outbreak

Work has been pretty busy this past week.  This is aside from the fact that I was on holiday last week and my food shopping/sampling schedule for the month is now condensed into 3 weeks instead of 4.  Originally I signed up for this enhanced sampling schedule under the premise that I would be getting help or coverage when I was out on vacations and days off...however, this was changed not long after I said I would do it and now its just me.  No help.  Fuck it though, at least I have a job.

Everyone else at work has been dealing with an E.coli O157 outbreak.  We have gotten a ton of samples sent into our lab.  Stools, isolates and now food even.  Isolates are easy to deal with, we set up biochemicals and send a sample to PCR, which get incubated and then read and run the next day respectively providing an answer.  Stools are a bit more complicated.  We plate them on selective media* and then enrich them in a selective broth and then incubate the both.  A portion of the broth gets sent to PCR, while we pick 3 pools of 5 colonies to send to PCR. When one pool comes up positive we deconstruct it by sending the 5 colonies individually to PCR.  The colony that is positive gets further work up with biochemicals and more PCR before it gets reported out.  If is negative, we pick more colonies (up to 100) before reporting it out as negative.

The food take a bit longer and smells alot more.  It has to be thawed, photographed and cataloged.  Then a portion of it gets stomached in selective enrichment media and incubated overnight at 37 degrees Celsius...this is the smell part.  The next day, we take a portion of this broth and send to PCR.  If it's positive we plate a dilution series of this broth on selective media, pick colonies and then we pick 3 pools of 5 colonies to send to PCR.  When one pool comes up positive we deconstruct it by sending the 5 colonies individually to PCR.  The colony that is positive gets further work up with biochemicals and more PCR before it gets reported out.  Sound familiar?  LOL.  If the broth was negative we repeat the process for the remainder of the food sample.  If it is still negative we report it as negative and wait for the Epidemiologists to get us more, or a different product or to determine that food had nothing to do with the outbreak.   

When we get food in everyone loses their shit.  They run around setting tests up, reading biochemicals and planning the next move.  You can't blame them though.  When food arrives it means people somewhere are really sick or dead possibly.  We are pretty close to nailing the source of this outbreak down though.  My advice is to wash food prep areas, cook your food thoroughly and wash your hands :)  

*(selects for certain organisms, killing the organisms not needed and encouraging growth of the organism that the scientist is looking for)