Resources

In this section you will find a list to resources on implementing pathogen sequencing, from major public health agencies and foundations, which can be used to design appropriate content, including real-work case studies, for pathogen genomics courses.

- Global Microbial Identifier: https://www.globalmicrobialidentifier.org/about-gmi

- WHO report on "The use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: technical guide" (https://apps.who.int/iris/handle/10665/274443)  

- ISO on Microbiology of the food chain — Whole genome sequencing for typing and genomic characterization of bacteria — General requirements and guidance (https://www.iso.org/standard/75509.html)

- GLASS 2020 report on Whole-genome sequencing for surveillance of antimicrobial resistance (https://apps.who.int/iris/bitstream/handle/10665/334354/9789240011007-eng.pdf)

-  Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States (https://www.fda.gov/food/science-research-food/whole-genome-sequencing-wgs-program)

- FIND report on Sequencing for antimicrobial resistance surveillance (https://www.finddx.org/wp-content/uploads/2022/04/20220211_Sequencing-for-AMR-surveillance.pdf)

- PHG foundation report Pathogen Genomics Into Practice (https://www.phgfoundation.org/report/pathogen-genomics-into-practice)

- PHE Expert opinion on whole genome sequencing for public health surveillance  (https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/731057/implementing_pathogen_genomics_a_case_study.pdf)

- UKHSA guidance on "Mycobacterium tuberculosis whole-genome sequencing and cluster investigation handbook" (https://www.gov.uk/government/publications/tb-strain-typing-and-cluster-investigation-handbook/mycobacterium-tuberculosis-whole-genome-sequencing-and-cluster-investigation-handbook)

- US CDC "Guide to the Application of Genotyping to Tuberculosis Prevention and Control" (https://www.cdc.gov/tb/programs/genotyping/manual.htm)