BIMS

Tag: bacterial identification

Whoooo Are You?

by gwilson on Mar.12, 2010, under A Day in the Life...

Crystal panel colorsWhen the CSI television show kicks off each episode with The Who singing “Who are you? Who-ooh Who-ooh?”, I’m often reminded that some of the most satisfying moments in science come when a mystery is solved and we come to understand something that was beyond our knowing.  In the TV show, the discovery is often the identity of a killer.  In the microbiology lab, it is often the identity of a microbe.  Sometimes, that microbe can also be a killer!

The traditional way for identifying bacteria is through completion of a series of biochemical tests conducted using tubes and plates of special growth media.  That was one of the things that drew me to microbiology – instead of trying to provide names to structures penetrated by pins stuck through cat muscles or plant leaves, test results in the micro lab were unambiguously black and white, or at least red and yellow.  I may nothave been sure whether the pin was in the semimembranosus or the pectineus, but I sure could tell the difference between red and yellow!

Today microbiologists still conduct the tests using tubes and plates, especially in the typical college teaching lab.  But the BIMS program is committed to exposing students to the tools that are used in hospitals and research labs to do things more quickly and accurately.  So, once students believe they know the identity of the bacteria they have isolated from nature, we follow up to confirm identity using a rapid ID system like those used in clinical labs.  This approach comes at a cost, but the experience is worth every penny.

There are many to choose from, and those schools exposing students to rapid ID systems typically choose to use either Enterotubes or API strips, which are on the “lower-tech” end of the spectrum.  We have decided to go a bit more high-tech and use the BD-BBL Crystal Rapid ID system.  Students place a colony or two of their purified unknown into the dilution broth and fill all 30 wells with inoculum.  A panel of 30 dehydrated media is snapped into place, enabling the inoculum to rehydrate the media, and the panels are tossed into an incubator overnight.  Ten-digit numerical codes are derived from the results and fed into a computer that spits out an identity.  Most recently, my students have used the panels for identifying bacteria contaminating foods – meats, fresh fruits and vegetables. 

Who are you?  When our students look at their plates of unknown bacteria and ask that question, they will find the answer is easy to determine using Crystal panels.   We fully believe by the time they graduate, BIMS students will be capable of answering the same question for CSI.  All it takes is the right tools, methods, and skills – something we are committed to providing.

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1-2-3’s of IRBs

by gwilson on Aug.07, 2009, under A Day in the Life..., Projects

staph bacitracin mannitoStudents in my Microbiology class this fall have a treat in store.  Instead of disconnected labs to teach the main principles of aseptic technique and identifying bacteria, students in this course are going to learn by doing research.  I have planned five research projects the student research teams will undertake:  conducting an air quality survey of campus buildings, screen fresh vegetables and fruits for E. coli, search for methicillin-resistant Staphylococcus aureus (MRSA) on campus, isolate endospore-formers and their bacteriophage from nature, and have groups design and conduct a research study of their own using the knowledge and skills learned.

One of these represents a first for our students – the MRSA study.  Our plan is to obtain nasal swabs from around 100 students on campus and compare the frequency of Staphylococcus aureus (SA) and MRSA among groups and with previous reports nationally.  Student research groups will collect nasal swabs and screen for SA and MRSA, identifying the most interesting isolates using our BD Crystal(TM) Rapid ID system.  They will analyze the data from a survey of participants and the results from the lab to see if on-campus residents differ in SA/MRSA occurence from off-campus residents, athletes vs. non-athletes, etc.  The results should be interesting!

Because we will be doing research involving human subjects, special approval is required from the campus oversight group:  the Institutional Review Board, or IRB.  Their job is to review proposed campus research to make sure it is ethical, responsible, and conforms to national standards for acceptable scientific research.  It is a first for me, since my lab research is typically environmentally-focused (bacteria don’t have to give informed consent!).    The “homework” required for the IRB is extensive – several federal reports and statutes to review, an online course through NIH for certification of training (yes, I missed a question!), and then a form  that asks all the hard questions needed to insure the research is well-thought, useful, and safe for all.  Reading the prescribed materials, thinking through how the project was structured in light of the training, going through the NIH course, and filling out the form took me the better part of three days. 

This bunny trail has been educational and informative, so much so that I’ll have all the Microbiology students go through the online training before they start the study in late September.  To know the trouble our scientific community goes through to protect the rights and dignity of its individuals is eye-opening and reassuring.  Sometimes things of great educational benefit are not on the main thoroughfares of our courses.  Oh, and ask those college sophomores you know whether they’ve done anything as exciting as this in their science classes!

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