Distance thresholds guidance for various pathogens

The distance threshold (either SNPs or TN93)cut-off in MicrobeTrace is an important factor in determining the composition of the molecular network. This value should be based on apriori knowledge of the pathogen, its mutation rate, as well as the question being asked about the outbreak. The table below is a compilation of suggested starting thresholds for various pathogens based on SME knowledge. These are only guidelines and users should establish the correct threshold based on your specific use-case.

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Pathogen	Distance metric	Cut-off
SARS-CoV-2	SNP	6-16
MPOX	SNP	0-1
HIV	TN93	0.005-0.015
HCV	TN93	0.052
Cyclospora	TN93	0.11
N. Gonorrhoea	SNP	16
HAV	SNP	0
Acinetobacter (CRAB)	SNP	2
N. meningitidis	SNP	35
Group A streptococcus	SNP	20
TB	SNP	5 or 15

References

• MPOX- Pers. Comm : SME deployed to CDC's Mpox response
• SARS CoV-2 Pers. Comm: Assistance with various state PHLs during pandemic response
• N. Gonorrhoea Exploring and Comparing the Structure of Sexual Networks Affected by Neisseria gonorrhoeae Using Sexual Partner Services Investigation and Genomic Data - PubMed (nih.gov)
• https://pubmed.ncbi.nlm.nih.gov/34310528/
• N. meningitidis- Pers. Comm. with SME (VA DOH)
• HAV Pers. Comm. FL DOH
• HCV- Pers. Comm. CDC/NCHHSTP/DVH
• TB - https://journals.asm.org/doi/10.1128/spectrum.00418-24