Pulmonary cryptococcosis (PC) is a lung infection caused by inhaling Cryptococcus neoformans or Cryptococcus gattii in the environment, which are two major cryptococcal pathogens in humans and animals; these two pathogens belong to the Cryptococcus neoformans species complex. When Cryptococcus spores are inhaled, they frequently enter the human lower respiratory tract. It is most common in immunocompromised patients. However, PC becomes one of the emerging diseases in immunocompetent patients [1], and epidemiological surveys in recent years have shown that the proportion of asymptomatic infections in immunocompetent PC patients is higher than that in immunocompromised patients (40.8% and 30.2%, respectively) [2]. For immunocompetent patients, their clinical symptoms are different from immunodeficiency patients [3]. PC can be confirmed by some conventional tests, e.g. taking specimens by lung puncture biopsy for culture, direct microscopy examination, and serum cryptococcal capsular polysaccharide antigen lateral flow assay (CrAg-LFA) test. CrAg-LFA detection is currently one of the most important methods for early diagnosis of cryptococcosis because it’s fast and low-cost. But the clinical manifestations of PC are non-specific [4], with cough, expectoration and fever being the most common symptoms. Moreover, Chest computed tomography (CT) of PC patients may show multiple nodular masses and cavities in some lesions [5], and some imaging of PC is similar to that of pulmonary tuberculosis, which may cause misdiagnosis. Since the clinical images of PC vary with the immune status of patients, and clinical symptoms are nonspecific and diverse [6], PC is easily misdiagnosed as other diseases, such as pulmonary tuberculosis, pneumonia and lung cancer. What is worse, patients have died in some cases due to the severe exacerbation of the disease because PC is misdiagnosed as pulmonary tuberculosis [7, 8].
Recently the incident rate of mixed pulmonary infection has increased, with mixed bacterial and fungal infections being common [9]. Mixed pulmonary infection is more common in the elderly or patients with compromised immunity and immunodeficiency. Different pathogens can cause mixed pneumonia at the same time, resulting in overlapping clinical manifestations that make it difficult to identify all pathogens in the early stage of diagnosis [10]. In addition, the long-term empirical treatment with broad-spectrum antibiotics may increase drug resistance in some pathogens. Conventional tests for infectious pathogens, such as microbial culture, microscopy methods, antigen detection techniques, and serologic tests, have deficiencies like long average detection turn-around time (TAT), low sensitivity and low positive rate. These shortcomings increase the risk that a mixed pulmonary infection is missed or misdiagnosed, hindering patients from receiving effective care in the timeliest manner possible.
Metagenomic next-generation sequencing (mNGS), an emerging pathogen detection method in recent years, can directly detect and identify pathogens by sequencing without culturing or classifying. Here, we retrospectively analyzed a female diagnosed with bacterial pneumonia complicated by PC and showed how mNGS contributes to the identification of infectious pathogens during diagnostic procedures.
Case presentation
A 43-year-old female was admitted to the Department of Respiratory and Critical Care Medicine, the First People’s Hospital of Qinzhou, because she had been coughing for over a month. One day before hospital admission, her chest CT at another local hospital showed space-occupying lesions in the right lower lobe, along with cavities and multiple nodules. Her preliminary diagnosis was a pulmonary infection. She was admitted to the hospital for further diagnosis and treatment. About 10 months ago, she underwent right plantar cyst resection at the Department of Joint and Sports Medicine of the hospital; the surgery was successful and she made a smooth recovery. She denied a history of cigarette-smoking, tuberculosis, intrafamilial infectious diseases, and a family history of genetic diseases. Physical examinations at the time of admission were normal, with the following parameters: body temperature 36.2 °C, breathing rate 20 times/min, heart rate 112 times/min, and blood pressure 116/83 mmHg. Her right lower lung breath sounds were slightly coarse, while her right upper lung and left lung breath sounds were clear, and there were no obvious rales or pleural friction rub in both lungs. Auxiliary examinations were as followed: WBC 12.32 × 109/L, absolute neutrophil count = 8.48 × 109/L, CRP = 16.04 mg/mL, ESR = 72.00 mm/h; serum CrAg-LFA test was positive; the M. tuberculosis antibody TB-Dot test was weakly positive; no abnormalities were found in G and GM test, liver and kidney function, blood gas, tumor markers test, and squamous cell carcinoma antigen examinations. Her contrast-enhanced chest CT image revealed multiple nodules and plaques in her right lung, as well as the formation of cavities, which is considered the characteristic of tuberculosis, but the fungal infection could not be ruled out (Fig. 1b). She was diagnosed with pulmonary infection due to the nature of the space-occupying lesions and cavities in the right lower lobe, and moxifloxacin (0.4 g, qd, by intravenous drip) was used for empirical anti-infective therapy.
Chronologically, on the3rd day of admission, her tuberculin skin test (PPD) was negative. On the 7th day, her body temperature was 36.5 °C. Her cough did not improve significantly, and she experienced occasional chest pain. No abnormality was found in bronchoscopy, and BALF samples were collected for microbial culture, G and GM test, M. tuberculosis DNA test, and fungal and Cryptococcus smear, all of which proved negative. In the meantime, a BALF specimen was directly sent to Clinical Genome Center, Guangxi Kingmed Diagnostics, for mNGS in accordance with the previous references [11, 12]. On the 9th day, the mNGS result (see Additional file 1 for the methods of mNGS) reported a total of 66521 single-end reads in the pathogen genomic DNA, of which 537 reads were Corynebacterium striatum, with a coverage of 1.37% (Fig. 2a). 144 reads were Pseudomonas aeruginosa, with a coverage of 0.11% (Fig. 2b). 20 reads were Streptococcus pneumoniae with a coverage of 0.03% (Fig. 2c), and 68 reads were Cryptococcus neoformans with a coverage of 0.03% (Fig. 2d). The species’ relative abundance values of Corynebacterium striatum, Pseudomonas aeruginosa, Streptococcus pneumoniae and Cryptococcus neoformans were 15.23%, 4.08%, 0.57% and 60.71%, respectively. There were no reads that were matched to M. tuberculosis. With the lung images and laboratory examination results in hand, the clinician considered a high possibility of bacterial and cryptococcal infection. Therefore, the diagnosis was changed to PC and bacterial pneumonia, and the anti-infection therapy was switched to mezlocillin (4 g, q8h, by intravenous drip) for antibacterial treatment and fluconazole sodium chloride injection (400 mg, qd, by intravenous drip) for antifungal treatment. Over the next 7 days, the patient gradually improved after anti-infective treatment, and because the treatment is effective, the current anti-infective regimen was maintained. On the 18th day, the re-examination CT showed that her right lung infection lesions were significantly reduced (Fig. 1c). On the 19th day, the woman was discharged from the hospital, and in a follow-up call two months later she self-reported that her symptoms had mostly subsided.
