PMC9577070_01
Chest CT of the patient. (A) The chest CT prior to admission showing high-density patchy and streak-like shadows in the lung, with unclear margin. (B) The chest CT of day 4 showing enhanced patchy and nodular high-density shadows in the lung, associated with diffused ground-glass opacities. (C) The chest CT of day 6 showing the relief of the patchy high-density shadow. (D) The chest CT of day 13 showing the absorption of the patchy high-density shadow.
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A chest CT on day 0 showed binary pulmonary infection, which was in suspicion of pulmonary tuberculosis (PTB) ( Figure 1A ). In association with the chest CT result ( Figure 1A ), the diagnosis of PTB was confirmed. Table 2 ,  Supplementary Figures 1A-C ). In combination with the heightened inflammation in bilateral lungs shown by the chest CT screen on day 4 ( Figure 1B ) as well as mental changes of the patient developed during the administration of sulperazone and moxifloxacin, the Jarisch-Herxheimer reaction (JHR) and leptospirosis-induced encephalopathy were of high suspicion. The chest CT of day 6 showed decreased infection foci and less amount of pleural effusion in the lung, in comparison to that of day 4 ( Figures 1B, C ). To further confirm the result of Xpert MTB RIF and CT, the sputum of the patient was also prepared for mNGS on day 6, from which the DNA sequences corresponding to MTBC (without L. interrogans) were detected with a read number of 4 (reported on day 8;  Table 2 ,  Supplementary Figure 1D ). The mNGS result of sputum was consistent with the Xpert MTB RIF result of day 3. On day 13, patchy shadows with high density were roughly absorbed as revealed by chest CT ( Figure 1D ); thus, the patient was transferred to the general ward of the infectious disease department for subsequent treatment. Moreover, the reads classified to L. interrogans or MTBC were subsequently aligned to a relevant microbial genome (i.e., L. interrogans or MTBC) using BLASTN v2.10.1+ for further validation ( Supplementary Figure 1D ).
Clinical course of the patient during hospitalization. The schematic shows the timeline from the onset of symptoms (11 November 2021) to transferring to the general ward (29 November). Major events, including diagnostics, manifestations, and medication during the course, are indicated. Sample collection for diagnostics is indicated in yellow, and the dates of corresponding reports available are shown in blue. Diagnostic examinations used for pathogen identification are highlighted by purple arrows. CSF, cerebrospinal fluid; Pl, plasma; U, urine; Pip.-Taz., Piperacillin sodium and tazobactam sodium for injection; Lev., Levofloxacin hydrochloride injection; Sul., sulperazone; Mox., moxifloxacin hydrochloride and sodium chloride injection; Met., methylprednisolone; Rif., rifampicin; Iso., isoniazid; Eth., ethambutol; Pyr., pyrazinamide; Pen., penicillin.
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The detailed clinical course of the patient during hospitalization is shown in  Figure 2 .