Diagnosis of pulmonary Scedosporium apiospermum infection from bronchoalveolar lavage fluid by metagenomic next-generation sequencing in an immunocompetent female patient with normal lung structure: a case report and literature review

Scedosporium apiospermum (S. apiospermum) belongs to the asexual form of Pseudallescheria boydii, which is widely distributed in various environments. S. apiospermum is one of the most common causes of invasive fungal infection in patients with immune deficiencies, particularly after organ transplantation, acquired immune deficiency syndrome (AIDS), cystic fibrosis lung disease, structural lung diseases, and long-term use of immunosuppressants or glucocorticoids. The most common infection site of S. apiospermum is the lungs, and the clinical symptoms are usually cough, expectoration, hemoptysis, fever, dyspnea, and pleuritic chest pain. Imaging changes associated with pulmonary S. apiospermum infection can be similar to those observed in pulmonary aspergillosis, such as typical fungal balls or non-specific, such as single or multiple nodular lesions with or without cavities, focal infiltration, phyllode infiltration, and bilateral diffuse infiltration. The key to effective treatment is an accurate and timely etiological diagnosis. Otherwise, delayed diagnosis may cause fatal consequences, especially for patients with suppressed immunity. However, it is noteworthy that S. apiospermum can also rarely infect people with normal immune function, similar to our case. Surgical resection has become an essential part of treatment [1‐3]. We presented a rare case of a 54-year-old non-immunocompromised female patient who developed pulmonary S. apiospermum infection and was diagnosed with pulmonary S. apiospermum infection by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF), as well as the first literature review of pulmonary S. apiospermum infection in immunocompetent patients.

A 54-year-old Chinese non-smoker female, who worked in a chicken processing factory, experienced intermittent right chest pain with occasional dry cough for 8 months with no apparent trigger. Although the patient’s sputum acid fast staining was negative, she was receiving empirical anti-tuberculosis therapy (2021.04.10) (the specific drug is unknown) in another hospital since her chest computed tomography (CT), dated April 2, 2021, suggested pulmonary tuberculosis. Further, the patient developed skin itching and systemic redness, prompting the anti-tuberculosis drugs to be changed (the specific drug is unknown), however, shortness of breath and shivering occurred following 3 days of medication, and the patient was eventually switched to isoniazid, rifampicin, ethambutol, and levofloxacin (HRE + Lfx) for tuberculosis therapy. Unfortunately, her symptoms and imaging manifestation did not improve, and the CT at Hechuan People’s Hospital on June 16, 2021, indicated a thick-walled cavity in the upper lobe of the right lung, with irregular morphology, uneven wall thickness, and mild soft tissue enhancement. On June 22nd, 2021, she was admitted to our department for further evaluation and treatment. During the investigation, the patient denied experiencing symptoms such as dyspnea, chest tightness, hot flashes, night sweats, hemoptysis, chills, or a high fever. No significant abnormality was observed in the physical examination, and auxiliary inspection results are demonstrated in Table 1. In particular, this patient had underwent the fungal culture of BALF and lung biopsy, but the results were all negative. The patient was initially diagnosed with bacteriologically negative pulmonary tuberculosis and continued with anti-tuberculosis therapy with HRE and Lfx. The BALF of the patient was sent to undergo mNGS analysis, and the mNGS result revealed that the patient suffered from S. apiospermum infection, and DNA sequencing reads were 426, followed by antifungal therapy with voriconazole (300 mg iv q12h d1; 200 mg q12h iv d2-d20). Chest enhanced CT suggested the possibility of lung cancer (Fig. 1A and B), and positron emission tomography/CT (PET-CT) indicated that peripheral lung adenocarcinoma was not excluded (SUVmax 2.8) (Fig. 2). No significant improvement was observed in her imaging manifestation after the post-treatment review (Fig. 1C and D), and the possibility of fungal infection along with pulmonary neoplasms was not completely excluded. Then a CT-guided percutaneous lung biopsy was performed, whose pathological report suggested fibroproliferation with chronic inflammatory cell infiltration (Fig. 3). Although no evidence of pulmonary neoplasms was observed during the lung biopsy, a thoracoscopic right upper lobectomy and lymph node dissection were performed. During the surgery, no pleural effusion was observed, and the lesion was located in the upper lobe of the right lung, measuring about 3*3 cm, with complete excision of the diseased lobe. The postoperative pathological results revealed visible silver-stained (Fig. 4A) and PAS-positive (Fig. 4B) oval spores in the alveolar septum, bronchiole wall, and alveolar cavity, thus, indicating fungal infection. Lung biopsy tissue from the upper lobe of the right lung revealed metaplasia from alveolar to bronchial, along with partial bronchiectasis. In and around the cavity, there was a large amount of inflammatory cell infiltration and foam cell aggregation, accompanied by lymphoid tissue hyperplasia. Fiber hyperplasia was observed in some regions, and alveolar epithelial hyperplasia was also visible (Fig. 5). The patient continued to consume voriconazole (200 mg po bid) for 2 months after surgery, and the diagnosis and treatment process are indicated in Fig. 6. Chest imaging was followed up at 1, 2, and 10 months after surgery, and no signs of recurrence were observed (Fig. 7).

We searched the keywords “Pulmonary” or “Lung” and “Scedosporium” or “Scedosporiums” or “Scedosporium apiospermum” on the PubMed database, which had a total of 1309 articles. Subsequently, we excluded studies unrelated to current research, patients without S. apiospermum infections, patients with immunocompromised lung, and patients with non-pulmonary infections. Finally, 25 medical records with complete case report data were retrospectively analyzed [4‐27]. The flow chart of the screening process is indicated in Fig. 8. The included patients were elaboratively summarized per the age, sex, major clinical manifestations, presence or absence of pre-existing disease, diagnostic methods, imaging manifestations, extensive or limited lesions, presence or absence of delay in diagnosis and treatment, treatment plan, and treatment outcome (Table 2).

A total of 25 immunocompetent patients with pulmonary S. apiospermum infection were reported on PubMed, and the basic characteristics of these patients are summarized in Table 3. In total, 12 females (48%) and 13 males (52%) were included; the average age of the patients was 50.96 years, ranging from 7 to 83 years. Of the included patients, 84% had the following symptoms: 16 with cough and expectoration (64%), 12 with hemoptysis (48%), 10 with fever (40%), nine with dyspnea (36%), and other symptoms including night sweats (12%), weight loss (12%), chest pain (8%), blood in the sputum (8%), anorexia (8%), fatigue (8%), and pneumothorax (4%). Cough and expectoration were the most common symptoms, followed by hemoptysis and fever. The severity of symptoms also varied, from inconspicuous pulmonary symptoms (three cases) to dyspnea (nine cases). Pulmonary tuberculosis was the most common underlying disease (11/25, 44%), followed by pulmonary cystic fibrosis (4/25, 16%) and bronchiectasis (3/25, 12%). The main diagnostic method was BALF culture in 13 cases (52%), followed by sputum culture in seven cases (28%), postoperative tissue culture in four cases (16%), lung biopsy and transbronchial lung biopsy in two cases (8%), gene sequencing of alveolar lavage fluid in two cases (8%), blood culture in one case (4%), and lung biopsy smear in one case (4%). Among the 25 patients included, four (16%) were treated with surgery, 15 (60%) with antifungal therapy (including one case with combined nebulized dornase Alfa and 7% hypertonic saline), and six (24%) were treated with surgery combined with antifungal therapy. Among these patients, treatment was delayed for nine (36%) patients, of which four (16%) were misdiagnosed as Aspergillus infections, one (8%) had empirical tuberculosis treatment, one (8%) whose prior bronchoalveolar lavage culture had later grown S. apiospermum and had been considered a contaminant, one patient (8%) had an unidentified fungus isolated from lung puncture biopsy, one patient (8%) had S. apiospermum detected in sputum three years prior deterioration, but the finding was disregarded, and one case (8%) was treated with antibiotics without finding etiological evidence. Fortunately, all of the above nine patients with delayed diagnosis were effectively treated after diagnosis of S. apiospermum infection. Out of the 25 reported cases, prognosis was not mentioned in two cases, in the remaining 23 cases mortality rate was 8.7% (2/23), cure rate was 82.6% (19/23), and 8.7% (2/23) of the patients showed improvement in their conditions. Of the cases that received only antifungal therapy, one died (6.7%, 1/15 cases). All four patients who received only surgical therapy were cured. Of the patients who received surgery in combination with antifungal therapy, treatment was effective in five cases (83.3%, 5/6 cases). The majority of hosts with normal immune function had a favorable prognosis, however, factors such as prolonged disease duration, underlying diseases, and delayed diagnosis and treatment may have caused the death.

S. apiospermum is widely distributed in various environments, such as contaminated water, wetlands, sewage, and saprobic heritage [28]. Most of the infections occur in patients with immune deficiency, such as those with AIDS, malignant tumors, long-term use of immunosuppressants or glucocorticoids, and organ transplantation, which can cause fatal disseminated infection [29‐32]. Additionally, it can occur in patients with normal immune function [4‐27]. Our literature review revealed that 11 patients (44%) had a history of pulmonary tuberculosis infection, which was consistent with Kantarcioglu et al.‘s hypothesis that pulmonary tuberculosis infection was the main risk factor for S. apiospermum pulmonary infection [33].

It has been reported that the risk factors for S. apiospermum infection in immunocompromised patients include lymphopenia, neutropenia, and serum albumin levels of < 3 mg/dL [30]. In immunocompetent patients, the main risk factors for S. apiospermum infection are surgery or trauma [34], and the lung and upper respiratory tract are the most infected sites. These infections fall into the following categories: Transient local colonization, bronchopulmonary saprobic involvement, fungus ball formation, and invasive S. apiospermum pneumonia [1]. Among the clinical features of S. apiospermum pulmonary infection, fever is the most common clinical sign and symptom in most cases, and other common symptoms are cough, expectoration, hemoptysis, dyspnea, and pleuritic chest pain [35]. The imaging manifestations of S. apiospermum pulmonary infection are similar to those of other infections, such as the formation of fungus balls in preexisting cavities, which is difficult to differentiate from an Aspergillus ball using radiograms. It may also exhibit solitary or multiple nodular lesions with or without cavitation, focal, lobar, or bilateral diffused infiltration [1]. Consistent with our literature review, S. apiospermum infection is frequently misdiagnosed as pulmonary aspergillosis or tuberculosis given the non-specific imaging features [6, 9, 11, 17]. The imaging of our patient presented thick-walled cavities in the right upper lobe, with uneven thickness, an irregular shape, and adjacent pleural adhesion, which are non-specific for pulmonary infections caused by S. apiospermum. Additionally, this patient experienced intermittent right chest pain and occasional dry cough for 8 months without an obvious trigger, which is consistent with tuberculosis symptoms. Prior to admission to our hospital, X-ray and CT conducted at another hospital was suggestive of pulmonary tuberculosis. Therefore, since tuberculosis was highly suggested based on symptoms and imaging, with no apparent risk factors for fungal infections, empirical anti-tuberculosis therapy was initiated prior to antifungal therapy consistent with other reports [4, 36, 37].

S. apiospermum infection can be diagnosed by microbiology (including direct staining and culture), histopathology, and polymerase chain reaction to identify fungal DNA [38‐41]. Additionally, serology can aid in the diagnosis as S. apiospermum infection through antigen detection using counter-immunoelectrophoresis and enzyme-linked immunosorbent assay [42, 43]. However, owing to the cross-reactions with antigens from other fungi such as Aspergillus spp, this method was not reported in cases [43]. To the best of our knowledge, this is the first reported case to use mNGS of BALF in the diagnosis of pulmonary S. apiospermum infection. Delays in diagnosis and treatment of S. apiospermum infection can be fatal, particularly in immunocompromised patients. mNGS can provide rapid and reliable method and offer a valuable diagnostic support, thereby avoiding delays in diagnosis and treatment.

In immunocompromised patients, infections caused by S. apiospermum are difficult to treat and usually fatal, whereas immunocompetent hosts had a better prognosis [1]. S. apiospermum infection is difficult to treat as it has been reported to be resistant to many antifungal agents, such as fluconazole, ketoconazole, flucytosine, terbinafine, itraconazole, and liposomal amphotericin B, however, it is susceptible to voriconazole, and a few studies have reported its efficacy in the treatment of S. apiospermum infection [5, 29, 44, 45]. According to the literature, surgical excision is an effective treatment for infections caused by S. apiospermum when lesions are localized [1]. Even in immunocompetent patients, infections caused by this pathogen often require surgical excision [1]. According to Liu et al.‘s a meta-analysis and systematic review of pulmonary S. apiospermum infection, more than half of the immunocompetent patients with pulmonary infection received surgical treatment, however, this did not cause a better overall survival rate [46]. However, since antifungal therapy failure is more common in immunocompromised patients, surgical resection may help to improve survival rates, whereas immunocompetent patients treated with antifungal therapy alone may have a good prognosis [46]. The overall mortality for pulmonary S. apiospermum infection in patients with the normal immune function was 12.5% (5/40), and among them who received surgery, the mortality was 9.09% (2/22), while the patients without surgery had a mortality of 16.67% (3/18) [46]. Our literature review revealed that the total mortality, the rate of patients who were cured, and improvement rates of 25 patients with normal immune function were 8.7%, 82.6%, and 8.7%, respectively. One patient who received antifungal treatment alone died (6.7%, 1/15), whereas four patients who received surgical treatment were cured, and five patients (83.3%, 5/6) responded favorably to surgery combined with antifungal therapy. In this case, the patient’s immune function and lung structure were normal. The reasons for surgical excision were as follows: (1) Based on the PET-CT report, it was suggested that the local metabolic activity of the upper lobe of the right lung was high (SUVmax = 2.8), and peripheral gonadal carcinoma was suspected; (2) Following antifungal treatment, the foci were not healed, and the possibility of pulmonary fungal infection complicated with lung cancer could not be excluded. The surgery aimed to remove the foci and actively resect the pulmonary tumor simultaneously based on a reported case of pulmonary S. apiospermum infection with pulmonary tumorlets in an immunocompetent patient [5]. The patient was followed up for 10 months after surgery, and the symptoms of dry cough and chest pain had improved, with the chest CT indicating effective treatment.

Based on our case and literature review, despite the absence of trauma or surgery, people with normal immune function and lung structure can also be infected with S. apiospermum. This case highlights mNGS in the clinical diagnosis of pulmonary invasive fungal disease. For traditional culture fail to provide clear pathogenic evidence, it is a rapid and reliable test to avoid the adverse consequences of delayed diagnosis and treatment. The combination of antifungal therapy and surgery is effective in the treatment of local lesions of pulmonary infection caused by S. apiospermum in hosts with normal immune function, especially when patients suffers from S. apiospermum infection combined with tumors.