Fungal and bacterial coinfections increase mortality of severely ill COVID-19 patients

Secondary Bacterial Infections in Critically Ill COVID-19 Patients Admitted in the Intensive Care Unit of a Tertiary Hospital in Romania

Background: The outbreak of the COVID-19 pandemic caught healthcare systems in many countries unprepared. Shortages of personnel, medicines, disinfectants, and intensive care unit (ICU) capacities, combined with inadvertent use of antibiotics and emergence of drug-resistant secondary infections, led to a surge in COVID-19-related mortality. Objective: We aimed to evaluate the prevalence of secondary bacterial infections and the associated antibiotic resistance in a temporary established ICU dedicated to COVID-19 patients. We also assessed the utility of clinical and routine laboratory data as predictors of secondary infections and mortality in these patients. Methods: We examined the medical records of 243 patients admitted to the COVID-19 Medical Support Unit of Târgu Mures, Romania, between 1 August 2020 and 31 January 2021. Results: Among the 243 patients admitted to the COVID-19 Medical Support Unit of Târgu Mures between 1 August 2020 and 31 January 2021, 59 (24.3%) presented secondary infections. Acinetobacter baumannii and Klebsiella pneumoniae were the most frequent isolates (31.1% and 18.9%, respectively), most of them multidrug resistant. Chronic obstructive pulmonary disease had a higher prevalence in patients who developed secondary infections (p = 0.012). Secondary infections were associated with longer stay in the ICU and with higher mortality (p = 0.006 and p = 0.038, respectively). Conclusions: Early identification of secondary infections and proper use of antibiotics are necessary to limit the spread of multidrug-resistant microorganisms in COVID-19 patients admitted in the ICU.

Microsporidian coinfection reduces fitness of a fungal pathogen due to rapid host mortality

Infection outcomes can be strongly context dependent, shifting a host-symbiont relationship along a parasitism-mutualism continuum. Numerous studies show that under stressful conditions, symbionts that are typically mutualistic can become parasitic. The reverse possibility, a parasite becoming mutualistic, has received much less study. We investigated whether the parasitic microsporidium Ordospora pajunii can become beneficial for its host Daphnia dentifera in the presence of the more virulent fungal pathogen Metschnikowia bicuspidata. We found that, even though infection with O. pajunii reduces the frequency of penetration of M. bicuspidata spores into the host body cavity, it does not improve the survival or reproduction of the host; conversely, coinfection increased the mortality of Daphnia. This shorter lifespan of coinfected hosts disrupted the life cycle of M. bicuspidata, greatly reducing its fitness. Thus, coinfection with both pathogens was detrimental to the host at the individual level but might be beneficial for the host population as a result of greatly reduced production of M. bicuspidata spores. If so, this would mean that O. pajunii outbreaks should delay or prevent M. bicuspidata outbreaks. In support of this, in an analysis of dynamics of naturally occurring outbreaks in two lakes where these pathogens co-occur, we found a time lag in occurrence between O. pajunii and M. bicuspidata, with M. bicuspidata epidemics only occurring after the collapse of O. pajunii epidemics. Thus, these results suggest that the interaction between co-occurring symbionts, and the net impact of a symbiont on a host, might be qualitatively different at different scales.IMPORTANCEUnderstanding the factors that modify infection probability and virulence is crucial for identifying the drivers of infection outbreaks and modeling disease epidemic progression, and increases our ability to control diseases and reduce the harm they cause. One factor that can strongly influence infection probability and virulence is the presence of other pathogens. However, while coexposures and coinfections are incredibly common, we still have only a limited understanding of how pathogen interactions alter infection outcomes or whether their impacts are scale dependent. We used a system of one host and two pathogens to show that sequential coinfection can have a tremendous impact on the host and the infecting pathogens and that the outcome of (co-)infection can be negative or positive depending on the focal organization level.

Candidemia Following Severe COVID-19 in Hospitalised and Critical Ill Patients: A Systematic Review and Meta-Analysis

RATIONALE

The epidemiology and clinical impact of COVID-19-associated candidemia (CAC) remained uncertain, leaving gaps in understanding its prevalence, risk factors and outcomes.

METHODS

A systematic review and meta-analysis were conducted by searching PubMed, Embase and Scopus for reports of CAC prevalence, risk factors and clinical outcomes up to June 18, 2024. The generalised linear mixed model was employed to determine the prevalence and 95% confidence intervals (CIs). The risk factors and clinical outcomes were compared between patients with and without CAC using the inverse variance method.

RESULTS

From 81 studies encompassing 29 countries and involving 351,268 patients, the global prevalence of CAC was 4.33% (95% Cl, 3.16%-5.90%) in intensive care unit (ICU) patients. In ICUs, the pooled prevalence of CAC in high-income countries was significantly higher than that of lower-middle-income countries (5.99% [95% Cl, 4.24%-8.40%] vs. 2.23% [95% Cl, 1.06%-4.61%], p = 0.02). Resistant Candida species, including C. auris, C. glabrata (Nakaseomyces glabratus) and C. krusei (Pichia kudriavzveii), constituted 2% of ICU cases. The mortality rate for CAC was 68.40% (95% Cl, 61.86%-74.28%) among ICU patients. Several risk factors were associated with CAC, including antibiotic use, central venous catheter placement, dialysis, mechanical ventilation, tocilizumab, extracorporeal membrane oxygenation and total parenteral nutrition. Notably, the pooled odds ratio of tocilizumab was 2.59 (95% CI, 1.44-4.65).

CONCLUSIONS

The prevalence of CAC is substantial in the ICU setting, particularly in high-income countries. Several risk factors associated with CAC were identified, including several that are modifiable, offering the opportunity to mitigate the risk of CAC.

Pulmonary microbial spectrum in late-stage SARS-CoV-2 infection: a case series

Coronavirus disease 2019 (COVID-19), a kind of respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), primarily spreads through the respiratory tract from human to human. Its extensive and rapid spread has led to a global pandemic, causing great harm to human health and economic development all over the world. Current known evidence indicates that SARS-CoV-2 has evolved accumulating multiple mutations, with altered infectivity and viral replication capacity. A better understanding of the complications of COVID-19 and its relationship with underlying diseases is crucial for the prevention and treatment of SARS-CoV-2. This case series reviewed case data of our 4 recent patients with severe or critical COVID-19, including treatment plan, status of pulmonary infection and their microbiology workup with metagenomic next-generation sequencing with bronchoalveolar lavage fluid. This report shed light on the significance of rapid and accurate clinical diagnosis and treatment on COVID-19.

Association between removable prosthesis-wearing and pneumonia: a systematic review and meta-analysis

BACKGROUND

A high burden of respiratory pathogens colonizing removable prosthesis surfaces suggests the potential of association between removable prosthesis-wearing and respiratory infections. Therefore, this systematic review and meta-analysis aimed to evaluate the evidence from clinical studies concerning the association between removable prosthesis-wearing and respiratory infections.

METHODS

Clinical studies that reported respiratory infections associated with adult patients wearing removable prostheses in any centers (hospitals and nursing homes) or communities were included. Literature was searched across five electronic databases (MEDLINE, Cochrane Library, EMBASE, Web of Science, and Scopus) to 28 May 2024. An additional search was performed for unpublished trials and references cited in related studies. The Newcastle-Ottawa Scale was employed for the quality assessment. The certainty assessment was established using GRADE. The results were pooled using a frequentist random-effects meta-analysis and the odds ratios generated.

RESULTS

A total of 1143 articles were identified. Thirteen articles had full-text articles screening and an additional two articles were added through reference linkage. Ultimately, six non-randomized clinical studies reporting various types of pneumonia contributed to this review. Overall odds of having pneumonia among prosthesis wearers were 1.43 (95% CI: 0.76 to 2.69) and 1.27 (95% CI: 1.11 to 1.46) using the random- and fixed-effects models, respectively. The heterogeneity in the meta-analysis was substantial. In subgroup analysis according to the study design, the heterogeneity within prospective studies was much reduced, I2 = 0% (p = 0.355). The certainty of the evidence evaluated using the GRADE approach was low to very low evidence for prosthesis wearers developing pneumonia based on studies.

CONCLUSIONS

There was no conclusive evidence from the non-randomized clinical studies supporting whether prosthesis-wearing is a risk factor for pneumonia based on outcomes from this review.

Tracking Antibiotic Resistance Trends in Central Iran Amidst the COVID-19 Pandemic From 2021 to 2023: A Comprehensive Epidemiological Study

Background

The emergence of coronavirus disease in 2019 (COVID-19) appears to be having an impact on antibiotic resistance patterns. Specific circumstances during the COVID-19 era may have played a role in the spread of antimicrobial resistance (AMR). This study aimed to look at the changes in AMR patterns of Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii at Al-Zahra Hospital.

Materials and Methods

From March 2021 to January 2023, 3651 clinical samples were collected from patients hospitalized at Isfahan's Al-Zahra Hospital. The Clinical and Laboratory Standards Institute recommended procedures for detecting gram-negative bacteria and assessing antibiotic susceptibility were used. We divided the information into three years.

Results

Highest resistance rates were seen in A. baumannii to Ciprofloxacin (98.0%) and Ampicillin-Sulbactam (97.0%). For P. aeruginosa the resistance rate for Ceftazidime (36.1), Levofloxacin (37.8), and Meropenem (47.1) dropped seriously in 2022.

Conclusion

During the second year of the pandemic in central Iran, all three species studied showed rising rates of AMR. This can be attributable to two peaks within Iran on May 6, 2021 and August 27, 2021. The results of this study show that P. aeruginosa, K. pneumoniae, and A. baumannii bacteria in central Iran have a higher level of antibiotic resistance than previously studied strains before the pandemic.

Prevalence of respiratory pathogens colonizing on removable dental prostheses in healthy older adults: A systematic review and meta-analysis

PURPOSE

This systematic review and meta-analysis aimed to investigate the prevalence of opportunistic respiratory pathogens colonizing removable dental prostheses in older adults without respiratory diseases.

METHODS

This review was registered with PROSPERO and conducted in accordance with the principles formed by the working group of the Joanna Briggs Institute (JBI) to evaluate systematic reviews of prevalence data. Literature searches were conducted across five electronic databases. Quality assessments were determined according to a revised JBI critical appraisal checklist across nine criteria. Comparison between fixed- and random-effects meta-analyses were performed for sensitivity analysis. Prediction intervals were also presented when three or more studies were included in the meta-analysis.

RESULTS

Across the databases, 1091 articles were identified, and 591 articles remained after the removal of duplicates. Twenty "potentially effective" studies were identified. Ultimately eight studies informed this review and meta-analyses were performed for 13 known respiratory pathogens. The meta-analyses identified the top three common respiratory pathogens residing on the removable prostheses were, in descending order: Staphylococcus aureus: 31.81% (95% CI: 13.34%-48.24%); Staphylococcus epidermidis: 14.07% (95% CI: 7.88%-21.48%); Klebsiella pneumoniae: 10.50% (95% CI: 2.55%-22.30%). The heterogeneity scores for nine respiratory pathogen analyses were classified as "unimportant inconsistency", I2 = 0% (p > 0.1). For sensitivity analysis, there was no difference between the random- and fixed-effects models.

CONCLUSION

The existing evidence demonstrated a high burden of certain opportunistic respiratory pathogens, which may be considered a major potential cause of respiratory infections in older adults wearing removable prostheses.

A comparison of the prevalence of respiratory pathogens and opportunistic respiratory pathogenic profile of 'clean' and 'unclean' removable dental prostheses

OBJECTIVES

To determine and compare the opportunistic respiratory pathogenic index (ORPI) and prevalence of respiratory pathogens between clean and unclean removable prostheses.

METHODS

A cross-sectional study was conducted among 97 removable prosthesis wearers at a teaching dental hospital. Participants' prosthesis hygiene was grouped into clean and unclean. After prosthesis plaque samples were sequenced using the Type IIB Restriction-site Associated DNA Sequencing for Microbiome method, the prevalence was assessed for the presence of respiratory pathogens on each sample. The ORPIs for clean and unclean prostheses were quantified based on the sum of the relative abundance of respiratory pathogenic bacteria in a microbiome using a reference database that contains opportunistic respiratory pathogens and disease-associated information.

RESULTS

A total of 30 opportunistic respiratory pathogens were identified on the removable prostheses. Eighty-one (83.5 %) removable prostheses harboured respiratory pathogenic bacteria. Stenotrophomonas maltophilia (34.0 %), Pseudomonas aeruginosa (27.8 %), and Streptococcus agalactiae (27.8 %) were the top three prevalent respiratory pathogens detected in plaque samples. There was a significantly higher prevalence of respiratory pathogens residing on unclean than clean prostheses (P = 0.046). However, the ORPIs in both groups showed no statistically significant difference (P = 0.516).

CONCLUSIONS

The ORPIs for both clean and unclean prostheses demonstrated a similar abundance of respiratory pathogens. However, the high prevalence of respiratory pathogens residing on unclean prostheses should not be underestimated. Therefore, maintaining good prosthesis hygiene is still important for overall oral and systemic health, even though the direct link between prosthesis cleanliness and reduced abundance of respiratory pathogens has not been established.

CLINICAL SIGNIFICANCE

The association between the prevalence of respiratory pathogens and unclean removable prostheses has been demonstrated and might increase the theoretical risk of respiratory disease development.

The characteristics of microbiome in the upper respiratory tract of COVID-19 patients

BACKGROUND

Co-infection with other pathogens in coronavirus disease 2019 (COVID-19) patients exacerbates disease severity and impacts patient prognosis. Clarifying the exact pathogens co-infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is premise of the precise treatment for COVID-19 patients.

METHODS

Sputum samples were collected from 17 patients in the COVID-19 positive group and 18 patients in the COVID-19 negative group. DNA extraction was performed to obtain the total DNA. Sequencing analysis using 16S and ITS rRNA gene was carried out to analyze the composition of bacterial and fungal communities. Meanwhile, all the samples were inoculated for culture.

RESULTS

We did not observe significant differences in bacterial composition between the COVID-19 positive and negative groups. However, a significantly higher abundance of Candida albicans was observed in the upper respiratory tract samples from the COVID-19 positive group compared to the COVID-19 negative group. Moreover, the Candida albicans strains isolated from COVID-19 positive group exhibited impaired secretion of aspartyl proteinases.

CONCLUSION

COVID-19 positive patients demonstrate a notable increase in the abundance of Candida albicans, along with a decrease in the levels of aspartyl proteinases, indicating the alteration of microbiota composition of upper respiratory tract.

Development and validation of machine learning-based models for predicting healthcare-associated bacterial/fungal infections among COVID-19 inpatients: a retrospective cohort study

BACKGROUND

COVID-19 and bacterial/fungal coinfections have posed significant challenges to human health. However, there is a lack of good tools for predicting coinfection risk to aid clinical work.

OBJECTIVE

We aimed to investigate the risk factors for bacterial/fungal coinfection among COVID-19 patients and to develop machine learning models to estimate the risk of coinfection.

METHODS

In this retrospective cohort study, we enrolled adult inpatients confirmed with COVID-19 in a tertiary hospital between January 1 and July 31, 2023, in China and collected baseline information at admission. All the data were randomly divided into a training set and a testing set at a ratio of 7:3. We developed the generalized linear and random forest models for coinfections in the training set and assessed the performance of the models in the testing set. Decision curve analysis was performed to evaluate the clinical applicability.

RESULTS

A total of 1244 patients were included in the training cohort with 62 healthcare-associated bacterial/fungal infections, while 534 were included in the testing cohort with 22 infections. We found that patients with comorbidities (diabetes, neurological disease) were at greater risk for coinfections than were those without comorbidities (OR = 2.78, 95%CI = 1.61-4.86; OR = 1.93, 95%CI = 1.11-3.35). An indwelling central venous catheter or urinary catheter was also associated with an increased risk (OR = 2.53, 95%CI = 1.39-4.64; OR = 2.28, 95%CI = 1.24-4.27) of coinfections. Patients with PCT > 0.5 ng/ml were 2.03 times (95%CI = 1.41-3.82) more likely to be infected. Interestingly, the risk of coinfection was also greater in patients with an IL-6 concentration < 10 pg/ml (OR = 1.69, 95%CI = 0.97-2.94). Patients with low baseline creatinine levels had a decreased risk of bacterial/fungal coinfections(OR = 0.40, 95%CI = 0.22-0.71). The generalized linear and random forest models demonstrated favorable receiver operating characteristic curves (ROC = 0.87, 95%CI = 0.80-0.94; ROC = 0.88, 95%CI = 0.82-0.93) with high accuracy, sensitivity and specificity of 0.86vs0.75, 0.82vs0.86, 0.87vs0.74, respectively. The corresponding calibration evaluation P statistics were 0.883 and 0.769.

CONCLUSIONS

Our machine learning models achieved strong predictive ability and may be effective clinical decision-support tools for identifying COVID-19 patients at risk for bacterial/fungal coinfection and guiding antibiotic administration. The levels of cytokines, such as IL-6, may affect the status of bacterial/fungal coinfection.

The effect of SARS-COV-2 variant on non-respiratory features and mortality among vaccinated and non-fully vaccinated patients

OBJECTIVE

To determine the effect of SARS-CoV-2 variants on non-respiratory features of COVID-19 in vaccinated and not fully vaccinated patients using a University of California database.

METHODS

A longitudinal retrospective review of medical records (n = 63,454) from 1/1/2020-4/26/2022 using the UCCORDS database was performed to compare non-respiratory features, vaccination status, and mortality between variants. Chi-square tests were used to study the relationship between categorical variables using a contingency matrix.

RESULTS

Fever was the most common feature across all variants. Fever was significantly higher in not fully vaccinated during the Delta and Omicron waves (p = 0.001; p = 0.001). Cardiac features were statistically higher in not fully vaccinated during Omicron; tachycardia was only a feature of not fully vaccinated during Delta and Omicron; diabetes and GI reflux were features of all variants regardless of vaccine status. Odds of death were significantly increased among those not fully vaccinated in the Delta and Omicron variants (Delta OR: 1.64, p = 0.052; Omicron OR: 1.96, p < 0.01). Vaccination was associated with a decrease in the frequency of non-respiratory features.

CONCLUSIONS

Risk of non-respiratory features of COVID-19 is statistically higher in those not fully vaccinated across all variants. Risk of death and correlation with vaccination status varied.

S, V. SD, Duvvur NR. An Experience in Laboratory Diagnosis of Fungal Infections in COVID -19 Patients

Introduction  Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has cast a gloom spell on healthcare worldwide, infecting millions of people. Objective  The aim of the present study is to determine the prevalence and review the contributing comorbidities and the precipitating factors leading to the emergence of the fungal infections in COVID-19-affected patients. To assess the utility of different laboratory techniques for confirmation of fungal infections. To assess the strengths and limitations of the diagnostic methods. Methods  We have studied 252 clinical samples obtained from 121 COVID-positive patients. Results  Among the 121 patients clinically diagnosed with fungal infections, 88 had diabetes and were given steroids for treatment ( p -value = 0.001). Ninety-five patients (78.5%) had a positive laboratory diagnosis (either culture positive, potassium hydroxide [KOH]-positive or positive histopathology report). Fungal culture was positive in 75 (61.9%) patients and histopathology report was positive in 62 (51.2%). Histopathology was positive in 7 (5.8%) patients in whom culture and KOH were negative. Conclusion  Aggressive treatment methods, administration of immune suppressants, and antibiotics, with an intention to salvage, have made patients susceptible to the benign fungus, causing it to evade the host immunity, thus leading to invasive infections. Applying different laboratory modalities would not only aid in providing fast and valuable information but also help in understanding the pathology which would assist the clinician in selecting the correct treatment for the patient.

Acute neutrophilic vasculitis (leukocytoclasia) in 36 COVID-19 autopsy brains

BACKGROUND

Hypercytokinemia, the renin-angiotensin system, hypoxia, immune dysregulation, and vasculopathy with evidence of immune-related damage are implicated in brain morbidity in COVID-19 along with a wide variety of genomic and environmental influences. There is relatively little evidence of direct SARS-CoV-2 brain infection in COVID-19 patients.

METHODS

Brain histopathology of 36 consecutive autopsies of patients who were RT-PCR positive for SARS-CoV-2 was studied along with findings from contemporary and pre-pandemic historical control groups. Immunostaining for serum and blood cell proteins and for complement components was employed. Microcirculatory wall complement deposition in the COVID-19 cohort was compared to historical control cases. Comparisons also included other relevant clinicopathological and microcirculatory findings in the COVID-19 cohort and control groups.

RESULTS

The COVID-19 cohort and both the contemporary and historical control groups had the same rate of hypertension, diabetes mellitus, and obesity. The COVID-19 cohort had varying amounts of acute neutrophilic vasculitis with leukocytoclasia in the microcirculation of the brain in all cases. Prominent vascular neutrophilic transmural migration was found in several cases and 25 cases had acute perivasculitis. Paravascular microhemorrhages and petechial hemorrhages (small brain parenchymal hemorrhages) had a slight tendency to be more numerous in cohort cases that displayed less acute neutrophilic vasculitis. Tissue burden of acute neutrophilic vasculitis with leukocytoclasia was the same in control cases as a group, while it was significantly higher in COVID-19 cases. Both the tissue burden of acute neutrophilic vasculitis and the activation of complement components, including membrane attack complex, were significantly higher in microcirculatory channels in COVID-19 cohort brains than in historical controls.

CONCLUSIONS

Acute neutrophilic vasculitis with leukocytoclasia, acute perivasculitis, and associated paravascular blood extravasation into brain parenchyma constitute the first phase of an immune-related, acute small-vessel inflammatory condition often termed type 3 hypersensitivity vasculitis or leukocytoclastic vasculitis. There is a higher tissue burden of acute neutrophilic vasculitis and an increased level of activated complement components in microcirculatory walls in COVID-19 cases than in pre-pandemic control cases. These findings are consistent with a more extensive small-vessel immune-related vasculitis in COVID-19 cases than in control cases. The pathway(s) and mechanism for these findings are speculative.

The Rapidly Changing Patterns in Bacterial Co-Infections Reveal Peaks in Limited Gram Negatives during COVID-19 and Their Sharp Drop Post-Vaccination, Implying Potential Evolution of Co-Protection during Vaccine-Virus-Bacterial Interplay

SARS-CoV-2 has caused the most devastating pandemic of all time in recent human history. However, there is a serious paucity of high-quality data on aggravating factors and mechanisms of co-infection. This study aimed to identify the trending patterns of bacterial co-infections and types and associated outcomes in three phases of the pandemic. Using quality hospital data, we have investigated the SARS-CoV-2 fatality rates, profiles, and types of bacterial co-infections before, during, and after COVID-19 vaccination. Out of 389 isolates used in different aspects, 298 were examined before and during the pandemic (n = 149 before, n = 149 during). In this group, death rates were 32% during compared to only 7.4% before the pandemic with significant association (p-value = 0.000000075). However, the death rate was 34% in co-infected (n = 170) compared to non-co-infected patients (n = 128), indicating a highly significant value (p-value = 0.00000000000088). However, analysis of patients without other serious respiratory problems (n = 28) indicated that among the remaining 270 patients, death occurred in 30% of co-infected patients (n = 150) and only 0.8% of non-co-infected (n = 120) with a high significant p-value = 0.00000000076. The trending patterns of co-infections before, during, and after vaccination showed a significant decline in Staphylococcus aureus with concomitant peaks in Gram negatives n = 149 before/n = 149 during, including Klebsiella pneumonian = 11/49 before/during, E. coli n = 10/24, A. baumannii n = 8/25, Ps. aeruginosa n = 5/16, and S. aureus 13/1. Nevertheless, in the post-vaccination phase (n = 91), gender-specific co-infections were examined for potential differences in susceptibility. Methicillin-resistant S. aureus dominated both genders followed by E. coli in males and females, with the latter gender showing higher rates of isolations in both species. Klebsiella pneumoniae declined to third place in male patients. The drastic decline in K. pneumoniae and Gram negatives post-vaccination strongly implied a potential co-protection in vaccines. Future analysis would gain more insights into molecular mimicry.

Clinical features of omicron SARS-CoV-2 variants infection associated with co-infection and ICU-acquired infection in ICU patients

Background

Although the decreasing rate of hospital admission in the omicron wave has led countries to loosen control, still the patients requires ICU admission. It is common for viral respiratory infections to be co-infected with bacteria. However, the difference between co-infection and ICU-acquired infection on their clinical characteristics and outcomes during the Omicron wave was little reported.

Methods

Clinical and microbiological data were collected from ICU patients with omicron infection between April 1st, 2022, and May 31th, 2022 and a comprehensive comparative study of the clinical characteristics and endpoint were conducted.

Results

The Omicron SARS-CoV-2 variants-infected patients requiring intensive care had high rates of co-infection (42.55%). Additionally, the ICU COVID-19 patients with co-infection showed more severe clinical features compared to those with ICU-acquired infection. Furthermore, Multivariate Cox analysis demonstrated that co-infection (hazard ratio: 4.670, p = 0.018) was a significant risk factor for poor outcomes in ICU patients with COVID-19. Besides, Kaplan-Meier survival curve analysis revealed that COVID-19 patients with co-infection had a significantly shorter 28-Day survival time compared to those with ICU-acquired infection (p < 0.001). Finally, our investigation identified a significant association between the presence of Candida app. in the broncho-alveolar lavage and an elevated risk of mortality (OR: 13.80, p = 0.002) and invasive ventilation (OR: 5.63, p = 0.01).

Conclusion

Co-infection is prevalent among patients requiring intensive care and is linked to unfavorable outcomes in the Omicron wave. Consequently, more attention may be needed for the empirical antibacterial treatment in ICU patients within the COVID-19 Omicron variant, especially anti-fungi.

Understanding clinical outcomes and factors influencing mortality in intensive care unit patients with COVID-19-associated candidemia

BACKGROUND

During the COVID pandemic, research has shown an increase in candidemia cases following severe COVID infection and the identification of risk factors associated with candidemia. However, there is a lack of studies that specifically explore clinical outcomes and mortality rates related to candidemia after COVID infection.

OBJECTIVES

The aim of this international study was to evaluate the clinical outcomes and identify factors influencing mortality in patients who developed candidemia during their COVID infection.

PATIENTS/METHODS

This study included adult patients (18 years of age or older) admitted to the intensive care unit (ICU) and diagnosed with COVID-associated candidemia (CAC). The research was conducted through ID-IRI network and in collaboration with 34 medical centres across 18 countries retrospectively, spanning from the beginning of the COVID pandemic until December 2021.

RESULTS

A total of 293 patients diagnosed with CAC were included. The median age of the patients was 67, and 63% of them were male. The most common Candida species detected was C. albicans. The crude 30-day mortality rate was recorded at 62.4%. The logistic regression analysis identified several factors significantly impacting mortality, including age (odds ratio [OR] 1.04, 95% confidence interval [CI] 1.02-1.07, p < .0005), SOFA score (OR 1.307, 95% CI 1.17-1.45, p < .0005), invasive mechanical ventilation (OR 7.95, 95% CI 1.44-43.83, p < .017) and duration of mechanical ventilation (OR 0.98, 95% CI 0.96-0.99, p < .020).

CONCLUSIONS

By recognising these prognostic factors, medical professionals can customise their treatment approaches to offer more targeted care, leading to improved patient outcomes and higher survival rates for individuals with COVID-associated candidemia.

Endocarditis caused by Aspergillus fumigatus in a patient 9 months after COVID-19 infection recovery: a case report and review of the literature

BACKGROUND

Aspergillus spp. are among the fungal pathogens that can cause life-threatening infections in patients with a history of COVID-19.

CASE PRESENTATION

We present the case of a 58-year-old Iranian woman with post-COVID-19 Aspergillus fumigatus endocarditis complicated by numerous thromboembolisms. She underwent mitral valve replacement surgery and multiple lower extremity embolectomies and was treated with voriconazole, which led to her final recovery.

CONCLUSIONS

Aspergillus endocarditis should be considered in any patient with suspected endocarditis who has a history of COVID-19 infection and does not respond to routine antibiotic and antifungal therapy, as COVID-19 interferes with proper immune function, and lack of underlying cardiac conditions and immunodeficiencies does not preclude the diagnosis. Culture and histopathological evaluation of vegetations and emboli, as well as PCR, can confirm the diagnosis. Early initiation of antifungal therapy and surgical removal of infected valves and emboli can improve prognosis in patients with Aspergillus endocarditis.

Cefiderocol and Sulbactam-Durlobactam against Carbapenem-Resistant Acinetobacter baumannii

Infections caused by carbapenem-resistant Acinetobacter baumannii (CRAB) remain a clinical challenge due to limited treatment options. Recently, cefiderocol, a novel siderophore cephalosporin, and sulbactam-durlobactam, a bactericidal β-lactam-β-lactamase inhibitor combination, have been approved by the Food and Drug Administration for the treatment of A. baumannii infections. In this review, we discuss the mechanisms of action of and resistance to cefiderocol and sulbactam-durlobactam, the antimicrobial susceptibility of A. baumannii isolates to these drugs, as well as the clinical effectiveness of cefiderocol and sulbactam/durlobactam-based regimens against CRAB. Overall, cefiderocol and sulbactam-durlobactam show an excellent antimicrobial activity against CRAB. The review of clinical studies evaluating the efficacy of cefiderocol therapy against CRAB indicates it is non-inferior to colistin/other treatments for CRAB infections, with a better safety profile. Combination treatment is not associated with improved outcomes compared to monotherapy. Higher mortality rates are often associated with prior patient comorbidities and the severity of the underlying infection. Regarding sulbactam-durlobactam, current data from the pivotal clinical trial and case reports suggest this antibiotic combination could be a valuable option in critically ill patients affected by CRAB infections, in particular where no other antibiotic appears to be effective.

Molecular Typing and Resistance Profile of Acinetobacter baumannii Isolates during the COVID-19 Pandemic: Findings from the "EPIRADIOCLINF" Project

Due to the COVID-19 pandemic, there has been a shift in focus towards controlling the spread of SARS-CoV-2, which has resulted in the neglect of traditional programs aimed at preventing healthcare-associated infections and combating antimicrobial resistance. The present work aims to characterize the colonization or infection with Acinetobacter baumannii of COVID-19 patients and to identify any clonality between different isolates. Specifically, data and resistance profiles of A. baumannii isolates were prospectively collected from patients recruited by the EPIRADIOCLINF project. Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were used for molecular typing. Overall, we analyzed 64 isolates of A. baumannii from 48 COVID-19 patients. According to our analysis, we have identified the spread of a clonally related isolate, referred to as B. The PFGE pattern B includes four subtypes: B1 (consisting of 37 strains), B2 (11), B3 (5), and B4 (2). Furthermore, in the isolates that were examined using MLST, the most observed sequence type was ST/281. In terms of resistance profiles, 59 out of the total isolates (92.2%) were found to be resistant to gentamicin, carbapenems, ciprofloxacin, and tobramycin. The isolation and identification of A. baumannii from COVID-19 patients, along with the high levels of transmission observed within the hospital setting, highlight the urgent need for the implementation of effective prevention and containment strategies.

Secondary and Co-Infections in Hospitalized COVID-19 Patients: A Multicenter Cross-Sectional Study in Malaysia

Bacterial and fungal secondary and co-infections are commonly identified with viral respiratory infections. This study was undertaken to determine the incidence and factors associated with bacterial and fungal infections in patients with COVID-19 as well as antibiotics prescription patterns within the first and second waves of the outbreak in Malaysia. Clinical records of 3532 COVID-19 patients admitted to hospitals in Malaysia between 4 February and 4 August 2020 were analyzed. Co-morbidities, clinical features, investigations, treatment, and complications were captured using the REDCap database. Culture and sensitivity test results were retrieved from the WHONET database. Univariate and multivariate regression analyses were used to identify associated determinants. A total of 161 types of bacterial and fungal infections were found in 81 patients, i.e., 2.3%. The most common bacterial cultures were Gram-negative, i.e., Pseudomonas aeruginosa (15.3%) and Klebsiella pneumoniae (13.9%). The most common fungal isolate was Candida albicans (41.2%). Augmentin, ceftriaxone, tazocin, meropenem, and azithromycin were the five most frequently prescribed antibiotics. The latter four were classified under the "Watch" category in the WHO AwaRe list. Our data showed that bacterial and fungal secondary and co-infections were frequently found in severely ill COVID-19 patients and were associated with a higher mortality rate.

[Candida albicans: risk factor in covid-19 patients]

The Candida Albicans fungus in our body can cause various conditions and will depend directly on the systemic condition of the host. Patients with COVID-19 who have previously presented this fungus can increase the likelihood of morbidity and mortality, since this microorganism can be located in areas that correspond to the respiratory system, generating a functional deficit. If not treated timely, it will proliferate into the blood and digestive system. Many patients with respiratory difficulties on account of this condition require mechanical ventilation to combat it.

Objective

To relate the presence of Candida Albicans as an aggravating factor in patients with COVID-19.

Materials and

methods: A literature review took place using the Redalyc, Scielo, PubMed, Research gate, Science direct, Google Scholar databases. The inclusion criteria used were: articles in English and Spanish, along with articles published from 2020 up to date. There were 65 scientific articles that met the search criteria and were analyzed. The analysis determined that oral candidiasis negatively affects patients with COVID-19 infection, increasing the risk of admission to the ICU with the use of artificial ventilators.

Evaluation of Blood Cultures from SARS-CoV-2-Positive and Negative Adult Patients

Bacteremia and fungemia are significant causes of morbidity and mortality that frequently occur as co-infections with viral respiratory infections, including SARS-CoV-2. The aim of this study was to evaluate the microorganisms that were isolated from the blood cultures of SARS-CoV-2-positive and negative patients and investigate their antimicrobial resistance patterns. A retrospective analysis was performed of 22,944 blood cultures sent to the laboratory between November 2020 and December 2021. Blood culture analyses were performed using the BD Bactec FX automated system. Identification was carried out using conventional methods, namely, VITEK-2 and MALDI-TOF MS. Antibacterial/antifungal susceptibility tests were performed according to EUCAST/CLSI recommendations. SARS-CoV-2 tests were performed with RT-PCR. Culture positivity was detected in 1630 samples from 652 patients. Of these 652 patients, 633 were tested for SARS-CoV-2; 118 (18.6%) were positive and 515 (81.3%) were negative. The bacteria and fungi that were isolated at the highest rate in SARS-CoV-2-positive patients were methicillin-resistant coagulase-negative staphylococci (MR-CoNS) (21.5%), Escherichia coli (12.4%), Klebsiella pneumoniae (12.4%), Candida albicans (1.65%), and Candida glabrata complex (1.65%), while in the negative patients, the highest rates were for E. coli (21.3%), MR-CoNS (13.5%), K. pneumoniae (12.05%), C. albicans (2.1%), Candida parapsilosis (1.1%), and Candida tropicalis (0.9%). No statistically significant difference was determined between COVID-19-positive and negative patients in terms of detection, such as with the Pseudomonas spp., Enterococcus spp., and methicillin-resistant Staphylococcus aureus isolated from the blood cultures (p > 0.05). The most common isolate was MR-CoNS in SARS-CoV-2-positive patients (p = 0.028). Acinetobacter baumannii was more frequent (p = 0.004) and carbapenem-resistant K. pneumoniae was isolated at a higher rate (60% vs. 43%) in SARS-CoV-2-positive patients compared to SARS-CoV-2-negative patients (p > 0.05). These findings highlight the fact that isolation procedures should not be disregarded and the distribution of bacterial/fungal agents of bloodstream infections and their antibiotic resistance should be followed up during a pandemic, such as in the case of COVID-19.

Fungal Infections Are Not Associated with Increased Mortality in COVID-19 Patients Admitted to Intensive Care Unit (ICU)

Introduction

Fungal infection is a cause of increased morbidity and mortality in intensive care patients. Critically unwell patients are at increased risk of developing invasive fungal infections. COVID-19 patients in the intensive care unit (ICU) may be at a particularly high risk. The primary aim of this study was to establish the incidence of secondary fungal infections in patients admitted to the ICU with COVID-19. Secondary aims were to investigate factors that may contribute to an increased risk of fungal infections and to calculate the mortality between fungal and nonfungal groups.

Methods

We undertook a retrospective observational study in a tertiary ICU in Wales, United Kingdom. 174 patients admitted with COVID-19 infection from March 2020 until May 2021 were included. Data were collected through a retrospective review of patient's clinical notes and microbiology investigation results obtained from the online clinical portal.

Results

81/174 (47%) COVID-19 patients developed fungal infections, 93% of which were Candida species, including Candida albicans (88%), and 6% had an Aspergillus infection. Age and smoking history did not appear to be contributing factors. The nonfungal group had a significantly higher body mass index (33 ± 8 vs. 31 ± 7, p=0.01). The ICU length of stay (23 (1-116) vs. 8 (1-60), p < 0.001), hospital length of stay (30 (3-183) vs. 15 (1-174) ± 7, p < 0.001), steroid days (10 (1-116) vs. 4 (0-28), p=0.02), and ventilation days (18 (0-120) vs. 2 (0-55), p < 0.001) were significantly higher in the fungal group. The mortality rate in both groups was similar (51% vs. 52%). The Kaplan-Meier survival analysis showed that the fungal group survived more than the nonfungal group (log rank (Mantel-Cox), p < 0.001).

Conclusion

Secondary fungal infections are common in COVID-19 patients admitted to the ICU. Longer treatment with corticosteroids, increased length of hospital and ICU stay, and greater length of mechanical ventilation significantly increase the risk of fungal infections. Fungal infection, however, was not associated with an increase in mortality.

COVID-19 and candiduria: an investigation of the risk factors and immunological aspects

Secondary fungal infections are frequently observed in COVID-19 patients. However, the occurrence of candiduria in these patients and its risk factors are underexplored. We evaluated the risk factors of candiduria in COVID-19 patients, including inflammatory mediators that could be used as prognostic markers. Clinical information, laboratory test results, and outcomes were collected from severely ill COVID-19 patients with and without candiduria. Candida species identification, antifungal susceptibility, and plasma inflammatory mediators' measurements were performed. Regression logistic and Cox regression model were used to evaluate the risk factors. A higher risk of longer hospitalization and mortality were observed in patients with candiduria compared to those with COVID-19 only. Candiduria was caused by Candida albicans, C. glabrata, and C. tropicalis. Isolates with intermediate susceptibility to voriconazole and resistant to caspofungin were identified. Classic factors such as the use of corticosteroids and antibacterials, the worsening of renal function, and hematological parameters (hemoglobin and platelets) were found to predispose to candiduria. The mediators IL-1β, IL-1ra, IL-2, CXCL-8, IL-17, IFN-γ, basic FGF, and MIP-1β were significantly increased in patients with COVID-19 and candiduria. Furthermore, IFN-γ, IL-1ra, and CXCL-8 were associated with the occurrence of candiduria in COVID-19 patients, whereas basic FGF, IL-1β, and CXCL-8 were associated with the risk of death in these patients. Classical and immunological factors were associated with worse prognosis among patients with COVID-19 and candiduria. Some mediators, especially CXCL-8, can be a reliable biomarker of fungal coinfection and may guide the diagnostic and the treatment of these patients.

Changes in the prevalence of pathogens causing hospital-acquired bacterial pneumonia and the impact of their antimicrobial resistance patterns on clinical outcomes: A propensity-score-matched study

BACKGROUND

This study aimed to evaluate changes in the prevalence of pathogens causing hospital-acquired bacterial pneumonia (HABP) and their antimicrobial resistance patterns in recent years, and to identify risk factors for 28-day all-cause mortality (ACM) in patients with HABP.

METHODS

A propensity-score-matched study was performed by randomly allocating patients with ventilator-associated and non-ventilator-associated bacterial pneumonia admitted to two university hospitals between 2011 and 2021.

RESULTS

In total, 17,250 patients with HABP were enrolled. The annual incidence of Staphylococcus aureus HABP decreased during the study period, while that of Klebsiella pneumoniae HABP increased significantly each year. Over the same period, the resistance rate of S. aureus to methicillin decreased from 88.4% to 64.4%, while the non-susceptibility rate of K. pneumoniae to carbapenems increased from 0% to 38%. HABP caused by A. baumannii [adjusted odds ratio (aOR) 1.50, 95% confidence interval (CI) 1.25-1.79], K. pneumoniae (aOR 1.28, 95% CI 1.16-1.40) and Stenotrophomonas maltophilia (aOR 1.32, 95% CI 1.05-1.66) was a risk factor for 28-day ACM. Patients with HABP caused by methicillin-resistant S. aureus and carbapenem-non-susceptible A. baumannii or K. pneumoniae had a significantly lower probability of survival. HABP with preceding coronavirus disease 2019 (COVID-19) was associated with high 28-day ACM (aOR 5.40, 955 CI 3.03-9.64) and high incidence of bacteraemic pneumonia (aOR 40.55, 95% CI 5.26-312.79).

CONCLUSIONS

This study showed shifting trends in HABP-causing pathogens in terms of annual incidence and resistance rates to major therapeutic antimicrobial agents. HABP-causing bacterial pathogens, their antimicrobial resistance phenotypes, and preceding COVID-19 were significantly associated with progression of HABP to bloodstream infection and 28-day ACM in infected patients.

Epidemiological Characteristics and Outcomes Predictors for Intensive Care Unit COVID-19 Patients in Al-Madinah, Saudi Arabia. Retrospective Cohort Study

Introduction

The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) increased the demand for intensive care unit (ICU) services. Mortality and morbidity rates among ICU COVID-19 patients are affected by several factors, such as severity, comorbidities, and coinfections. In this study, we describe the demographic characteristics of COVID-19 patients admitted to an ICU in Saudi Arabia, and we determined the predictors for mortality and prolonged ICU length of stay. Additionally, we determined the prevalence of bacterial coinfection and its effect on the outcomes for ICU COVID-19 patients.

Methods

We retrospectively studied the medical records of 142 COVID-19 patients admitted to the ICU at a tertiary hospital in Madinah, Saudi Arabia. Data on demographics, medical history, mortality, length of stay, and presence of coinfection were collected for each patient.

Results

Neutrophil-to-Lymphocyte ratio (NLR) and intubation were reliable predictors of mortality and ICU length of stay among these ICU COVID-19 patients. Moreover, bacterial coinfections were detected in 23.2% of the patients and significantly (p < 0.001) prolonged their ICU length of stay, explaining the 10% increase in the length of stay for these patients. Furthermore, mortality reached 70% among the coinfected patients, and 60.8% of the isolated coinfecting pathogens were multidrug-resistant (MDR) strains of Klebsiella pneumoniae, Acinetobacter baumannii, and Staphylococcus aureus.

Conclusion

Increased NLR and intubation are predictors of mortality and prolonged length of stay in COVID-19 patients admitted to the ICU. Coinfection with MDR bacterial strains potentially results in complications and is a high-risk factor for prolonged ICU length of stay.

New Phocoenamicin and Maklamicin Analogues from Cultures of Three Marine-Derived Micromonospora Strains

Antimicrobial resistance can be considered a hidden global pandemic and research must be reinforced for the discovery of new antibiotics. The spirotetronate class of polyketides, with more than 100 bioactive compounds described to date, has recently grown with the discovery of phocoenamicins, compounds displaying different antibiotic activities. Three marine Micromonospora strains (CA-214671, CA-214658 and CA-218877), identified as phocoenamicins producers, were chosen to scale up their production and LC/HRMS analyses proved that EtOAc extracts from their culture broths produce several structurally related compounds not disclosed before. Herein, we report the production, isolation and structural elucidation of two new phocoenamicins, phocoenamicins D and E (1-2), along with the known phocoenamicin, phocoenamicins B and C (3-5), as well as maklamicin (7) and maklamicin B (6), the latter being reported for the first time as a natural product. All the isolated compounds were tested against various human pathogens and revealed diverse strong to negligible activity against methicillin-resistant Staphylococcus aureus, Mycobacterium tuberculosis H37Ra, Enterococcus faecium and Enterococcus faecalis. Their cell viability was also evaluated against the human liver adenocarcinoma cell line (Hep G2), demonstrating weak or no cytotoxicity. Lastly, the safety of the major compounds obtained, phocoenamicin (3), phocoenamicin B (4) and maklamicin (7), was tested against zebrafish eleuthero embryos and all of them displayed no toxicity up to a concentration of 25 μM.

COVID-19-associated candidiasis and the emerging concern of Candida auris infections

The incidence of COVID-19-associated candidiasis (CAC) is increasing, resulting in a grave outcome among hospitalized patients with COVID-19. The most alarming condition is the increasing incidence of multi-drug resistant Candida auris infections among patients with COVID-19 worldwide. The therapeutic strategy towards CAC caused by common Candida species, such as Candida albicans, Candida tropicalis, and Candida glabrata, is similar to the pre-pandemic era. For non-critically ill patients or those with a low risk of azole resistance, fluconazole remains the drug of choice for candidemia. For critically ill patients, those with a history of recent azole exposure or with a high risk of fluconazole resistance, echinocandins are recommended as the first-line therapy. Several novel therapeutic agents alone or in combination with traditional antifungal agents for candidiasis are potential options in the future. However, for multidrug-resistant C. auris infection, only echinocandins are effective. Infection prevention and control policies, including strict isolation of the patients carrying C. auris and regular screening of non-affected patients, are suggested to prevent the spread of C. auris among patients with COVID-19. Whole-genome sequencing may be used to understand the epidemiology of healthcare-associated candidiasis and to better control and prevent these infections.

Implications of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infected Hospitalised Patients with Co-Infections and Clinical Outcomes

The clinical severity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection may rise because of acquiring a co-infection during the hospital stay of the patients. The rate of hospital co-infection alongside COVID-19 infection remains low. However, the mortality rates and intensive care unit (ICU) admission remains ambiguous. The present study investigates the implications of COVID-19 hospitalised infected patients with co-infection and the clinical outcomes. In this study, 142 patients were included. The eligible patients who tested positive for COVID-19 infection were hospitalised for more than two days. Each patient's characteristics and laboratory results were collected, such as who was admitted to the intensive care unit and who was discharged or expired. The results revealed that out of the 142 hospitalised patients, 25 (17.6%) were co-infection positive, and 12 identified types of co-infection: two Gram-positive bacterial infections, one fungal infection and nine Gram-negative bacterial infections. In addition, 33 (23.2%) were ICU admitted, 21 were co-infection negative and 12 were co-infection positive. Among the 12 ICU admitted with co-infection, 33.4% were discharged. The death rate and ICU admission had a p-value < 0.05, indicating statistical significance for co-infected patients compared to non-co-infected patients. It was concluded that co-infection remains very low within hospitalised COVID-19-infected patients but can have severe outcomes with increased ICU admission and increased mortality rates. Thus, implementing infection preventive measures to minimize the spread of hospital-acquired infections among COVID-19 hospitalised patients.

Association of SARS-CoV-2 status and antibiotic-resistant bacteria with inadequate empiric therapy in hospitalized patients: a US multicenter cohort evaluation (July 2019 - October 2021)

BACKGROUND

Antibiotic usage and antibiotic resistance (ABR) patterns changed during the COVID-19 pandemic. Inadequate empiric antibiotic therapy (IET) is a significant public health problem and contributes to ABR. We evaluated factors associated with IET before and during the COVID-19 pandemic to determine the impact of the pandemic on antibiotic management.

METHODS

This multicenter, retrospective cohort analysis included hospitalized US adults who had a positive bacterial culture (specified gram-positive or gram-negative bacteria) from July 2019 to October 2021 in the BD Insights Research Database. IET was defined as antibacterial therapy within 48 h that was not active against the bacteria. ABR results were based on susceptibility testing and reports from local facilities. Multivariate analysis was used to identify risk factors associated with IET in patients with any positive bacterial culture and ABR-positive cultures, including multidrug-resistant (MDR) bacteria.

RESULTS

Of 278,344 eligible patients in 269 hospitals, 56,733 (20.4%) received IET; rates were higher in patients with ABR-positive (n = 93,252) or MDR-positive (n = 39,000) cultures (34.9% and 45.0%, respectively). Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2)-positive patients had significantly higher rates of IET (25.9%) compared with SARS-CoV-2-negative (20.3%) or not tested (19.7%) patients overall and in the ABR and MDR subgroups. Patients with ABR- or MDR-positive cultures had more days of therapy and longer lengths of stay. In multivariate analyses, ABR, MDR, SARS-CoV-2-positive status, respiratory source, and prior admissions were identified as key IET risk factors.

CONCLUSIONS

IET remained a persistent problem during the COVID-19 pandemic and occurred at higher rates in patients with ABR/MDR bacteria or a co-SARS-CoV-2 infection.

Sequential Extracorporeal Blood Purification Is Associated with Prolonged Survival among ICU Patients with COVID-19 and Confirmed Bacterial Superinfection

INTRODUCTION

This study investigates the impact of sequential extracorporeal treatments with oXiris® or CytoSorb® plus Seraph-100® on the clinical and laboratory parameters of critically ill COVID-19 patients with bacterial superinfection.

METHODS

Patients admitted to the intensive care unit with COVID-19, bacterial superinfection, and undergoing blood purification (BP) were enrolled in this prospective, single-center, observational study. "standard BP" with oXiris® or CytoSorb® were used in 35 COVID-19 patients with bacterial infection. Seraph-100® was added in 33 patients when available serially in the same oXiris® circuit or as sequential treatment with CytoSorb® as a sequential BP.

RESULTS

A significant reduction in SOFA score 3 days after treatment was observed in patients undergoing sequential BP (11.3 vs. 8.17, p < 0.01) compared to those undergoing "standard BP" (11.0 vs. 10.3, p > 0.05). The difference between the observed and expected mortality rate based on APACHE IV was greater in the sequential BP group (42.4% vs. 81.7%, p < 0.001) than the "standard BP" (74.2% vs. 81.7%, p > 0.05). Patients treated with sequential BP had a longer survival than those treated with "standard BP" (22.4 vs. 18.7 months; p < 0.001).

CONCLUSIONS

The sequential approach may enhance the positive effect of BP on organ dysfunction among critically ill patients with COVID-19 and bacterial superinfection.

Impact of COVID-19 on the distribution of pathogenic bacteria in the lower respiratory tract of the elderly

BACKGROUND

To investigate the distribution of bacterial pathogens of lower respiratory tract infection (LRTI) in hospitalized elderly patients during the COVID-19 epidemic and to explore the influence of COVID-19 on the distribution of bacterial pathogens, to provide guidance for clinical diagnosis.

METHODS

Specimens of sputum from elderly LRTIs patients at Fuding Hospital of China were consecutively collected from October 2022 to January 2023. Cultures and identification were done, and RT-PCR was employed to detect SARS-Cov-2 nucleic acid.

RESULTS

A total of 195 isolates were characterized in 163 sputum samples of consecutive hospitalized elderly patients, of which 11.3% were Gram-positive bacteria and 88.7% were Gram-negative. The top of frequently isolated pathogens was Klebsiella pneumonia (30.3%), Pseudomonas aeruginosa (19.0%), Acinetobacter baumannii (12.8%), Stenotrophomonas maltophili, (7.7%), Escherichia coli (7.2%). According to the results of novel coronavirus nucleic acid detection, the 163 patients were divided into COVID-19 group and non-COVID control (CNT) group. The comparison of bacterial distribution between the groups revealed that Stenotrophomonas maltophilia was lower in the COVID-19 than in the CNT group, while A. baumannii was higher in the COVID-19 group, and the difference was statistically significant (p < .05).

CONCLUSION

The major bacteria identified in sputum culture of hospitalized elderly patients were K. pneumonia, P. aeruginosa, A. baumannii, S. maltophilia, and E. coli. Furthermore, the distribution of S. maltophilia and A. baumannii between the COVID-19 and CNT groups was found to be significantly different (p < .05), while there were no significant differences in the distribution of other bacteria.

Carbapenem-Resistant Acinetobacter spp Infection in Critically Ill Patients With Limited Treatment Options: A Descriptive Study of Cefiderocol Therapy During the COVID-19 Pandemic

Background

Carbapenem-resistant Acinetobacter baumannii infections are difficult to treat and are a significant public health threat due to intrinsic/acquired resistance and limited treatment options.

Methods

A retrospective, observational cohort study in patients receiving cefiderocol via Shionogi's early access program for Acinetobacter spp infections (1 April 2020-30 April 2021; 27 sites; Italy, Spain, Germany, France). Primary outcome was clinical success, defined as clinical resolution of infection at day 14 or day 28 survival.

Results

Overall, 147 patients were included. Primary infection sites were respiratory (65.3%) and bloodstream (unknown source [15.6%]; catheter-related [10.9%]); 24.5% of patients had polymicrobial infection. Of 136 patients in intensive care (92.5%), 85.3% (116/136) received mechanical ventilation. Septic shock (55.6% [70/126]) and coronavirus disease 2019 (COVID-19) (81.6%) were prevalent. Prior to cefiderocol, 85.0% of patients received gram-negative treatment, 61.2% received ≥2 antimicrobials, and most received colistin (58.5%; median duration, 11.5 days). Cefiderocol monotherapy was used in 30.6% of patients. Clinical success rate was 53.1% and was higher in patients without septic shock (62.5%), without COVID-19 (77.8%), and with lower Sequential Organ Failure Assessment (SOFA) scores (quartile 1 [median, 3; range, 0-5]: 82.9%). Day 28 survival was 44.9% and was higher in patients without septic shock (60.7%), without COVID-19 (59.3%), with lower SOFA score (quartile 1: 82.9%), and receiving first-line cefiderocol (68.2% [15/22]). Resolution of infection at day 14 occurred in 39.5% of patients.

Conclusions

Despite use in complex patients with limited treatment options and high septic shock/COVID-19 rates, cefiderocol treatment was associated with an overall clinical success rate of 53%.

Collateral Changes in Cell Physiology Associated with ADC-7 β-Lactamase Expression in Acinetobacter baumannii

The ADC (AmpC) β-lactamase is universally present in the Acinetobacter baumannii chromosome, suggesting it may have a yet-to-be-identified cellular function. Using peptidoglycan composition analysis, we show that overexpressing the ADC-7 β-lactamase in A. baumannii drives changes consistent with altered l,d-transpeptidase activity. Based on this, we tested whether cells overexpressing ADC-7 would exhibit new vulnerabilities. As proof of principle, a screen of transposon insertions revealed that an insertion in the distal 3' end of canB, encoding carbonic anhydrase, resulted in a significant loss of viability when the adc-7 gene was overexpressed. A canB deletion mutant exhibited a more pronounced loss of viability than the transposon insertion, and this became amplified when cells overexpressed ADC-7. Interestingly, overexpression of the OXA-23 or TEM-1 β-lactamases also led to a pronounced loss of viability in cells with reduced carbonic anhydrase activity. In addition, we demonstrate that reduced CanB activity led to increased sensitivity to peptidoglycan synthesis inhibitors and to the carbonic anhydrase inhibitor ethoxzolamide. Furthermore, this strain exhibited a synergistic interaction with the peptidoglycan inhibitor fosfomycin and ethoxzolamide. Our results highlight the impact of ADC-7 overexpression on cell physiology and reveal that the essential carbonic anhydrase CanB may represent a novel target for antimicrobial agents that would exhibit increased potency against β-lactamase-overexpressing A. baumannii. IMPORTANCE Acinetobacter baumannii has become resistant to all classes of antibiotics, with β-lactam resistance responsible for the majority of treatment failures. New classes of antimicrobials are needed to treat this high-priority pathogen. This study had uncovered a new genetic vulnerability in β-lactamase-expressing A. baumannii, where reduced carbonic anhydrase activity becomes lethal. Inhibitors of carbonic anhydrase could represent a new method for treating A. baumannii infections.

Altered Anti-Viral Immune Responses in Monocytes in Overweight Heavy Drinkers

Alcohol abuse causes increased susceptibility to respiratory syndromes like bacterial pneumonia and viral infections like SARS-CoV-2. Heavy drinkers (HD) are at higher risk of severe COVID-19 if they are also overweight, yet the molecular mechanisms are unexplored. Single-cell RNA-seq (scRNA-seq) was performed on peripheral blood mononuclear cells from lean or overweight HD and healthy controls (HC) after challenge with a dsRNA homopolymer (PolyI:C) to mimic a viral infection and/or with lipopolysaccharide (LPS). All monocyte populations responded to both PolyI:C and LPS with pro-inflammatory gene expression. However, expression of interferon stimulated genes, essential for inhibiting viral pathogenesis, was greatly reduced in overweight patients. Interestingly, the number of upregulated genes in response to PolyI:C challenge was far greater in monocytes from HD compared to HC, including much stronger pro-inflammatory cytokine and interferon-γ signaling responses. These results suggest increased body weight reduced anti-viral responses while heavy drinking increased pro-inflammatory cytokines.

The Impact of Coronavirus Disease 2019 on Viral, Bacterial, and Fungal Respiratory Infections

Although coronavirus disease 2019 (COVID-19) remains an ongoing threat, concerns regarding other respiratory infections remain. Throughout the COVID-19 pandemic various epidemiologic trends have been observed in other respiratory viruses including a reduction in influenza and respiratory syncytial virus infections following onset of the COVID-19 pandemic. Observations suggest that infections with other respiratory viruses were reduced with social distancing, mask wearing, eye protection, and hand hygiene practices. Coinfections with COVID-19 exist not only with other respiratory viruses but also with bacterial pneumonias and other nosocomial and opportunistic infections. Coinfections have been associated with increased severity of illness and other adverse outcomes.

The emergence of multidrug-resistant bacteria causing healthcare-associated infections in COVID-19 patients - a retrospective multi-centre study

INTRODUCTION

We evaluated the prevalence, aetiologies and antibiotic resistance patterns of bacterial infections in hospitalized patients with laboratory-confirmed SARS-CoV-2. We also investigated comorbidities, risk factors, and the mortality rate in COVID-19 patients with bacterial infections.

METHODS

This retrospective observational study evaluated medical records of 7249 randomly selected patients with COVID-19 admitted to three clinical centres between January 1 2021 and February 16, 2022. A total of 6478 COVID-19 patients met the eligibility criteria for analysis.

RESULTS

The mean age of the patients with SARS-CoV-2 and bacterial infections was 68.6 ± 15.5 years (range: 24 to 94 years). The majority of patients (68.7%) were older than 65 years. The prevalence of bacterial infections among hospitalized COVID-19 patients was 12.9%, most of them being hospital-acquired (11.5%). Bloodstream (37.7%) and respiratory tract infections (25.6%) were the most common bacterial infections. Klebsiella pneumoniae and Acinetobacter baumannii caused 25.2% and 23.6% of all bacterial infections, respectively. Carbapenem-resistance in Enterobacterales, A. baumannii, and Pseudomonas aeruginosa were 72.6%, 93.7%, and 69.1%. Age >60 years and infections caused by ≥3 pathogens were significantly more prevalent among deceased patients compared to survivors (p<0.05). Furthermore, 95% of patients who were intubated developed ventilator-associated pneumonia. The overall in-hospital mortality rate of patients with SARS-CoV-2 and bacterial infections was 51.6%, while 91.7% of patients who required invasive mechanical ventilation died.

CONCLUSIONS

Our results reveal a striking association between healthcare-associated bacterial infections as an important complication of COVID-19 and fatal outcomes.

Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections

The immune system has to fight off hundreds of microbial invaders every day, such as the human-pathogenic fungus Aspergillus fumigatus. The fungal conidia can reach the lower respiratory tract, swell and form hyphae within six hours causing life-threatening invasive aspergillosis. Invading pathogens are continuously recognized and eliminated by alveolar macrophages (AM). Their number plays an essential role, but remains controversial with measurements varying by a factor greater than ten for the human lung. We here investigate the impact of the AM number on the clearance of A. fumigatus conidia in humans and mice using analytical and numerical modeling approaches. A three-dimensional to-scale hybrid agent-based model (hABM) of the human and murine alveolus allowed us to simulate millions of virtual infection scenarios, and to gain quantitative insights into the infection dynamics for varying AM numbers and infection doses. Since hABM simulations are computationally expensive, we derived and trained an analytical surrogate infection model on the large dataset of numerical simulations. This enables reducing the number of hABM simulations while still providing (i) accurate and immediate predictions on infection progression, (ii) quantitative hypotheses on the infection dynamics under healthy and immunocompromised conditions, and (iii) optimal AM numbers for combating A. fumigatus infections in humans and mice.

Procalcitonin Values Fail to Track the Presence of Secondary Bacterial Infections in COVID-19 ICU Patients

The development of secondary bacterial infections in COVID-19 patients has been associated with increased mortality and worse clinical outcomes. Consequently, many patients have received empirical antibiotic therapies with the potential to further exacerbate an ongoing antimicrobial resistance crisis. The pandemic has seen a rise in the use of procalcitonin testing to guide antimicrobial prescribing, although its value remains elusive. This single-centre retrospective study sought to analyse the efficacy of procalcitonin in identifying secondary infections in COVID-19 patients and evaluate the proportion of patients prescribed antibiotics to those with confirmed secondary infection. Inclusion criteria comprised patients admitted to the Grange University Hospital intensive care unit with SARS-CoV-2 infection throughout the second and third waves of the pandemic. Data collected included daily inflammatory biomarkers, antimicrobial prescriptions, and microbiologically proven secondary infections. There was no statistically significant difference between PCT, WBC, or CRP values in those with an infection versus those without. A total of 57.02% of patients had a confirmed secondary infection, with 80.2% prescribed antibiotics in Wave 2, compared to 44.07% with confirmed infection and 52.1% prescribed antibiotics in Wave 3. In conclusion, procalcitonin values failed to indicate the emergence of critical care-acquired infection in COVID-19 patients.

Altered infective competence of the human gut microbiome in COVID-19

BACKGROUND

Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.

RESULTS

We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls.

CONCLUSIONS

Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.

A two-year retrospective study of multidrug-resistant Acinetobacter baumannii respiratory infections in critically Ill patients: Clinical and microbiological findings

BACKGROUND

Acinetobacter baumannii infection is a serious public health problem because it is highly resistant to antimicrobial therapy and causes a high fatality rate in critically ill patients. The aim of the study is to examine the demographics, microbiological findings, clinical presentation, and outcomes of multi-drug-resistant Acinetobacter baumannii respiratory infections in adult ICU intubated patients during COVID-19 pandemic.

METHODS

This study included 115 mechanically ventilated adult ICU patients who had multi-drug-resistant Acinetobacter baumannii retrieved from respiratory samples during the COVID-19 pandemic in Albaha, Saudi Arabia. The information was obtained from medical and laboratory files. Univariate analysis was used to compare gender, COVID-19 infection, and outcomes.

RESULTS

The rate of Acinetobacter baumanni respiratory infections among adult ICU patients was 6.2 %. Almost 93 % developed ventilator-associated pneumonia, and five of them developed bacteremia. The isolates had significant antibiotic resistance patterns, of which 3 % were pandrug-resistant bacteria. The death rate was 74 %, with major risk factors including sepsis, septic shock, VAP, liver diseases, and the use of inappropriate antibiotic therapy that lacked both colistin and tigecycline. Patients with COVID-19 coinfection had worse outcomes compared to non-COVID-19 patients.

CONCLUSIONS

The identification of MDR-AB as a threat highlights the importance of surveillance studies in this region.

Next-Generation Sequencing in Critically Ill COVID-19 Patients with Suspected Bloodstream Infections: A Retrospective Cohort Study

BACKGROUND

Rapid pathogen identification and appropriate antimicrobial therapy are crucial in critically ill COVID-19 patients with bloodstream infections (BSIs). This study aimed to evaluate the diagnostic performance and potential therapeutic benefit of additional next-generation sequencing (NGS) of microbial DNA from plasma in these patients.

METHODS

This monocentric descriptive retrospective study reviewed clinical data and pathogen diagnostics in COVID-19 ICU patients. NGS (DISQVER^®) and blood culture (BC) samples were obtained on suspicion of BSIs. Data were reviewed regarding the adjustment of antimicrobial therapy and diagnostic procedures seven days after sampling and analyzed using the Chi²-test.

RESULTS

Twenty-five cases with simultaneous NGS and BC sampling were assessed. The NGS positivity rate was 52% (13/25) with the detection of 23 pathogens (14 bacteria, 1 fungus, 8 viruses), and the BC positivity rate was 28% (7/25, 8 bacteria; p = 0.083). The NGS-positive patients were older (75 vs. 59.5 years; p = 0.03) with a higher prevalence of cardiovascular disease (77% vs. 33%; p = 0.03). These NGS results led to diagnostic procedures in four cases and to the commencement of four antimicrobial therapies in three cases. Empirical treatment was considered appropriate and continued in three cases.

CONCLUSIONS

In COVID-19 patients with suspected BSIs, NGS may provide a higher positivity rate than BC and enable new therapeutic approaches.

The clinical outcomes of COVID-19 critically ill patients co-infected with other respiratory viruses: a multicenter, cohort study

BACKGROUND

Previous studies have shown that non-critically ill COVID-19 patients co-infected with other respiratory viruses have poor clinical outcomes. However, limited studies focused on this co-infections in critically ill patients. This study aims to evaluate the clinical outcomes of critically ill patients infected with COVID-19 and co-infected by other respiratory viruses.

METHODS

A multicenter retrospective cohort study was conducted for all adult patients with COVID-19 who were hospitalized in the ICUs between March, 2020 and July, 2021. Eligible patients were sub-categorized into two groups based on simultaneous co-infection with other respiratory viruses throughout their ICU stay. Influenza A or B, Human Adenovirus (AdV), Human Coronavirus (i.e., 229E, HKU1, NL63, or OC43), Human Metapneumovirus, Human Rhinovirus/Enterovirus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), Parainfluenza virus, and Respiratory Syncytial Virus (RSV) were among the respiratory viral infections screened. Patients were followed until discharge from the hospital or in-hospital death.

RESULTS

A total of 836 patients were included in the final analysis. Eleven patients (1.3%) were infected concomitantly with other respiratory viruses. Rhinovirus/Enterovirus (38.5%) was the most commonly reported co-infection. No difference was observed between the two groups regarding the 30-day mortality (HR 0.39, 95% CI 0.13, 1.20; p = 0.10). The in-hospital mortality was significantly lower among co-infected patients with other respiratory viruses compared with patients who were infected with COVID-19 alone (HR 0.32 95% CI 0.10, 0.97; p = 0.04). Patients concomitantly infected with other respiratory viruses had longer median mechanical ventilation (MV) duration and hospital length of stay (LOS).

CONCLUSION

Critically ill patients with COVID-19 who were concomitantly infected with other respiratory viruses had comparable 30-day mortality to those not concomitantly infected. Further proactive testing and care may be required in the case of co-infection with respiratory viruses and COVID-19. The results of our study need to be confirmed by larger studies.

Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential

Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct < 35 and for mNGS samples it was >40% target coverage, median depth of 1X and RPKM > 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify^® Platform (Illumina^® Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration-with promise to reduce morbidity and mortality.

Pneumocystis jirovecii Infections Among COVID-19 Patients: A Case Series and Literature Review

Background

Pneumocystis jirovecii pneumonia (PCP) is a serious, emerging complication of coronavirus disease 2019 (COVID-19).

Methods

We performed a systematic review of published cases. We describe 6 new cases of PCP/COVID-19 coinfection. Among our cases (n = 6) and those in the literature (n = 69) with available data, the median age (interquartile range [IQR]) was 59 (44-77) years (n = 38), 72% (47/65) were male, and the mortality rate was 30.9% (21/68).

Results

Long-term corticosteroid use was noted in 45.1% (23/51), advanced HIV infection (defined as a CD4 count <200 cells/μL) in 17.6% (9/51), and antineoplastic chemotherapy in 13.7% (7/51), consistent with known PCP risk factors. Notably, 56.7% (38/47) had verifiable risk factors for PCP (high-dose corticosteroids, immunosuppressive therapy, and HIV infection) before COVID-19 infection. A median absolute lymphocyte count (IQR) of 0.61 (0.28-0.92) ×103 cells/mm3 (n = 23) and CD4 count (IQR) of 66 (33-291.5) cells/mm3 (n = 20) were also discovered among the study population.

Conclusions

These findings suggest a need for greater attention to PCP risk factors among COVID-19 patients and consideration of PCP prophylaxis in these high-risk populations.

Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors

The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.

Invasive Fungal Infections in Hospitalized Patients with COVID-19: A Non-Intensive Care Single-Centre Experience during the First Pandemic Waves

Invasive fungal infections (IFIs) represent a severe complication of COVID-19, yet they are under-estimated. We conducted a retrospective analysis including all the COVID-19 patients admitted to the Infectious Diseases Unit of the Federico II University Hospital of Naples until the 1 July 2021. Among 409 patients, we reported seven cases of IFIs by Candida spp., seven of Pneumocystis jirovecii pneumonia, three of invasive pulmonary aspergillosis, and one of Trichosporon asahii. None of the cases presented underlying predisposing conditions, excluding one oncohematological patient treated with rituximab. Ten cases showed lymphopenia with high rates of CD4+ < 200/µL. All cases received high-dose steroid therapy (mean duration 33 days, mean cumulative dosage 1015 mg of prednisone equivalent), and seven cases had severe COVID-19 disease (OSCI ≥ 5) prior to IFI diagnosis. The cases showed a higher overall duration of hospitalization (63 vs 24 days) and higher mortality rate (23% vs. 7%) compared with the COVID-19 patients who did not developed IFIs. Cases showed a higher prevalence of high-dose steroid therapy and lymphopenia with CD4+ < 200/µL, primarily due to SARS-CoV-2 infection and not related to underlying comorbidities. IFIs strongly impact the overall length of hospitalization and mortality. Therefore, clinicians should maintain a high degree of suspicion of IFIs, especially in severe COVID-19 patients.

Comparison of clinical outcomes in critically ill COVID-19 patients on mechanical ventilation with nosocomial pneumonia between Alpha and Omicron variants

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a pandemic that has resulted in millions of deaths worldwide. Critically ill COVID-19 patients who require intubation and develop nosocomial pneumonia, commonly caused by gram-negative bacilli, have a higher mortality rate than those without nosocomial pneumonia.

OBJECTIVES

The aim of this study is to compare the clinical characteristics and outcomes and associated risk factors of Alpha and Omicron SARS-CoV-2 variants in critically ill patients on mechanical ventilation (MV) with nosocomial pneumonia.

DESIGN

This is a retrospective single-center cohort study.

METHODS

This observational study was conducted at Taipei Veterans General Hospital, Taiwan from May 2021 to September 2022. Critically ill patients who had confirmed SARS-CoV-2 infection and intubated on a MV with bacterial pneumonia were enrolled. Demographic data, laboratory results, and treatment information were collected and analyzed. In addition, clinical outcomes among different SARS-CoV-2 variants were examined.

RESULTS

This study included 94 critically ill COVID-19 patients who required intubation and intensive care unit (ICU) admission. The Alpha group had a longer duration of SARS-CoV-2 viral shedding, MV days, and ICU stay, while the Omicron group had older age, more comorbidities, higher APACHE II scores, and higher in-hospital mortality (47.0% versus 25.0%, p = 0.047). However, independent risk factors for in-hospital mortality included malignancy, lower serum albumin levels, and lack of Remdesivir treatment, except for the SARS-CoV-2 variant.

CONCLUSION

Our study discovered a higher in-hospital mortality rate in severe COVID-19 patients with MV and secondary pneumonia infected with the Omicron variant compared to the Alpha variant; however, real independent risk factors for in-hospital mortality are malignancy, lower serum albumin level, and lack of Remdesivir treatment.

Bacterial coinfections in hospitalized children with COVID-19 during the SARS-CoV-2 Omicron BA.2 variant pandemic in Taiwan

Background

Bacterial coinfections have been widely recognized in adults with coronavirus disease 2019 (COVID-19). However, bacterial coinfections in hospitalized children with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have not been sufficiently researched. This study aimed to determine the clinical presentations and risk factors for bacterial coinfections of pediatric inpatients during the SARS-CoV-2 Omicron BA.2 variant pandemic.

Methods

This retrospective, observational study included patients younger than 18 years of age who were hospitalized for COVID-19 confirmed by polymerase chain reaction (PCR) or antigen rapid tests during the SARS-CoV-2 Omicron BA.2 variant pandemic. Data and outcomes of these patients with or without bacterial coinfections were compared.

Results

During this study period, 161 children with confirmed COVID-19 were hospitalized. Twenty-four had bacterial coinfections. The most frequently reported concurrent diagnosis was bacterial enteritis, followed by lower respiratory tract infections. Children with bacterial coinfections had higher white blood cell (WBC) counts and PCR cycle threshold values. The bacterial coinfection group comprised a relatively greater proportion of patients who required high-flow nasal cannula oxygen and remdesivir. The length of stay in the hospital and that in the intensive care unit were longer for children with COVID-19 with bacterial coinfections. Mortality was not observed in either group. Abdominal pain, diarrhea, and comorbidity with neurologic illnesses were risk factors for bacterial coinfections with COVID-19.

Conclusion

This study provides clinicians with reference points for the detection of COVID-19 in children and its possible association with bacterial infections. Children with COVID-19 and neurologic diseases who present with abdominal pain or diarrhea are at risk of bacterial coinfections. Prolonged fever duration and higher PCR test cycle threshold values, WBC levels, and high-sensitivity C-reactive protein (hsCRP) levels may indicate bacterial coinfections in children with COVID-19.