Primers used for the preliminary analysis of a subset of PNG samples.

<p>Primers used for the preliminary analysis of a subset of PNG samples.</p

Phylogenetic relationships of the <i>tp0136</i> typing region.

<p><i>tp0136</i> types are shown for <i>T</i>.<i>p</i>. <i>pertenue</i> and Fribourg Blanc isolates and PNG samples; typing designations are as described in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.g003" target="_blank">Fig 3</a>. Sequences were first aligned using the Muscle algorithm, using default parameters. The evolutionary history was inferred using the Neighbor-Joining method. The optimal tree is shown, with branch lengths equivalent to the evolutionary distance as indicated by the scale. Evolutionary distance was measured using the number of differences per sequence, with pairwise deletion of gaps. The percentage of replicate trees in which the associated molecular types clustered together in the bootstrap test (1000 replicates) is shown next to the branches. Analyses were conducted in MEGA version 7.0 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref032" target="_blank">32</a>].</p

Sequence alignment of <i>tp0326</i> typing region.

<p>Sequence alignment of <i>tp0326</i> types from <i>T</i>. <i>pallidum</i> subsp. <i>pertenue</i> isolates and Papua New Guinea samples. Nucleotide numbering between 2031and 2342 in the alignment refers to coordinates in strain CDC2 in GenBank (Accession No. CP002375.1) as indicated by **. The sequences between coordinates 2117 and 2297 are conserved in all strains examined. 1: Samoa D, Samoa F; 2: Gauthier; 3: Ghana051, CDC1; 4: CDC2; 5: Fribourg-Blanc; 6–8: Papua New Guinea samples.</p

Phylogenetic relationships of the <i>tp0326</i> types.

<p><i>tp0326</i> types are shown for <i>T</i>.<i>p</i>. <i>pertenue</i> and Fribourg Blanc isolates and PNG samples; typing designations are as described in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.g006" target="_blank">Fig 6</a>. Sequences were first aligned using the Muscle algorithm, using default parameters. The evolutionary history was inferred using the Neighbor-Joining method. The optimal tree is shown, with branch lengths equivalent to the evolutionary distance as indicated by the scale. Evolutionary distance was measured using the number of differences per sequence, with pairwise deletion of gaps. The percentage of replicate trees in which the associated molecular types clustered together in the bootstrap test (1000 replicates) is shown next to the branches. Analyses were conducted in MEGA version 7.0 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref032" target="_blank">32</a>].</p

Primers used for the MLST scheme.

<p>Primers used for the MLST scheme.</p

<i>Treponema pallidum</i> subsp. <i>pertenue</i> strains used in this study.

<p><i>Treponema pallidum</i> subsp. <i>pertenue</i> strains used in this study.</p

Phylogenetic analysis of <i>Tp</i> multilocus sequence types.

<p>Multilocus Sequence Types (MLSTs) were defined by sequencing regions of three genes: <i>tp0548</i>, <i>tp0136</i> and <i>tp0326</i>. Concatenated sequences were first aligned using the Muscle algorithm, using default parameters. The evolutionary history of the MLSTs was inferred using the Neighbor-Joining method. The optimal tree is shown, with branch lengths equivalent to the evolutionary distance as indicated by the scale. Evolutionary distance was measured using the number of differences per sequence, with pairwise deletion of gaps. The percentage of replicate trees in which the associated molecular types clustered together in the bootstrap test (1000 replicates) is shown next to the branches. Analyses were conducted in MEGA version 7.0 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref032" target="_blank">32</a>].</p

Sequence alignment of <i>Tp0548</i> types A through X.

<p>Sequence alignment is for different strains of <i>T</i>. <i>pallidum</i> subsp. <i>pallidum</i> and <i>T</i>. <i>pallidum</i> subsp. <i>pertenue</i>. The coordinates of nucleotides 130–212 shown above the alignment are based on the Nichols strain genome (AE 000520.1) as indicated by **. Published reference sequences for each <i>tp0548</i> type are as follows: Types A-I:[<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref011" target="_blank">11</a>]; Type J: [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref036" target="_blank">36</a>]; Type K: [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref017" target="_blank">17</a>]; Type L: [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref037" target="_blank">37</a>]; Type M-N:[<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref038" target="_blank">38</a>]; Type O:[<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref033" target="_blank">33</a>]; Type P: [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref034" target="_blank">34</a>] Type Q: [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref035" target="_blank">35</a>]; Type R,V,W: [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref005" target="_blank">5</a>]; Type S-T and X: this work; Type U: [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.ref007" target="_blank">7</a>] Type Q (indicated by *) was originally incorrectly published as Type O; it was renamed in this manuscript.</p

Sequence alignment of <i>tp0136</i> type G with <i>Treponema paraluiscuniculi</i> A.

<p>The very unusual sequence (Type G) found in <i>tp0136</i> from the majority of PNG samples was more closely aligned with the sequence from <i>T</i>. <i>paraluiscuniculi</i> than with the other <i>T</i>.<i>p</i>. <i>pertenue</i> strains (types A-F in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006113#pntd.0006113.g003" target="_blank">Fig 3</a>). The coordinates in the alignment are in reference to <i>T</i>. <i>paraluiscuniculi</i> A strain (Accession No. CP002103) as indicated by **.</p

Linkage disequilibrium between 8 markers (MS2, MS7, MS9, MS10, MS12, MS15, MS16, MS20) determined by LIAN software.

a<p>Linkage in Sigimaru was not significant if only unique haplotypes were analyzed (11 samples, <i>I_A^S</i> = 0.0037, <i>P</i> = 0.400.</p