<table><thead><tr><th>Strain</th><th>Accession#</th><th>Year</th><th>Source</th><th>District</th><th>Commune</th><th>Lineage</th></tr></thead><tbody><tr><td>201/07</td><td>SRR4175444</td><td>2007</td><td>Human</td><td>Ambatofinandrahana</td><td>Ambatofinandrahana</td><td>y05</td></tr><tr><td>27/17</td><td>SRS4032734</td><td>2017</td><td>Human</td><td>Manandriana</td><td>Ambohimahazo</td><td>y03</td></tr><tr><td>50/17</td><td>SRS4032746</td><td>2017</td><td>Human</td><td>Ambositra</td><td>Ivato</td><td>y03</td></tr><tr><td>62/09</td><td>SRR4175420</td><td>2009</td><td>Human</td><td>Antanifotsy</td><td>Ambohitompina</td><td>z06</td></tr><tr><td>38/17</td><td>SRS4032757</td><td>2017</td><td>Human</td><td>Mandritsara</td><td>Andratamarina</td><td>α</td></tr><tr><td>55/08</td><td>SRR4175435</td><td>2008</td><td>Human</td><td>Antsirabe II</td><td>Tsarahonenana Sahanivotry</td><td>w02</td></tr><tr><td>67/09</td><td>SRR4175423</td><td>2009</td><td>Human</td><td>Antsirabe II</td><td>Manandona</td><td>t02</td></tr><tr><td>49/17</td><td>SRS4032744</td><td>2017</td><td>Human</td><td>Manandriana</td><td>Ambovombe Centre</td><td>t11</td></tr><tr><td>45/04</td><td>SRR4175421</td><td>2004</td><td>Human</td><td>Antsirabe II</td><td>Manandona</td><td>t11</td></tr><tr><td>12/09</td><td>SRR4175436</td><td>2009</td><td>Human</td><td>Fandriana</td><td>Miarinavaratra</td><td>u03</td></tr><tr><td>145/08</td><td>SRR4175428</td><td>2008</td><td>Human</td><td>Ambatofinandrahana</td><td>Soavina</td><td>h04</td></tr><tr><td>18/06</td><td>SRR4175425</td><td>2006</td><td>Human</td><td>Antsirabe II</td><td>Mangarano</td><td>h10</td></tr><tr><td>46/12</td><td>SRR4175429</td><td>2012</td><td>Human</td><td>Betafo</td><td>Alakamisy Marososona</td><td>h06</td></tr><tr><td>214/07</td><td>SRR4175427</td><td>2007</td><td>Human</td><td>Antsirabe II</td><td>Ambohitsimanova</td><td>h16</td></tr><tr><td>36/17</td><td>SRS4032756</td><td>2017</td><td>Human</td><td>Arivonimamo</td><td>Mahatsinjo Est</td><td>x01</td></tr><tr><td>24/09</td><td>SRR4175438</td><td>2009</td><td>Human</td><td>Faratsiho</td><td>Ramainandro</td><td>x03</td></tr><tr><td>102/06</td><td>SRS4032747</td><td>2006</td><td>Human</td><td>Faratsiho</td><td>Ramainandro</td><td>x03</td></tr><tr><td>09/12</td><td>SRR4175434</td><td>2012</td><td>Human</td><td>Betafo</td><td>Mahaiza</td><td>v03</td></tr><tr><td>30/10</td><td>SRR4175432</td><td>2010</td><td>Human</td><td>Antsirabe II</td><td>Ambohitsimanova</td><td>v06</td></tr><tr><td>95/07</td><td>SRR4175431</td><td>2007</td><td>Human</td><td>Betafo</td><td>Manohisoa</td><td>v13</td></tr><tr><td>197/11</td><td>SRR4175433</td><td>2011</td><td>Human</td><td>Betafo</td><td>Ambohimanambola</td><td>v09</td></tr><tr><td>69/04</td><td>SRR4175430</td><td>2004</td><td>Human</td><td>Mandoto</td><td>Ankazomiriotra</td><td>v10</td></tr><tr><td>CO92<br>(root)</td><td>GCA_001293415.1</td><td>1992</td><td>Human</td><td>N/A</td><td>N/A</td><td>N/A</td></tr></tbody></table>

<table><caption>**Appendix Table 2.** Residual sputum samples from 42 probable or confirmed cases used for *Y. pestis* DNA capture, enrichment, and sequencing*</caption><thead><tr><th>Sputum sample</th><th>District</th><th>Collection date</th><th>RDT result</th><th>Culture result</th><th>PCR (IPM) result</th><th>Case classification</th><th>PCR (NAU) result (Ct)</th></tr></thead><tbody><tr><td>121–2017</td><td>Mahajanga I</td><td>14-Sep-17</td><td>POS</td><td>POS</td><td>POS</td><td>Confirmed</td><td>27.3</td></tr><tr><td>135–2017</td><td>Toamasina I</td><td>15-Sep-17</td><td>POS</td><td>NEG</td><td>POS</td><td>Confirmed</td><td>35.0</td></tr><tr><td>125–2017</td><td>Faratsiho</td><td>16-Sep-17</td><td>POS</td><td>NEG</td><td>POS</td><td>Confirmed</td><td>29.6</td></tr><tr><td>133–2017</td><td>Faratsiho</td><td>16-Sep-17</td><td>POS</td><td>NEG</td><td>POS</td><td>Confirmed</td><td>38.8</td></tr><tr><td>129–2017</td><td>Faratsiho</td><td>16-Sep-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>37.7</td></tr><tr><td>184–2017</td><td>Vohemar</td><td>22-Sep-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.4</td></tr><tr><td>597–2017</td><td>Antananarivo Renivohitra</td><td>10-Oct-17</td><td>NEG</td><td>-</td><td>POS</td><td>Probable</td><td>37.0</td></tr><tr><td>630–2017</td><td>Toamasina I</td><td>11-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.3</td></tr><tr><td>647–2017</td><td>Toamasina I</td><td>11-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>39.8</td></tr><tr><td>653–2017</td><td>Toamasina I</td><td>11-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>37.2</td></tr><tr><td>663–2017</td><td>Toamasina I</td><td>11-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>46.5</td></tr><tr><td>632–2017</td><td>Toamasina I</td><td>11-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.9</td></tr><tr><td>636–2017</td><td>Toamasina I</td><td>11-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>39.3</td></tr><tr><td>641–2017</td><td>Toamasina I</td><td>11-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.5</td></tr><tr><td>666–2017</td><td>Toamasina I</td><td>11-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>36.8</td></tr><tr><td>819–2017</td><td>Antananarivo Renivohitra</td><td>12-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>40.8</td></tr><tr><td>841–2017</td><td>Antananarivo Renivohitra</td><td>12-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>39.0</td></tr><tr><td>843–2017</td><td>Antananarivo Renivohitra</td><td>12-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>37.2</td></tr><tr><td>1100–2017</td><td>Antananarivo Renivohitra</td><td>16-Oct-17</td><td>POS</td><td>NEG</td><td>POS</td><td>Confirmed</td><td>36.1</td></tr><tr><td>1074–2017</td><td>Antananarivo Renivohitra</td><td>16-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>39.7</td></tr><tr><td>1078–2017</td><td>Antananarivo Atsimondrano</td><td>16-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.5</td></tr><tr><td>1115–2017</td><td>Antananarivo Renivohitra</td><td>16-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>37.8</td></tr><tr><td>1002–2017</td><td>Antananarivo Renivohitra</td><td>16-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>37.9</td></tr><tr><td>1006–2017</td><td>Antananarivo Renivohitra</td><td>16-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>39.4</td></tr><tr><td>1015–2017</td><td>Antananarivo Renivohitra</td><td>16-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.8</td></tr><tr><td>1028–2017</td><td>Antananarivo Renivohitra</td><td>16-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.6</td></tr><tr><td>1040–2017</td><td>Antananarivo Renivohitra</td><td>16-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>37.7</td></tr><tr><td>1164–2017</td><td>Antananarivo Renivohitra</td><td>17-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>37.6</td></tr><tr><td>1147–2017</td><td>Antananarivo Renivohitra</td><td>17-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.4</td></tr><tr><td>1237–2017</td><td>Antananarivo Renivohitra</td><td>18-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>37.9</td></tr><tr><td>1307–2017</td><td>Antananarivo Renivohitra</td><td>20-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>37.3</td></tr><tr><td>1470–2017</td><td>Antananarivo Renivohitra</td><td>23-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>37.7</td></tr><tr><td>1468–2017</td><td>Antananarivo Renivohitra</td><td>23-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.0</td></tr><tr><td>1494–2017</td><td>Antananarivo Renivohitra</td><td>24-Oct-17</td><td>NEG</td><td>-</td><td>POS</td><td>Probable</td><td>36.3</td></tr><tr><td>1633–2017</td><td>Antananarivo Renivohitra</td><td>26-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.2</td></tr><tr><td>1659–2017</td><td>Antananarivo Renivohitra</td><td>26-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>39.7</td></tr></tbody></table>

<footnote>*Sequences are ordered as they appear in the phylogeny (Figure 2 in main text) from top to bottom.</footnote>
<table><thead><tr><th>Sputum sample</th><th>District</th><th>Collection date</th><th>RDT result</th><th>Culture result</th><th>PCR (IPM) result</th><th>Case classification</th><th>PCR (NAU) result (Ct)</th></tr></thead><tbody><tr><td>1661–2017</td><td>Antananarivo Renivohitra</td><td>26-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>48.5</td></tr><tr><td>1686–2017</td><td>Antananarivo Renivohitra</td><td>27-Oct-17</td><td>POS</td><td>NEG</td><td>POS</td><td>Confirmed</td><td>38.9</td></tr><tr><td>1762–2017</td><td>Antananarivo Renivohitra</td><td>30-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>48.3</td></tr><tr><td>1866–2017</td><td>Antananarivo Renivohitra</td><td>2-Nov-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.3</td></tr><tr><td>2093–2017</td><td>Antananarivo Renivohitra</td><td>10-Nov-17</td><td>NEG</td><td>-</td><td>POS</td><td>Probable</td><td>39.1</td></tr><tr><td>2152–2017</td><td>Antananarivo Renivohitra</td><td>15-Nov-17</td><td>POS</td><td>NEG</td><td>POS</td><td>Confirmed</td><td>38.2</td></tr></tbody></table>

<table><caption>**Appendix Table 3.** Percent coverage of *Y. pestis* sequencing reads generated from seven enriched samples across the four genomic components of the CO92 reference</caption><thead><tr><th>Enriched sample</th><th>CO92 chromosome (NC_003143.1)</th><th>CO92 plasmid pMT1 (AL117211.1)</th><th>CO92 plasmid pCD1 (AL117189.1)</th><th>CO92 plasmid pPCP1 (AL109969.1)</th></tr></thead><tbody><tr><td>121–2017</td><td>96.11</td><td>40.86</td><td>97.97</td><td>30.23</td></tr><tr><td>125–2017</td><td>95.49</td><td>41.69</td><td>98.37</td><td>32.92</td></tr><tr><td>135–2017</td><td>16.20</td><td>10.81</td><td>46.80</td><td>11.97</td></tr><tr><td>1494–2017</td><td>6.18</td><td>3.10</td><td>7.75</td><td>5.08</td></tr><tr><td>184–2017</td><td>8.65</td><td>5.60</td><td>12.56</td><td>17.27</td></tr><tr><td>2093–2017</td><td>4.26</td><td>1.66</td><td>5.45</td><td>4.44</td></tr><tr><td>819–2017</td><td>8.34</td><td>4.02</td><td>12.98</td><td>5.77</td></tr></tbody></table>

<table><caption>**Appendix Table 4.** Primers, TaqMan®-MGB probes, and annealing temperatures for *Y. pestis* SNP genotyping assays*</caption><thead><tr><th>SNP position in CO92 reference</th><th>Primer sequences (5' to 3')</th><th>Probe sequences (5' to 3')</th><th>Annealing temperature</th></tr></thead><tbody><tr><td>3490108</td><td>F-GATAGGCGTAAGGCATTAAATAATGAC<br/>R-GGTTTATATGCATTCGCTGGTCATTATT</td><td>D-6FAM-CCATAAGCGACACCAT<br/>A-VIC-CCATAAGCGGCACCA</td><td>63</td></tr><tr><td>2297224</td><td>F-TCATACCATCAAGGACGACTGC<br/>R-TTTGTGCTGAACTGGGCGA</td><td>D-6FAM-CTAACATCGTCATTGAA<br/>A-VIC-TAACATCGCCATTGAA</td><td>60</td></tr><tr><td>2275118</td><td>F-GTTGGCGGAACAAGGCTATA<br/>R-CGTGAATATCTTCAATGCGGTAA</td><td>D-6FAM-GTATCAAGGCGTGAGTG<br/>A-VIC-TATCAAGGCGCGAGTG</td><td>60</td></tr><tr><td>2524044</td><td>F-CAATATGGCCATAGGCAGCG<br/>R-GCTGTTACCGGATTTGTCCGT</td><td>D-6FAM-CCATGGAGTTGCCA<br/>A-VIC-CCATGGTGTTGCCA</td><td>60</td></tr><tr><td>2569128</td><td>F-GCCGTGCCAAGCGCTATC<br/>R-AGGCCTTGCCCAGCACTTC</td><td>*D-6FAM-CTGGCTAAAATTGGTGATG<br/>*A-VIC-TCTGGCTAAAATCGGTGAT</td><td>60</td></tr><tr><td>3289728</td><td>F-ACACTTGGAAGAATAACTCATGTACATCAG<br/>R-CTGTGCGCCGTAAGCCATAT</td><td>D-6FAM-TCGATTTCATCTTACAACAC<br/>A-VIC-TCGATTTCATCTAACAACAC</td><td>60</td></tr></tbody></table>

<footnote>*RDT, culture, and initial PCR results were performed on the original sputum samples as detailed in Section 1 above.</footnote>

<footnote>*Annealing temperatures are in C°. F: forward primer; R: reverse primer; D: probe for derived SNP state; A: probe for ancestral SNP state; Red text in probe sequence: SNP state; *: probe designed on the reverse complement</footnote>
<table><thead><tr><th>Sputum sample</th><th>District</th><th>Collection date</th><th>RDT result</th><th>Culture result</th><th>PCR (IPM) result</th><th>Case classification</th><th>PCR (NAU) result (Ct)</th></tr></thead><tbody><tr><td>1661–2017</td><td>Antananarivo Renivohitra</td><td>26-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>48.5</td></tr><tr><td>1686–2017</td><td>Antananarivo Renivohitra</td><td>27-Oct-17</td><td>POS</td><td>NEG</td><td>POS</td><td>Confirmed</td><td>38.9</td></tr><tr><td>1762–2017</td><td>Antananarivo Renivohitra</td><td>30-Oct-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>48.3</td></tr><tr><td>1866–2017</td><td>Antananarivo Renivohitra</td><td>2-Nov-17</td><td>POS</td><td>NEG</td><td>NEG</td><td>Probable</td><td>38.3</td></tr><tr><td>2093–2017</td><td>Antananarivo Renivohitra</td><td>10-Nov-17</td><td>NEG</td><td>-</td><td>POS</td><td>Probable</td><td>39.1</td></tr><tr><td>2152–2017</td><td>Antananarivo Renivohitra</td><td>15-Nov-17</td><td>POS</td><td>NEG</td><td>POS</td><td>Confirmed</td><td>38.2</td></tr></tbody></table>

<table><caption>**Appendix Table 3.** Percent coverage of *Y. pestis* sequencing reads generated from seven enriched samples across the four genomic components of the CO92 reference</caption><thead><tr><th>Enriched sample</th><th>CO92 chromosome (NC_003143.1)</th><th>CO92 plasmid pMT1 (AL117211.1)</th><th>CO92 plasmid pCD1 (AL117189.1)</th><th>CO92 plasmid pPCP1 (AL109969.1)</th></tr></thead><tbody><tr><td>121–2017</td><td>96.11</td><td>40.86</td><td>97.97</td><td>30.23</td></tr><tr><td>125–2017</td><td>95.49</td><td>41.69</td><td>98.37</td><td>32.92</td></tr><tr><td>135–2017</td><td>16.20</td><td>10.81</td><td>46.80</td><td>11.97</td></tr><tr><td>1494–2017</td><td>6.18</td><td>3.10</td><td>7.75</td><td>5.08</td></tr><tr><td>184–2017</td><td>8.65</td><td>5.60</td><td>12.56</td><td>17.27</td></tr><tr><td>2093–2017</td><td>4.26</td><td>1.66</td><td>5.45</td><td>4.44</td></tr><tr><td>819–2017</td><td>8.34</td><td>4.02</td><td>12.98</td><td>5.77</td></tr></tbody></table>

<table><caption>**Appendix Table 4.** Primers, TaqMan®-MGB probes, and annealing temperatures for *Y. pestis* SNP genotyping assays*</caption><thead><tr><th>SNP position in CO92 reference</th><th>Primer sequences (5' to 3')</th><th>Probe sequences (5' to 3')</th><th>Annealing temperature</th></tr></thead><tbody><tr><td>3490108</td><td>F-GATAGGCGTAAGGCATTAAATAATGAC<br/>R-GGTTTATATGCATTCGCTGGTCATTATT</td><td>D-6FAM-CCATAAGCGACACCAT<br/>A-VIC-CCATAAGCGGCACCA</td><td>63</td></tr><tr><td>2297224</td><td>F-TCATACCATCAAGGACGACTGC<br/>R-TTTGTGCTGAACTGGGCGA</td><td>D-6FAM-CTAACATCGTCATTGAA<br/>A-VIC-TAACATCGCCATTGAA</td><td>60</td></tr><tr><td>2275118</td><td>F-GTTGGCGGAACAAGGCTATA<br/>R-CGTGAATATCTTCAATGCGGTAA</td><td>D-6FAM-GTATCAAGGCGTGAGTG<br/>A-VIC-TATCAAGGCGCGAGTG</td><td>60</td></tr><tr><td>2524044</td><td>F-CAATATGGCCATAGGCAGCG<br/>R-GCTGTTACCGGATTTGTCCGT</td><td>D-6FAM-CCATGGAGTTGCCA<br/>A-VIC-CCATGGTGTTGCCA</td><td>60</td></tr><tr><td>2569128</td><td>F-GCCGTGCCAAGCGCTATC<br/>R-AGGCCTTGCCCAGCACTTC</td><td>*D-6FAM-CTGGCTAAAATTGGTGATG<br/>*A-VIC-TCTGGCTAAAATCGGTGAT</td><td>60</td></tr><tr><td>3289728</td><td>F-ACACTTGGAAGAATAACTCATGTACATCAG<br/>R-CTGTGCGCCGTAAGCCATAT</td><td>D-6FAM-TCGATTTCATCTTACAACAC<br/>A-VIC-TCGATTTCATCTAACAACAC</td><td>60</td></tr></tbody></table>

<footnote>*RDT, culture, and initial PCR results were performed on the original sputum samples as detailed in Section 1 above.</footnote>

<footnote>*Annealing temperatures are in C°. F: forward primer; R: reverse primer; D: probe for derived SNP state; A: probe for ancestral SNP state; Red text in probe sequence: SNP state; *: probe designed on the reverse complement</footnote>
<table><caption>Appendix Table 5. *Y. pestis* SNP genotyping calls in seven enriched sputum samples*</caption><thead><tr><th>SNP position in CO92</th><th>TaqMan assay?</th><th>CO92 allele (outgroup, ancestral state)</th><th>Sputum 135-2017 (Case 4)</th><th>Sputum 121-2017 (Case 7; isolate 17/17)</th><th>Sputum 125-2017 (Case 15)</th><th>Sputum 184-2017 (Case 22)</th><th>Sputum 2093-2017</th><th>Sputum 819-2017</th><th>Sputum 1494-2017</th><th>SNP specificity in the phylogeny</th></tr></thead><tbody><tr><td>812303</td><td>NO</td><td>A</td><td></td><td>G (S)</td><td>G (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>2681067</td><td>NO</td><td>A</td><td></td><td>G (S)</td><td>G (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>3490108</td><td>YES</td><td>G</td><td></td><td>A (S/T)</td><td>A (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>4545787</td><td>NO</td><td>T</td><td></td><td>A (S)</td><td>A (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>1902978</td><td>NO</td><td>G</td><td>A (S)</td><td>A (S)</td><td>A (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>2274467</td><td>NO</td><td>G</td><td></td><td>A (S)</td><td>A (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>1539852</td><td>NO</td><td>C</td><td>T (S)</td><td>T (S)</td><td>T (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and some older isolates but no other 2017 isolates</td></tr><tr><td>2297224</td><td>YES</td><td>C</td><td>T (S/T)</td><td>T (S/T)</td><td>T (S/T)</td><td>T (S)</td><td>T (T)</td><td></td><td></td><td>SNP on branch unique to 17/17 in WGS phylogeny</td></tr><tr><td>2275118</td><td>YES</td><td>C</td><td></td><td>T (S/T)</td><td>T (S/T)</td><td></td><td></td><td></td><td></td><td>SNP on branch unique to 17/17 in WGS phylogeny</td></tr><tr><td>2524044</td><td>YES</td><td>T</td><td></td><td>A (S/T)</td><td>A (S/T)</td><td></td><td>A (T)</td><td>T (S/T)</td><td></td><td>SNP on branch unique to 17/17 in WGS phylogeny</td></tr><tr><td>2569128</td><td>YES</td><td>G</td><td></td><td>A (S/T)</td><td>A (S/T)</td><td></td><td></td><td></td><td></td><td>SNP on branch unique to 17/17 in WGS phylogeny</td></tr><tr><td>3289728</td><td>YES</td><td>A</td><td></td><td>T (S/T)</td><td>T (S/T)</td><td></td><td>T (T)</td><td></td><td></td><td>SNP on branch unique to 17/17 in WGS phylogeny</td></tr><tr><td>420544</td><td>NO</td><td>C</td><td></td><td>C (S)</td><td>C (S)</td><td></td><td></td><td>T (S)</td><td></td><td>J group SNP found in all J group isolates in the phylogeny, including multiple 2017 isolates</td></tr><tr><td>2383628</td><td>NO</td><td>T</td><td></td><td>T (S)</td><td>T (S)</td><td></td><td></td><td></td><td>C (S)</td><td>β group SNP found in 2017 isolates 30/17,</td></tr></tbody></table>
<table><caption>Appendix Table 5. *Y. pestis* SNP genotyping calls in seven enriched sputum samples*</caption><thead><tr><th>SNP position in CO92</th><th>TaqMan assay?</th><th>CO92 allele (outgroup, ancestral state)</th><th>Sputum 135-2017 (Case 4)</th><th>Sputum 121-2017 (Case 7; isolate 17/17)</th><th>Sputum 125-2017 (Case 15)</th><th>Sputum 184-2017 (Case 22)</th><th>Sputum 2093-2017</th><th>Sputum 819-2017</th><th>Sputum 1494-2017</th><th>SNP specificity in the phylogeny</th></tr></thead><tbody><tr><td>812303</td><td>NO</td><td>A</td><td></td><td>G (S)</td><td>G (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>2681067</td><td>NO</td><td>A</td><td></td><td>G (S)</td><td>G (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>3490108</td><td>YES</td><td>G</td><td></td><td>A (S/T)</td><td>A (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>4545787</td><td>NO</td><td>T</td><td></td><td>A (S)</td><td>A (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>1902978</td><td>NO</td><td>G</td><td>A (S)</td><td>A (S)</td><td>A (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>2274467</td><td>NO</td><td>G</td><td></td><td>A (S)</td><td>A (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and multiple other 2017 isolates and older isolates</td></tr><tr><td>1539852</td><td>NO</td><td>C</td><td>T (S)</td><td>T (S)</td><td>T (S)</td><td></td><td></td><td></td><td></td><td>S group SNP found in isolate 17/17 and some older isolates but no other 2017 isolates</td></tr><tr><td>2297224</td><td>YES</td><td>C</td><td>T (S/T)</td><td>T (S/T)</td><td>T (S/T)</td><td>T (S)</td><td>T (T)</td><td></td><td></td><td>SNP on branch unique to 17/17 in WGS phylogeny</td></tr><tr><td>2275118</td><td>YES</td><td>C</td><td></td><td>T (S/T)</td><td>T (S/T)</td><td></td><td></td><td></td><td></td><td>SNP on branch unique to 17/17 in WGS phylogeny</td></tr><tr><td>2524044</td><td>YES</td><td>T</td><td></td><td>A (S/T)</td><td>A (S/T)</td><td></td><td>A (T)</td><td>T (S/T)</td><td></td><td>SNP on branch unique to 17/17 in WGS phylogeny</td></tr><tr><td>2569128</td><td>YES</td><td>G</td><td></td><td>A (S/T)</td><td>A (S/T)</td><td></td><td></td><td></td><td></td><td>SNP on branch unique to 17/17 in WGS phylogeny</td></tr><tr><td>3289728</td><td>YES</td><td>A</td><td></td><td>T (S/T)</td><td>T (S/T)</td><td></td><td>T (T)</td><td></td><td></td><td>SNP on branch unique to 17/17 in WGS phylogeny</td></tr><tr><td>420544</td><td>NO</td><td>C</td><td></td><td>C (S)</td><td>C (S)</td><td></td><td></td><td>T (S)</td><td></td><td>J group SNP found in all J group isolates in the phylogeny, including multiple 2017 isolates</td></tr><tr><td>2383628</td><td>NO</td><td>T</td><td></td><td>T (S)</td><td>T (S)</td><td></td><td></td><td></td><td>C (S)</td><td>β group SNP found in 2017 isolates 30/17,</td></tr></tbody></table>
<table><thead><tr><th>SNP position in CO92</th><th>TaqMan assay?</th><th>CO92 allele (outgroup, ancestral state)</th><th>Sputum 135-2017 (Case 4)</th><th>Sputum 121-2017 (Case 7; isolate 17/17)</th><th>Sputum 125-2017 (Case 15)</th><th>Sputum 184-2017 (Case 22)</th><th>Sputum 2093-2017</th><th>Sputum 819-2017</th><th>Sputum 1494-2017</th><th>SNP specificity in the phylogeny</th></tr></thead><tbody><tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>32/17, 33/17, 34/17, 48/17, and 55/17</td></tr></tbody></table>

<footnote>*Colors in the first row and first and last columns correspond to the colors assigned to specific phylogenetic groups in the maximum likelihood phylogeny (Figure 2 in the main text). Blue and yellow colors indicated ancestral and derived state of SNPs, respectively. (S): SNP call from sequencing data only; (T): SNP call from TaqMan data only; (S/T): SNP call from both sequencing and TaqMan data.</footnote>
<table><thead><tr><th>SNP position in CO92</th><th>TaqMan assay?</th><th>CO92 allele (outgroup, ancestral state)</th><th>Sputum 135-2017 (Case 4)</th><th>Sputum 121-2017 (Case 7; isolate 17/17)</th><th>Sputum 125-2017 (Case 15)</th><th>Sputum 184-2017 (Case 22)</th><th>Sputum 2093-2017</th><th>Sputum 819-2017</th><th>Sputum 1494-2017</th><th>SNP specificity in the phylogeny</th></tr></thead><tbody><tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td>32/17, 33/17, 34/17, 48/17, and 55/17</td></tr></tbody></table>

*Colors in the first row and first and last columns correspond to the colors assigned to specific phylogenetic groups in the maximum likelihood phylogeny (Figure 2 in the main text). Blue and yellow colors indicated ancestral and derived state of SNPs, respectively. (S): SNP call from sequencing data only; (T): SNP call from TaqMan data only; (S/T): SNP call from both sequencing and TaqMan data.