Table 1.
Treponema pallidum subsp. pertenue strains used in this study.
Table 2.
Primers used for the preliminary analysis of a subset of PNG samples.
Table 3.
Primers used for the MLST scheme.
Fig 1.
Sequence alignment of Tp0548 types A through X.
Sequence alignment is for different strains of T. pallidum subsp. pallidum and T. pallidum subsp. pertenue. 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 tp0548 type are as follows: Types A-I:[11]; Type J: [36]; Type K: [17]; Type L: [37]; Type M-N:[38]; Type O:[33]; Type P: [34] Type Q: [35]; Type R,V,W: [5]; Type S-T and X: this work; Type U: [7] Type Q (indicated by *) was originally incorrectly published as Type O; it was renamed in this manuscript.
Fig 2.
Phylogenetic relationships of the tp0548 types.
tp0548 types are shown for T.p. pallidum, T.p. pertenue, and Fribourg Blanc isolates/strains and for PNG samples, as shown in Fig 1. 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 [32].
Fig 3.
Sequence alignment of Tp0136 types A through G from T. pallidum subsp. pertenue isolates and Papua New Guinea samples.
The coordinates in the alignment between nucleotides 223 and 675 in T. pallidum subsp. pertenue strains and Papua Guinea samples are in reference to strain CDC2 in GenBank (Accession No. CP002375.1) as indicated by **. A: Fribourg-Blanc, CDC2; B: Samoa D, Samoa F; C: Gauthier, F: CDC1, Ghana051; D, E, and G: Papua New Guinea samples.
Fig 4.
Sequence alignment of tp0136 type G with Treponema paraluiscuniculi A.
The very unusual sequence (Type G) found in tp0136 from the majority of PNG samples was more closely aligned with the sequence from T. paraluiscuniculi than with the other T.p. pertenue strains (types A-F in Fig 3). The coordinates in the alignment are in reference to T. paraluiscuniculi A strain (Accession No. CP002103) as indicated by **.
Fig 5.
Phylogenetic relationships of the tp0136 typing region.
tp0136 types are shown for T.p. pertenue and Fribourg Blanc isolates and PNG samples; typing designations are as described in Fig 3. 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 [32].
Fig 6.
Sequence alignment of tp0326 typing region.
Sequence alignment of tp0326 types from T. pallidum subsp. pertenue 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.
Fig 7.
Phylogenetic relationships of the tp0326 types.
tp0326 types are shown for T.p. pertenue and Fribourg Blanc isolates and PNG samples; typing designations are as described in Fig 6. 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 [32].
Fig 8.
T. pallidum subsp. pertenue types collected on Lihir Island, Papua New Guinea, from May 2013 and October 2016.
Data for the 194 fully typeable samples are included here, and proportions for each type are shown.
Fig 9.
Phylogenetic analysis of Tp multilocus sequence types.
Multilocus Sequence Types (MLSTs) were defined by sequencing regions of three genes: tp0548, tp0136 and tp0326. 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 [32].