Identifying resistance genes from WGS data

The sequencing of the isolates using the Illumina Hiseq 2000 platform (Illumina, Inc., San Diego, CA, USA), de novo assembly and sequence annotation was reported by Musicha et al.15

The final annotated sequences were screened for acquired AMR genes using NCBI BLAST against a bespoke database of genes curated by the Wellcome Trust Sanger Institute based on the ResFinder database. A cut-off of >95% for nucleotide identity and >90% for coverage against the database was used to confirm gene identity.