key: cord-0868650-mj9xc5fv
authors: Silva, Danielle L.; Lima, Caroline M.; Magalhães, Vanessa C.R.; Baltazar, Ludmila M.; Peres, Nalu T.A.; Caligiorne, Rachel B.; Moura, Alexandre S.; Fereguetti, Tatiani; Martins, Juliana C.; Rabelo, Lívia F.; Abrahão, Jônatas S.; Lyon, Ana C.; Johann, Susana; Santos, Daniel A.
title: Fungal and bacterial coinfections increase mortality of severely ill COVID-19 patients
date: 2021-04-20
journal: J Hosp Infect
DOI: 10.1016/j.jhin.2021.04.001
sha: 24995289f3de63fdd494c2cb337ed7e871781c0f
doc_id: 868650
cord_uid: mj9xc5fv

BACKGROUND: SARS-CoV-2 predisposes patients to secondary infections; however, a better understanding of the impact of coinfections on the outcome of hospitalized COVID-19 patients is still necessary. AIM: To analyse death risk due to coinfections in COVID-19 patients. METHODS: We evaluated the Odds of death of 212 severely ill COVID-19 patients, with detailed focus on the risks for each pathogen, site of infection, comorbidities and length of hospitalization. FINDINGS: The mortality rate was 50.47%. Fungal and/or bacterial isolation occurred in 89 patients, of which 83.14% died. Coinfected patients stayed hospitalized longer and had an increased Odds of dying (OR = 13.45, R(2)=0.31). The risk of death was increased by bacterial (OR=11.28) and fungal (OR=5.97) coinfections, with increased levels of creatinine, leukocytes, urea and C-reactive protein. Coinfections increased the risk of death if patients suffer from cardiovascular disease (OR= 11.53), diabetes (OR=6.00) or obesity (OR=5.60) in comparison with patients with these comorbidities but without pathogen isolation. The increased risk of death was detected for negative-coagulase Staphylococcus (OR=25.39), Candida non-albicans (OR=11.12), S. aureus (OR=10.72), Acinetobacter spp. (OR=6.88), Pseudomonas spp. (OR=4.77) and C. albicans (OR=3.97). The high-risk sites of infection were blood, tracheal aspirate and urine. Patients with coinfection undergoing invasive mechanical ventilation were 3.8 times more likely to die than those without positive cultures. CONCLUSIONS: Severe COVID-19 patients with secondary coinfections required longer hospitalization and had higher risk of death. The early diagnosis of coinfections is essential to identify high-risk patients and to determine the right interventions to reduce mortality.

Background SARS-CoV-2 predisposes patients to secondary infections; however, a better understanding of the impact of coinfections on the outcome of hospitalized COVID-19 patients is still necessary.

To analyse death risk due to coinfections in COVID-19 patients.

We evaluated the Odds of death of 212 severely ill COVID-19 patients, with detailed focus on the risks for each pathogen, site of infection, comorbidities and length of hospitalization.

The mortality rate was 50.47%. albicans (OR=3.97). The high-risk sites of infection were blood, tracheal aspirate and urine. Patients with coinfection undergoing invasive mechanical ventilation were 3.8 times more likely to die than those without positive cultures.

Since December 2019, SARS-CoV-2 led to more than 100 million COVID-19 cases around the world, resulting in almost three million deaths [1] . SARS-CoV-2 infects primarily the lungs and there is no effective treatment available [2] . Most of COVID-19 patients present a mild or moderate disease; but patients with comorbidities may require mechanical ventilation and intensive care, which predispose to secondary and opportunistic infections [3] .

Considering previous data from other respiratory virus diseases such as Severe Acute Respiratory Syndrome (SARS-1), Middle Eastern Respiratory Syndrome (MERS) [3] , some authors pointed that COVID-19 patients may also be more susceptible to bacterial/fungal coinfection [4] . These coinfections represent a severe risk of morbidity and mortality as observed during influenza A (H1N1) pandemic in 2009 [5] and may be present in 8% (62/806) of COVID-19 patients [6] . Goyal and colleagues reported a rate of 6% of bacteraemia during hospital admission [7] , while Wang and colleagues, reported that 29 of 69 patients had bacterial/fungal coinfection [8] . Acinetobacter, Klebsiella, Enterobacter, Aspergillus and Candida are among the main genera that cause secondary infection in COVID-19 patients [8, 9, 10] .

Although some studies report coinfections and pathogens isolated [11] , it is still unclear the risk imposed by these infections on patient's morbidity and mortality. In this study we aimed to analyse the association between fungal/bacterial coinfections and mortality of patients with severe COVID-19 admitted to a public tertiary hospital in Belo Horizonte, Brazil. Our primary endpoint was the risk of death comparing patients with and without fungal and bacterial secondary infection; secondary endpoints included (i) patient's risk of death in the presence of both coinfection and comorbidities, (ii) risks associated with the opportunistic pathogen, (iii) site of isolation, and (iv) implications J o u r n a l P r e -p r o o f on length of hospitalization. This knowledge will help to improve the diagnostic approaches to identify high-risk patients, and also to determine interventions that reduce mortality.

In this cohort we evaluated data from 212 severely ill COVID-19 patients (from May to November 2020) admitted to the Eduardo de Menezes hospital (Fundação Hospitalar do Estado de Minas Gerais), Belo Horizonte, Brazil, which is exclusively dedicated to attend COVID-19 patients during pandemic. All patients received laboratory diagnosis of COVID-19 (SARS-CoV-2 RT-PCR positive in nasopharyngeal samples) and were followed from admission until the outcome (discharge or death). Most of the patients required critical care unit admission. Either written or oral informed consent from patients or their legal representatives were obtained previous to the enrolment. Both National Ethics Committee (Comissão Nacional de Ética em Pesquisa -CONEP) and

the Hospital's Ethics Committee approved the study (CAAE: 30627320.6.0000.0008).

Upon enrolment, information about age, sex, comorbidities and length of hospital stay were obtained from medical records. Other data such as signs and symptoms, use of Patients with signs and symptoms of coinfection during COVID-19 hospitalization and with further positive cultures, as defined by CDC, were also included in this study [13] .

Only health care associated infections were included. Data on the growth of the microorganisms were analysed in relation to the risk of death. Microbiological findings not related to a higher risk of death were considered as colonization. The presence of positive cultures related to increased risk of death was considered as an infection. The clinical specimens analysed included blood, tracheal aspirate, urine, catheter tip, Mini-BAL, sputum and refluid (blood collected at the access to the central venous catheter).

Data on antimicrobials were collected, whose prescription was carried out according to the Guidelines Assistance for COVID-19 [14] .

Upon the determination of the main factors influencing patients' deaths, we focused our analyses on comparing patients with and without fungal and/or bacterial isolation.

Multiple regression and stratified univariate analysis were used to assess the risk of death for patients with comorbidities in the presence and absence of positive cultures.

We calculated the death risk associated to each isolated pathogen, site of infection and J o u r n a l P r e -p r o o f the implications of coinfection on length of hospitalization. The Odds ratios (OR) were presented with 95% confidence intervals and P<0.05 was considered statistically significant. Data were expressed as absolute values, mean±SD or percentages.

Categorical variables were compared using the chi-square test. Continuous variables were compared using Student's t-test or Mann-Whitney test. EpiInfo 7.2, GraphPad Prism 5.0 and Microsoft Excel 2007 software were used in the analyses

The patients' demographic and clinical characteristics are shown in Figure 1 . 

The mean hospitalization length was significantly longer (P=0.043) among patients who died (13.59 days) compared to those who were discharged (10.3 days) (Figure 2A ).

Patients with positive cultures stayed hospitalized (17.28 days) longer than those without them (9.27 days) (P=0.001) ( Figure 2B ).

We performed stratified analyses to assess whether the pathogen isolation increases the risk of death in patients with comorbidities (Table 1) COPD: Chronic obstructive pulmonary disease. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using stratified univariate analysis and P<0.05 was considered statistically significant.

*Undefined because odds ratio could not be calculated with a zero cell. R 2 was calculated using regression model ( ⁋ P<0.05).

Next, we verified biochemical and haematological markers comparing COVID-19 patients with and without positive cultures (Table 2) . Creatinine, total leukocyte count, urea and C-reactive protein (CRP) were increased in patients with positive cultures, while the levels of haemoglobin were decreased. Platelet numbers and lactate concentrations were not different between the two groups. 

Data related to the identified microorganisms, their anatomical sites of origin, as well as administered antimicrobials are described in table 3. Candida albicans (OR=3.97) were isolated (Table 4 ). 

Bacteria were frequently isolated from tracheal aspirate (n=45), followed by catheter tip (n=21), blood (n=19), urine (n=4) and bronchoalveolar lavage (Mini-BAL) (n=1) ( Table   5 ). Bacteria in the blood (OR= 21.03) and tracheal aspirate (OR= 11.94) were J o u r n a l P r e -p r o o f associated with an increased risk of death (P≤0.001). On the other hand, their isolation from the urine did not increased risk of death (P=0.9848).

Fungi were frequently isolated from tracheal aspirate (n=33), followed by urine (n=25), blood (n=4), catheter tip (n=4), sputum (n=3) and Mini-BAL (n=1). The isolation of fungi in the tracheal aspirate (OR = 7.09) and urine (OR = 5.45) were associated with an increased risk of death (P≤0.002), which did not occur with isolation from sputum (OR=0.49) ( Table 5 ). in China and Brazil [10, 15] . The mortality data from our study corroborate a Brazilian study, in which 59% of the patients admitted to the ICU and 80% of those who were mechanically ventilated died [15] . Different from a previous report [16] , we did not find higher mortality among male patients. The average age of deceased ones was higher than that of those discharged, which is in line with previous studies that showed that 65% of patients over 50 are more likely to develop severe COVID-19 [10, 15, 17] .

Dyspnoea, oxygen saturation <95% and cough were the main symptoms reported at admission and are compatible with that previously described [18] . Cardiovascular disease, diabetes and obesity, the main comorbidities found in our study, are also cited by other authors as related to severe COVID-19. Organ damage in these patients can contribute to multiple organ failure and consequent mortality [19] .

Patients with COVID-19 may present reduction in the lymphocyte count, which affect cell-mediated immune response by decreasing CD4 and CD8 T cells, suggesting that SARS-CoV-2 consumes many immune cells and inhibits the cellular immune function [20, 21] . Therefore, the immune dysregulation increases susceptibility to coinfection, which can be diagnosed in 50% (27/54) of patients with COVID-19 who died [22] . In our analysis, the presence of coinfections significantly increased the length of hospitalization and death risk, which has an impact on public health costs and the scarcity of beds available for new patients.

Coinfections also cause haematological and biochemical disbalance, worsening the general clinical condition [23] . We found significant changes in the levels of creatinine, J o u r n a l P r e -p r o o f haemoglobin, leukocyte count and urea in patients with positive cultures compared to those without them.

In our cohort, the secondary pathogen isolation increases the risk of death in patients with cardiovascular disease, diabetes, obesity and also when invasive mechanical ventilation was used. Interestingly, Non-aureus Staphylococcus was associated with a higher risk of death. Despite being often considered as a commensal microorganism, it is one of the most common causes of catheter-related infections, and its treatment may be complicated by the presence of biofilms and resistance to antibiotics [24] . In most cases of isolation of NC Staphylococcus from catheter, other microorganisms were also isolated from this clinical sample, pointing out that the catheter can act as a reservoir for colonization by multiple microorganisms, possibly in biofilms. In this study, 97.17% of the patients received antibacterial drugs, a higher rate than that described by other authors [25] . As previously discussed [26] , the possibility of coinfections should not be ignored, but it is essential that the need for antibacterial treatments is carefully evaluated, so the selection of resistant microorganisms is not accelerated.

Although bacterial infections are more common in critically ill patients, fungal infections should not be underestimated [27] , as they are also associated with increased mortality, longer hospital stays and increased hospital costs. We detected a high prevalence of Candida spp., which is the main fungus causing infections in critically ill patients [28] . It can be part of the human microbiota, making it difficult to distinguish between colonization and infection.

The increased risk of death (depending on the site of isolation and species) may indicate that they are in fact acting as pathogens. The higher risk of death from infections by

Candida non-albicans may be related to the lower sensitivity of some species to antifungals. It is worth mentioning that patients with severe COVID-19 undergo many J o u r n a l P r e -p r o o f interventions that favour opportunistic infections (mechanical ventilation, broadspectrum antibacterial, corticosteroids, parenteral nutrition, central venous catheter). If a patient's condition provides strong evidence of a fungal infection, this possibility should not be ignored [29] .

Overall, this study has some limitations. First, because of its retrospective nature, data availability was limited to the medical records at the hospital. Second, the total population in the analysed period was larger than those presented in this study, since data from patients who were transferred to other hospitals and those who evaded from the hospital were excluded. Third, we must consider the small sample size related to some analysed data. In these cases, studies with a larger sample size should be performed in order to offer more data. Finally, our analyses were limited to the available laboratory data. However, we believe that our data lead to the better understanding of fungal and bacterial coinfections in patients with severe COVID-19.

In conclusion, our results point that severely ill COVID-19 patients with bacterial and/or fungal coinfections require longer hospital stays and present a higher relative risk of death compared to those without coinfections. Furthermore, coinfections can increase the risk of death in subsets of patients with different comorbidities. Thus, we emphasize that the early identification of bacterial and fungal infections, since it will help to identify high-risk patients, and also to determine the right interventions to reduce mortality.

J o u r n a l P r e -p r o o f

World Health Organization. WHO Coronavirus Disease (COVID-19) Dashboard

Treatment for COVID-19: An overview

Coinfections in people with COVID-19: a systematic review and meta-analysis

Risk Factors Associated with Acute Respiratory Distress Syndrome and Death in Patients with Coronavirus Disease

Why is coinfection with influenza virus and bacteria so difficult to control

Bacterial and Fungal Coinfection in Individuals with Coronavirus: A Rapid Review to Support COVID-19 Antimicrobial Prescribing

Clinical characteristics of COVID-19 in New York City

Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China

High Prevalence of Putative Invasive Pulmonary Aspergillosis in Critically Ill COVID-19 Patients

Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

Bacterial and viral coinfections in patients with severe SARS-CoV-2 pneumonia admitted to a French ICU

Surveillance Definitions for Specific Types of Infections

Guidelines Assistance for COVID-19, FHEMIG 2021

Characterisation of the first 250 000 hospital admissions for COVID-19 in Brazil: a retrospective analysis of nationwide data

Male sex identified by global COVID-19 meta-analysis as a risk factor for death and ITU admission

Centre for the Mathematical Modelling of Infectious Diseases COVID-19 working group. Global, regional, and national estimates of the population at increased risk of severe COVID-19 due to underlying health conditions in 2020: a modelling study

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19

COVID-19 and multiorgan response

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

Pathological inflammation in patients with COVID-19: a key role for monocytes and macrophages

Bacterial and fungal infections in COVID-19 patients: A matter of concern

COVID-19 and the clinical hematology laboratory

Staphylococcus epidermidis--the 'accidental' pathogen

Bacterial coinfection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis

SARS-CoV-2, bacterial coinfections, and AMR: the deadly trio in COVID-19?

Fungal infections should be part of the core outcome set for COVID-19

EPIC II Group of Investigators. International study of the prevalence and outcomes of infection in intensive care units

We declare that we have no conflicts of interest.