Tour a Fully-Automated Clinical Microbiology Lab

Summary

Join Andrea Howard on a tour of the University of Rochester Medical Center's clinical microbiology lab, where diagnostic testing identifies infectious microorganisms. Learn about rapid antigen detection, PCR, automated microbiology, and AST for guiding antibiotic choices. Explore the role of clinical microbiology in patient care, including allergy testing, viral load monitoring, and COVID-19 diagnostics.

Takeaways

• 🔬 Clinical microbiology laboratories are crucial for patient care by identifying microorganisms causing infections.
• 🏥 The UR Medicine lab performs tests in bacteriology, virology, immunology, mycology, parasitology, serology, and mycobacteriology.
• 🧪 Specimens are received from various hospitals, logged, and sorted by sample type before testing.
• ⏱️ STAT tests, requiring rapid results, include detection for malaria, Legionella, and streptococcus pneumonia.
• 💉 Automated systems like the Keystra and Cepheid are used for culture growth, sample processing, and rapid diagnostics.
• 🔎 Bacterial identification is conducted using mass spectrometry and antimicrobial susceptibility testing (AST) to guide treatment.
• 🦠 PCR and multiplex systems are used for detecting viral, bacterial, and parasitic pathogens, including those causing gastrointestinal and sexually transmitted infections.
• 🧬 The laboratory also processes serological tests for diseases like syphilis, hepatitis, HIV, and autoimmune disorders.
• ⚗️ Mycology tests are performed to identify fungal infections through macroscopic and microscopic examination.
• 👩‍🏫 The lab trains medical technology students, fellows, and pathology residents, contributing to clinical microbiology education.

Q & A

What is the primary role of a clinical microbiology laboratory?

The primary role of a clinical microbiology laboratory is to detect, isolate, and identify microorganisms that cause infections to aid clinicians in diagnosing and managing patients with infectious diseases and immunological disorders.

What types of diagnostic testing are performed at UR Medicine’s clinical microbiology laboratory?

The laboratory performs bacteriology, immunology, mycobacteriology, mycology, parasitology, serology, and virology testing.

What is a STAT test, and why is it important?

A STAT test is a test with a quick turnaround time, generally less than one hour. It is important because results are urgently needed for immediate patient care and treatment decisions.

What is the purpose of the Cepheid PCR system in the lab?

The Cepheid PCR system is used to detect nucleic acid targets for bacterial and viral pathogens, including Mycobacterium tuberculosis, Staphylococcus aureus, Streptococcus pyogenes, and viruses like COVID-19, influenza, and RSV. It also detects antibiotic resistance markers such as methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacteriaceae.

How does the Keystra automated microbiology system improve traditional microbiology methods?

The Keystra system automates processes traditionally done manually, such as specimen processing, culture inoculation, and colony isolation on agar plates. It streamlines high-volume sample handling by using conveyor belts and automated tracking, improving efficiency and accuracy.

What is the role of technologists at the 'reader' and 'worker' benches in the bacteriology lab?

Technologists at the reader benches evaluate microbial growth on agar plates to identify potential pathogens. Those at the worker benches perform further workup of suspicious colonies for bacterial identification using mass spectrometry.

How is antimicrobial susceptibility testing (AST) conducted in the laboratory?

AST is conducted using automated systems like the Phenix AST system, which inoculates panels with a standardized inoculum of an organism to detect bacterial growth in the presence of various antibiotics. Manual AST methods, such as broth microdilution and diffusion assays, are also used for certain organisms and drug combinations.

What is the significance of performing AST in clinical microbiology?

AST guides clinicians in selecting the appropriate antibiotics for infections, helping to ensure effective treatment. It also contributes to antimicrobial stewardship by helping develop antibiograms, which summarize the susceptibility patterns of common isolates in a particular hospital.

What kind of tests are performed using the BD Max system in the laboratory?

The BD Max system is used for detecting gastrointestinal pathogens using multiplex PCR. It differentiates between viral, bacterial, and parasitic causes of infectious diarrhea, identifying pathogens such as Salmonella, Shigella, Campylobacter, norovirus, adenovirus, astrovirus, Giardia, Cryptosporidium, and Entamoeba histolytica.

What types of specimens are processed for sexually transmitted infection (STI) testing in the lab?

STI testing is performed on urine specimens, vaginal, rectal, and throat swabs for nucleic acid detection of pathogens such as gonorrhea, chlamydia, Trichomonas vaginalis, and Mycoplasma genitalium.

How are fungal infections diagnosed in the mycology section of the laboratory?

Fungal infections are diagnosed by processing patient samples for the growth of yeast and molds on agar plates. Molds are identified based on the macroscopic appearance of growth and microscopic examination of fungal structures.

What kind of testing is performed using the Architect system in the serology and immunology section?

The Architect system is used for detecting antibodies and antigens for various infections, including syphilis, hepatitis A, B, and C, and for fourth-generation HIV testing, which combines antibody and antigen detection for early identification of HIV infection.

What is the purpose of the Quantiferon assay in the laboratory?

The Quantiferon assay is used to diagnose tuberculosis (TB) infection by detecting immune responses to TB-specific antigens in a patient’s blood sample.

What are some of the professional career fields represented among the laboratory staff?

The laboratory staff includes technicians with two-year associate degrees, technologists with four-year bachelor’s degrees, and doctoral-level directors with postdoctoral training in clinical microbiology.

What role do clinical microbiologists play besides performing laboratory testing?

Clinical microbiologists serve as educators and consultants. They train medical technology students, postdoctoral fellows, and pathology residents, preparing them to join clinical microbiology and public health labs in the future.