At the end of 2022, the global COVID-19 outbreak resumed, with the Omicron variant becoming dominant. This variant has numerous mutations that boost its ability to evade humoral immunity and increase transmissibility (Rana et al., 2022). Although Omicron infections are generally less severe, the extreme transmissibility led to a surge in cases and an increase in critically ill patients (Brüssow, 2022; Wu Y. et al., 2022). COVID-19 patients in intensive care units (ICUs) face higher risks of co-infections and mortality (Binkhamis et al., 2023). Pulmonary aspergillosis, an opportunistic infection linked to mechanical ventilation, predominantly affects ICU patients with chemotherapy, transplants, or immunosuppression (Thompson et al., 2020). During COVID-19 epidemics, the virus was found to damage alveolar epithelial and tissue endothelial cells, disrupting lung barriers (Short et al., 2016). Combined with prolonged hospital stays, steroid and immunomodulator use, and the need for invasive mechanical ventilation in most patients with acute respiratory distress syndrome, this makes critically ill COVID-19 patients more prone to bacterial and opportunistic fungal lung infections (Aspergillus, Candida, Cryptococcus, and Trichinella), with Aspergillus being the most common (Chiurlo et al., 2021). Some studies have reported that the prevalence of CAPA in patients with severe COVID-19 ranges from 2.4% to 34.3% (Kariyawasam et al., 2022). The prognosis for severe CAPA is relatively poor, characterized by high morbidity and mortality rates that range from 22.2% to 71.4% (Kariyawasam et al., 2022; Lamoth et al., 2021; Pasquier et al., 2021). This situation poses a significant threat to public health. Since the beginning of the COVID-19 pandemic, many studies on CAPA have been reported, and the prevalence of CAPA in COVID-19 ICU patients reported in different studies varies widely, which may be related to inconsistent surveillance methods and diagnostic criteria (Chong et al., 2022). In 2020, the European Confederation of Medical Mycology/International Society for Human and Animal Mycoses consensus developed relevant diagnostic criteria and disposition consensus for CAPA. The diagnosis of Aspergillosis was categorized as Proven CAPA (histopathological confirmation or Aspergillus positive in sterile samples), Probable CAPA (host factors + clinical deterioration + mycological evidence e.g., BALF GM ≥1.0), and Possible CAPA(clinical suspicion with insufficient mycological evidence/non-specific findings), and the relevant host factors that predispose to aspergillosis were defined (Asperges et al., 2024). While this consensus aids in diagnosing and treating CAPA, it remains a clinical challenge (Skóra et al., 2023).

There are few studies on the incidence, prognosis, and associated risk factors of CAPA in the Omicron variant. This retrospective study analyzed CAPA incidence in the Omicron variant, identified risk factors, and assessed their relationship with patient prognosis. The findings may guide future viral pneumonia treatment, reduce secondary pulmonary mycoses, and improve severe COVID-19 pneumonia survival rates.

With the global spread of COVID-19, there are more and more reports about patients with combined bacterial and fungal infections, among which fungal infections, especially Aspergillus infections, whose higher infection rate and mortality pose a severe threat to the life and health of patients, so it is essential to diagnose the co-infections at an early stage and to make the correct clinical interventions [14]. In our study, the incidence of COVID-19 co-infection with pulmonary mycosis was 29.3%, with a mortality rate of 52.9% (9/17) ( Table 2 ). The mortality rate of COVID-19 patients with co-infections with bacterial fungi was as high as 57.14% (4/7). In comparison, the 90-day mortality rate of non-CAPA patients was significantly lower 24.4% (10/41) than that of patients with co-infections with fungal infections (P = 0.035) ( Table 2 ). Graciela et al. described the clinical, microbiological, and radiological characteristics of 86 patients diagnosed with probable CAPA in a Mexican hospital. They described the mortality rate, which was as high as 60% in their CAPA patients (Hernández-Silva et al., 2024). In a meta-analysis, the incidence and mortality of CAPA in patients admitted to the ICU were estimated to be 10.2% and 54.9% (Mitaka et al., 2021), and their mortality rate remained high. A meta-analysis by Woon et al. included a total of 729 patients with COVID-19, of whom 14.9% (109/729) were diagnosed with CAPA, with a prevalence ranging from 3.3 to 34.4% between 3.3 and 34.4%, with an all-cause hospitalization mortality rate of 42.6% (OR 3.39; 95% CI,1.97-5.86; P < 0.001) (Chong et al., 2022). It is evident that despite the overall better prognosis of mildly ill patients with Omicron infections, there is a high incidence of CAPA in critically ill patients and an extremely high mortality rate in patients with CAPA.

In treating COVID-19 pneumonia, glucocorticoids, and immunosuppressants have been used as standard therapeutic tools, which play an essential role in controlling the inflammatory response and reducing the mortality of the patients. However, when steroids and immunosuppressants are applied, the risk of CAPA in patients increases. In our study, whether steroids therapy was used or not had no effect on whether CAPA occurred; however, with the prolongation of steroids use (P = 0.002, OR: 1.603 (95% CI: 1.181~2.176)) and the increase in cumulative dose of steroids use ((P < 0.001, OR: 1.012 (95% CI: 1.009~1.015) ( Figure 2 ). The incidence of CAPA increased. Hashim et al. concluded in a meta-analysis of 21 studies and 5174 patients that the risk of CAPA was associated with the use of high-dose glucocorticoids and not significantly correlated with low-dose steroids and that patients with COVID-19 were at risk of CAPA even without steroids therapy (Hashim et al., 2023). Gregoire et al. studied 141 patients with CAPA in a single-center retrospective observational study analyzing the incidence and risk factors for COVID-19-associated pulmonary aspergillosis in an intensive care unit. In univariate analyses, patients using steroids had a higher probability of developing CAPA. However, multivariate analyses did not observe an association between steroids and CAPA development (Gregoire et al., 2021). Currently, there are conflicting results in different studies about whether steroids are a risk factor for the development of CAPA, probably because steroids were heavily used as an effective treatment during the COVID-19 period. The baseline conditions of the patients, as well as the dosage of steroids used and the duration of their use, varied in each study center, resulting in conflicting results.

In the present study, we found that the incidence of CAPA increased only when glucocorticoids were used for an extended period. This may be because the steroids were used for a shorter period and did not have a significant immunomodulatory effect on the patients. In our univariate and multivariate analyses of risk factors for CAPA mortality, we found that neither the use of steroids nor the duration of steroids use significantly affected CAPA mortality ( Table 3 ). Tolizumab and baricitinib were also commonly used as immunomodulators during the COVID-19 pneumonia epidemic. Several previous studies have identified the use of tocilizumab as a risk factor for CAPA (Cadena et al., 2021; Prattes et al., 2022), and our study found that the use of tocilizumab (P = 0.020) increased the incidence of CAPA. In contrast, the use of baricitinib did not affect the presence of CAPA; in a retrospective study conducted at the National Institute of Respiratory Research (INER) in Mexico City, the incidence of CAPA at its center was only 4.13%. One factor contributing to its low prevalence was the rare use of immunomodulators such as tocilizumab at this center (Hernández-Silva et al., 2024). A meta-analysis showed that the combination of baricitinib with dexamethasone and anti-il-6 inhibitors significantly reduced 28-day mortality (Selvaraj et al., 2022); Albuquerque et al. found that the efficacy of baricitinib was not inferior to that of tocilizumab, and that baricitinib had a shorter half-life compared to tocilizumab, and the shorter half-life of baricitinib compared with tocilizumab was beneficial in reducing the risk of secondary infections (Albuquerque et al., 2023), and the present study found that the use of baricitinib did not increase the prevalence of CAPA as tocilizumab did, and the role that glucocorticosteroids and various types of immunosuppressants and immunomodulators have played in the treatment of COVID-19 pneumonia is well documented, and previous studies have confirmed that glucocorticosteroids may increase the prevalence of COVID-19 pneumonia and that glucocorticosteroids may reduce the risk of secondary infections. Previous studies have also confirmed that glucocorticoids can reduce the mortality rate of COVID-19 ventilated patients (Recovery: Randomised Evaluation of Covid-19 Therapy, 2020), but the side effects should be considered comprehensively, and steroids and immunomodulators can be used in the right amount and at the right time. In addition, we found that patients with diabetes mellitus (P = 0.018), renal insufficiency (P = 0.002), and COPD (P = 0.003) were more prone to CAPA. In the follow-up treatment and monitoring of clinical indicators of patients with COVID-19, we observed an increase in interleukin-6 (P = 0.022), mechanical ventilation (P = 0.002), and an increase in the hospitalization duration (P = 0.021), and increased type of antibiotic use (P = 0.002) were risk factors for the development of CAPA ( Table 2 ).

Currently, the incidence of bacterial co-infections in patients with COVID-19 is low, but in the intensive care unit, the incidence of co-infections with bacterial infections and the mortality rate is high due to the prolonged stay in the ICU, the need for prolonged mechanical ventilation, and the high incidence of pulmonary infections in the critically ill patients (Wu H. Y. et al., 2022), and the current reports on both bacterial and fungal co-infections in COVID-19 are extremely rare, and inherently there is no accurate incidence and prognosis of the In our study, we found that the probability of COVID-19 co-infection with both fungal and bacterial infections was about 41.18%, and the mortality rate was as high as 57.14%, and the most common bacterial strain was Acinetobacter baumannii, and some previous studies have found that most of the co-infections with bacterial infections of COVID-19 in the ICU were gram-negative (Pseudomonas aeruginosa, Enterobacteriaceae, and Klebsiella pneumoniae) (Bardi et al., 2021; Naseef et al., 2022). Our findings showed that the primary co-infected strain was Acinetobacter baumannii. In a retrospective study by Yang et al., a total of 20 critically ill patients with COVID-19, all of whom were admitted to the ICU, were enrolled. The reasons for this may lie in the different ICU environments in different study centers, the use of antibiotics, and the small number of cases preventing a uniform conclusion. All patients with CAPA had large numbers of Aspergillus found on more than two sputum cultures or BALF cultures. All patients underwent a serum GM test, which had a positive rate of 41.2% (7/17), and five patients with CAPA underwent an BALF GM test, which was positive in all cases. A previous report found the sensitivity of alveolar lavage fluid GM to be 66.7% in CAPA cases, but only 21.4% were positive for serum GM (Armstrong-James et al., 2020). We can see that BALF is vital in diagnosing CAPA. However, fiberoptic bronchoscopy is rare in many healthcare institutions because the COVID-19 virus can be transmitted by aerosol. CAPA patients with negative serum GM tests are present; some CAPA patients may be underdiagnosed. Therefore, the diagnosis of CAPA should not be limited to serum GM but should be based on sputum culture, CT manifestations, clinical symptoms, and host factors of ECMM/ISHAM.

In this study, the mortality rate of CAPA patients was 57.14% (4/7), which was much higher than the 90-day mortality rate of 24.4% (10/41) in non-CAPA patients (P = 0.004, OR: 0.28, (95% CI: 0.087~0.942)) ( Table 2 ), and among CAPA patients, the use of mechanical ventilation (P = 0.040 OR: 10.500, (95% CI: 1.115~98.914)), advanced age (P = 0.043 OR: 1.212, (95% CI: 1.006~1.460)) and significantly elevated CRP levels (P = 0.042 OR: 1.043, (95% CI: 1.002~1.078)) had a poor prognosis ( Figure 3 ), and all CAPA patients were treated with antifungal therapy when they were found to be Aspergillus, and of the 17 patients with CAPA, nine patients were treated with voriconazole, five patients were treated with esaconazole, and three patients were treated with antifungal therapy with amphotericin B. However, we found that timely antifungal therapy did not significantly improve the patient’s prognosis, which may be related to the patient’s severe condition and prolonged disease duration. For the targets of the drugs as antifungal mainly include: 1. Clinical resolution: ≥72-hour fever remission + respiratory symptom improvement (SOFA score decrease ≥2 points); 2. Microbiological clearance: Negative fungal culture/PCR from respiratory samples on sequential testing; 3. Radiographic stabilization: ≥50% reduction in pulmonary infiltrates on CT within 14 days; 4. Inflammatory normalization: CRP <20 mg/L + IL-6 <40 pg/mL sustained for 5 days (Verweij et al., 2021). The CAPAs mainly occurred in the ICUs. In patients with prolonged disease duration and poor prognosis, their COVID-19 disease duration mainly determines their mortality rate. Antifungal therapy did not improve the prognosis of either proven CAPA, probable CAPA, or possible CAPA (Russo et al., 2024; van Grootveld et al., 2023). Therefore, preventing CAPA is essential in managing critically ill patients with COVID-19.

Our study still needs some improvement. Firstly, this study is a single-center study with a small sample size, so some of the conclusions may differ from those of other centers due to the different diagnostic methods and treatments in each treatment center. Secondly, this study needs more drug resistance monitoring of Aspergillus and has limited reference value for using antibiotics to treat COVID-19 combined Aspergillus strains. Furthermore, because all patients were COVID-19 critically ill, we excluded patients who died or were automatically discharged within 48 hours of admission. However, these patients may have had a longer course of the disease and fungal infection before admission, so our study found the CAPA incidence and mortality rates. However, they were already at a high level and may be biased compared to the facts. Finally, because critically ill COVID-19 patients are too sick to be diagnosed by histology or direct microscopy, this study was limited to patients with proposed CAPA and suspected CAPA and lacked studies of patients with confirmed CAPA.

In conclusion, we found a high prevalence of CAPA (29.3%) in cases of severe COVID-19 pneumonia and a mortality rate of 52.9% in patients with CAPA. Risk factors associated with the development of CAPA include underlying diseases such as diabetes, IL-6 elevation, renal insufficiency, and chronic obstructive pulmonary disease, as well as mechanical ventilation, tocilizumab use, and prolonged hospitalization. Previous studies on the use of glucocorticoids have been controversial, with some suggesting that the use of glucocorticoids increases the incidence of CAPA and may worsen the prognosis. In contrast, others have found that using glucocorticoids does not make a significant difference in the occurrence of CAPA and leads to a favorable prognosis. However, our study found that short-term use of glucocorticosteroids in appropriate doses did not increase the incidence of CAPA and helped to improve the prognosis of patients; when glucocorticosteroids were used for a prolonged period, they led to an increase in the incidence of CAPA. Of note, mortality is significantly higher in patients with CAPA compared with non-CAPA patients, and mechanical ventilation, advanced age, and elevated C-reactive protein levels are considered poor prognostic indicators in patients with CAPA. Prevention of CAPA through careful monitoring of high-risk patients, rational use of glucocorticoids and immunomodulators, and effective infection control measures remains a top priority in managing severe COVID-19 cases.

However, we must also note the limitations of our study, including the single-centre design, small sample size, and exclusion of specific patient groups that could have biased our findings. In order to validate our findings and gain further insight into the epidemiology, risk factors, and CAPA management strategies of critically ill COVID-19 patients, future multicenter collaborative studies with larger sample sizes are warranted.