On the other hand, microbial genomes are cheap, fast, and you can provide epidemiologically relevant information to clinical laboratories, hospital networks, and public health departments. I’m not arguing that we will or should sequence everything–and today that’s not feasible–but in two or three years, I don’t see any technical hurdles to routine microbiological surveillance in hospitals. This is something already being done, just with mid-20th century technology.
So this joint venture between bioMérieux, a laboratory diagnostic company, and the sequencing behemoth Illumina seems promising (boldface mine):
The first application will be an NGS epidemiological solution offered by service labs for genotyping disease agents. The high resolution of NGS combined with bioMerieux’s industry-leading knowledge in microbiology will provide easily accessible and highly accurate information to communities and hospitals to track, prevent, contain and stop the spread of disease agents.
The solution will combine Illumina’s MiSeq® sequencing system with a jointly developed pathogen genome database based on bioMérieux’s culture collection. This collection, which contains over 80,000 references, constitutes one of the largest libraries of bacterial strains in the world, and will contribute to creating a database of unprecedented scope with information about virulence and microbial resistance characteristics. The service will deliver a standardized report with a genomic profile of the infectious agents, with sequence-level accuracy and depth of information…
The ultimate goal of the Illumina-bioMérieux epidemiology solution will be to enable public health and hospital microbiology laboratories to contain an epidemic, avoid transmission of infectious agents, and improve hospital practices where needed. Those facing a suspected epidemic or health crisis will be able to send the relevant isolates to a designated laboratory equipped with an Illumina sequencing system. The genetic sequences will be sent via a secure cloud platform to be analyzed, using the database and software developed by bioMérieux, which will also generate a customized report for the customer.
The devil will be in the details–the bioinformatics details–but this is a good development. It’s time clinical epidemiology entered the 21st century.