Enhanced molecular typing of <i>Treponema pallidum</i> identified a new tp0548 Gene type in Shandong, China

Li, Zhen; Xiao, Hailu; Zhao, Wei; Li, Zhongwei; Zheng, Ruisheng; Hou, Jin; Huang, Na; Tian, Haijun

doi:10.1111/apm.12724

Cited by 10 publications

(7 citation statements)

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“…[ 34 ] and the other was incorrectly defined as type O by Li et al et al . [ 35 ] (here re-defined as Q). Analysis of the PNG samples resulted in the identification of two tp0548 genotypes (sequences designated S and T) that had not previously been identified in the literature.…”

Section: Resultsmentioning

confidence: 99%

“…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.…”

Section: Resultsmentioning

confidence: 99%

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Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea

et al. 2017

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BackgroundYaws is a neglected tropical disease, caused by Treponema pallidum subsp. pertenue. The disease causes chronic lesions, primarily in young children living in remote villages in tropical climates. As part of a global yaws eradication campaign initiated by the World Health Organization, we sought to develop and evaluate a molecular typing method to distinguish different strains of T. pallidum subsp. pertenue for disease control and epidemiological purposes.Methods and principal findingsPublished genome sequences of strains of T. pallidum subsp. pertenue and pallidum were compared to identify polymorphic genetic loci among the strains. DNA from a number of existing historical Treponema isolates, as well as a subset of samples from yaws patients collected in Lihir Island, Papua New Guinea, were analyzed using these targets. From these data, three genes (tp0548, tp0136 and tp0326) were ultimately selected to give a high discriminating capability among the T. pallidum subsp. pertenue samples tested. Intragenic regions of these three target genes were then selected to enhance the discriminating capability of the typing scheme using short readily amplifiable loci. This 3-gene multilocus sequence typing (MLST) method was applied to existing historical human yaws strains, the Fribourg-Blanc simian isolate, and DNA from 194 lesion swabs from yaws patients on Lihir Island, Papua New Guinea. Among all samples tested, fourteen molecular types were identified, seven of which were found in patient samples and seven among historical isolates or DNA. Three types (JG8, TD6, and SE7) were predominant on Lihir Island.ConclusionsThis MLST approach allows molecular typing and differentiation of yaws strains. This method could be a useful tool to complement epidemiological studies in regions where T. pallidum subsp. pertenue is prevalent with the overall goals of improving our understanding of yaws transmission dynamics and helping the yaws eradication campaign to succeed.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea

et al. 2017

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“…Interestingly, ECDCT TP0548 subtypes d, f and g were further differentiated using longer PCR products of the TP0548 locus ( Fig 2 ). In fact, there were 19 different ECDCT subtypes of TP0548 identified among 1904 samples tested in several studies (data taken from [ 5 , 18 , 48 , 50 , 53 , 56 , 58 ]. In comparison, among the 191 samples characterized by MLST in this and the previous study [ 21 ], 18 different allelic variants of TP0548 were found.…”

Section: Discussionmentioning

confidence: 99%

“…The remaining 94% of samples belonged to the SS14-like group of TPA strains. A previous analysis of 2,506 clinical samples, which were classified with respect to the Nichols-like or the SS14-like cluster, revealed 177 (7.1%) clinical samples belonged to the Nichols-like cluster of TPA strains [ 18 , 34 , 50 , 53 ]. Data from the present study are therefore in agreement with the meta-analysis of Nichols-like and SS14-like clinical samples.…”

Section: Discussionmentioning

confidence: 99%

Multi-locus sequence typing of Treponema pallidum subsp. pallidum present in clinical samples from France: Infecting treponemes are genetically diverse and belong to 18 allelic profiles

et al. 2018

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Treponema pallidum subsp. pallidum, the causative agent of sexually transmitted syphilis, detected in clinical samples from France, was subjected to molecular typing using the recently developed Multilocus Sequence Typing system. The samples (n = 133) used in this study were collected from 2010–2016 from patients with diagnosed primary or secondary syphilis attending outpatient centers or hospitals in several locations in France. Altogether, 18 different allelic profiles were found among the fully typed samples (n = 112). There were five allelic variants identified for TP0136, 12 for TP0548, and eight for TP0705. Out of the identified alleles, one, seven, and three novel alleles were identified in TP0136, TP0548, and TP0705, respectively. Partial allelic profiles were obtained from 6 samples. The majority of samples (n = 110) belonged to the SS14-like cluster of TPA isolates while 7 clustered with Nichols-like isolates. Patients infected with Nichols-like samples were more often older (p = 0.041) and more often diagnosed with secondary syphilis (p = 0.033) compared to patients infected with SS14-like samples. In addition, macrolide resistance caused by the A2058G mutation was found to be associated with allelic profile 1.3.1 or with strains belonging to the 1.3.1 lineage (p<0.001). The genetic diversity among TPA strains infecting the European population was surprisingly high, which suggests that additional studies are needed to reveal the full genetic diversity of TPA pathogens infecting humans.

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“…In the present study, we found that a tp0548 sequence-type in the clinical isolate X-4 that had not been previously identified through the ECDC or MLST typing system [4,11,17,20,[22][23][24][25][26][27][28][29]. Based on an analysis of an 83-bp region in the tp0548 locus, the phylogenetic tree revealed that this novel sequence-type, "ao", clustered with SS14-like genotypes.…”

Section: Discussionmentioning

confidence: 65%

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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Enhanced molecular typing of Treponema pallidum identified a new tp0548 Gene type in Shandong, China

Abstract: Enhanced molecular typing of Treponema pallidum identified a new tp0548 Gene type in Shandong, China APMIS 125: 937-939

Cited by 10 publications

References 8 publications

Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea

Development of a Multilocus Sequence Typing (MLST) scheme for Treponema pallidum subsp. pertenue: Application to yaws in Lihir Island, Papua New Guinea

Multi-locus sequence typing of Treponema pallidum subsp. pallidum present in clinical samples from France: Infecting treponemes are genetically diverse and belong to 18 allelic profiles

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

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