A 57-year-old man was admitted because of abdominal distension, anorexia and constipation for 5 weeks, chest pain for 1 week, and fever for 1 day on 16 April 2020. On 8 March 2020, the patient developed abdominal distension, anorexia, constipation, and decreased anus exhaust, and was given drugs to promote gastrointestinal motility but with no improvement. On 9 April 2020, the patient was accidentally hit by a wrench on the left side of the chest at work, and it was accompanied by chest pain. The chest CT at the local hospital revealed Wegener's granulomatosis, which did not exclude the possibility of tuberculosis, and no further diagnosis or treatment were performed. On 15 April 2020, the patient developed chills and fever with a body temperature of 39C during his visit to our outpatient department. The blood routine showed a WBC of 7.33 x 109/L, hemoglobin of 98 g/L, a neutrophil ratio of 87.1%, and a C-reactive protein of 119.72 mg/L. The results of plain chest and abdomen films showed multiple lesions in bilateral lungs, with the nature to be determined, and enterostasis. Then, the patient was admitted for further treatment.
The patient had chronic viral hepatitis B and type 2 diabetes mellitus, and was given entecavir 0.5 mg qd for anti-hepatitis B virus treatment. He was diagnosed with hepatitis B virus-associated membranous nephropathy in 2019 and had received high-dose hormone therapy (Medrol 48 mg qd) for 2 months before the onset of the disease. His lymphocytes were decreased: total T lymphocytes 427 cells/mul, helper T cells 210 cells/mul, and suppressor T cells 209 cells/mul. Two months ago, the patient was given methylprednisolone 48 mg qd because there was no improvement in urine protein, and the dose was reduced to 44 mg qd 2 days before the admission. The patient was engaged in furniture manufacturing and works in a dusty environment.
On admission, his body temperature was 39.5 C, the respiratory rate was 22 breaths per minute, and his consciousness was clear. There was no yellowing of the whole body skin mucosa, rash, or subcutaneous hemorrhage. Liver palm was notable but without obvious spider nevus. The oral cavity and pharynx were found to have a bean curd-like attachment, and the tongue was thick with white spots. The patient's breath sounds were weak bilaterally, with the left lung more pronounced, and there was pressure pain around the umbilicus. The cardiovascular system and nervous systems and the limbs were unremarkable.
The laboratory tests showed interleukin-6 of 137.2 pg/ml, serum ferritin of 1,642.3 ng/ml, and an erythrocyte sedimentation rate of 83 mm/h. The T-lymphocyte subsets shown by flow cytometry indicated an absolute value of total T cells of 427 cells/mul, an absolute value of helper T cells (Th) of 210 cells/mul, and an absolute value of suppressor T cells (Ts) of 209 cells/mul. Seven items of immune functions demonstrated a total complement hemolytic activity of 68 IU/L and immunoglobulin G of 6.29 g/L. For liver function, globulin was 19.3 g/L and albumin was 24.6 g/L. Glycosylated hemoglobin was 10.7%. The tuberculosis immune spot test was negative. Fungal D-glucan was 745 ng/L. The fungal culture with throat wipes detected Candida albicans. The routine urine test was positive for urine protein and urine glucose.
After the admission, the patient was given fluconazole injection 200 mg qd, latamoxef 1 g q12 h for anti-infection, entecavir 0.5 mg qd for anti-hepatitis B virus, methylprednisolone 44 mg qd for anti-hepatitis B virus, and blood glucose control, urine protein reduction, kidney protection, and other treatments. On the 2nd day of admission, the patient's temperature returned to normal, and the re-examination showed a high-sensitivity C-reactive protein of 20.98 mg/L and procalcitonin <0.05 ng/ml. Since the pathogens of pulmonary infection were unknown, on the 7th day of admission, bronchofiberscopy was performed and bronchoalveolar lavage fluid (BALF) was collected for pathogen detection (culture + tuberculosis gene probe). The patient presented with a postoperative transient temperature of 38.5 C with chills and was considered to have an acute upper respiratory tract infection. After antiviral treatment with oseltamivir 75 mg bid, the body temperature returned to normal on the same day. Sputum specimens and BALF specimens were sent several times for sputum smears and cultures, and no M. tuberculosis was found in the smears or cultures. However, the BALF specimens were positive for M. tuberculosis gene probes A, B, C, and E and negative for rifampicin resistance mutation. A. fumigatus was cultured from the bronchoalveolar lavage fluid, and the preliminary diagnosis was pulmonary tuberculosis and pulmonary Aspergillus infection. Glucocorticoids were discontinued on the 8th day of admission, and fluconazole and latamoxef were discontinued. The anti-tuberculosis regimen was changed to isoniazid 0.3 g qd, ethambutol 1 g qd, pyrazinamide 1 g qd, and levofloxacin 0.4 g qd, and the antifungal therapy was changed to Voriconazole 200 mg q12 h.
On the 10th day of admission, the patient again developed hyperthermia, with a temperature of 39.4 C, accompanied by chills, left-sided chest pain with blood in the sputum, and shortness of breath. The repeat examination showed high-sensitivity a C-reactive protein of 98.58 mg/L, procalcitonin of 0.09 ng/ml, and a decreased oxygenation index compared to before. The repeat chest CT showed multiple infectious lesions, some nodules with cavities in both upper lungs, a small amount of pleural and pericardial effusion, and progressive lesions compared with the CT film from another hospital (Figure 1). Considering that the fever was caused by aggravation of the pulmonary infection, levofloxacin was changed to moxifloxacin hydrochloride in sodium chloride injection 0.4 g qd. Fever peak decreased slightly, but the body temperature did not decrease to normal. On the 13th day of admission, the patient had a high fever again, with the highest body temperature of 39.5 C. The infection indicators continued to rise on recheck, with a high-sensitivity C-reactive protein of 123.54 mg/L and procalcitonin of 0.11 ng/ml.
BALF samples were submitted for PACEseq metagenomic next-generation sequencing (mNGS) (Hugobiotech, Beijing, China), and A. fumigatus (227 reads), N. nova (148 reads), M. tuberculosis (1 read), human alphaherpesvirus 1 (39 reads), and human cytomegalovirus (11 reads) were detected (Figure 2). Briefly, for the mNGS method, the collected BALF specimen was centrifuged at 5,000 g and at room temperature for 10 min, and DNA was extracted from the supernatant using the TIANamp Micro DNA Kit (DP316, Tiangen Biotech). Sequencing libraries were constructed with the QIAseq   Ultralow Input Library Kit (Illumina). Qualified libraries with different tags were pooled together and amplified and then sequenced with a Nextseq550 system (Illumina) for 150 cycles. Kytococcus sedentarius (51 reads), Streptococcus gordonii (36 reads), Rothia dentocariosa (82 reads), Nocardia mikamii (10 reads), Streptococcus mitis (21 reads), Lactobacillus salivarius (25 reads), and Streptococcus pseudopneumoniae (43 reads) were also detected by the mNGS but were considered as oral colonizing microorganisms and were not considered as pathogenic microorganisms.
A needle biopsy of the left upper lung tissue was also performed, and the mNGS of the lung tissue revealed N. nova (92 reads) and human cytomegalovirus (2 reads) (Figure 2). The serum viral examination was CMV-IgG positive and CMV DNA-positive. Herpes simplex virus type I IgG was positive and herpes simplex virus type I IgM was negative. The histopathological examination of the lungs revealed purulent inflammation with fibrinous inflammation (Figure 3). Combined with the characteristics of imaging changes, mNGS results of BALF and lung tissues, the patient was considered to have a multi-pathogen infection (N. nova, M. tuberculosis, A. fumigatus, and cytomegalovirus). The pulmonary imaging features of this patient were predominantly cavernous and not consistent with viral pneumonia manifestation features, so respiratory infection caused by human alphaherpesvirus 1 was not considered.
The treatment regimen was then adjusted to co-trimoxazole 3 tablets tid and imipenem and cilastatin sodium injection 1 g, q8 h for the treatment of N. nova, and ganciclovir 0.25 g, q12 h for the treatment of cytomegalovirus. The anti-tuberculosis and Aspergillus treatments were also continued. The fever peak was decreased, and his chest pain was relieved, with normal temperature on the 17th day of admission. The dynamic reexamination revealed that the infection indicators had decreased gradually. On day 24 of admission, the repeat chest CT showed improvement of the pulmonary infection (Figure 4), CMV DNA was negative, and "ganciclovir" was discontinued. On day 44 of admission, the patient recovered and was discharged. The patient continued to receive the anti-tuberculosis and antifungal treatments with Voriconazole 200 mg q12 h and sulfonamide Tablets 3 tablets tid for N. nova in the outpatient department. A review of the chest CT at 1 and 3 months after discharge showed that the lesion was gradually absorbed.