDOM Illumina MiSeq SRX1737521 SJV_7 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418076 SAMN04901229 SJV_7 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737522 B5773_Brazil SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418077 SAMN04901283 B5773_Brazil WGS GENOMIC RANDOM Illumina MiSeq SRX1737523 Tucson_24 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418078 SAMN04901284 Tucson_24 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737524 GT017_Paraguay SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418079 SAMN04901285 GT017_Paraguay WGS GENOMIC RANDOM Illumina MiSeq SRX1737525 GT002_Texas SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418080 SAMN04901286 GT002_Texas WGS GENOMIC RANDOM Illumina MiSeq SRX1737526 730332_Guatemala SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418081 SAMN04901287 730332_Guatemala WGS GENOMIC RANDOM Illumina MiSeq SRX1737527 730333_Guatelama SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418082 SAMN04901288 730333_Guatelama WGS GENOMIC RANDOM Illumina MiSeq SRX1737528 730334_Guatemala SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418083 SAMN04901289 730334_Guatemala WGS GENOMIC RANDOM Illumina MiSeq SRX1737529 SJV_8 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418084 SAMN04901230 SJV_8 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737530 SJV_9 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418085 SAMN04901231 SJV_9 WGS GENOMIC RANDOM Illumina HiSeq 2500 SRX1737531 SJV_10 SRP074212 PRJNA274372 DNA samples were prepared for multiplexed, paired-end sequencing following the manufacturers protocol. For each isolate, 1-5ug dsDNA in 200ul was sheared and then purified using the QIAquick PCR Purification kit (Qiagen). Enzymatic processing of the DNA followed the guidelines as described in the Illumina protocol, with the exceptions of processing enzymes obtained from New England Biolabs (New England Biolabs, Ipswich, MA) and oligonucleotides and adaptors from Illumina (Illumina Inc). After ligation of the adaptors, the DNA was run on a 2% agarose gel for 2 hours; subsequently a gel slice containing 500-600 bp fragments of each DNA sample was isolated and purified using the QIAquick Gel Extraction kit (Qiagen). Individual libraries were quantified with qPCR on the ABI 7900HT (Life Technologies Corp.) using the Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Based on the individual library concentrations, equimolar pools of twelve S. aureus libraries were prepared at a concentration of at least 1nM. To ensure accurate loading onto the flowcell, the same quantification method was used to quantify the final pools. SRS1418086 SAMN04901232 SJV_10 WGS GENOMIC RANDOM Illumina HiSeq 2500