Microbiology Exercises

BWH Microbiology Rotation: Hands-On Exercises

The following exercises are covered in the first month of the rotation for clinical pathology residents. They provide a hands-on learning experience for you to become "re-acquainted" with microbiology. In addition to perfecting your sterile technique and general handling of microorganisms, the exercises are intended to bring you up to speed with many of the tests and organisms you will encounter at the reading bench.

Week 1: Learning (re-learning) microbiological stains.
Residents will perform Gram stains on accessioned sputum samples. You goals are to:

Determine if the specimen is adequate.
Identify organisms on the smear.
Assess whether the pattern of organisms seen reflects oral flora vs. true pathogens.
Follow the work-up of the samples in the microbiology lab.

        In the mycology lab you will perform lactophenol blue and KOH preps on fungal isolates.
        In the parasitology lab you will perform the Kinyoun modified acid fast stain on isolates of
        Nocardia, Rhodococcus and M. avium, and on recently received sputum samples.

Your results will be covered in the weekly teaching session.

Week 2: Antimicrobial Susceptibility Testing.
        Residents will be given 4 isolates each to evaluate by Kirby-Bauer testing. Follow the instructions in
        SOP #171-02 (Antimicrobial Susceptibility Testing) and, as needed SOP #152-03 (identification of
        ESBL), SOP # 151-06 (Identification & reporting of MRSA). In addition, read through the articles
        in the antimicrobial-resistance folder for general background on common molecular mechanisms of
        resistance. You will present your findings on Friday at "Resistance Rounds." Your evaluation should
        include:

Interpretation of the KB results.
Hypothesized genetic mechanisms of resistance, and common means of transmissibility for the given organism.
Comparison of the pattern of resistance with data for that species in the BWH WHONET database.
Proposed course of treatment given the location from which the organism was cultured, and the susceptibility results.

Week 3: Gram negative enterics.
Residents will be given a panel of 8 enteric organisms and different types of media on which to isolate them:

MacConkey Agar
Hektoen Enteric Agar
XLD Agar
TSI or KIA slants.

        The goal is to speciate to the genus level with the above media, and to become familiar with the results seen
        when using the above selective media. Later on you will use the Vitek and API systems for speciation of
        organisms.

Week 4: Gram positive organisms.
        Residents will be given a panel of 8-12 organisms that stain "Gram positive." Over the course of the week you
        will speciate each organism. For fun we usually perform an isolation of motile Bacillus species from
        soil, and cover cell/spore morphology in the identification of pathogenic and non-pathogenic Bacillus species.

In the second month of the rotation residents will be given a panel of unknown specimens containing aerobes, anaerobes, yeasts and fungal species. You will have the resources within the microbiology laboratory to speciate organisms you identify.