Low genetic diversity of Treponema pallidum ssp. pertenue (TPE) isolated from patients' ulcers in Namatanai District of Papua New Guinea: Local human population is infected by three TPE genotypes

Abstract

Yaws is an endemic disease caused by Treponema pallidum subsp. pertenue (TPE) that primarily affects children in rural regions of the tropics. The endemic character of yaws infections and the expected exclusive reservoir of TPE in humans opened a new opportunity to start a yaws eradication campaign. We have developed a multi-locus sequence typing (MLST) scheme for TPE isolates combining the previously published (TP0548, TP0488) and new (TP0858) chromosomal loci, and we compared this typing scheme to the two previously published MLST schemes. We applied this scheme to TPE-containing clinical isolates obtained during a mass drug administration study performed in the Namatanai District of Papua New Guinea between June 2018 and December 2019. Of 1081 samples collected, 302 (28.5%) tested positive for TPE DNA, from which 255 (84.4%) were fully typed. The TPE PCR-positivity in swab samples was higher in younger patients, patients with single ulcers, first ulcer episodes, and with ulcer duration less than six months. Non-treponemal serological test positivity correlated better with PCR positivity compared to treponema-specific serological tests. The MLST revealed a low level of genetic diversity among infecting TPE isolates, represented by just three distinct genotypes (JE11, SE22, and TE13). Two previously used typing schemes revealed similar typing resolutions. Two new alleles (one in TP0858 and one in TP0136) were shown to arise by intragenomic recombination/deletion events. Compared to samples genotyped as JE11, the minor genotypes (TE13 and SE22) were more frequently detected in samples from patients with two or more ulcers and patients with higher values of specific TP serological tests. Moreover, the A2058G mutation in the 23S rRNA genes of three JE11 isolates was found, resulting in azithromycin resistance.

Fig 1. Sequence differences between alleles detected among TPE-containing samples from Namatanai, Papua New Guinea.

The S_E22 genotype is highly related to the sequence of TPE Samoa D, a strain isolated initially in Polynesia in 1953 [17] and sequenced later [15]. The T_E allele was divergent from TPE Samoa D and TP0858 allele 3. The TP0858 allele 3 appears to result from the intragenomic reshuffling of the TP0856 locus, a mechanism suggested earlier [18]. The predominant J_E11 genotype resembles the TPE Samoa D sequence except for allele TP0858, which was described as recombinant in the Indonesian TPE strain Kampung Dalan K363 [18]. The numbers above nucleotide positions indicate gene coordinates in the TPE Samoa D.

Fig 2. Geographical locations of detected genotypes in sampled wards in Namatanai, Papua New Guinea.

The map is based on information from 164 participants from the first round. The minor T_E13 genotype was only detected in two neighboring wards in the central part of the sampled Namatanai District and in one patient who was coinfected with both J_E11 and T_E13 genotypes from the northern part. The S_E22 genotype was detected in four individual wards relatively distant from each other. This map was constructed using QGIS 3.28.0, baselayer made with Natural Earth. Free vector and raster map data @ naturalearthdata.com.

Fig 3. Modular structure of TPE TP0858 alleles 1, 2, and 3 from TPE-containing samples from Namatanai, Papua New Guinea.

While TP0858 allele 2 has a modular structure similar to TPE Samoa D, TP0858 allele 1 has a similar modular structure as Kampung Dalan K363 [18]. The TP0858 allele 3 represents a novel allele with a unique modular structure. The arrows denote recombinant regions. The figure was modified according to Strouhal et al. (2018) [18], and an additional donor site is shown. All sequences shown correspond to the Samoa D sequences, while the sequences determined in this study differ in several nucleotide positions. Not all identified donor sites were found among TPE strains and isolates.

Fig 4

A. Modular structure of TPE TP0136 alleles D, E, and U from TPE-containing samples from Namatanai, Papua New Guinea. Both alleles D and E (shown in bold) have identical modular structures with TPE CDC-2, CDC2575, Ghana-051, LMNP-1, and Fribourg-Blanc; however, both alleles D and E differ in several individual nucleotide positions. Allele U (shown in bold) has a different modular structure identical to TPE Samoa D and Gauthier. For comparison, the modular structure of TP0136 from Indonesian TPE strains Kampung Dalan K363 and Sei Geringging K403 and TPA strain SS14 have different modular structures [18]. B. Sequences of individual repeat motifs. Please note that the r0 motif does not repeat in TPE but was found repetitive in TPA TP0136 from a clinical isolate from the Czech Republic (Allelic profile: 18.1.1; [24]). The figure was modified according to Strouhal et al. (2018) [18].