Public Health Microbiology strategy

The Public Health Microbiology (PHM) strategy for Scotland, 2019 to 2023, identified the important role that Whole Genome Sequencing (WGS) will play in the future.

The strategy has a particular focus on moving to Pathogen Genome Sequencing (PGS) – this is WGS for microbial pathogens.

Integrating PGS into PHM will improve our:

  • national surveillance
  • alert and response systems
  • national epidemic preparedness

Value of the service

Using PGS on the SARS-CoV-2 virus as part of the COVID-19 pandemic response has demonstrated the value of this technology.

It has shown that high-resolution genotyping helps quickly identify outbreaks and trace the spread of pathogens.

Where mutations are detected with resistance to therapeutics, it provides genetic information we can use to inform treatment choices.

This then informs public health and infection prevention control interventions, where high-risk clones or variants are identified.

Upscaling the sequencing capacity

Before the investment in SARS-CoV-2 genomics, and through the course of the pandemic, the Scottish Mycobacteria Reference Laboratory (SMRL) in Lothian (external website) and Greater Glasgow & Clyde (external website) were using PGS on a limited number of bacterial pathogen species.

As a result of the success of SARS-CoV-2 sequencing, the service is expanding to sequence new pathogens. 

In February 2022, SMRL in Lothian introduced PGS for possible tuberculosis and Non-Tuberculous Mycobacterial (NTM) infection.

There are also several pathogens in development for roll-out throughout this year.

Contact the service

You can contact the SMRL Lothian at

You can contact the SMRL Glasgow at

Last updated: 17 October 2022
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