Week 3: Allison [A Dishing of Microbiology]

     It was a dark and stormy day in Chelsea. As Dr. Glesby bent over the exam table, using gloved hands and mint green Q-tipped swabs to take samples from the unmentionables of patients, he explained to me the risk of uncontrolled HIV. 

    HIV is a retrovirus; within the helper T-cell (CD4+)  the HIV RNA integrates into the host cell's DNA. As the cell's genes become activated, new copies of the virus are produced using the host's cellular machinery. Medical professionals can get a reading on this by measuring the viral load, the amount of RNA copies detected in a milliliter of blood plasma. As the HIV infection continues, the number of CD4+ helper T-cells decreases, disarming the body's ability to coordinate the immune system and attack infections.  At low CD4 counts within 100s range, HIV patients become at risk for rare bacterial infections, viruses, and cancers that wouldn't be a cause for concern in high CD4+ count individuals. Medical professionals call these opportunistic infections. This is why Dr. Glesby was so diligent in ensuring the vaccinations and antibiotic medications of his at-risk patients as well as swabbing them for potential microbiology samples. 

    At this point, I interjected. "Would it be possible for me to see what happens with the swabs after you take samples?” Dr. Glesby said he’d see what he could do. That very night, I received an email from Dr. Lars Westblade who had invited me to follow along the microbiology rounds in the pathology department. Dr. Glesby had reached out on my behalf. He was, after all, a very good doctor and very dedicated to instructing students like myself! 

    The next day, I made my way across the street to the microbiology department, and donned myself in PPE to begin rounds. Dr. Westblade was an English gentleman with salt-pepper hair and thick rimmed glasses. In the past, he worked in Industry at Emeryville, expressing therapeutic agents from yeast but had since then transitioned to his role at Weill Cornell Medical Center. Wearing a pristine lab coat and well fitting gloves, he led residents and us summer students to each station and the plates - chocolate, blood, and MacConkey agar - to gain some visual recognition. 

    The main microbiology lab was divided into three stations: blood, stool/urine, and respiratory. Over by the far end of the room at the blood station, Dr. Westblade explained how the bacteria in blood samples taken in the clinic are incubated and then cultured on agar plates before checking each one for visual morphologies, colors, scents, and changes in the agar color. For example, a strain of Streptococcus anginosus could be identified by the scent of caramel in the air, its ability to break down blood in the blood agar, and many other features that Dr. Westblade would quiz the pathology residents on as we continued to walk to the next stations.  He acknowledged that most diagnotics nowadays are performed using MALDI mass spectroscopy to identify surface protein on the cell coat of the bacteria withholding a few exceptions. 

    "And yet, some fields hadn't changed at all," he told us as we walked into the fungal and yeast station. He pulled out a thick book full of diagrams. "The field of fungal identification in microbiology hasn't changed for 100 years, and that is because the fruiting bodies of the fungus are incredibly distinct and identifiable." And once again, it was a great change fastforwarding back to the present after a dip into microbiology's fungal past as we descended past what locals called the pet graveyard to the Covid-19 testing facilities below. 

    In the peak of the pandemic, technicians described, the high throughput covid instruments used to test where run 24/7 and carefully managed by an around the clock shift of technologists and anyone who graduated with some type of biology degree that could be trained. But it was quieter now, with only 80 tests run a day in comparison to the thousands that piled up last summer. Thinking not only about the high throughput instruments but also the mRNA vaccines, I was appreciative of the need for innovative engineering products that could do so much to save lives. I only hope we can continue to improve their functionality in the future.    

That night, the rain poured down and the subways flooded but the next day was bright and sunny as things should be when its summer in the city. 

    To Be Continued!

Fig 1. Aspergillus Niger originating from bronchial wash of cancer patient
Fig 2. Unidentified fungus originating from bronchial wash 
Fig 3,4. Two high throughput PCR for Covid-19 testing.

  

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