Comparative Genomics and Full-Length TprK Profiling ofTreponema pallidumsubsp.pallidumReinfection

Abstract

AbstractDeveloping a vaccine againstTreponema pallidumsubspeciespallidum, the causative agent of syphilis, remains a public health priority. Syphilis vaccine design efforts have been complicated by lack of an in vitroT. pallidumculture system, prolific antigenic variation in outer membrane protein TprK, and lack of functional annotation for nearly half of the genes. Understanding the genetic basis ofT. pallidumreinfection can provide insights into variation among strains that escape cross-protective immunity. Here, we present comparative genomic sequencing and deep, full-lengthtprKprofiling of twoT. pallidumisolates from blood from the same patient that were collected six years apart. Notably, this patient was diagnosed with syphilis four times, with two of these episodes meeting the definition of neurosyphilis, during this interval. Outside of the highly variabletprKgene, we identified 14 coding changes in 13 genes. Nine of these genes putatively localized to the periplasmic or outer membrane spaces, consistent with a potential role in serological immunoevasion. Using a newly developed full-lengthtprKdeep sequencing protocol, we profiled the diversity of this gene that far outpaces the rest of the genome. Intriguingly, we found that the reinfecting isolate demonstrated less diversity across eachtprKvariable region compared to the isolate from the first infection. Notably, the two isolates did not share any full-length TprK sequences. Our results are consistent with an immunodominant-evasion model in which the diversity of TprK explains the ability ofT. pallidumto successfully reinfect individuals, even when they have been infected with the organism multiple times.Author SummaryThe causative agent of syphilis,Treponema pallidumsubspeciespallidum, is capable of repeat infections in people, suggesting that the human immune response does not develop sufficiently broad or long-lasting immunity to cover treponemal diversity. Here, we examined the genomes from two blood-derived isolates ofT. pallidumderived 6 years apart from a patient who had syphilis four times during the same period to understand the genetic basis of reinfection. We found a paucity of coding changes across the genome outside of the highly variabletprKgene. Using deep profiling of the full-lengthtprKgene, we found surprisingly that the two isolates did not share any full-length TprK sequences.