Persistent Borrelia burgdorferi protein antigen in CD16 + monocytes is associated with monocyte-skewed immune dysregulation in post-treatment Lyme disease syndrome (PTLDS)

Abstract Post-treatment Lyme disease syndrome (PTLDS) is characterized by persistent symptoms after antibiotic therapy for Borrelia burgdorferi infection. The mechanisms underlying these symptoms remain incompletely understood and have been attributed to ongoing low-level infection, autoimmunity, or immune dysregulation driven by residual bacterial antigens. We investigated whether Borrelia burgdorferi protein antigen persists in long-lived monocyte subsets in PTLDS patients and is associated with broader immune dysregulation. CD14 ⁺ CD16 ⁺ monocytes from 10 patients with PTLDS were analyzed by mass spectrometry; plasma from all 10 was profiled on a 14-plex cytokine panel against 50 healthy donors; PBMCs from 6 patients (3 antigen-positive and 3 antigen-negative) underwent RT-qPCR and bulk RNA-seq with immune-compartment profiling. FlaB and OspC were detected in CD14 ⁺ CD16 ⁺ monocytes months to years after treatment, whereas Borrelia burgdorferi transcript was not detected. Plasma IFN-γ exceeded the healthy donor median in all 10 participants. Antigen-positive samples showed an antigen-associated inflammatory transcriptional profile, including increased TNFSF14/LIGHT, GSDMD, GBP5, and KCNJ2 expression, together with a compartment-level pattern of monocyte-skewed myeloid reconfiguration, higher neutrophil-related features, and selective T-cell-state changes. These findings link residual Borrelia burgdorferi protein in CD14 ⁺ CD16 ⁺ monocytes to monocyte-skewed immune remodeling in PTLDS, paralleling observations in long COVID and supporting a model in which post-infectious syndromes are sustained by antigen-fueled immune remodeling rather than ongoing infection. Importance Many people treated for Lyme disease go on to experience fatigue, pain, and difficulty thinking for months or years, and the reason is unknown. Persistent infection has been a leading explanation, yet longer courses of antibiotics do not help. We found proteins from Borrelia burgdorferi , the bacterium that causes Lyme disease, inside long-lived blood monocytes of patients with lasting symptoms, years after treatment and with no sign that the bacterium was still active. Patients carrying these proteins showed a distinct inflammatory immune profile. These findings point to leftover bacterial material, rather than ongoing infection, as a possible driver of persistent symptoms, echo observations in long COVID, and argue that treatments directed at the immune response deserve study.