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.

[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.

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.

Pulmonary Complications after COVID-19.

Coronavirus disease 2019 (COVID-19) is a threat to patients not only because of its acute course, but also because of various complications occurring in the following period, that is, more than 28 days after the onset of acute infection. The present study identified a total of 121 patients hospitalized 29 or more days after the first positive result of a PCR test for SARS-CoV-2, of whom 98 patients were included in the study. Patients were divided into two groups by the time interval between the positive COVID-19 test result and hospitalization date. The time intervals were week 5-11 in an ongoing-COVID group (57.1% of patients) and 12 or more weeks in a post-COVID-group (42.9%). The most frequent reason for hospitalization was respiratory tract infection (58.2%). Pneumonia accounted for 77.2% of these cases. Other reasons for hospitalization were interstitial lung disease (22.4%), pulmonary embolism (8.2%), and sarcoidosis (6.1%). The study group was further divided according to the causes of hospitalization into subgroups with infections and other causes. In the group with infectious diseases, there was a shorter time period between PCR positivity and hospitalization and there were significantly more frequent non-respiratory complications. In the entire sample, the in-hospital mortality was 5.1%.

[Enterococcal infections and their treatment options].

AIM: The study aimed to characterize enterococcal infections at the University Hospital Olomouc and to define antibiotic treatment options. MATERIAL AND METHODS: The data was obtained from the ENVIS LIMS laboratory information system. Between 1 January 2015 and 31 December 2019, clinically relevant enterococci in the hospital and their resistance to antibiotics were retrospectively evaluated. Until mid-2016, criteria defined by Facklam and Collins and biochemical properties determined with the Encoccus test were used for identification. Subsequently, all enterococci were identified using the MALDI-TOF MS system. The susceptibility to antibiotics was determined using a standard microdilution method according to the EUCAST criteria. RESULTS: A total of 8 239 clinically relevant enterococci were isolated over the 5-year period. The most frequently isolated species were Enterococcus faecalis and Enterococcus faecium, which accounted for more than 90% in the period 2017-2019. Enterococci were most frequently isolated from urine (35 %), surgical wounds (17 %) and urethral/vaginal swabs (17 %). Clinically relevant enterococci were most commonly isolated from patients with oncological diagnoses (22%), those with urinary and genital diseases (15%) and respiratory diseases (9%). Enterococcus faecalis strains showed very low resistance to the antibiotics tested. Enterococcus faecium was shown to have 24 % proportion of vancomycin-resistant strains (VRE). CONCLUSION: Primary antibiotics suitable for treating infections with the etiological role of Enterococcus faecalis include aminopenicillins, in case of severe infections in combination with aminoglycosides, in particular gentamicin. For Enterococcus faecium strains, glycopeptides must be chosen. To treat VRE, linezolid or tigecycline are indicated.

Bacterial Pathogens and Evaluation of a Cut-Off for Defining Early and Late Neonatal Infection.

Bacterial infections are an important cause of mortality and morbidity in newborns. The main risk factors include low birth weight and prematurity. The study identified the most common bacterial pathogens causing neonatal infections including their resistance to antibiotics in the Neonatal Department of the University Hospital Olomouc. Additionally, the cut-off for distinguishing early- from late-onset neonatal infections was assessed. The results of this study show that a cut-off value of 72 h after birth is more suitable. Only in case of early-onset infections arising within 72 h of birth, initial antibiotic therapy based on gentamicin with ampicillin or amoxicillin/clavulanic acid may be recommended. It has been established that with the 72-h cut-off, late-onset infections caused by bacteria more resistant to antibiotics may be detected more frequently, a finding that is absolutely crucial for antibiotic treatment strategy.

Implementation of Antibiotic Stewardship in a University Hospital Setting.

The article describes activities of an antibiotic center at a university hospital in the Czech Republic and presents the results of antibiotic stewardship program implementation over a period of 10 years. It provides data on the development of resistance of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus to selected antibiotic agents as well as consumption data for various antibiotic classes. The genetic basis of resistance to beta-lactam antibiotics and its clonal spread were also assessed. The study showed significant correlations between aminoglycoside consumption and resistance of Escherichia coli and Klebsiella pneumoniae to gentamicin (r = 0.712, r = 0.869), fluoroquinolone consumption and resistance of Klebsiella pneumoniae to ciprofloxacin (r = 0.896), aminoglycoside consumption and resistance of Pseudomonas aeruginosa to amikacin (r = 0.716), as well as carbapenem consumption and resistance of Pseudomonas aeruginosa to meropenem (r = 0.855). Genotyping of ESBL- positive isolates of Klebsiella pneumoniae and Escherichia coli showed a predominance of CTX-M-type; in AmpC-positive strains, DHA, EBC and CIT enzymes prevailed. Of 19 meropenem-resistant strains of Klebsiella pneumoniae, two were identified as NDM-positive. Clonal spread of these strains was not detected. The results suggest that comprehensive antibiotic stewardship implementation in a healthcare facility may help to maintain the effectiveness of antibiotics against bacterial pathogens. Particularly beneficial is the work of clinical microbiologists who, among other things, approve administration of antibiotics to patients with bacterial infections and directly participate in their antibiotic therapy.

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.

[Bacterial complications in surgical management of esophageal cancer].

One of the most common cancers is esophageal carcinoma. The basic therapeutic approach is esophagectomy, one of the most extensive procedures in general surgery, potentially leading to serious postoperative complications, in particular respiratory complications. The objective was clinical and microbiological characterization of patients after the surgical removal of the esophagus for carcinoma. In 2020, a total of 14 patients underwent the surgery. Respiratory complications occurred in 57 % of them, with pneumonia leading to respiratory failure and acute respiratory distress syndrome being noted in 21 %. The identified bacterial pathogens were strains of Acinetobacter johnsonii, Enterobacter cloacae, Serratia marcescens, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Enterococcus faecium. In one case, the patient's condition was complicated by fungal infection caused by Candida krusei. The study results warrant the need for close collaboration between the physician caring for a particular patient and a microbiologist that must be continuous and based on daily assessment of both microbiology test results and the patient's clinical condition.

[Bacteremia pathogens in the University Hospital Olomouc].

OBJECTIVES: To provide an overview of the most common bacterial species isolated from blood cultures in the University Hospital Olomouc in the years 2015-2019 and their antibiotic resistance patterns. MATERIAL AND METHODS: The data were obtained from the laboratory information management system ENVIS LIMS. The results were analyzed retrospectively for the period from January 1, 2015 to December 31, 2019. Among positive blood cultures, the prevalence of bacterial species was assessed and the most frequent species were evaluated for resistance to selected antibiotics. Each sample was processed using standard microbiology methods with the MALDI-TOF MS system. Susceptibility to antibiotics was tested with the microdilution method according to the EUCAST recommendations. RESULTS: Over the study period, a total of 3 400 isolates from blood cultures were included. Coagulase-negative staphylococci were the most prevalent (37 %), followed by Escherichia coli (16 %), Klebsiella pneumoniae (9 %), Staphylococcus aureus (7 %), Streptococcus spp. (5 %), Pseudomonas aeruginosa (4 %), Enterobacter cloacae (2 %), Enterococcus faecalis (2 %) and Enterococcus faecium (2 %). Resistance of E. coli to 3rd generation cephalosporins, piperacillin/tazobactam, gentamicin and fluoroquinolones ranged from 7 % to 33 %. A high percentage of Klebsiella pneumoniae strains (33 %-65 %) was resistant to the above antibiotics. The prevalence of methicillin-resistant Staphylococcus aureus reached 3-7 %. Pseudomonas aeruginosa exhibited resistance to piperacillin/tazobactam, ceftazidime, cefepime, meropenem, ciprofloxacin and gentamicin ranging from 3 % to 46 %. CONCLUSION: Knowing the prevalence of bacterial species from blood cultures and their antimicrobial resistance patterns is important for empirical antibiotic therapy in case of an existing infection. It is advisable to conduct such epidemiological studies as part of antibiotic stewardship.

Analysis of Vancomycin-Resistant Enterococci in Hemato-Oncological Patients.

Enterococci are important bacterial pathogens, and their significance is even greater in the case of vancomycin-resistant enterococci (VRE). The study analyzed the presence of VRE in the gastrointestinal tract (GIT) of hemato-oncological patients. Active screening using selective agars yielded VRE for phenotypic and genotypic analyses. Isolated strains were identified with MALDI-TOF MS, (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry) their susceptibility to antibiotics was tested, and resistance genes (vanA, vanB, vanC-1, vanC2-C3) and genes encoding virulence factors (asa1, gelE, cylA, esp, hyl) were detected. Pulsed-field gel electrophoresis was used to assess the relationship of the isolated strains. Over a period of three years, 103 VanA-type VRE were identified in 1405 hemato-oncological patients. The most frequently detected virulence factor was extracellular surface protein (84%), followed by hyaluronidase (40%). Unique restriction profiles were observed in 33% of strains; clonality was detected in 67% of isolates. The study found that 7% of hemato-oncological patients carried VRE in their GIT. In all cases, the species identified was Enterococcus faecium. No clone persisted for the entire 3-year study period. However, genetically different clusters were observed for shorter periods of time, no longer than eight months, with identical VRE spreading among patients.