MLST databases for Staphylococcus aureus, Streptococcus pneumoniae, Salmonella enterica, Escherichia coli, Enterococcus faecium, Listeria monocytogenes and Enterobacter cloaceae were downloaded from pubmlst.org using the getmlst.py script included with SRST2 (June 2014).
Antimicrobial resistance gene detection was performed using the ARG-Annot database of acquired resistance genes [18 (link)]. Allele sequences (DNA) were downloaded in fasta format [43 ] (May, 2014). Sequences were clustered into gene groups with ≥80% identity using CD-hit [44 (link)] and the headers formatted for use with SRST2 using the scripts provided (cdhit_to_csv.py, csv_to_gene_db.py). A copy of the formatted sequence database used in this study is included in the SRST2 github repository [35 ].
Representative sequences for 18 plasmid replicons were extracted from GenBank using the accessions and primer sequences specified by Carattoli et al. [45 (link)]. A copy of the formatted sequence database used in this study is included in the SRST2 github repository [35 ].
Antimicrobial resistance gene detection was performed using the ARG-Annot database of acquired resistance genes [18 (link)]. Allele sequences (DNA) were downloaded in fasta format [43 ] (May, 2014). Sequences were clustered into gene groups with ≥80% identity using CD-hit [44 (link)] and the headers formatted for use with SRST2 using the scripts provided (cdhit_to_csv.py, csv_to_gene_db.py). A copy of the formatted sequence database used in this study is included in the SRST2 github repository [35 ].
Representative sequences for 18 plasmid replicons were extracted from GenBank using the accessions and primer sequences specified by Carattoli et al. [45 (link)]. A copy of the formatted sequence database used in this study is included in the SRST2 github repository [35 ].