On sunspots, click science and molecular iconography

Area of Science:

• Microbiology
• Genetics
• Epidemiology

Background:

• CRISPR-spoligotyping and MIRU-VNTR typing are standard for Mycobacterium tuberculosis genotyping.
• Online tools like SITVIT_WEB and MIRU-VNTRplus aid in genotype family assignment and clustering analysis.
• These methods are crucial for molecular epidemiology of tuberculosis.

Purpose of the Study:

• To critically evaluate the practical aspects and limitations of widely used Mycobacterium tuberculosis genotyping tools.
• To address issues of inadequate (sub)clade assignment and scientifically unsound phylogenies.
• To propose improvements for more accurate and reliable molecular epidemiological studies.

Main Methods:

• Critical essay based on practical application of SITVIT_WEB and MIRU-VNTRplus.
• Analysis of decision rules and methodological options in spoligotyping data analysis.
• Review of limitations in understanding the evolution of targeted genome loci.

Main Results:

• Identified inadequate (sub)clade assignment due to imperfect decision rules in online tools.
• Highlighted outdated methodological options leading to scientifically unsound phylogenies from spoligotyping data.
• Noted confusing terminology, misclassification, and false clustering as significant issues.

Conclusions:

• Current genotyping tools and their application present significant limitations for accurate Mycobacterium tuberculosis classification.
• Improvements in decision rules, terminology, and methodological options are necessary for robust molecular epidemiology.
• Addressing these issues is vital for meaningful scientific discussion and reliable tuberculosis outbreak investigations.