Characterisation of the novel clinical isolate X-4 containing a new tp0548 sequence-type

Author:

Liu Dan,Tong Man-Li,Liu Li-Li,Lin Li-Rong,Zhang Hui-Lin,Yang Tian-CiORCID

Abstract

ObjectivesA 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.MethodsThe pooled segment genome sequencing method followed by Illumina sequencing was performed.ResultsThis 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.ConclusionThe 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.

Funder

National Natural Science Foundation of China

Key Projects for Province Science and Technology Program of Fujian

Natural Science Foundation of Fujian Province

Publisher

BMJ

Subject

Infectious Diseases,Dermatology

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