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Scientists dont exactly know why this reaction happens but suspect that one reason is that the killed spirochetes break down and release toxins, and our immune systems response to this spill is what causes the symptoms of the Jarisch Herxheimer reaction

10.1016/j.cbpa.2023.102358

The infected cells were subsequently resuspended in lysis buffer (containing 50 mM Tris, 10% sucrose, 50 M ATP, 1 mM phenylmethylsulfonyl fluoride (PMSF), 5 mM dithiothreitol (DTT), 1% NP40, 10 mM imidazole, 1 protease inhibitor and phosphatase inhibitor, pH 7.0, with HCl)

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ESM Cambrian: revealing the mysteries of proteins with unsupervised learning