The case involved a 62-year-old male farmer with a history of alcoholic liver disease. He was admitted to the hospital on March 2, 2022, and the chief complaint was "fever and cough with difficult breathing for 4 d". Four days before admission, the patient had a fever with no obvious cause, a maximum temperature of 41.0C, chills, poor appetite, fatigue, headache and generalised muscle aches, intermittent disordered speech, cough, expectoration, and gradually worsening dyspnoea, for which he visited a local hospital. Chest computed tomography (CT) suggested infection and partial consolidation of the right lung. The patient was diagnosed to have "severe pneumonia" and administered the antibiotics piperacillin sulbactam, meropenem, and levofloxacin, and antiviral agent oseltamivir; however, a recurrent persistent fever and worsening dyspnoea were observed. The patient was admitted to the RICU of Huizhou Central People's Hospital for further treatment.
Physical examination presented the following findings: body temperature: 39.2C, pulse: 93 beats/min, respiratory rate: 35 breaths/min, blood pressure: 113/76 mmHg, pulse oximetry: 90% (5 L/min oxygen by face mask). The patient was conscious and lethargic and had no yellowing of the skin, mucosa, or sclera and no enlargement of superficial lymph nodes. He was tachypnoeic with coarse breath sounds in both lungs, and wet rales could be heard in the bilateral lower lungs. The heart rate was 93 beats/min and regular; no pathological murmurs were heard in any of the valve auscultation areas and no other significant abnormalities were observed.
Laboratory examination presented the following findings: negative for novel coronavirus RNA and influenza A and B virus antigens; blood gas analysis (FiO2: 41%): pH: 7.445, PO2: 49.0 mmHg, PCO2: 25.4 mmHg, HCO3: 18.7 mmol/L, base excess: -4 mmol/L, oxygen saturation index: 119.5. Complete blood count was as follows: white blood cell (WBC): 3.7 x 109/L, neutrophil percentage: 86.1%, lymphocyte count: 0.24 x 109/L, haemoglobin: 105 g/L, platelets: 69 x 109/L; high-sensitivity C-reactive protein (hs-CRP): 320.25 mg/L, procalcitonin (PCT): 47.86 ng/mL. The liver function test results were as follows: alanine aminotransferase (ALT): 116 U/L, aspartate aminotransferase (AST): 696 U/L, total bilirubin: 32.3 micromol/L, albumin: 23.5 g/L. The kidney function test results were as follows: urea: 11.8 mmol/L, serum creatinine: 119 mumol/L, lactate: 1.22 mmol/L, plasma ammonia: 42.3 mumol/L, blood potassium: 3.53 mmol/L, blood sodium: 130 mmol/L. Coagulation function: fibrinogen: 9.95 g/L, D-dimer: 12,500 ng/mL; creatine kinase (CK): 8454 U/L, lactate dehydrogenase (LDH): 785 U/L. Brain natriuretic peptide precursor: 1470 pg/mL and high-sensitivity troponin T: 35.73 ng/L. Chest CT at the time of admission (Figure 1A-C) showed multiple patchy exudative opacities in the right lung and a large consolidated shadow in the right lower lung. Six hours after admission, the patient's condition worsened, obvious respiratory distress was observed, and the oxygen saturation index dropped to 95 mmHg. A diagnosis of severe community-acquired pneumonia (SCAP) with acute respiratory distress syndrome (ARDS) was considered, and the patient was administered tracheal intubation with invasive mechanical ventilation, methylprednisolone (40 mg) as an anti-inflammatory and liver protective drug, and an antibiotic regimen of meropenem injection (1.0 g q. 8 h), moxifloxacin injection (0.4 g q.d.), and oseltamivir capsules (75 mg q. 12 h). The patient had a severe infection with rapidly progressing pulmonary lesions, the efficacy of conventional antibiotics was poor, and the causative pathogen was not obvious. After obtaining written consent from his family members, 10 mL of bronchoalveolar fluid (BALF) collected via fibreoptic bronchoscopy was sent to the Daan Gene sequencing platform (Daan Gene Co., Ltd. of Sun Yat-sen University) for metagenomic next-generation sequencing (mNGS). During this period, the Widal test, Weil-Felix test, tuberculosis antibodies, anti-neutrophil cytoplasmic antibodies, and IgM antibodies for respiratory pathogens (Legionella pneumophila, Chlamydia pneumoniae, Mycoplasma pneumoniae, Q fever Rickettsia, adenovirus, respiratory syncytial virus, influenza A virus, influenza B virus, and parainfluenza virus) were all negative. The bacterial and fungal cultures of blood, phlegm, and BALF were negative. After the initial antibiotic treatment, the patient's condition did not improve; he still had a persistent fever and showed limited improvement in oxygenation, decreased platelets, and progressive increase in liver enzymes and blood creatinine. On March 4 (day 3), laboratory re-examination showed the following: platelets: 52 x 109/L, ALT: 559 U/L, AST: 1548 U/L, and serum creatinine: 341 micromol/L. On the same day, the DNA mNGS results indicated the presence of C. psittaci, with a sequence number of 14940, coverage of 97%, and relative abundance of 74.2%. Follow-up based on the patient's medical history indicated that he raised chickens, ducks, and other fowl at home. Taking together, the patient's clinical presentation and mNGS results led to a diagnosis of severe C. psittaci pneumonia. The patient had severe hepatic and renal insufficiency, and treatment with respiratory quinolones, macrolides, and antibiotics, such as doxycycline and minocycline, was not appropriate. After consultation with the hospital clinical pharmacist, the antibiotic regimen was adjusted to omadacycline injection (first dose: 100 mg IV q. 12 h, followed by: 100 mg IV q.d.). After 72 h of treatment, the patient's temperature gradually decreased to a normal level (Figure 2), and a complete blood count re-examination on March 7 (day 6) showed the following: WBC: 6.3 x 109/L, neutrophil percentage: 85.1%, lymphocyte count: 0.64 x 109/L, haemoglobin: 85 g/L, platelets: 116 x 109/L, hs-CRP: 127.14 mg/L, PCT: 5.53 ng, ALT: 228 U/L, AST: 430 U/L, serum creatinine: 202 micromol/L. The patient's condition gradually improved; inflammation indices decreased significantly; and liver enzymes, creatinine, CK, and LDH gradually returned to normal levels (Figures 3-7). On March 14 (day 13), the patient was successfully extubated and high-flow oxygen therapy was continued. Chest CT re-examination indicated significant resorption of the right lung lesion (Figure 1D-F). The patient's condition was considered stable and his gastrointestinal function improved. On March 16 (day 15), the omadacycline injection was changed to an oral preparation (300 mg p.o. q.d.), and the patient was administered low-flow oxygen therapy and transferred to the general ward. On March 23 (day 22), chest CT re-examination indicated further resorption of the right lung lesion (Figure 1G-I), and the patient was discharged the following day. The final diagnosis was psittacosis, severe community-acquired pneumonia, ARDS, multiple organ system failure (type I respiratory failure, liver failure, and renal failure), rhabdomyolysis, and alcoholic liver disease. Outpatient follow-up at 1 month after discharge indicated no significant abnormalities in inflammation indices (hs-CRP and PCT) and liver and kidney functions, and chest CT indicated that the lung lesions were largely resorbed, leaving only a small number of fibrous linear opacities (Figure 1J-L).