…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.
It looks like Ion Torrent is making a real move to claim this sequencing niche (boldface mine):
Ion Torrent technology allows genome sequencing with reduced costs, leading to its widespread use in bacterial genomics. Given the abundance of information produced by this platform, intuitive bioinformatics tools demanding minimal training are required in order to translate such a technology into the clinical settings routine.
IonGAP is a publicly available integrated pipeline designed for the assembly and subsequent analysis of Ion Torrent bacterial sequence data. Both its components and their configuration are based on a research process aimed to discover the optimal combination of tools for obtaining good results from single-end reads generated by the Ion Torrent PGM sequencer.
Here’s what it offers:
On the antibiotic resistance front, the underlying data are pretty good, but not perfect. Nonetheless, this product could help Ion Torrent, which I think is a poorer sequencing technology compared to Illumina, gain access to clinical labs. Not only are the start up costs cheaper (the Ion Torrent machine costs less), but there’s out-of-the-box software for clinicians.
Curious to see how this plays out.