Immunosequencing of the T-cell receptor repertoire reveals signatures specific for diagnosis and characterization of early Lyme disease

Abstract

Lyme disease, the most common tick-borne illness in the United States, is most frequently caused by infection with Borrelia burgdorferi. Although early antibiotic treatment can prevent development of severe illness and late manifestations, diagnosis is challenging in patients who do not present with a typical erythema migrans rash. To support a diagnosis of Lyme disease in such cases, guidelines recommend 2-tiered serologic testing. However, 2-tiered testing has numerous limitations, including ambiguity in interpretation and lower sensitivity in early disease. We developed a diagnostic approach for Lyme disease based on the T-cell response to B. burgdorferi infection by immunosequencing T-cell receptor (TCR) repertoires in blood samples from 3 independent cohorts of patients with laboratory-confirmed or clinically diagnosed early Lyme disease, as well as endemic and non-endemic controls. We identified 251 public, Lyme-associated TCRs that were used to train a classifier for detection of early Lyme disease with 99% specificity. In a validation cohort of individuals with early Lyme disease, TCR testing demonstrated a 1.9-fold increase in sensitivity compared to standard 2-tiered testing (STTT; 56% versus 30%), with a 3.1-fold increase <=4 days from the onset of symptoms (44% versus 14%). TCR positivity predicted subsequent seroconversion in 37% of initially STTT-negative patients, suggesting that the T-cell response is detectable before the humoral response. While positivity for both tests declined after treatment, greater declines in posttreatment sensitivity were observed for STTT compared to TCR testing. Higher TCR scores were associated with clinical measures of disease severity, including abnormal liver function test results, disseminated rash, and number of symptoms. A subset of Lyme-associated TCRs mapped to B. burgdorferi antigens, demonstrating high specificity of a TCR immunosequencing approach. These results support the clinical utility of T-cell-based testing as a sensitive and specific diagnostic for early Lyme disease, particularly in the initial days of illness.

T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity

“…However, a subset of TCRs can be detected across multiple individuals, more commonly among those with shared HLA alleles; these public TCRs may be the result of exposure to a common antigen and can serve as a biomarker of disease (19,20). We have developed classifiers leveraging thousands of public TCR sequences shared across individuals with a history of infection for identification of prior CMV infection and Lyme disease, in addition to prior SARS-CoV-2 infection (17,21,22). These classifiers are highly specific for the disease of interest; for example, the initial SARS-CoV-2 classifier was developed to have a target specificity of 99.8% across 1702 prepandemic controls, presumably including individuals exposed to other coronaviruses (17).…”

Large-Scale Sequencing of Borreliaceae for the Construction of Pan-Genomic-Based Diagnostics

“…Next-generation sequencing has been used to detect host responses to acute Lb rather than attempting to directly detect the Borreliellal genome. Sequencing human T-cell receptors (TCRs) is a novel approach to Lyme disease diagnostics and began clinical trials in 2021 [ 214 ]. T-cells respond to Lb infection earlier than B-cells can produce antibodies, and thus the expansion of Borreliellal -specific T-cell receptor sequences in a patient’s circulating lymphocytes has the potential to confirm acute cases of Lyme disease earlier than traditional serologic methods [ 151 ].…”

Progress in kidney transplantation: The role for systems immunology

“…Quantifying the presence of these antigen-specific TCRs by frequency in the overall repertoire, which has been termed breadth for unique clones and depth for total templates, may inform the quantity and quality of the anti-pathogen T-cell response. Following CMV, this approach was later applied successfully in both Lyme disease and Epstein-Barr Virus (EBV) (142,143).…”

“…Prior exposure and T-cell mediated immunity can be inferred by comparing an individual's TCR repertoire against a classifier developed from a database of known public SARS-CoV-2 associated TCRs (145,146). This methodology has recently been expanded to diagnosis of other vector-borne disease and has the potential to be applied to innumerable viral pathogens (143). TCR repertoire has proved to be useful in evaluating response to vaccination, and may be a useful adjunct in screening patients for baseline protective immunity prior to transplantation to guide prophylaxis or duration of therapy (147,148).…”