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).

[Resistance of bacterial pathogens isolated from the lower respiratory tract and their clonality in intensive care patients in a post-COVID-19 period]

OBJECTIVES

The period of the COVID-19 pandemic had a significant impact on the healthcare system, including its effect on compliance with the established procedures of a rational antibiotic policy, especially in the context of nosocomial pneumonia, where it was very difficult to distinguish a possible bacterial superinfection from a severe inflammatory reaction caused by the SARS-CoV-2 virus. The aim of the present study was to analyze the antimicrobial resistance of bacterial pathogens isolated from the lower respiratory tract and their clonality in intensive care patients in 2022 and to compare it with the previous COVID-19 period.

MATERIAL AND METHODS

Bacterial strains isolated from the lower respiratory tract (LRT) of patients hospitalized at the Department of Anaesthesiology, Resuscitation and Intensive Care, Olomouc University Hospital (DARIC) over a three-year period (January 1, 2020 - December 31, 2022) were included in the study. The susceptibility to antibiotics was determined by the standard microdilution method according to the EUCAST criteria, and selected isolates were compared using pulsed-field gel electrophoresis (PFGE).

RESULTS

The resistance of the most common bacterial pathogens isolated from the LRT of patients hospitalized at DARIC did not change significantly during the COVID-19 (2020-2021) and post-COVID-19 (2022) periods, with the exception of Serratia marcescens and Enterococcus faecium species. These two showed an increase in the number of strains during the COVID-19 pandemic, as well as a significant increase in the proportion of resistant strains. In the case of Serratia marcescens, there was a subsequent decrease in the number of isolates and their resistance in 2022. For Enterococcus faecium, the total number of isolates also decreased significantly, but the frequency of vancomycin-resistant isolates (VRE) continued to increase. During the COVID-19 pandemic, increased VRE detection can be linked to proven clonal spread, but significant clonality was no longer confirmed in 2022. Comparison of similarity by PFGE in other bacterial species also did not reveal significant horizontal transmission between patients in the post-COVID-19 period, as most isolates (85%) showed a unique restriction profile.

CONCLUSIONS

The results indicate that the frequency and antimicrobial resistance of the majority of the most common bacterial pathogens from the LRT of patients hospitalized at DARIC in the post-pandemic period remain comparable to the time before and during the COVID-19 pandemic outbreak. An exception is Enterococcus faecium, which showed an increase in vancomycin resistance in both the COVID-19 and the post-COVID-19 periods.

Bacterial Resistance to Antibiotics and Clonal Spread in COVID-19-Positive Patients on a Tertiary Hospital Intensive Care Unit, Czech Republic

This observational retrospective study aimed to analyze whether/how the spectrum of bacterial pathogens and their resistance to antibiotics changed during the worst part of the COVID-19 pandemic (1 November 2020 to 30 April 2021) among intensive care patients in University Hospital Olomouc, Czech Republic, as compared with the pre-pandemic period (1 November 2018 to 30 April 2019). A total of 789 clinically important bacterial isolates from 189 patients were cultured during the pre-COVID-19 period. The most frequent etiologic agents causing nosocomial infections were strains of Klebsiella pneumoniae (17%), Pseudomonas aeruginosa (11%), Escherichia coli (10%), coagulase-negative staphylococci (9%), Burkholderia multivorans (8%), Enterococcus faecium (6%), Enterococcus faecalis (5%), Proteus mirabilis (5%) and Staphylococcus aureus (5%). Over the comparable COVID-19 period, a total of 1500 bacterial isolates from 372 SARS-CoV-2-positive patients were assessed. While the percentage of etiological agents causing nosocomial infections increased in Enterococcus faecium (from 6% to 19%, p < 0.0001), Klebsiella variicola (from 1% to 6%, p = 0.0004) and Serratia marcescens (from 1% to 8%, p < 0.0001), there were significant decreases in Escherichia coli (from 10% to 3%, p < 0.0001), Proteus mirabilis (from 5% to 2%, p = 0.004) and Staphylococcus aureus (from 5% to 2%, p = 0.004). The study demonstrated that the changes in bacterial resistance to antibiotics are ambiguous. An increase in the frequency of ESBL-positive strains of some species (Serratia marcescens and Enterobacter cloacae) was confirmed; on the other hand, resistance decreased (Escherichia coli, Acinetobacter baumannii) or the proportion of resistant strains remained unchanged over both periods (Klebsiella pneumoniae, Enterococcus faecium). Changes in pathogen distribution and resistance were caused partly due to antibiotic selection pressure (cefotaxime consumption increased significantly in the COVID-19 period), but mainly due to clonal spread of identical bacterial isolates from patient to patient, which was confirmed by the pulse field gel electrophoresis methodology. In addition to the above shown results, the importance of infection prevention and control in healthcare facilities is discussed, not only for dealing with SARS-CoV-2 but also for limiting the spread of bacteria.

[Impact of the COVID-19 pandemic on antimicrobial resistance]

OBJECTIVES

The COVID-19 pandemic has had a major impact on the healthcare system, which has been forced to manage large numbers of patients, including those with respiratory insufficiency and in need of oxygen therapy. Due to concerns about bacterial co-infection, antibiotic therapy was administered to many patients. The aim of the present study was to compare antimicrobial resistance in intensive care patients in the pre-pandemic and pandemic periods.

MATERIAL AND METHODS

Patients hospitalized at the Department of Anesthesiology, Resuscitation and Intensive Care Medicine of the University Hospital Olomouc in the pre-COVID-19 period (2018-2019) and during the pandemic (2020-2021) were enrolled in the study. Clinical samples from the lower respiratory tract were routinely collected twice a week, with one strain of a given species first isolated from each patient being included in the study.

RESULTS

While several bacterial species (Escherichia coli, Proteus mirabilis and Haemophilus influenzae) were found to occur less frequently, an increased occurrence was documented for Enterococcus faecium, Serratia marcescens and Klebsiella variicola. Overall, however, it can be concluded that there was no major change in the frequency of bacterial pathogens isolated from the lower respiratory tract during the COVID-19 period. Similarly, with only a few exceptions, antimicrobial resistance did not change significantly. More significant increases in resistance to piperacillin/tazobactam, cefotaxime, ciprofloxacin and gentamicin have been demonstrated for Serratia marcescens. However, a decrease in the resistance of Pseudomonas aeruginosa and Burkholderia cepacia complex to meropenem was also observed.

CONCLUSIONS

There was no significant change in the frequency of bacterial pathogens and their resistance to antibiotics during the COVID-19 pandemic. However, there was an increase or decrease in the percentage of some species and in their resistance.

[Acute care treatment of COVID-19 pneumonia with acute respiratory failure]

Treatment of COVID-19 patients and their extreme numbers represented an unprecedented challenge for the intensive care system in healthcare facilities throughout the Czech Republic, a country particularly affected by the new coronavirus SARS-CoV-2 pandemic. A steep increase in the need for intensive care placed an excess burden on bed and staff capacity. For a severe and critical course of COVID-19, bilateral pneumonia with acute hypoxemic respiratory failure is pathognomonic. In the intensive care setting, COVID-19 therapy is primarily symptomatic, supporting failing respiratory function to gain time needed to restore it and to repair the lungs. The aggressiveness and comprehensiveness of respiratory support depend on the severity of failure, ranging from simple oxygen therapy, to non-invasive support and mechanical ventilation, to extracorporeal support. By contrast, specific COVID-19 therapy is directly targeted against SARS-CoV-2 or modulates the organism's response to the virus. Primary, virus-induced lung injury may be secondarily complicated by coinfection or superinfection, most commonly bacterial, increasing the severity and lethality of the disease. Therefore, anti-infective therapy is crucial for the prognosis and outlook of intensive care COVID-19 patients. Among nosocomial infections complicating COVID-19, ventilator-associated pneumonia (developing in mechanically ventilated patients) is particularly important and challenging, and so are issues related to bacterial resistance and rational antibiotic therapy.

Clostridioides difficile and Vancomycin-Resistant Enterococci in COVID-19 Patients with Severe Pneumonia

Broad-spectrum antibiotics administered to patients with severe COVID-19 pneumonia pose a risk of infection caused by Clostridioides difficile. This risk is reduced mainly by strict hygiene measures and early de-escalation of antibiotic therapy. Recently, oral vancomycin prophylaxis (OVP) has also been discussed. This retrospective study aimed to assess the prevalence of C. difficile in critical COVID-19 patients staying in an intensive care unit of a tertiary hospital department of anesthesiology, resuscitation, and intensive care from November 2020 to May 2021 and the rates of vancomycin-resistant enterococci (VRE) after the introduction of OVP and to compare the data with those from controls in the pre-pandemic period (November 2018 to May 2019). During the COVID-19 pandemic, there was a significant increase in toxigenic C. difficile rates to 12.4% of patients, as compared with 1.6% in controls. The peak rates were noted in February 2021 (25% of patients), immediately followed by initiation of OVP, changes to hygiene precautions, and more rapid de-escalation of antibiotic therapy. Subsequently, toxigenic C. difficile detection rates started to fall. There was a nonsignificant increase in VRE detected in non-gastrointestinal tract samples to 8.9% in the COVID-19 group, as compared to 5.3% in the control group. Molecular analysis confirmed mainly clonal spread of VRE.

Antibiotic treatment issues in patients with COVID-19

The COVID-19 pandemic may increase the current threat of antimicrobial resistance and exacerbate another, rather silent, pandemic posed by the increasing frequency of multidrug-resistant bacterial pathogens and the associated potential for loss of effective antibiotics. Antibiotic treatment has often been used in patients hospitalized for COVID-19 due to concerns about possible bacterial co-infection, as confirmed by previous experience with viral respiratory infections such as H1N1 influenza, SARS and MERS. Concerns or unknowns related to the COVID-19 pandemic have also affected physicians behavior, including the use of antibiotics. However, the high rate of antibiotic use in patients, especially those with mild to moderate COVID-19 disease, is inconsistent with the actual incidence of bacterial co-infections and/or secondary respiratory infections. Thus, it is clear that a careful assessment of the role of antibiotic treatment in patients hospitalized for COVID-19 is required. According to the current WHO recommendation, the application of antibiotics is especially suitable for patients with severe/critical degree of respiratory insufficiency requiring intensive oxygen therapy, artificial lung ventilation or support by extracorporeal membrane oxygenation.

Nosocomial pneumonias

The paper provides clear definitions of the basic concepts of nosocomial pneumonias. Specifically, definitions and classifications of HAP and VAP, general treatment principles and specific recommended procedures for antibiotic therapy are given as applicable in the Czech Republic.

Human myotubularin-related protein 9 regulates ER-to-Golgi trafficking and modulates WNT3A secretion

Regulation of phosphatidylinositol phosphates plays a crucial role in signal transduction, membrane trafficking or autophagy. Members of the myotubularin family of lipid phosphatases contribute to phosphoinositide metabolism by counteracting the activity of phosphoinositide kinases. The mechanisms determining their subcellular localization and targeting to specific membrane compartments are still poorly understood. We show here that the inactive phosphatase MTMR9 localizes to the intermediate compartment and to the Golgi apparatus and is able to recruit its active phosphatase partners MTMR6 and MTMR8 to these locations. Furthermore, MTMR8 and MTMR9 co-localize with the small GTPase RAB1A and regulate its localization. Loss of MTMR9 expression compromises the integrity of the Golgi apparatus and results in altered distribution of RAB1A and actin nucleation-promoting factor WHAMM. Loss or overexpression of MTMR9 leads to decreased rate of protein secretion. We demonstrate that secretion of physiologically relevant cargo exemplified by the WNT3A protein is affected after perturbation of MTMR9 levels.

[Hospital-acquired pneumonia in the light of current recommendations - is there a space for improving patient care?]

Hospital-acquired pneumonia (HAP) is an infection of the lung parenchyma. It is the second most frequent nosocomial infection and the leading cause of death from infection in critically ill patients. Hospital-acquired and, particularly, ventilator-associated pneumonia prolong the hospital stay and increase treatment costs. The clinical signs of pneumonia are rather non-specific, with limited possibilities to distinguish the lung condition from other nosological entities. The yield, effectiveness and cost of new rapid diagnostic procedures as well as early biochemical markers specific for pneumonia have not been sufficiently verified and clinical translation of technological innovations is slow. In bedside clinical practice, the diagnosis continues to be based on clinical examination together with imaging methods, most frequently X-ray. The spectrum of etiologic agents changes, with an increase in the prevalence of multidrug-resistant (MDR) bacterial pathogens. Initial antibiotic therapy, particularly in critically ill ventilated patients, needs to include broad-spectrum agents due to the risk of the presence of MDR bacteria. The likelihood of successful treatment may be increased by regular updates of recommendations for adequate initial antibiotherapy with regard to the epidemiological situation and knowledge of bacterial resistance to antimicrobials in a particular hospital and region. As part of the current valid guidelines, recommendation were newly translated; however, their level of evidence is often very low and the strength of recommendation is mostly weak or moderate. Their benefit to everyday practice is questionable. The article points to changes brought about by the recent European guidelines published in fall 2017 and summarizes current issues concerning HAP pathogens in intensive care units in the Czech Republic.

Detection of the etiological agents of hospital-acquired pneumonia - validity and comparison of different types of biological sample collection: a prospective, observational study in intensive care patients

BACKGROUND

There is still a lack of evidence as to which method of biological sample collection is optimal for identifying bacterial pathogens causing hospital-acquired pneumonia (HAP). Much effort has been made to find an easy and valid approach to be used in clinical practice.

METHODS

The primary endpoint of this prospective, observational study was to determine the predictive value of oropharyngeal swab (OS) and gastric aspiration (GA) as simple and non-invasive methods for diagnosing HAP. Their efficacy was compared to endotracheal aspiration (ETA) and protected specimen brushing (PSB), the standard methods approved for HAP diagnosis.

RESULTS

Initially, 56 patients were enrolled. Significant amounts of bacterial pathogens were detected in 48 patients (79 isolates) in Round A and in 39 patients (45 isolates) in Round B (after 72 hours). The sensitivity rates were: ETA 98%, PSB 31%, OS 64% and GA 67% in Round A and ETA 87%, PSB 32%, OS 74% and GA 42% in Round B. Strains of 12 bacterial species were identified in the samples. The three most common etiological agents (both rounds together) were Klebsiella pneumoniae (23.7%), Burkholderia multivorans (21.1%) and Pseudomonas aeruginosa (15.8%).

CONCLUSIONS

Blind ETA is an optimum method for obtaining biological samples for identification of etiological agents causing HAP in intubated patients. Microbial etiological agents were more frequently detected in ETA samples than in those collected by PSB. If ETA/PSB results are negative, samples may be collected by OS and/or GA as these techniques followed ETA in terms of the frequency of pathogen detection.

[Validity comparison of various biological samples from lower airway and their contribution for the detection of nosocomial pneumonia etiological agents]

BACKGROUND

The aim of the study was to compare the validity of bronchial secretion sampling and bronchoscopy-assisted protected specimen brushing (PSB) in patients with hospital-acquired pneumonia (HAP).

MATERIALS AND METHODS

In patients with HAP, bronchial secretion samples (aspiration of lower airway secretions from an orotracheal tube with a suctioning catheter) and PSB (bronchoscopy-assisted sampling from the most affected area of the lung, verified by CT scan) were taken at the same time. Both samples were processed by semiquantitative routine microbiological techniques. Identification of microorganisms was performed by standard microbiological techniques using the MALDI-TOF automated system. For similarity or identity determination of bacterial isolates from bronchial secretion sampling and PSB, pulsed-field gel electrophoresis was used.

RESULTS

Thirty patients were enrolled into the study. Thirty pairs of bronchial secretion samples and PSB samples were obtained and processed. The samples were positive in 23 patients (77 %) and 15 patients (50 %), respectively. In 15 cases, the same pathogen was determined in both samples, and in all those cases, the isolates were genetically identical.

CONCLUSION

The results of the study show that bronchial secretion samples analysis enabled identification of all pathogens that were identified by PSB. Given the high sensitivity of the bronchial secretion aspiration technique and genetic identity of isolates in both samples, bronchial secretion sampling may be recommended for determining HAP etiological agents as the samples are much easier to obtain from patients.

Binding of the Galanthus nivalis agglutinin to thymocytes reveals alterations in surface glycosylation during T-cell development

Surface binding of the Galanthus nivalis agglutinin (GNA) to thymocyte subsets has been studied in pigs and rodents by multicolour flow cytometry. In all the species examined, analogous staining profiles have been recorded. Counter-staining with anti-CD3epsilon, anti-CD4 and anti-CD8 monoclonal antibodies (MoAb) revealed that a significant increase of the GNA targets on the cell surface occurred during early thymocyte differentiation and reached its maximum at the level of the CD3loCD4+CD8+ small cortical thymocyte. This was followed by a decrease in the GNA binding capacity upon terminal maturation to the single positive thymocytes. PAGE analysis has revealed a dominant GNA-binding glycoprotein (molar mass approx. 90 kDa) present on thymocyte plasma membranes and absent on the surface of splenic lymphocytes, although both the whole cell lysates from both organs contained GNA ligands of the same size. Our findings are in agreement with previous data showing that immature thymocytes differ from their mature counterparts and peripheral T lymphocytes in the surface glycosylation pattern, and support the hypothesis that lectin-glycoprotein interaction plays a significant role in the cell-to-cell crosstalk in the thymic cortex.