Characteristics of Viral Pneumonia in Immunocompromised and Immunocompetent Patients: A Retrospective Cohort Study

Background: Viral pneumonia has a high incidence and mortality and often presents with bacterial or fungal infections. However, only a few studies have examined viral infection in immunocompromised patients. In this study, we compared the clinical and etiologic characteristics of viral pneumonia in immunocompetent and immunocompromised patients. Methods: We retrospectively recruited patients hospitalized with viral pneumonia from 6 academic hospitals in China between August 2016 and December 2019. We measured the prevalence of comorbidities, coinfections, nosocomial infections, and in-hospital mortalities. Results: Of the 806 patients, 370 were immunocompromised and 436 were immunocompetent. Cytomegalovirus (CMV) was most common (58.1%) in immunocompromised patients, followed by inuenza A virus (IFV-A, 21.4%), respiratory syncytial virus (RSV, 19.2%), and parainuenza virus (PIV, 7.3%). IFV-A (46.1%) was the most common in immunocompetent patients, followed by RSV (20.6%), adenovirus (AdV, 10.6%), PIV (10.1%), and rhinovirus (HRV, 9.2%). Disease severity and in-hospital mortality of immunocompromised patients were higher than those of immunocompetent patients. Pneumocystis jirovecii pneumonia (PCP) (22.4%), Aspergillus (14.1%) and bacteria (13.8%) were most frequent coinfections in immunocompromised patients as to Aspergillus (10.8%), bacteria (7.1%) and mycoplasma (5.3%) in immunocompetent patients. Viral shedding was signicantly longer in immunocompromised patients. Conclusions: Immunocompromised patients have a high frequency of coinfections, and persistent viral shedding makes them contagious for prolonged periods. Most deaths were reported among those with CMV and two-or-more viruses, and we found the same


Data collection
The following data were collected on patient and disease characteristics, initial oxygenation strategy, laboratory and microbiological data (blood, nasopharyngeal swabs, sputum, and/or bronchoalveolar lavage samples; bacterial or fungal cultures; viral nucleic acid detection; and antibiotic susceptibility patterns), associated organ dysfunction, and patient outcomes at hospital discharge.

Microbiological methods
Microbiological samplings were performed, bronchoalveolar lavage (BAL) samples were obtained according to clinical indication or judgement of the attending physician. Sputum, BAL samples or nasopharyngeal swabs were performed for atypical pathogen and viral PCR ampli cation tests .Respiratory viruses including CMV, RSV, IFV types A and B, PIV, HRV, human metapneumovirus (HMPV), or adenovirus (AdV) and Mycoplasma pneumoniae, Chlamydia pneumoniae, L. pneumophila , Pneumocystisjirovecii (PCP) were detected in nasopharyngeal swab, sputum, endotracheal aspirate (ETA), or BAL uid using reverse-transcription real time polymerase chain reaction (RT-PCR) (Shanghai Zhijiang Biological Technology, China). Sputum, ETA, BAL samples were evaluated for bacteria cultures and fungal cultures; The Platelia Aspergillus test was used for galactomannan detection (Bio-Rad Laboratories, Marnes-la-Coquette, France).

Pathogen-speci c diagnostic criteria
For diagnosing pneumonia caused by Aspergillus, one or more of the following criteria were required: (1) histopathologic or direct microscopic evidence of dichotomous septate hyphae with a positive culture for Aspergillus from tissue, (2) a positive Aspergillus culture from BAL uid, (3) a galactomannan optical index in BAL uid ≥ 1, (4) a galactomannan optical index in serum ≥ 0.5; (5) Aspergillus species identi ed by culture characteristics and microscopically [16,17].
The diagnosis of Pneumocystisjirovecii pneumonia (PCP) required one of the following: (1) high-resolution computed tomography imaging showing diffuse ground glass opacity with patchy distribution; (2) mycological criteria: microscopic examination of the respiratory sample revealing the presence of Pneumocystis cystic or trophic forms; or (3) a positive PCR test for Pneumocystis DNA [18].
Coinfection was considered if bacteria or fungi were isolated from lower respiratory tract specimens (qualified sputum, endotracheal aspirate, and BAL) and/or it was indicated by blood samples within 48 h of hospitalization. Nosocomial infection was diagnosed when patients showed clinical signs or symptoms of pneumonia or bacteremia and had a positive culture of a new pathogen obtained from lower respiratory tract specimens and/or blood samples taken ≥ 48 h after admission.

Statistical analysis
The demographics, clinical characteristics, and pathogen testing results were expressed as mean (± standard deviation), median (interquartile range), or numbers (percentage). Group comparisons were conducted using the Student's t-test or Wilcoxon rank-sum test for continuous variables with and without normal distributions, respectively. Categorical variables of the two groups were compared using the c 2 test.
Statistical analyses were performed using SPSS version 19.0 (SPSS, Inc., Chicago, Illinois). All tests were two-sided, and P-values < 0.05 were considered statistically signi cant.

Patient and public involvement
No patient or the public were involved in the development of the research question, study design, recruitment, and the conduct of the study.
Patients with nephrotic syndrome and chronic glomerulonephritis had a lower oxygenation index and lymphocyte count, higher PCP infection rate, more noninvasive ventilator use and need for ICU treatment, and the highest in-hospital mortality rate. The in-hospital mortality rate of patients with connective tissue disease was the second highest (30%), while that of solid-organ transplantation patients was the lowest (10%) ( Table 4). Viral shedding was signi cantly longer in immunocompromised hosts than in immunocompetent hosts (Table 5).

Discussion
This study was a large-scale, multi-center, retrospective study of the etiology and clinical risk factors for CAP in immunocompromised patients. The main ndings were as follows: (1) The disease severity and in-hospital mortality rate of immunocompromised patients were higher than those of immunocompetent patients; (2) CMV was more common in the immunocompromised group, and IFV-A, HRV, and AdV were more common in the immunocompetent group; (3) Among the coinfections of immunocompromised patients, PCP was the main pathogen, followed by Aspergillus and bacteria, and in the immunocompetent group, Aspergillus was the most common pathogen, followed by bacteria and mycoplasma; (4) The in-hospital mortality rates of the non-IFV infection groups were lower than those of the CMV group and the two-or-more viruses group, ; (5) The in-hospital mortality rate of patients with nephrotic syndrome or chronic glomerulonephritis was the highest, while that of solid-organ transplantation patients was the lowest; (6) Whether IFV (H1N1) or RSV, the period of viral shedding was signi cantly longer in immunocompromised hosts that in immunocompetent hosts.
In recent years, several studies have focused on respiratory virus infection in patients after hematopoietic cell transplantation (HCT) [19][20][21][22][23][24]. Sachiko studied HRV in the lower respiratory tract of patients with HCT and found that 55% of patients had coinfections and that the 90-day mortality rate was 41% [19], which was similar to lower respiratory tract infection caused by RSV, PIV, or IFV [20][21][22]. Among immunocompromised patients with IFV pneumonia, nearly 60% had an associated infection with at least one other organism, and the mortality rate among these patients was between 15-30% [23]. The mortality rate among hematologic malignancy patients with RSV was approximately 18%, and in HCT recipients who developed RSV lower respiratory tract infections, it can be as high as 83%. [24].
Similarly, our study showed that the disease severity and in-hospital mortality (26.5% vs 18.8%) of immunocompromised patients were higher than those of immunocompetent patients.
CMV, especially with PCP coinfection, has a high mortality rate in immunocompromised patients [25,26]. However, at present, there are few comparative studies examining CMV and other respiratory viruses. Our ndings indicate that non-CMV viral infections may also have PCP coinfection albeit less frequent. Comparably [27][28], we found no difference in the rate of virus-aspergillus coinfections irrespective of the type of viral infection.
The disease severity, complications, and outcomes in immunocompetent patients with CAP were similar between IFV and non-IFV related respiratory diseases [29][30][31]. We found that the in-hospital mortality was signi cantly higher in immunocompromised patients with CMV or two-or-more viruses infections. This suggests that when viral infection is suspected in an immunocompromised host, healthcare providers should look for the presence of CMV and other viral etiology, as early diagnosis and treatment are essential to improve outcome. We also found the highest mortality rate in patients with nephrotic syndrome or chronic glomerulonephritis, which there was a higher rate of CMV and PCP infection. This indicates that routinely screening for PCP and CMV infections should be considered in this group.
It has been suggested that viral respiratory infections in immunocompromised patients involves persistent viral shedding, making them contagious for prolonged periods [32][33][34]. Memoli reported the viral shedding period of immunocompromised patients was longer than that of immunocompetent patients with IFV pneumonia (19.04 vs. 6.38 days, respectively; P < 0.05) [33]. Virus detection for more than 30 days was reported in 29% of infected patients with hematological disorders [32]. In this study, we demonstrated that bothH1N1 and RSV infections have longer viral shedding period in immunocompromised hosts, which made it necessary to extend the duration of antiviral therapy.
There were several limitations to this study. First, it had a retrospective design and might not capture all patients. Second, not every patient with pneumonia underwent a full array of pathogen testing. As such, the pathogen identi cation and diagnosis could have been incomplete. Third, many patients had been administered antibiotics before. Despite these limitations, our results were consistent with the literature and provided a detail insight into the clinical characteristics, pathogenic characteristics, and outcomes of different viral infections in immunocompromised hosts.