MIDI Sherlock™ Microbial Identification System with E-FAME Methods

Importance of the Topic

The rapid and reliable identification of bacteria and yeast is essential across clinical diagnostics, pharmaceutical quality control, food safety, environmental monitoring and biodefense. Gas chromatographic analysis of fatty acid methyl esters (FAMEs) offers a standardized, high‐throughput approach that reduces operator variability and accelerates decision‐making in microbial workflows.

Objectives and Study Overview

This specification sheet presents the Sherlock™ Microbial Identification System enhanced by E‐FAME methods. The goal is to automate microbial identification by combining robust sample preparation, pattern‐recognition software, extensive reference libraries and integration with Agilent Technologies GC platforms and ChemStation software.

Methodology and Instrumentation

The Sherlock E‐FAME workflow involves:

• Pure culture subculture: a single colony incubated for 24–48 hours depending on growth rate.
• Sample preparation: a three‐step liquid–liquid extraction and heat block reaction completed in under 3 minutes per sample, yielding FAME derivatives.
• GC analysis: vials loaded into an autosampler for unattended injection. Typical throughput is six samples per hour on Agilent 6850 or single‐channel 7890 Series GCs.
• Data processing: Sherlock software performs pattern matching against calibrated FAME libraries and offers optional modules for clustering, trend analysis, DNA sequence integration and 21 CFR Part 11–compliant electronic records.

Key Results and Discussion

No manual calibration is required because Sherlock’s pattern‐recognition algorithms use an internal calibration standard. Users without chromatographic expertise can achieve consistent identifications. The E‐FAME libraries cover over 500 species, including Environmental Aerobes (240 entries) and Clinical Aerobes (267 entries), plus selected yeast, fungal and anaerobic strains. Per‐sample reagent cost is approximately USD 6, excluding culture media. Software visualization tools (dendrograms, PCA plots, neighbor‐joining trees) and data‐export capabilities support research and quality‐control reporting.

Benefits and Practical Applications

The Sherlock E‐FAME system delivers:

• High throughput and rapid turnaround: sample prep under 20 minutes; six analyses per hour.
• Low cost per sample and minimal training requirements.
• Comprehensive automation: from FAME derivatization to GC run and library matching.
• Flexible software modules: contamination tracking (Tracker/Cluster), custom library generation, DNA‐based identification and polyphasic reporting.
• Regulatory compliance: audit trails, electronic signatures and secure data vaults.

Instrumentation Used

• Sherlock system on Windows® 7 Pro or XP Pro PC with MIDI Sherlock and Agilent ChemStation software.
• Agilent 6850 Series GC (29 kg; operating range 15–35 °C; 5–95% RH) or 7890 Series GC (49 kg; same conditions).
• Autosampler with 27-vial tray for uninterrupted sequence runs.

Future Trends and Applications

Emerging directions include integration of machine‐learning algorithms for improved pattern recognition, expansion of reference libraries to cover rare and newly described taxa, miniaturized and portable GC systems for field use, cloud‐based data sharing and integration with multiomics platforms to achieve holistic microbial phenotyping.

Conclusion

The Sherlock Microbial Identification System with E‐FAME methods provides a turnkey solution for automated, reproducible and cost‐effective microbial identification. Its combination of rapid sample preparation, robust GC analysis, integrated software modules and extensive libraries meets the diverse needs of modern analytical laboratories.