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. When you first load your files into MicrobeTrace use the settings (gear) button to select the distance metric (SNPs or TN93) and to enter the initial cut-off value for your pathogen (Link Threshold field).
Once the network is rendered, you can adjust the distance threshold values, making them less or more stringent to look at the effect on your network. The more stringent the threshold, fewer the links. This is done using Global Settings menu; accessed by selecting Settings on the main menu bar in the upper left window. This menu option has three tabs: the Filtering tab, used to modify cut-off values and other features of the network, the Styling tab used to color nodes, links and background, and the Timeline tab, which gives you a time player to track cluster growth over time.
Select Filtering tab, increase or decrease your threshold value using the arrows, and use the mini histogram as a guide. (hovering over bars in the histogram tells you the distance threshold at that point)
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.
| 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 |
- 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