Interpretation
Isolates are pre-processed using cell lysis and nucleic acid purification procedures.
Library preparation is performed using Illumina DNA library kits and NGS is performed on MiSeq (Illumina).
NGS read data (fastq files) are quality checked and then analysed using reference based mapping programs to generate variant calls.
Variants in regions of interest are then compared to data-bases and WHO catalogue of mutations.
Phenotypic susceptibility testing is also performed as not all resistance mechanism/mutations are understood.
Option: All data can be made available via file share service if NGS only required without bioinformatic analysis.
Consultation: All antimicrobial resistance strains are reviewed by a Microbiologist.
