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Brian Raphael , PhD , has been a research microbiologist at CDC since 2005 and currently leads the agency ’ s Legionella activities , with a major focus on advanced molecular detection in the Pneumonia Response and Surveillance Laboratory in the Respiratory Diseases Branch . Before this , he led research involving molecular subtyping of botulinum toxin-producing clostridia at CDC ’ s Enteric Diseases Laboratory Branch . Raphael graduated from the University of Arizona with a PhD in microbiology and immunology and completed a postdoctoral fellowship at Washington State University , studying mechanisms of Campylobacter jejuni pathogenesis . Here he discusses current and future applications of whole genome sequencing in the microbiology laboratory .

As a research microbiologist for the past decade or so , you have been at the forefront of next-generation sequencing ( NGS ) in public health . What are the benefits of this technology ?

Before whole genome sequencing ( WGS ), we used various molecular methods to subtype bacteria , including PCR , PFGE and microarray technologies . But we were examining hundreds of targets instead of the entire genome , with millions of bases with potential diversity . With WGS , we ’ re looking at the nucleotide variation all at once and we can begin to use comparative genomics to learn how strains differ from one another . Already , we are gaining an unprecedented understanding of the incredible diversity of microorganisms . For Legionella , some of the most important questions WGS can help us answer are : How can we confidently attribute an environmental source to isolates from patients ? How common or rare is a particular strain ? And how dangerous is it ?

CDC maintains extensive culture collections . By sequencing these strains we can actually place the differences we detect among strains isolated from an outbreak within the context of the greater diversity that we now know exists . This information can help us understand if an outbreak strain is something new or unusual . One of the huge benefits of sequencing is that all of the data can be entered into public databases and queried by people all over the world . This greatly improves the value of this information by expanding the knowledge base . Bottom line : WGS gives us information very rapidly that would have taken weeks or months to learn previously .

You have experience using various bioinformatics tools and certifications in Linux , R programming and Python . Is access to bioinformatics expertise necessary to gain the full value of NGS ?

Yes , it is absolutely necessary ! As a microbiologist , I had to learn about bioinformatics tools to keep up with the changes that NGS brings . I am constantly evaluating new tools to determine if they are quicker , more streamlined and likely to perform better . Many of these tools have to be used with a command line interface . I think a lot of microbiologists may be intimidated by the command line . I say , “ Don ’ t fear the command line .” I think it ’ s great . It opens up the prospect of all kinds of new scientific software , most of which is open source , so anyone can use it .

What three pieces of advice would you offer to PHL scientists just now unpacking their laboratory ’ s first Ion Torrent or MiSeq NGS platform ?

The very first thing on the agenda : You should actually speak with local representatives of the instrument manufacturer and get a copy of the manual before your instrument arrives . This will probably save a lot of troubleshooting later .

The second thing : Make a plan right now to deal with data , including how to store , share and back up . Also , come up with a plan to systematically name your files . If you don ’ t think about this now , you ’ re going to have a mountain of data and important data may be hard to retrieve later .