Seqsphere version 7

The genomic search of chlR, efrE, and efrF genes (reference strain E. faecalis V583; GenBank accession no. AE016830.1; locus-tag EF_2225 to EF_2227) was performed in the 666 E. faecalis sequenced genomes by using the MyDBfinder tool available at the Center for Genomic Epidemiology (www.genomicepidemiology.org). The chlR-efrEF genes identified in each genome were translated into the corresponding amino acid sequences by the DNA translate tool of ExPASy SIB Bioinformatics Resource Portal (https://web.expasy.org/translate/), and the occurrence of incomplete ChlR-EfrEF proteins was evaluated.
For the sequenced E. faecalis included in the phenotypic assays, a comparison of the amino acid sequences with the reference strain E. faecalis V583 was performed using Clustal Omega software (https://www.ebi.ac.uk/Tools/msa/clustalo/) to identify specific mutations. Their clonal relationship was also established by MLST and cgMLST (46 (link), 47 (link)) (http://pubmlst.org; Ridom SeqSphere+, version 7.2). A phylogenetic tree based on their cgMLST allelic profiles was constructed using Ridom SeqSphere+ software, and isolate information was added to the tree using iTol software (https://itol.embl.de).

The genomic search of chlR, efrE, and efrF genes (reference strain E. faecalis V583; GenBank accession no. AE016830.1; locus-tag EF_2225 to EF_2227) was performed in the 666 E. faecalis sequenced genomes by using the MyDBfinder tool available at the Center for Genomic Epidemiology (www.genomicepidemiology.org). The chlR-efrEF genes identified in each genome were translated into the corresponding amino acid sequences by the DNA translate tool of ExPASy SIB Bioinformatics Resource Portal (https://web.expasy.org/translate/), and the occurrence of incomplete ChlR-EfrEF proteins was evaluated.
For the sequenced E. faecalis included in the phenotypic assays, a comparison of the amino acid sequences with the reference strain E. faecalis V583 was performed using Clustal Omega software (https://www.ebi.ac.uk/Tools/msa/clustalo/) to identify specific mutations. Their clonal relationship was also established by MLST and cgMLST (46 (link), 47 (link)) (http://pubmlst.org; Ridom SeqSphere+, version 7.2). A phylogenetic tree based on their cgMLST allelic profiles was constructed using Ridom SeqSphere+ software, and isolate information was added to the tree using iTol software (https://itol.embl.de).