Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis.

Area of Science:

• Genomics
• Molecular Epidemiology
• Microbiology

Background:

• Genome sequencing is crucial for molecular epidemiology, particularly for tracking infectious disease transmission.
• Short sequence reads are typically aligned to a reference strain to identify genetic variations like single nucleotide polymorphisms.

Purpose of the Study:

• To evaluate the impact of reference genome selection on Mycobacterium tuberculosis transmission inferences.
• To determine if the choice of reference strain affects phylogenetic analyses in molecular epidemiology.

Main Methods:

• Alignment of short sequence reads from 162 closely related Mycobacterium tuberculosis lineage 4 isolates.
• Comparison of phylogenetic trees generated using 7 different reference genomes.
• Assessment of single nucleotide polymorphism detection across different reference alignments.

Main Results:

• Phylogenetic trees were largely consistent regardless of the reference genome used.
• Inferences of transmission patterns remained stable with most reference genome choices.
• Only the most divergent reference genomes led to significant deviations in phylogenetic analysis.

Conclusions:

• Reference genome selection has a limited impact on Mycobacterium tuberculosis epidemiological inferences for closely related isolates.
• The choice of reference strain for sequencing can be based on factors beyond strict lineage matching.
• This finding offers flexibility in selecting reference genomes for molecular epidemiology studies of M. tuberculosis.