Objectives A 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 characterise a new clinical isolate, we performed further genome-scale molecular analysis.
Methods The pooled segment genome sequencing method followed by Illumina sequencing was performed.
Results This novel sequence-type contained a unique nucleotide substitution ‘T’ at position 167 and belonged to the SS14-like clade of TPA strains, as determined by phylogenetic analysis. Multi-locus sequence analysis of nine chromosomal loci demonstrated that the X-4 isolate was clustered within a monophyletic group of TPA strains. Whole-genome phylogenetic analysis subsequently corroborated the TPA strain classification of the X-4 isolate and revealed that the isolate was closely 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 might indicate that this gene of the X-4 isolate is likely involved in phase variation events. The length heterogeneity of the poly A/T tracts was lower than the genetic variability of the poly G/C tracts, and all the observed intrastrain variations fell within coding regions.
Conclusion The novel tp0548 sequence-type was determined to belong to a new TPA isolate, X-4. The identification of variable length in homopolymetic tracts (G/C and A/T) could provide a snapshot of the genes that potentially involved in genotype–phenotype variations. These findings provide an unequivocal characterisation for better understanding the molecular variation of this emerging isolate.
- molecular typing
- molecular genetics
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Handling editor Federico Garcia
DL and M-LT contributed equally.
Contributors T-CY conceived the study. DL, M-LT and T-CY designed the study. DL, LL and LiL performed the wet laboratory experiments. DL and H-LZ performed bioinformatics analyses. DL, M-LT and LiL and T-CY performed research and analysed data. LL performed sample collection. DL, M-LT and T-CY wrote the manuscript. All authors read and approved the final manuscript.
Funding This work was supported by the National Natural Science Foundation under grant numbers 81871729, 81772260, 81771312, 81672094, 81471967, 81471231 and 81401749; the Key Projects for Province Science and Technology Program of Fujian under grant number 2018D0014; and the Natural Science Foundation of Fujian Province under grant number 2016J01628.
Competing interests None declared.
Patient consent for publication Not required.
Ethics approval This study was approved by the Ethics Committee of Zhongshan Hospital, Xiamen University, and conformed with the Declaration of Helsinki. Written informed consent was obtained according to institutional guidelines prior to the study. All rabbit experiments strictly followed the parameters outlined by the Institutional Animal Care and Use Committee (IACUC) and were approved by the animal experimental ethics committee of School of Medicine, Xiamen University.
Provenance and peer review Not commissioned; externally peer reviewed.
Data availability statement All data relevant to the study are included in the article or uploaded as online supplemental information. The complete genome sequences of the X-4 isolate were deposited in GenBank under accession number CP040555. The raw data sequences were deposited in the SRA database (BioProject ID: PRJNA544173) under the following BioSample accession number: SAMN11812273.