One of the remits in the Genomics, Proteomics and Bioinformatics Unit (GPBU) of the UK Health Protection Agency is to utilise genomics in infection control by the use of accelerated genomic information and enhanced biotechnological methods to streamline the traditional approaches used in classical molecular genetics to instigate advances in Public Health Protection.

Alteration in gene expression patterns or DNA sequence can have profound effects on biological functions and pathological processes. In GPBU, systems are developed for identifying genetic variations and gene expression and our key developmental objectives are to reformat sequence-based typing into fast, high throughput systems, to explore microbial genome sequences for VNTRs and SNP targets as tools for high resolution strain comparison and to provide tools for molecular-based surveillance of high priority infections.

To this end, Pyrosequencing technology has been evaluated for its utility in SNP characterisation (including antibiotic/drug resistance) and genotyping in Public Health Microbiology in the UK. An overview of applications will be presented including:

HIV-1

–drug resistance

–subtyping

Hepatitis C virus

–genotyping

–minor genotype analysis

Antibiotic resistance

–Neisseria gonorrhoeae

–Salmonella enterica

–Mycobacterium tuberculosis

Mycobacterium tuberculosis

–screening from sputum samples

–VNTR typing

H antigen typing of Salmonella