Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure. The annotation was done by ENSEMBL and includes annotations from RefSeq, CCDS as. As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future. All annotated protein coding genes for human reference sequence GRCh37(hg19). Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories.
The raw sequencing reads were mapped to the reference human genome (hg19). The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology. VariantStudio (Illumina) and CLC Genomics Workbench (CLCbio-Qiagen) softwares. The initial de novo assemblies were created for both male and female sequence data using CLC Genomics Workbench.
Genomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology.