In-Depth Notes on Automation in Microbiology

Automation in Microbiology

Introduction

• Overview of Automation in Microbiology
  • Not as advanced as other medical disciplines.
  • Recent significant developments.
  • Limited availability of advanced instruments, e.g., MALDI-TOF, Total Lab Automation (TLA).
  • Basic tests (e.g., biochemical tests, Gram stains, colonial morphology) still prevalent in modern labs.
  • Microbiology remains a predominantly hands-on discipline.

Specimen Processing

• Challenges of Automation
  • Varied specimens and identification methods complicate automation.
  • Different streaking techniques for different specimens (e.g., urines).
• Common Specimen Types
  • Urine: one of the most frequently processed specimens.
  • Collection in diverse containers.
• Focus of Automation
  • Mainly targeted at organism identification and Antimicrobial Susceptibility Testing (AST).

Commercial Identification & AST Methods

• Automated Systems
  • Automate basic biochemical testing, results setup, and interpretation.
  • Utilizes spectrophotometry and fluorometry for analysis in identification and AST.

Examples of Automated Systems

• BD Phoenix
• MicroScan WalkAway
• VITEK 2 Compact

Total Laboratory Automation (TLA)

• Functionality of TLA Systems
  • Manage specimen handling, streaking plates, incubation, and digital imaging of cultures.
• Common Systems Available
  • BD Kiestra, FMLA (Biomerieux), WASPLab (Copan).
• Key Features
  • Conveyor/track systems for moving plates.
  • Digital cameras for reading plates.
  • Robotic management for automated processing.

Mass Spectrometry (MALDI-TOF MS)

• Innovation Significance
  • Major leap in microbial identification technology.
  • Utilizes Matrix Assisted Laser Desorption Ionization-Time of Flight approach.
• Process Overview
  • Chemical compounds ionized into charged molecules; measures mass-to-charge ratio (m/z).
  • Minimal organism needed compared to older technologies.
  • Applicable for early identification of infectious diseases from bacteria, viruses, fungi.

MALDI-TOF Operation

• Requirements
  • Pure isolate necessary for reliable results (high scores for accuracy).
  • Formic acid enhances ionization and identification accuracy.
• Limitations
  • Mixed cultures may yield obscure results; high confidence thresholds (90% generally acceptable).
  • Direct spotting from specimens (blood/urine) possible but requires lab validation.

MALDI-TOF Sample Preparation

1. Add matrix solution.
2. Spot target slide with colony (up to 5 days old).
3. Air dry matrix.
4. Load target slides and create spectra.

MALDI-TOF Mechanism

• Process Components
  • Sample ionization by matrix absorption and UV laser pulse.
  • Drift region for mass spectrum generation; results in identification confidence scores for organisms.

Performance Evaluation of MALDI-TOF

• Identification Accuracy
• Comparative studies showing high % species identification accuracy using MALDI vs. traditional biochemical methods.
• Example:
  • 1,371 isolates; conventional vs MALDI-TOF identified 93% matches.
  • 92% identification for Enterobacteriaceae, nonfermenting Gram-negative bacilli 92%, etc.

Downsides to MALDI-TOF

• Technical Challenges
  • Spotting plates relies on skillful technique; prone to concentration errors.
  • Complexity of updated species nomenclature can lead to confusion.
  • Some organisms (e.g., S. pneumoniae, Streptococcus dysgalactiae) may not differentiate effectively due to capsule density.
  • No performance of antimicrobial testing during the process.

Conclusion

• Current Status of Microbiology Automation
  • Recent improvements, yet many technologies hindered by high costs.
  • Basic automation tools (e.g., Vitek, Phoenix) are commonplace.
  • Growing acceptance of MALDI-TOF in labs, despite its limitations.
  • Total Laboratory Automation is projected to form the future direction of microbiology labs.

Learning Check Questions

1. What is the main quality control organism used as a calibration spot for MALDI?
2. What is the CHCA reagent?
3. What is Formic Acid used for?
4. What are some limitations of MALDI?
5. How does MALDI differentiate various organisms, and how are spectra generated?