On September 25th, 2021, a 38-year-old Chinese man went to a local hospital for his left lower abdominal pain (Figure 1). The patient was hospitalized and given symptomatic treatment such as fasting, antispasmodic, analgesic, enema and nutritional support. Subsequently, the abdominal diseases were ruled out by examinations. On October 2nd, 2021, after one week of empirically treated with levofloxacin intravenously (unknown dose), his abdominal pain was relieved and he was discharged. 
However, on October 5th, 2021, the patient complained of left lower abdominal pain again, which could spread to the entire abdomen quickly. Meanwhile, he began to suffer from continuous low back pain and a low-grade fever in the afternoon (fluctuations at 37-38 degrees Celsius). Based on the symptoms and the lumbar spine magnetic resonance (MR) images (Supplementary Figure 1) of the patient, the local doctors thought there was a possibility of lumbar (L3/4) tuberculosis (TB). After receiving anti-TB treatment, the patient was discharged.
On November 24th, 2021, the patient was transferred to Sun Yat-sen memorial hospital as his condition continued to deteriorate. His vital signs were within normal limits, his body weight dropped 10% in two months and he went without a bowel movement for a week. On detailed consultation, the history of underlying diseases, bites, surgery, betel nut addiction and oral uncleanness were excluded. Then, a systematic physical examination confirmed that he had lower abdominal pain, especially in his left lower abdomen. Apart from that, he had percussion pain in the spinous process of the lumbar spine (L3, L4) and limited lumbar mobility. The patient reported his visual analogue scale (VAS) score of lower abdominal pain was 8, the VAS score of low back pain was 6 and the lumbar spine Japanese Orthopaedic Association Scores (JOA) was 8.
After admission to Sun Yat-sen memorial hospital, MR, computed tomography (CT), ultrasonography and endoscopy ruled out visceral organ diseases. X-ray images showed the intervertebral space height between L3 and L4 was decreased (Figure 2). His lumbar spine CT images showed a large vertebral bone defect at L3 (Figure 3A and D). Subsequent MR imaging revealed disc inflammation and osteomyelitis at L3 and L4 (Figure 3B and C). Due to the unclear diagnosis of bacterial infection, we initially let him continue to use anti-TB drugs (Isoniazid 300 mg qm, Rifampicin 450mg qm, Ethambutol 750mg qm, Pyrazinamide 500mg tid) until the TB-related tests confirmed negative. In addition, considering the possibility of his potential gastrointestinal bacterial infection, we empirically used levofloxacin (0.5 g qd) intravenously since admission. However, the patient's condition gradually deteriorated while taking anti-TB drugs and levofloxacin, and the patient had a low-grade fever (Figure 4). In the following days, the results of TB-related and tumor marker-related test were confirmed to be negative and the patient stopped taking anti-TB drugs. In a series of preoperative cultures, no bacteria were found in his blood.   
On December 7th, 2021, considering the large vertebral bone defect and high-intensity activity required for his job could lead to spinal instability, an operation was performed (Supplementary surgical Technique and Supplementary Figure 2). After the operation, his abdominal symptoms disappeared and vital signs were stable. Then, his intraoperative samples were sent for pathological examination, culture and metagenomic next-generation sequencing (mNGS). Of all the intraoperative lesion samples submitted, only mNGS (Supplementary Figure 3) and anaerobic culture confirmed the presence of Eikenella corrodens. The procedure and quality control of mNGS records are in Supplementary Material Method. On the first postoperative day, his wound drainage fluid was re-cultured and no bacteria was found.
On December 11th, 2021, according to the mNGS and drug susceptibility results, we switched the patient's levofloxacin to Piperacillin Sodium and Tazobactam Sodium (PSTS, 4.5g q8h). PSTS was administered intravenously until the patient was discharged on December 25th, 2021, during which time his infection-related indicators gradually improved (Figures 4 and 5). After discharge, the patient continued to take amoxicillin and clavulanate potassium tablets (457mg bid) orally for four weeks. 
On January 7th, 2022, the patient returned to our hospital for the first follow-up visit. His inflammatory indicators were normal and nutritional status had improved significantly (Figure 6). X-ray examination of lumbar showed that the lumbar spine (L3/4) had recovered well (Figure 7A and B). At this time, he could gradually extend his standing and walking time to about 2 hours and his lumbar spine JOA score was 22. Except for his wound pain, symptoms of lower abdominal pain, lumbar pain and other discomfort were relieved.  
On March 4th, 2022, the patient finished his second follow-up visit. Three months after the operation, the patient could go back to his work and live a completely normal life. Under the protection of the waist brace (Supplementary Figure 4B), the bone fusion and spinal stability were good (Figure 7C). His lumbar spine JOA score was 27 and all relevant test indicators had returned to normal (Figures 4-6).
On December 25th, 2022, the patient had completed a 12-month follow-up. During multiple telephone follow-up visits, the patient did not report any pain, fever or other discomfort.