Secrets learned from sequencing the bacterium that causes syphilis

From the Greninger Lab, UW Virology

The secrets are in the sequence. Drs. Nicole Lieberman and Alex Greninger from the Greninger Lab generated 196 near-complete Treponema pallidum genome sequences to gain a better understanding of the bacterium that causes syphilis infection and provide insight into vaccine targets. Their findings were recently published in PLOS Neglected Tropical Diseases.

Rates of global syphilis infection are increasing despite effective treatment using penicillin. For this reason, developing a vaccine against T. pallidum may prove effective in curtailing the climbing rates of disease. FDA-approved vaccines are routinely employed to restrict bacterial infections that cause significant human diseases including typhoid fever, tetanus, diphtheria, whooping cough (pertussis), pneumonia, meningococcal disease, cholera, and anthrax. Yet, the selection of a comprehensive vaccine target is complex, especially when considering strain diversity.

To develop an effective vaccine, global sampling of circulating T. pallidum is necessary to identify vaccine targets that are broadly represented. Dr. Lieberman commented that one of the challenges in reaching this goal is that “the bacterium that causes syphilis, T. pallidum subsp. pallidum, cannot be grown in a laboratory as can many other bacterial species.” Additionally, “isolating and sequencing its DNA directly from a lesion swab is technically challenging.” Nonetheless, the researchers successfully generated close to 200 near-complete genome sequences for T. pallidum from diverse geographical regions including China, Ireland, Italy, Japan, Madagascar, Peru, and the United States of America. These publicly available sequences significantly expanded the geographical sampling range of T. pallidum, especially from under-sampled regions like China, Madagascar, and Peru.

With these new sequences in-hand, the researchers generated a phylogenetic tree of modern T. pallidum genomes which diverged into several subclades. To annotate sequence differences between subclades, the researchers characterized which genomes contained protein alterations for known or suspected antigens. Suspected antigens included T. pallidum proteins that were known to be surface exposed or reacted with pooled sera from individuals with syphilis infection. Intriguingly, mutations in antigenic proteins were enriched over non-antigenic proteins for some subclades. This finding suggested that in these cases the human immune response could be a robust driver of divergent variant selection in T. pallidum genomes, a common theme in host-pathogen evolution.

Percentage of mutations that occur in non-antigenic proteins as compared to known or suspected antigenic proteins (including surface proteins) for several T. pallidum strains.
Percentage of mutations that occur in non-antigenic proteins as compared to known or suspected antigenic proteins (including surface proteins) for several T. pallidum strains.

Furthermore, proteins targeted by the immune response often display multiple, independent mutations to evolve and evade host detection. To dissect the outcome of this selective pressure on key antigenic proteins, the researchers constructed protein structure models for the mutant forms of five highly mutated proteins. Intriguingly, a deletion in TP0136, a multidomain adhesion protein, occurs independently in multiple geographical locations and overlaps with a known recombination hotspot in the T. pallidum genome. This finding suggests that T. pallidum TP0136 sequence variability is necessary for the evolution of the bacteria and likely enables evasion of the human immune response.

In addition to the study of antigenic proteins expressed by T. pallidum, mutations in non-antigenic proteins can also provide insight into bacterium evolution and possible vaccine targets. For example, a mutation of the putative ERCC3-like DNA repair helicase TP0380 was only found in the Nichols A subclade and surprisingly correlated with an increased rate of mutation for this clade compared to circulating stains of the other six subclades. Together these data identify one potential mechanism of how the bacteria increase the rate of mutation in current circulating strains and may indicate a boost in bacterium fitness as observed by continued evasion of the human immune response.

“These data provide vaccine researchers a wealth of information on T. pallidum antigenic variability across the entire world and allows them to prioritize targets that will provide protection equally well against strains circulating in Seattle and those circulating in Lima or Antananarivo or Dublin,” said Dr. Lieberman. In the future, Dr. Lieberman intends to sequence T. pallidum genomes from samples in other under-sampled countries. “With that in mind, we have initiated collaborations on strain collection with clinical sites in Sri Lanka, India, and Argentina, as well as continuing our work with collaborators in Peru, China, and throughout the USA.” In parallel with additional sequencing, Dr. Lieberman stated that follow-up studies include “functional profiling to examine which of the sequence variants we have discovered interact with the human immune system, and which may help it evade immune clearance.”

The research spotlighted in this article was funded by the National Institutes of Health, the Ministry of Education, Culture, Sports, Science, and Technology of Japan, and the Japan Agency for Medical Research and Development.

Lieberman NAP, Lin MJ, Xie H, Shrestha L, Nguyen T, Huang ML, Haynes AM, Romeis E, Wang QQ, Zhang RL, Kou CX, Ciccarese G, Dal Conte I, Cusini M, Drago F, Nakayama SI, Lee K, Ohnishi M, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Mitjà O, Rompalo A, Mulcahy F, Hook EW 3rd, Lukehart SA, Casto AM, Roychoudhury P, DiMaio F, Giacani L, Greninger AL. 2021. Treponema pallidum genome sequencing from six continents reveals variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar. PLoS Negl Trop Dis. 15(12):e0010063.