Bacterial and fungal co-infections among ICU COVID-19 hospitalized patients in a Palestinian hospital: a retrospective cross-sectional study

Introduction

Severe Acute Respiratory Syndrome Coronavirus 2 (SAR-CoV-2) is a highly contagious novel viral pathogen that provokes an immediate spread among hospitalized patients with Community-Acquired Pneumonia (CAP)¹; extending from mild symptoms in approximately 84% of patients to life-threatening hypoxic conditions necessitating admittance into the Intensive Care Unit (ICU) and oxygen support.² Additionally, it causes multi-organ failure that involves sepsis and thromboembolic complications, which progresses into an acute kidney and cardiac injury.³ On March 11^th, 2020, the World Health Organization (WHO) deemed coronavirus disease 2019 (COVID-19) a pandemic disease due to its unusual transmission speed and the wide scale of infection.⁴

The bacterial and fungal co-infections are frequently recurring due to respiratory viral diseases. For example, most deaths in the Spanish flu pandemic in 1918 were due to subsequent bacterial infection.⁵ The possibility of co-infections raises concerns as it hinders COVID-19 management, worsens prognosis, and might increase the fatality rate. The reported prevalence of bacterial co-infection varies between studies. Previous studies showed a low prevalence of early bacterial coinfection.^6,7 On the other hand, data from France pointed to a high prevalence of early bacterial coinfection during severe COVID-19 pneumonia.⁸

Throughout the pandemic, evaluation of gathered specimens from hospitalized COVID-19 patients reported the following as the most prevalent organisms that induce co-bacterial infection: S. aureus, S. epidermidis, H. influenzae, Streptococcus spp., E. coli, K. pneumoniae, and P. aeruginosa.⁹ Therefore, many COVID-19 treatment protocols include empirical antibiotic therapy to cover suspected organisms. Thirty studies were summarized in a systematic review, including 3834 COVID-19 patients. Overall, only 7% of the hospitalized patients were confirmed to have bacterial co-infection with one or more pathogens, primarily in seriously ill patients.¹⁰ On the contrary, diagnosis and/or treatment of fungus infections in COVID-19 patients are neglected or delayed, and the actual prevalence of fungal co-infection is yet to be established. Few studies addressed this issue; one systematic review meta-analysis research was carried out in China on 2780 confirmed SAR-CoV-2 participants from nine relevant articles. After fungal culturing at admission, 0.12%-0.15% of the cases were positive for fungal infection, and Asian patients were more likely to acquire fungal co-infection than the patients in the studies from the U.K. The infecting fungi include Aspergillus, Candida, Cryptococcus neoformans, and Pneumocystis.¹¹

The exact mechanism of microbial co-infection is inadequately understood. Virologists assumed that the viruses attach and penetrate the host's airway epithelial cells creating an inflammatory response, desensitizing Toll-like receptors, and leading to cellular apoptosis in numerous mechanisms.¹² In addition, it debilitates the body's defense and induces cellular dysfunction and death.¹²

Viruses aid in proliferation, colonization, and invasive infection of opportunistic nosocomial pathogens or normal respiratory tract flora, hindering the innate immune response, compressing airway mucus, and disrupting the cilia allowing the virus to spread and adhere to more sites.³ Furthermore, various researchers^13,14 highlighted the synergy regulations among viruses and bacteria; both are jointly advantageous, aggravating clinical outcomes. If this cooperation is confirmed, the management of some viral infections with antibiotics becomes further necessary.¹⁵

COVID-19 has been chiefly linked to high levels of inflammatory markers, such as elevated levels of C-reactive protein and procalcitonin. Accordingly, the similarity between Sar-CoV-2 and bacterial infections in radiological infiltrates and laboratory findings makes it challenging to provide a precise diagnosis in daily medical practice.¹⁶ However, according to current studies, most COVID-19 patients did not have bacterial or fungal co-infections upon admission or through the hospital stay, even though they received antibiotics upon admission or before diagnosis.¹⁷ Furthermore, many factors advocated escalation of antimicrobial consumption during the pandemic: lack of specific antiviral agents, the overload of the health services’ capacities, saturated laboratories, and diagnosis uncertainty.¹⁸ As a result, clinicians are obliged to prescribe broad-spectrum multi-antibiotic regimens to treat all the possible infected pathogens.¹⁹ Therefore, this study aimed to investigate and evaluate bacterial and fungal co-infection burden and prevalence among COVID-19 patients admitted to a treatment facility at Beit-Jala hospital in Palestine. In addition, it reveals the etiology of the infection, provides the antimicrobial stewardship that was used in the hospital and provides insight into the association of clinical outcomes with several factors and comorbidities.

Methods

Results

Discussion

In this research, the characteristics of co-infection in 321 severely ill COVID-19 patients were evaluated. The mortality rate of 8.1% (26) for patients admitted to the ICU due to Covid-19 coinfections found by this study is much lower than other reported rates of 25.7 % in a systematic review that included 15 studies in different countries.²⁰ Despite the absence of antimicrobial stewardship in urgent response, the hospital's initiation of drastic empirical administration was crucial for preventing or treating suspected infections. In addition, the hospital’s guideline adherence to empiric antimicrobial therapy and the other drugs was adequate. Furthermore, many factors could affect this finding, including the age and living situations; in our sample, two-thirds of participants were less than 65 years old. In addition, all participants did not live in nursing homes or elderly homes where a higher rate of antimicrobial resistance is expected.

COVID-19 patients are at risk of fungal infections during the latter stages of the disease due to seriously damaged alveoli and the decline in leukocyte counts.²¹ Based on the knowledge of SARS in 2003 and the invasive Aspergillosis, it is vital to consider the possibility of a life-threatening fungal infection accompanying COVID-19. At the beginning of blood/sputum culturing, the number of cases infected by A. fumigatus was 48.9% (157). Those patients were initially given antibacterial regimens before and during their ICU stay without fluconazole due to medication cost. Fluconazole was added to the hospital formulary by January and confirmed fungal infections were treated with fluconazole. The addition of fluconazole to empirical therapy had reduced the average ICU stay from six days to less than two days, and the mortality rate from A. fumigatus decreased from 4.5% to 0%. Infection disease specialists realized the risk of fungal co-infection through the pandemic; the French High Council for Public Health recommended that clinicians concentrate on fungal infections in COVID patients, particularly in severe disease cases.²¹

Bacterial co-infection was recorded in 51.1% (164) of cases, with higher mortality rates among Enterobacter infected patients; this may be due to its known drug resistance. It should be noted that normal oral flora colonization or contamination may occur, particularly in the sputum specimens. In general, the empirical treatment with ceftriaxone or ampicillin/sulbactam showed minimal benefits to the clinical status. However, we observed a better prognosis with ceftriaxone than ampicillin/sulbactam, with mortality rates at 4% (9) and 17.3% (17), respectively; more studies are needed to confirm this association.

The wide-spectrum antimicrobial regimens are administered once the bacterial co-infection is confirmed and the patient is admitted into the ICU. Unfortunately, there is no available data to compare COVID-19 patients who received antibacterial agents with those who did not, which could help determine therapeutic efficacy. However, a regimen of piperacillin with tazobactam and levofloxacin resembles meropenem and vancomycin in terms of clinical outcomes and management rate. Other studies had revealed a higher rate of mortality and organ failure in patients administered meropenem.¹⁷ Furthermore, after the recovery and discharge from the hospital, all outpatients were prescribed azithromycin, which also has antiviral activity and may decrease the incidence of acute organ failure.¹⁷

Earlier examinations illustrated that multiple antibiotic administrations did not alter the disease progression or patients' higher mortality rates.²² In our study, it appeared to induce a good prognosis. Ceftriaxone, meropenem, and vancomycin regimens have been linked with more favorable outcomes and lower mortality rates. Until solid evidence is available, antimicrobials should be maintained for critical cases and constantly re-evaluated based on the patient's progress. The antimicrobial therapy must only cover the suspected or confirmed bacterial infection.

Antibiotic resistance and allergic reactions are multifactorial issues, and the pandemic has impacted the health system and provided a suitable environment for bacteria to become resistant to antimicrobials. In our study, all COVID-19 patients were admitted to the ICU and received at least four diverse types of broad-spectrum antibacterial agents; in addition, the accessibility of over-the-counter antimicrobials had undeniably grown through the pandemic.¹⁹ This inappropriate behavior will lead to the evolution of high levels of antibiotic-resistant bacteria.

This study's unusual incidence of bacterial or fungal infections and mortality rates differs from other published studies.^11,23 This significant finding is due to the characteristics of critically ill patients receiving therapy via invasive catheters and being at risk of infection by nosocomial pathogens. Moreover, the unusual rate of infection has been credited to the exhaustion in the clinical care system, creating a prolonged hospital exposure, principally in the major waves of the virus.

Patients included in this study were 100% severe-critical ill. Therefore, it is necessary to differentiate between mild-moderate and severe patients and prioritize the ICU admittance. Fever was the notable symptom of SARS-CoV-2 infection identified at the early stages of the disease. Regarding laboratory findings, leukocytosis occurred in critically ill patients with distinct grades, and it was observed in 11.4% of severe COVID-19 cases.²⁴ Leukocytosis aids in the disease progress evaluation and reflects the severity of COVID-19 infection; it is exacerbated by the cytokine storm and inflammatory mediators that drive apoptosis and pulmonary microvascular destruction, creating alveolar oedema. The increased level of CRP is a diagnostic biomarker for coronavirus in distinguishing moderate and critical patients. The pathogenesis of COVID-19 involves a vigorous inflammatory response that manages a dysregulated flood of immune cells and signaling molecules.²⁵ In general, viral respiratory infections have been linked to hypoxia. COVID-19 patients are considered hypoxic if their oxygen saturation level is <90%, while the normal SpO₂ is ≥95% at rest in healthy people. Hypoxia is a fearful condition that is monitored and adjusted by mechanical ventilation.²⁶ Although several studies^27,28 reported links between laboratory findings and clinical outcomes, our cases did not show a significant link.

Throughout the coronavirus pandemic, tobacco smoking issues and the risk of infection was constantly reviewed. Published research²⁹ indicated that smokers are twice as likely to develop severe COVID-19 as nonsmokers, as smoking tobacco induces alterations in the respiratory tract and cell-mediated immune response.²⁹ Furthermore, current smokers have higher ACE-2 gene expression than non-smokers; this gene is responsible for ACE-2 receptors production, which COVID-19 attaches to and penetrates the cells, thus raising the chance of infection.³⁰ Our study did not find an association between smoking habits and the duration of ICU stay or clinical prognosis.

Numerous investigations^31,32 found that older COVID-19 patients aged ≥50 years were correlated with a higher risk for severe signs, atypical presentation, the opportunity for co-infections, and higher fatality rates than patients <50 years of age. The rate usually increases rapidly with age, which is not surprising due to the drop in natural immunity with aging and associated comorbidities. In addition, it is believed that older people are prone to adverse drug reactions.³² In general, people of older ages are more prone to becoming infected with the COVID virus than younger people.³² A review reported that the fatality rate is doubled in males compared to females; it stated that male patients might have higher ACE-2 enzyme activity, directed by male sex hormones, contributing to more risk factors for SARS-CoV-2 infection worsening clinical outcomes.³³ Additionally, the smoking rate is higher in males.³³

Effects of comorbidities such as hypertension, diabetes mellitus, coronary heart disease, and cancer were compared between survivors and non-survivors of COVID-19. Participants with comorbid conditions have a significantly greater fatality rate than those without them because they have decreased natural immunity and are poly-pharmacy patients.^34,35 There was no association between age, gender, or comorbidities with the clinical outcomes and ICU stay duration in our study.

Previous reports described mild anemia in COVID-19 patients at the ICU; due to severe inflammation that consumes iron,³⁶ the innate immune system limits the bioavailability of iron in order to diminish viral replication and infection. Accordingly, iron absorption from the diet is reduced, and the liver generates hepcidin, which blocks iron from carrying out of the cell. Accordingly, iron supplementation may exacerbate the disease and increase the inflammatory process.³⁷ However, no solid investigations were performed on the relation between iron and clinical results in COVID-19 patients. In the study, 62.6% of the patients received IV iron supplements for three days based on a randomized clinical trial. 99% had improved and stayed for a shorter time (1-6 days) in the ICU than those who did not receive IV iron; thus, it can be suggested that the iron provided an enhancement to immunity. Therefore, there is a strong association between low serum levels of iron and an increased infection rate and morbidity.

COVID-19 produces oxidative stress irregularity, and this process has been enhanced by glutathione reduction. Thiones are synthesized in a multi-step process involving N-acetyl-cysteine (NAC). Thiones are also ACE-2 blockers, thereby diminishing SARS-CoV-2 penetration into the cell. In a placebo-controlled study, NAC administration had reduced plasma inflammatory biomarker levels via several mechanisms. Besides antioxidant activity, NAC has vasodilator activity, especially in the intravenous route. In addition, it has mucolytic properties, inhibits RNA virus replication, and has confirmed protective effects against comorbid conditions, including cardiovascular diseases.³⁸ In our study, patients received NAC 1200 mg/day during the hospital stay, and even after discharge, they showed a good prognosis and improvement in their health status.

Conclusion

The COVID-19 pandemic exerts pressure on healthcare professionals, including a high probability of infection. It is eminent to save lives during this pressure, even if it means multi-drug antimicrobial regimens for prevention or treatment. However, the insufficiency of data about antibiotic types, dosage, and duration of treatment through the pandemic continues to be challenging to health care providers. In addition, bacterial and fungal co-infection is common among COVID-19 patients at the ICU in Palestine; it is not evident if these cases are attributed to SARS-CoV-2 or coincidental as there is little available data. Finally, antimicrobial stewardship, appropriate patient assessment, and selecting the appropriate antimicrobial agents for the right patient at the right time will decrease hospital stay, mortality, and health care costs.

Data availability

Author contributions

HN Project Administration, Supervision, Writing – Review & Editing, UM and YS Data Curation, Writing – Original Draft Preparation, Formal Analysis, NA Formal Analysis, Writing – Original Draft Preparation, AA Methodology, Writing – Review & Editing, MD Methodology, Writing – Review & Editing, IA Data Curation, MF Writing – Review & Editing. All authors read and approved the final manuscript.