Molecular strain typing of the yaws pathogen, Treponema pallidum subspecies pertenue

Katz, Samantha S.; Chi, Kai-Hua; Nachamkin, Eli; Danavall, Damien; Taleo, Fasihah; Kool, Jolanda; Addo, Kennedy Kwasi; Ampofo, William; Simpson, Shirley V.; Ye, Tun; Asiedu, Kingsley; Ballard, Ronald C.; Chen, Cheng Y.; Pillay, Allan

doi:10.1371/journal.pone.0203632

Cited by 8 publications

(9 citation statements)

References 37 publications

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“…A subsequently introduced enhanced typing system included a portion of the TP0548 locus 33 . While the enhanced typing system has also been used for the typing of human TPE strains 12 , it did not overcome the difficulties associated with amplification of 60-bp repeats of the arp gene or the uncertainties associated with amplification of three different tpr -subfamily II genes in one single assay, followed by subsequent restriction enzyme analysis 11 . A recently published alternative method for MLST included the widely used TP0548 locus but also two additional loci located in the TP0136 and TP0326 genes 11 .…”

Section: Discussionmentioning

confidence: 99%

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Strain diversity of Treponema pallidum subsp. pertenue suggests rare interspecies transmission in African nonhuman primates

Chuma

Roos

Atickem

et al. 2019

Sci Rep

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In our most recent study, we found that in Tanzania infection with Treponema pallidum (TP) subsp. pertenue (TPE) is present in four different monkey species. In order to gain information on the diversity and epidemiological spread of the infection in Tanzanian nonhuman primates (NHP), we identified two suitable candidate genes for multi-locus sequence typing (MLST). We demonstrate the functionality of the MLST system in invasively and non-invasively collected samples. While we were not able to demonstrate frequent interspecies transmission of TPE in Tanzanian monkeys, our results show a clustering of TPE strains according to geography and not host species, which is suggestive for rare transmission events between different NHP species. In addition to the geographic stability, we describe the relative temporal stability of the strains infecting NHPs and identified multi-strain infection. Differences between TPE strains of NHP and human origin are highlighted. Our results show that antibiotic resistance does not occur in Tanzanian TPE strains of NHP origin.

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Section: Discussionmentioning

confidence: 99%

“…10 , subtype composition. Two recent studies suggested new typing systems for human yaws 11,12 . It was unclear though, whether the existing molecular typing systems for TPA or TPE of human origin can be applied to TP strains originating from NHPs.…”

Section: Introductionmentioning

confidence: 99%

Strain diversity of Treponema pallidum subsp. pertenue suggests rare interspecies transmission in African nonhuman primates

Chuma

Roos

Atickem

et al. 2019

Sci Rep

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“…In recent times, methods for differentiating T. pallidum subspecies have been developed. These include a real-time PCR assay, nested PCR, a combination of PCR/RFLP analysis, and sequencing analysis [ 44 , 45 , 46 , 47 , 48 , 49 , 50 ]. Since some yaws variants harbor a primer binding-site mutation, which tends to yield false-negative PCR results, molecular diagnosis in such a case should employ primers that are targeted towards highly conserved regions [ 47 ].…”

Section: Resultsmentioning

confidence: 99%

A Systematic Review on Suitability of Molecular Techniques for Diagnosis and Research into Infectious Diseases of Concern in Resource-Limited Settings

Yalley

Ahiatrogah

Kafintu-kwashie

et al. 2022

CIMB

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Infectious diseases significantly impact the health status of developing countries. Historically, infectious diseases of the tropics especially have received insufficient attention in worldwide public health initiatives, resulting in poor preventive and treatment options. Many molecular tests for human infections have been established since the 1980s, when polymerase chain reaction (PCR) testing was introduced. In spite of the substantial innovative advancements in PCR technology, which currently has found wide application in most viral pathogens of global concern, the development and application of molecular diagnostics, particularly in resource-limited settings, poses potential constraints. This review accessed data from sources including PubMed, Google Scholar, the Web of Knowledge, as well as reports from the World Health Organization’s Annual Meeting on infectious diseases and examined these for current molecular approaches used to identify, monitor, or investigate some neglected tropical infectious diseases. This review noted some growth efforts in the development of molecular techniques for diagnosis of pathogens that appear to be common in resource limited settings and identified gaps in the availability and applicability of most of these molecular diagnostics, which need to be addressed if the One Health goal is to be achieved.

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“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted December 16, 2019. ; https://doi.org/10.1101/2019.12.16.877886 doi: bioRxiv preprint tp0548 locus (nucleotides 130-212 according to tp0548 in the Nichols strain genome [AE 000520.1]) with published data, including a known TPA pattern and a known TPE pattern in silico, showed that the tp0548 genotype in the X-4 isolate was novel. The known tp0548 genotypes (a-ak) were assigned in a unique list containing TPA strains and TPE strains [20][21][22], and three other tp0548 genotypes of TPA strains were recently published: two were defined as type "r" and "s" by Grillová el al. [11], and one was defined as type "y" by Kumar et al [23].…”

Section: Classification Of the X-4 Isolatementioning

confidence: 99%

Characterization of the novel clinical isolate X-4 containing a newtp0548sequence-type

Liú

Tong

Liu

et al. 2019

Preprint

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BackgroundA novel tp0548 sequence-type was identified in one clinical isolate (X-4) from a patient diagnosed with primary syphilis in Xiamen, China. To precisely define and characterize this new clinical isolate, we performed further genome-scale molecular analysis. Methodology/Principal findingsThe alignment of all published tp0548 genotypes revealed that this new genotype had a unique nucleotide substitution G->T at position 167, and the letter "ao" was assigned to the genotype. Phylogenetic analysis showed that the "ao" genotype belonged to the SS14-like clade of Treponema pallidum (TPA) strains. The genome of the X-4 isolate was then sequenced and analyzed, and the result of a multi-locus sequence analysis using a set of nine chromosomal loci showed that the X-4 isolate was clustered with a monophyletic group of TPA strains, which clearly identified the isolate as a TPA strain.Whole-genome phylogenetic analysis was subsequently conducted to corroborate the TPA strain classification of the X-4 isolate. And the isolate was genetically related to the SS14 strain, with 42 single nucleotide variations and 12 insertions/deletions. In addition, high intrastrain heterogeneity in the length of the poly G/C tracts was found in the TPAChi_0347 locus, which indicated that this gene was most likely involved in phase variation events. The first investigation of the length heterogeneity of the poly A/T tracts showed the variability of the ploy A/T was lower, and all the observed intrastrain variations fell within coding regions. Conclusions/Significance 3The study demonstrated the X-4 isolate was a TPA isolate containing a novel tp0548 sequence-type. The identification of intrastrain genetic heterogeneity at poly G/C tracts and poly A/T tracts of the isolate could provide a snapshot of the genes that potentially involved in genotype-phenotype variations. These findings provide an unequivocal characterization for better understanding the molecular variation of this emerging isolate. 4 Author summaryThree subspecies of Treponema pallidum (pallidum, pertenue, and endemicum) are increasingly showing overlap in terms of transmission and clinical manifestations. We recently identified a novel tp0548 genotype in the X-4 isolate, which was obtained from an adult male with genital lesions. The novel genotype contained a unique nucleotide substitution G->T at position 167 and belonged to the SS14-like clade of TPA strains, as determined by phylogenetic analysis. We conducted an in-depth exploration of the genome of the X-4 isolate using the pooled segment genome sequencing method followed by Illumina sequencing. Multi-locus sequence analysis of nine chromosomal loci demonstrated that the X-4 isolate was clustered within a monophyletic group of TPA strains, which identified the isolate as a TPA strain. Whole-genome phylogenetic analysis subsequently corroborated the TPA strain classification of the X-4 isolate and revealed that the isolate was very closely related to the SS14 strain, with 42 single nucleotide variations and 12 inserti...

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Molecular strain typing of the yaws pathogen, Treponema pallidum subspecies pertenue

Cited by 8 publications

References 37 publications

Strain diversity of Treponema pallidum subsp. pertenue suggests rare interspecies transmission in African nonhuman primates

Strain diversity of Treponema pallidum subsp. pertenue suggests rare interspecies transmission in African nonhuman primates

A Systematic Review on Suitability of Molecular Techniques for Diagnosis and Research into Infectious Diseases of Concern in Resource-Limited Settings

Characterization of the novel clinical isolate X-4 containing a newtp0548sequence-type

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