Multiple emm Hits Detected in emmtyper Output – Consistent Pairing Observed

[Daniel-VM]

Hello, I ran emmtyper using a Singularity image and noticed that while most predicted emm types have a single hit, a few output two hits. See the examples below. Additionally, these pairs of emm hits consistently appear together. I haven't found an explanation for this in the documentation—does anyone know why this happens?

EMM49.3;EMM141.3;
(EMM6.0)(EMM6.125);
EMM89.0;EMM203.4
EMM141.2;EMM11.0

Command:

singularity exec \\
--bind ${scratch_dir} \\
--bind ${scratch_dir}/../../ \\
--bind \$blastdb_path \\
singularity-emmtyper.0.2.0--py_0 emmtyper \\
-w blast \\
--keep \\
--blast_db "\${blastdb_path}/cdc_emm_database" \\
--percent-identity 100 \\
--culling-limit 5 \
--output 01-typing/results_emmtyper.out \\
--output-format verbose \\
./fasta_inputs/*.fa

[erinyoung]

Out of ~700 S. pyogenes isolates that we've sequenced 2023-2024, ~20 had multiple emm types. When we re-isolated and re-sequenced the multiple emm-type isolates, they only had one. In my case, the assumption is that it's a mixed isolate.