Coinfection and superinfection in ICU critically ill patients with severe COVID-19 pneumonia and influenza pneumonia: are the pictures different?

Background Similar to influenza, coinfections and superinfections are common and might result in poor prognosis. Our study aimed to compare the characteristics and risks of coinfections and superinfections in severe COVID-19 and influenza virus pneumonia. Methods The data of patients with COVID-19 and influenza admitted to the intensive care unit (ICU) were retrospectively analyzed. The primary outcome was to describe the prevalence and pathogenic distribution of coinfections/ICU-acquired superinfections in the study population. The secondary outcome was to evaluate the independent risk factors for coinfections/ICU-acquired superinfections at ICU admission. Multivariate analysis of survivors and non-survivors was performed to investigate whether coinfections/ICU-acquired superinfections was an independent prognostic factor. Results In the COVID-19 (n = 123) and influenza (n = 145) cohorts, the incidence of coinfections/ICU-acquired superinfections was 33.3%/43.9 and 35.2%/52.4%, respectively. The most common bacteria identified in coinfection cases were Enterococcus faecium, Pseudomonas aeruginosa, and Acinetobacter baumannii (COVID-19 cohort) and A. baumannii, P. aeruginosa, and Klebsiella pneumoniae (influenza cohort). A significant higher proportion of coinfection events was sustained by Aspergillus spp. [(22/123, 17.9% in COVID-19) and (18/145, 12.4% in influenza)]. The COVID-19 group had more cases of ICU-acquired A. baumannii, Corynebacterium striatum and K. pneumoniae. A. baumannii, P. aeruginosa, and K. pneumoniae were the three most prevalent pathogens in the influenza cases with ICU-acquired superinfections. Patients with APACHE II ≥18, CD8+ T cells ≤90/μL, and 50 < age ≤ 70 years were more susceptible to coinfections; while those with CD8+ T cells ≤90/μL, CRP ≥120 mg/L, IL-8 ≥ 20 pg./mL, blood glucose ≥10 mmol/L, hypertension, and smoking might had a higher risk of ICU-acquired superinfections in the COVID-19 group. ICU-acquired superinfection, corticosteroid administration for COVID-19 treatment before ICU admission, and SOFA score ≥ 7 were independent prognostic factors in patients with COVID-19. Conclusion Patients with COVID-19 or influenza had a high incidence of coinfections and ICU-acquired superinfections. The represent agents of coinfection in ICU patients were different from those in the general ward. These high-risk patients should be closely monitored and empirically treated with effective antibiotics according to the pathogen.


Introduction
The coronavirus disease 2019 (COVID-19) outbreak has caused a global health crisis and led to a high rate of critical illness (1).Although the Omicron variant might cause milder cases, mortality increased during the Omicron period, even in a highly vaccinated population (2).Influenza virus infection is also a global public health problem that has caused major morbidity and mortality in many countries (3).Both predispose patients to coinfections and superinfections, especially with bacteria, which could promote severe disease and necessitate timely diagnosis (4)(5)(6).
Coinfections in patients with COVID-19 seem uncommon, ranging from 0 to 19% (7)(8)(9)(10)(11)(12).However, similar to influenza, superinfections are common in COVID-19, which can follow the initial infection phase or occur during recovery (13).Early recognition of patients with a high risk of coinfections/superinfections is important for the early use of antibiotics and in implementing measures to limit the possibility of superinfection, which may, in turn, reduce mortality, especially in the intensive care unit (ICU).It could even reduce antibiotic resistance caused by the unnecessary use of antibiotics.However, as of March 2023, the risk factors and characteristics related to coinfections/superinfections in COVID-19 and influenza cases in the same ICU have not been described.
Therefore, we aimed to describe the prevalence, pathogenic distribution and clinical characteristics of coinfections/superinfections in patients with COVID-19 and influenza in the same ICU.We also explored the predictive factors of coinfections/superinfections, which might help choose the appropriate application time and variety of antibiotics.

Study design and patients
This retrospective observational study included patients with severe influenza virus pneumonia from December 1, 2017, to February 28, 2022, and patients with severe COVID-19 from December 1, 2022, to February 28, 2023, admitted to the respiratory ICU (RICU) of China-Japan Friendship Hospital in China.Patients younger than 18 years of age were excluded.
Demographics, clinical data, and results of microbiological examinations were extracted from the electronic medical record management system.Due to the study's retrospective nature, the need for informed consent from the patients or their legal guardians was waived.The study was approved by the institutional ethics committees of China-Japan Friendship Hospital.
The primary outcome in our study was a description of the prevalence and pathogenic distribution of coinfections and ICU-acquired superinfections in patients with COVID-19 and influenza.The secondary outcome was an evaluation of the independent risk factors for coinfections/ICU-acquired superinfections at ICU admission.Multivariate analysis of survivors and non-survivors was performed to investigate whether coinfections/ ICU-acquired superinfections was an independent prognostic factor.

Diagnostic criteria
All patients with influenza infection underwent testing using nasopharyngeal swabs or lower respiratory tract (LRT) specimens.Two methods were used for laboratory diagnosis: polymerase chain reaction (PCR) and serological testing (14,15).Severe influenza virus pneumonia was defined as the presence of influenza infection and severe community-acquired pneumonia (CAP) (16).
SARS-CoV-2 infection was confirmed via viral genome positivity in PCR or antigen, according to the Diagnosis and Treatment of Novel Coronavirus Infection Interim Guidance Report by the National Health Commission of the People's Republic of China (17).Severe COVID-19 was defined as any one of the following: (1) shortness of breath with respiratory rate ≥ 30 per minute; (2) pulse oxygen saturation ≤ 93% in the resting state; and (3) partial pressure of oxygen/fraction of inspiration oxygen (PaO 2 /FiO 2 ) ≤300 mmHg.Critically ill patients satisfied any one of the following criteria: (1) respiratory failure where invasive ventilation is needed, (2) shock, and (3) failure of any other organ and need for ICU care (17).

Definitions
Coinfection was defined as pathogen detection via diagnostic test at the time of or within the first 48 h of ICU admission.If detection occurred ≥48 h after ICU admission, the infection was defined as an ICU-acquired superinfections.These tests included cultures of the respiratory tract secretions (sputum, bronchoalveolar lavage fluid, and endotracheal aspiration), multiplex respiratory PCRs performed on a nasopharyngeal swab or on respiratory tract secretions, metagenomic next-generation sequencing (mNGS) for respiratory tract secretions, and urinary antigen test for Streptococcus pneumoniae.The final diagnosis of causative agents was made according to the clinical physician expert groups combining imaging and clinical symptoms.Tracheobronchitis was defined as follows: The combination of fever (>38°C) with no other recognizable cause, new or increased sputum production, and a positive tracheal aspirate culture without radiographic evidence of pneumonia (18).Pneumonia was defined by the presence of new or progressive radiographic infiltrate associated with two of the following criteria: (1) Fever, temperature above 38°C; (2) leukocyte count above 10 × 10 9 /L or below 4 × 10 9 /L, and (3) purulent endotracheal

Statistical analysis
Continuous variables are presented as mean ± standard deviation or median (interquartile range) and compared using a t-test or Mann-Whitney U test.Categorical variables were described using percentages and compared using the chi-square or Fisher's exact tests.All significance tests were two-tailed, and statistical significance was defined as p ≤ 0.05.Factors associated with coinfections/ICU-acquired superinfections were evaluated using univariate and multivariate analyzes.The multivariate analysis included all variables (p < 0.1) from the univariate analysis and the factors reported to be associated with coinfections/ICU-acquired superinfections.All results were analyzed using SPSS for Windows, version 26 (IBM Corp, Armonk, NY, United States).

Risk factors for coinfections
The univariate analysis of patients with COVID-19 showed no significant differences in age, APACHE II, SOFA, and comorbidities on diagnosis between patients with and without coinfections (Supplementary    2).
In the COVID-19 group, the hospital survival rate was lower in patients with ICU-acquired superinfections (18.5% vs. 56.5%,p < 0.001).By comparing survivors and non-survivors, we found that ICU-acquired superinfection (OR: 3.677; 95%CI: 1.518-8.906;p = The Prevalence of ICU -acquired infection distribution of Pathogens in patients with Inluenza.2).However, the hospital survival rate was similar regardless of ICU-acquired superinfection in patients with severe influenza virus pneumonia.

Discussion
In this study, the prevalence of respiratory coinfections/ ICU-acquired superinfections in the COVID-19 and influenza cohorts were 33.3%/43.9and 35.2%/52.4%,respectively.Bacteria were isolated more frequently not only in coinfection but also in ICU-acquired superinfections cases.The most common bacteria identified in coinfection cases were P. aeruginosa, E. faecium, and A. baumannii in patients with COVID-19 and P. aeruginosa, A. baumannii, and K. pneumoniae in patients with influenza.Besides, a significant higher proportion of coinfection events was sustained by Aspergillus spp.The COVID-19 group had more cases of ICU-acquired A. baumannii, C. striatum and K. pneumoniae.P. aeruginosa, A. baumannii, and K. pneumoniae were the three most prevalent pathogens in the influenza cases with ICU-acquired superinfections.In addition, ICU-acquired superinfection was an independent prognostic factor in the COVID-19 group.
Our study demonstrated a higher proportion of patients with coinfections in the COVID-19 group (33.3%).Previous studies and reviews have reported variable coinfection rates, ranging from 3.5 to 14%, focusing on patients from general wards with bacterial infections (7,8,11,12,(22)(23)(24).Only a few studies have reported coinfection data from COVID-19 cohort in the ICU (26.9-28%) (11,25,26).The coinfection rate in our ICU was higher than that in others.In addition, the main pathogens were gram-negative bacilli and Aspergillus spp., which was not in accordance with previous studies that reported that S. aureus and other common community-acquired bacteria were prevalent in coinfections (8,11,26).In our influenza cohort, the prevalence of coinfections was similar to most of previous study (4,27), but higher than others (28,29).
Meanwhile, unlike other studies, which reported S. aureus, S. pneumoniae and Hemophilus influenza were the most commonly isolated co-infectious agents (4,5,27,29), we found typical pathogens of nosocomial infections such as A. baumannii and P. aeruginosa.Some factors may explain this phenomenon.First, in our study, the time from onset to ICU admission was longer than in other studies (9 vs. 3-5.6days).Only, 17.2% of the patients in our study were admitted directly from the emergency or outpatient department.The rest were hospitalized in general wards and other ICUs before being transferred to the ICU in our study.Second, we supposed that it was due to the inclusion bias in different studies but not the actual situation.The diagnostic criteria for coinfection were not standardized, which confounded pathogenicity and colonization.Most of studies that assumed coinfection as the pathogen were detected.In addition, the time of diagnosis of coinfection was not uniform.Many studies included secondary infection or mixed coinfection and secondary infection.Obviously, the proportion of coinfection with Aspergillus spp. was quite high in our study.Awareness of the possibility of fungal coinfection in COVID-19 is essential to initiate empirical antifungal therapy and fungal infection test as early as possible, which assisted in preventing severe illness and death from coinfection.
In the COVID-19 cohort, patients aged 50-70 years had the highest prevalence of coinfection (OR: 2.680), which was in agreement with studies that reported that older adult patients tended to have coinfection (30,31).Hughes et al. (8) indicated that the age group of 55-81 years were predisposed to coinfection, which concorded with our study (50-70 years).APACHE II ≥18 and CD8+ T cell ≤90/μL were also independent risk factors for coinfection.These findings might imply that critical conditions due to disease and declined immune ability due to aging are the causes of coinfection in the older adult (32).In addition, BMI ≤23.5 kg/m 2 and WBC ≥10 × 10 9 /L were predictive factors of influenza coinfection.A higher WBC count was a manifestation of coinfection.A large prospective study conducted by Langouche et al. reported that critical illness evokes adipose tissue accumulation of alternatively active M2 macrophages, which have local anti-inflammatory functions (33).Patients with a lower BMI may have weak anti-inflammatory abilities.Our study showed that patients with high-risk factors could be treated empirically with antibiotics after ICU admission.Antibiotics should cover both gram-positive and gram-negative bacteria.It should also be noted that patients with COVID-19 may have coinfection with fungi, and these patients should be promptly treated with antifungal therapy.
The pathogenesis of influenza coinfection has been elaborated.Influenza virus contributes to respiratory epithelial cell damage, bacterial mucociliary clearance dysfunction, and immune response dampening, enabling increased bacterial adherence and invasion (34,35).As for COVID-19, the mechanism of the pathogenesis of coinfection remains indistinct, and we lack evidence to support the bacteria-virus association (7).
The incidence of ICU-acquired superinfections was similar in the COVID-19 and influenza cohort (43.9% vs. 53.4%).In both cohorts, gram-negative bacilli were responsible for most ICU-acquired superinfections.A. baumannii, K. pneumoniae, and P. aeruginosa were the most commonly identified bacteria.However, the COVID-19 Further, the incidence of MDR bacteria was similar between COVID-19 and influenza.In the COVID-19 group, 2 patients had ICU-acquired superinfections with Aspergillus spp.and Rhizopus spp.They all experienced kidney transplantation and took immunosuppressants for long periods, which accounted for the immune disorder.In a multicenter cohort study conducted by Rouze et al. (37), the incidence of ventilator-associated lower respiratory tract infection was significantly higher in the COVID-19 group (50.5%) than in the influenza group (30.3%).However, we did not reach this conclusion.The shorter duration of IPPV for COVID-19 in our study may have contributed to this difference.
Like VAP in other diseases (38), ICU-acquired superinfection was associated with longer IPPV time, ICU stay and hospital stay.
Another key finding from our study was that ICU-acquired superinfection was associated with a reduced survival rate in patients with COVID-19.This results agrees with those of other studies that have shown a negative association between secondary infection and an increased risk of death (39,40).
This study identified many predictive factors for ICU-acquired superinfection of COVID-19.The decrease in CD8+ T cells and the increase of IL-8 levels indicated the cytokine storm activation and subsequent immunosuppression (41).Immune response dysfunction may be associated with a higher risk of ICU-acquired superinfection.Moreover, high blood glucose levels, hypertension, and smoking have all reported to be related to secondary infection (42)(43)(44).Based on the above results, early identification of high-risk patients for ICU-acquired superinfection and active examination for pathogens will facilitate timely and appropriate antibiotics, which is beneficial to prognosis.To our knowledge, this is the first study to focus on the coinfections/ICU-acquired superinfections of COVID-19 versus influenza ICU patients in Asia.We clearly defined the time of sample positivity time from the date of ICU admission (<48 h vs. ≥ 48 h).However, this study had several limitations.First, this was a single-center retrospective study, and the study population was relatively small; therefore, possible selection and report biases exist, and it is difficult to generalize the results to other centers.Second, ICU management, ICU isolation measures, sampling methods, and infection diagnostic techniques differed between the COVID-19 and influenza pandemics.In addition, we distinguished infection and colonization using clinical judgment rather than bacterial count, which may have affected the detection rate.Most importantly, some patients were exposed to antibiotics and stayed in general wards or other ICUs before our ICU admission.This could have impacted pathogenic microorganism detection and potentially underestimated or overestimated the real coinfection rate.

Conclusion
Coinfections and ICU-acquired superinfections were frequent not only in COVID-19 patients but also in influenza patients admitted to the ICU.The represent agents of coinfections in ICU patients were different from those in the general ward.Our study provides evidence supporting close monitoring and empirical choice of antibiotics according to the pathogen for COVID-19 and influenza cases at risk of coinfections/ICU-acquired superinfections in the ICU.Apart from the limited study population, ICU management, ICU isolation measures, sampling methods, and infection diagnostic techniques may have impact on we conducted a multivariate analysis.APACHE II ≥18 (OR: 2.309; 95%CI: 1.005-5.304;p = 0.049), CD8+ T cells ≤90/μL (OR: 2.466; 95%CI: 1.084-5.612;p = 0.031), and 50 < age ≤ 70 years (OR: 2.680; 95%CI: 1.183-6.072;p = 0.018) were independent risk factors for coinfection (Table vs. 8 (5.5-11.5),p = 0.001].Patients with coinfections had a lower body mass index (BMI) than those without coinfections [23.38 (21.40-25.90)vs. 25.34 (22.49-28.01),p = 0.012].The white blood cell count and prothrombin time were higher in patients with coinfection (Supplementary Tables

FIGURE 1 The
FIGURE 1The Prevalence of coinfection and distribution of Pathogens in patients with COVID-19.

FIGURE 2 The
FIGURE 2The Prevalence of coinfection and distribution of Pathogens in patients with Inluenza.

FIGURE 4
FIGURE 4 (21)al infection was diagnosed according to the taskforce report on the diagnosis and clinical management of COVID-19 associated pulmonary aspergillosis(20)and clinical practice guideline for the management of candidiasis: 2016 Update by the Infectious Diseases Society of America(21).

Table 4 )
. Combining the factors reported in the literature associated with coinfection,

TABLE 1
Pathogens in COVID-19 and influenza patients with co-infections and ICU-acquired superinfections.

TABLE 2
Independent risk factors for coinfection of COVID-19 and influenza.

TABLE 3
Treatment and outcomes of COVID-19 and influenza patients with coinfection.

TABLE 4
Treatment and outcomes of COVID-19 and influenza patients with ICU-acquired superinfections., continuous renal replacement therapy; ECMO, extracorporeal membrane oxygenation; IPPV, intensive positive-pressure ventilation; ICU, intensive care unit.our conclusion.A large-scale and well-designed RCT is needed in the future. CRRT