Bacterial and fungal superinfections are detected at higher frequency in critically ill patients affected by SARS CoV-2 infection than negative patients and are associated to a worse outcome

Epidemiology of bacterial respiratory tract infections during the pre-pandemic, COVID-19 pandemic and post-pandemic era: A retrospective study of hospitalized adults in northern Greece between 2018 and 2023

INTRODUCTION

The COVID-19 pandemic has had impact on global healthcare and respiratory disease patterns. The aim was to evaluate the changes in positive respiratory cultures during the pandemic.

METHODS

A retrospective analysis of respiratory specimens in Papanikolaou Hospital during 2018-2023 was performed. In total, 18,852 samples (12,277 males, 6575 females) of respiratory samples were recorded.

RESULTS

During 2018-2019, 684 BAL samples were received, of which 12.3 % were positive. Positive pharyngeal smears constituted 24.8 %, compared to 18.5 % in pandemic years, and 29.6 % in 2023. In PTC, pre-pandemic, positives were 12.3 %, while in 2021 the maximum percentage of positives (21.9 %) was observed. Positive levels remained high in 2023 (18.3 %). Concerning bronchial secretions, there was an increase (55.3 % in 2022 vs 47.0 % in 2019). The predominant bacteria were Acinetobacter spp, Klebsiella spp and Pseudomonas spp.

CONCLUSION

Except for the bronchial secretions, the rest of the respiratory specimens do not exhibit any definite trends.

Bacterial infections and outcomes of inpatients with COVID-19 in the intensive care unit during the delta-dominant phase: the worst wave of pandemic in Iran

Background

Epidemiological data regarding the prevalence of bacterial multidrug-resistant (MDR) Gram-negative infections in patients with COVID-19 in Iran are still ambiguous. Thus, in this study we have investigated the epidemiology, risk factors for death, and clinical outcomes of bacterial infections among patients with COVID-19 in the intensive care unit (ICU).

Method

This retrospective cohort study included patients with COVID-19 hospitalized in the ICU of a university hospital in Iran between June 2021 and December 2021. We evaluated the epidemiological, clinical, and microbiological features, outcomes and risk factors associated with death among all COVID-19 patients. Data and outcomes of these patients with or without bacterial infections were compared. Kaplan-Meier plot was used for survival analyses.

Results

In total, 505 COVID-19 patients were included. The mean age of the patients was 52.7 ± 17.6 years and 289 (57.2%) were female. The prevalence of bacterial infections among hospitalized patients was 14.9%, most of them being hospital-acquired superinfections (13.3%). MDR Klebsiella pneumoniae and Staphylococcus aureus were the most common pathogens causing respiratory infections. Urinary tract infections were most frequently caused by MDR Escherichia coli and K. pneumoniae. The overall in-hospital mortality rate of COVID-19 patients was 46.9% (237/505), while 78.7% (59/75) of patients with bacterial infections died. Infection was significantly associated with death (OR 6.01, 95% CI = 3.03-11.92, p-value <0.0001) and a longer hospital stay (p < 0.0001). Multivariate logistic regression analysis showed that Age (OR = 1.04, 95% CI = 1.03-1.06, p-value <0.0001), Sex male (OR = 1.70, 95% CI = 1.08-2.70, p-value <0.0001), Spo2 (OR = 1.99, 95% CI = 1.18-3.38, p-value = 0.010) and Ferritin (OR = 2.33, 95% CI = 1.37-3.97, p-value = 0.002) were independent risk factors associated with in-hospital mortality. Furthermore, 95.3% (221/232) of patients who were intubated died.

Conclusion

Our findings demonstrate that bacterial infection due to MDR Gram-negative bacteria associated with COVID-19 has an expressive impact on increasing the case mortality rate, reinforcing the importance of the need for surveillance and strict infection control rules to limit the expansion of almost untreatable microorganisms.

Interferon-responsive neutrophils and macrophages extricate SARS-CoV-2 Omicron critical patients from the nasty fate of sepsis

The SARS-CoV-2 Omicron variant is characterized by its high transmissibility, which has caused a worldwide epidemiological event. Yet, it turns ominous once the disease progression degenerates into severe pneumonia and sepsis, presenting a horrendous lethality. To elucidate the alveolar immune or inflammatory landscapes of Omicron critical-ill patients, we performed single-cell RNA-sequencing (scRNA-seq) of bronchoalveolar lavage fluid (BALF) from the patients with critical pneumonia caused by Omicron infection, and analyzed the correlation between the clinical severity scores and different immune cell subpopulations. In the BALF of Omicron critical patients, the alveolar violent myeloid inflammatory environment was determined. ISG15+ neutrophils and CXCL10+ macrophages, both expressed the interferon-stimulated genes (ISGs), were negatively correlated with clinical pulmonary infection score, while septic CST7+ neutrophils and inflammatory VCAN+ macrophages were positively correlated with sequential organ failure assessment. The percentages of ISG15+ neutrophils were associated with more protective alveolar epithelial cells, and may reshape CD4+ T cells to the exhaustive phenotype, thus preventing immune injuries. The CXCL10+ macrophages may promote plasmablast/plasma cell survival and activation as well as the production of specific antibodies. As compared to the previous BALF scRNA-seq data from SARS-CoV-2 wild-type/Alpha critical patients, the subsets of neutrophils and macrophages with pro-inflammatory and immunoregulatory features presented obvious distinctions, suggesting an immune disparity in Omicron variants. Overall, this study provides a BALF single-cell atlas of Omicron critical patients, and suggests that alveolar interferon-responsive neutrophils and macrophages may extricate SARS-CoV-2 Omicron critical patients from the nasty fate of sepsis.

Bloodstream infections in the era of the COVID-19 pandemic: Changing epidemiology of antimicrobial resistance in the intensive care unit

The Coronavirus disease 2019 (COVID-19) pandemic increased the burden of critically ill patients who required hospitalization in the intensive care unit (ICU). Bacterial and fungal co-infections, including bloodstream infections (BSIs), increased significantly in ICU patients with COVID-19; this had a significant negative impact on patient outcomes. Reported data pertaining to BSI episodes from the ICU setting during the COVID-19 pandemic were collected and analyzed for this narrative review. We searched the PubMed database for articles published between March 2020 and October 2023; the terms "COVID-19" AND "bloodstream infections" AND "ICU" were used for the search. A total of 778 articles were retrieved; however, only 27 were exclusively related to BSIs in ICU patients with COVID-19. Data pertaining to the epidemiological characteristics, risk factors, characteristics of bacterial and fungal BSIs, patterns of antimicrobial resistance, and comparisons between ICU and non-ICU patients during and before the COVID-19 pandemic were obtained. Data on antimicrobial stewardship and infection-control policies were also included. The rates of BSI were found to have increased among ICU patients with COVID-19 than in non-COVID-19 patients and those admitted during the pre-pandemic period. Male gender, 60-70 years of age, increased body mass index, high Sequential Organ Failure Assessment scores at admission, prolonged hospital and ICU stay, use of central lines, invasive ventilation, and receipt of extracorporeal membrane oxygenation were all defined as risk factors for BSI. The use of immune modulators for COVID-19 appeared to increase the risk of BSI; however, the available data are conflicting. Overall, Enterococci, Acinetobacter baumannii, and Candida spp. emerged as prominent infecting organisms during the pandemic; along with Enterobacterales and Pseudomonas aeruginosa they had a significant impact on mortality. Multidrug-resistant organisms prevailed in the ICU, especially if antimicrobial resistance was established before the COVID-19 pandemic and were significantly associated with increased mortality rates. The unnecessary and widespread use of antibiotics further increased the prevalence of multidrug-resistant organisms during COVID-19. Notably, the data indicated a significant increase in contaminants in blood cultures; this highlighted the decline in compliance with infection-control measures, especially during the initial waves of the pandemic. The implementation of infection-control policies along with antibiotic stewardship succeeded in significantly reducing the rates of blood contamination and BSI pathogens. BSIs considerably worsened outcomes in patients with COVID-19 who were admitted to ICUs. Further studies are needed to evaluate adequate preventive and control measures that may increase preparedness for the future.

Bacterial Community- and Hospital-Acquired Pneumonia in Patients with Critical COVID-19-A Prospective Monocentric Cohort Study

The impact of bacterial pneumonia on patients with COVID-19 infection remains unclear. This prospective observational monocentric cohort study aims to determine the incidence of bacterial community- and hospital-acquired pneumonia (CAP and HAP) and its effect on mortality in critically ill COVID-19 patients admitted to the intensive care unit (ICU) at University Hospital Olomouc between 1 November 2020 and 31 December 2022. The secondary objectives of this study include identifying the bacterial etiology of CAP and HAP and exploring the capabilities of diagnostic tools, with a focus on inflammatory biomarkers. Data were collected from the electronic information hospital system, encompassing biomarkers, microbiological findings, and daily visit records, and subsequently evaluated by ICU physicians and clinical microbiologists. Out of 171 patients suffering from critical COVID-19, 46 (27%) had CAP, while 78 (46%) developed HAP. Critically ill COVID-19 patients who experienced bacterial CAP and HAP exhibited higher mortality compared to COVID-19 patients without any bacterial infection, with rates of 38% and 56% versus 11%, respectively. In CAP, the most frequent causative agents were chlamydophila and mycoplasma; Enterobacterales, which were multidrug-resistant in 71% of cases; Gram-negative non-fermenting rods; and Staphylococcus aureus. Notably, no strains of Streptococcus pneumoniae were detected, and only a single strain each of Haemophilus influenzae and Moraxella catarrhalis was isolated. The most frequent etiologic agents causing HAP were Enterobacterales and Gram-negative non-fermenting rods. Based on the presented results, commonly used biochemical markers demonstrated poor predictive and diagnostic accuracy. To confirm the diagnosis of bacterial CAP in our patient cohort, it was necessary to assess the initial values of inflammatory markers (particularly procalcitonin), consider clinical signs indicative of bacterial infection, and/or rely on positive microbiological findings. For HAP diagnostics, it was appropriate to conduct regular detailed clinical examinations (with a focus on evaluating respiratory functions) and closely monitor the dynamics of inflammatory markers (preferably Interleukin-6).