Category Archives: Genomics

The Clinical And Bioinformatic CTX-M Problem

We’ll get to what CTX-M is in a bit, but first some biology background. Let’s talk about some game theory carbapenem antibiotics (also referred to as carbapenems): Before we get started, let’s do a quick biology review. A serious health … Continue reading

Posted in Antibiotics, Genomics, KPC | Leave a comment

PacBio Finally Makes A Move It Desperately Needed To Make

While everyone hunts for the Holy Grail of human genomic sequencing (and other large genome critters), I’ve noted before there’s an obvious, if less sexy, market: …microbial genomes are cheap, fast, and you can provide epidemiological relevant information to clinical … Continue reading

Posted in Genomics | 5 Comments

A Failure Of Data Transmission: The CRE Edition

There’s a very interesting article that came out recently describing the first public report of carbapenem resistance in E. coli from the U.S. food supply. Maryn McKenna provides a good overview: Bacteria containing a gene that confers resistance to a … Continue reading

Posted in Antibiotics, Data Stuff, Genomics | 1 Comment

Prospective Bacterial Genomic Surveillance

One of the things the evul federal gummint is gearing up to every food borne bacterial disease isolate that is sent to either the CDC or public health labs in what is known as the GenomeTrakr Network (I’ve heard this … Continue reading

Posted in E. coli, Food, Genomics, Public Health

Bacterial Whole Genome Sequencing And The Clinic: The Future Is Almost Here

I heard this talk almost a year ago*, so I’m glad this paper is finally out (I’ll translate into English below; boldface mine): The increasing prevalence of multidrug-resistant (MDR) bacteria is a serious global challenge. Here, we studied prospectively whether … Continue reading

Posted in Antibiotics, E. coli, Genomics, KPC, MRSA, NDM-1, Public Health | 1 Comment

Barriers To Data Sharing

I’ve made this point about the role of funders before, but Fiona Nelson is absolutely right (boldface mine): Genomics is a data science. The human genome is vast – 3 billion base pairs. To make any significant findings from the … Continue reading

Posted in Data Stuff, Funding, Genomics

Just As We’re Getting Good At Genomic Surveillance…

…we run into a problem. From Morbidity and Mortality Weekly Report (what you don’t read it? Loser. Boldface mine): To evaluate progress toward prevention of enteric and foodborne illnesses in the United States, the Foodborne Diseases Active Surveillance Network (FoodNet) … Continue reading

Posted in Genomics, Public Health