Disease-Associated Multimolecular Signature in the Urine of Patients with Lyme Disease Detected Using Raman Spectroscopy and Chemometrics

Abstract

A urine-based screening technique for Lyme disease (LD) was developed in this research. The screen is based on Raman spectroscopy, iterative smoothing-splines with root error adjustment (ISREA) spectral baselining, and chemometric analysis using Rametrix software. Raman spectra of urine from 30 patients with positive serologic tests (including the US Centers for Disease Control [CDC] two-tier standard) for LD were compared against subsets of our database of urine spectra from 235 healthy human volunteers, 362 end-stage kidney disease (ESKD) patients, and 17 patients with active or remissive bladder cancer (BCA). We found statistical differences ( p < 0.001) between urine scans of healthy volunteers and LD-positive patients. We also found a unique LD molecular signature in urine involving 112 Raman shifts (31 major Raman shifts) with significant differences from urine of healthy individuals. We were able to distinguish the LD molecular signature as statistically different ( p < 0.001) from the molecular signatures of ESKD and BCA. When comparing LD-positive patients against healthy volunteers, the Rametrix-based urine screen performed with 86.7% for overall accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), respectively. When considering patients with ESKD and BCA in the LD-negative group, these values were 88.7% (accuracy), 83.3% (sensitivity), 91.0% (specificity), 80.7% (PPV), and 92.4% (NPV). Additional advantages to the Raman-based urine screen include that it is rapid (minutes per analysis), is minimally invasive, requires no chemical labeling, uses a low-profile, off-the-shelf spectrometer, and is inexpensive relative to other available LD tests.

Alterations in the molecular composition of COVID-19 patient urine, detected using Raman spectroscopic/computational analysis

“…Previously published computational methods were used [ 19 , 28 , 29 , 42 ] with the Rametrix ® Toolbox (LITE v1.1 and PRO v1.0) with added capabilities for ISREA baselining [ 40 , 41 ]. Calculations were performed in MATLAB R2018A (Mathworks; Natick, MA).…”

“…ISREA was applied using nodes (or ‘knots’) at wavenumbers of 400, 950, 1100,1500, and 1800 cm -1 . In specified cases, the placement of nodes was also allowed to vary, as described previously [ 19 ], to exclude specific Raman shift regions of spectra selectively. Spectra were analyzed by principal component analysis (PCA) and discriminant analysis of principal components (DAPC) in the Rametrix ® LITE Toolbox, and models were cross-validated with leave-one-out analysis with Rametrix ® PRO.…”

“…Spectra were analyzed by principal component analysis (PCA) and discriminant analysis of principal components (DAPC) in the Rametrix ® LITE Toolbox, and models were cross-validated with leave-one-out analysis with Rametrix ® PRO. These methods have been implemented and described previously [ 19 , 28 , 32 , 35 – 39 ]. This procedure allowed calculation of overall prediction accuracy, sensitivity, specificity, positive-predictive value (PPV), and negative-predictive value (NPV) for detecting COVID-19 in human urine.…”

“…Of spectra were performed through the calculation of total spectral distance (TSD), as has been demonstrated [ 15 , 16 , 18 , 19 , 29 , 32 ]. In calculation of TSD, the difference between each urine spectrum and that of Surine ™ was calculated at each wavenumber and summed.…”

“…We have successfully applied this method of urinalysis to determining the molecular characteristics and physical properties of urine specimens from healthy human volunteers (n = 235 urine samples) [ 15 ], patients with chronic kidney disease (CKD) (n = 362 urine samples) [ 16 ], bladder cancer (BCa) and non-neoplastic genitourinary pathologies (such as cystitis and benign prostatic hypertrophy/urinary retention, among others) (n = 56 urine samples) [ 17 , 18 ], and post-acute patients following exposure to Lyme pathogen ( Borrelia sp.) (n = 30 urine samples) [ 19 ]. Data cited in these references was derived from Rametrix ® analysis of urine specimens collected prior to December 2018.…”