Week 2 - Finishing up Clinical Microbiology Bench rotations

For Week 2, I've picked up where I left off with bench rotations in Dr. Westblade's microbiology lab, as well as getting a look at clinical consultations with Dr. Spector. On Monday, we started patrolling the halls according to schedule as Dr. Spector touched base with his patients pre- and post- operation. It was heartwarming to see how relieved and happy his patients were, as well as some of the aftercare required for their different surgeries. There were a variety of vases, ranging from breast reductions to burn victims. For the remainder of the week, I was able to sit at the CSF (Cerebral-spinal Fluid), Blood, MALDI and AST (Susceptibility Testing) benches in the Westblade Lab. 

I began at the CSF bench. Here, lab technicians are able to work with CSF samples collected from many different patients, and address concerns related to bacterial growths in said samples. From the CSF, Blood Agar (BAP), Chocolate Agar (CBA) and MacConkey Agar plates were streaked and incubated overnight. Thioglycolate broth was also used to suspend a liquid culture. The next day, visible bacterial growths were quantified and analyzed from each medium to determine the nature of the growth. Based on the technician's analysis, additional tests can be performed to confirm the identity of the organism. To do this, a gram stain is prepared as a preliminary  step. The morphology of the culture is also crucial (and most times very indicative) of the organism present. For instance, an organism that does not grow on a MacConkey plate (which is selective for gram negative bacteria), but grows well on a BAP and CBA is definitely gram positive. Furthermore, small, white, beta hemolytic colonies with these characteristics are indicative of Staphylococcus-genus bacteria. To confirm the organism is Staphylococcus, and to identify Staphylococcus Aureus specifically, biochemical tests (Coagulase) can be used.  The gram stain (which should depict blue, gram positive cocci in clusters) is used validate this observation or to identify different bacteria strains within the same culture. Isolates can also be prepared based on the amount of organisms per plate or as needed for culture workup (i.e. further identification). After a preliminary observation is recorded, the samples are sent to ID via MALDI-tof, and eventually susceptibility testing to determine the best treatment options for the patient. 

On the Bloods bench, a similar procedure is followed, with a few exceptions related to the type of bacteria present on the aforementioned plates. Here, a BCID (or preliminary identification done by an instrument called the BioFire) is obtained that lets technicians know the bacteria strain, but only for commonly identified types (ex. P. Aeruginosa, S. Aureus, E. Coli, etc). Using the BCID and biochemical tests, techs can determine if further identification is needed (via MALDI) or if susceptibility testing is required for strains like Staphylococcus Aureus, which can be methicillin resistant or susceptible. This is also needed for  other organisms where susceptibility can be induced or hindered by the presence of other drugs such as clindamycin or vancomycin. Testing is done using an Epsilometer test (E-test) or D-disk diffusion test. Depending on the result, additional susceptibility testing using a micro scan can be performed. 

At the MALDI bench, I was able to see the sample preparation steps needed to perform identification runs as well as some of the challenges that come with them. Who knew yeast was so difficult to ID?

This was definitely another jam-packed week. Since starting my rotation, I've learned so much- I can (semi-accurately) identify different organisms by genus with just one look. I can't wait to learn more and start working with my own samples soon!

- Taylor D