The Prevalence and Impact of Coinfection and Superinfection on the Severity and Outcome of COVID-19 Infection: An Updated Literature Review

Kinetic Patterns of Antibiotic Consumption in German Acute Care Hospitals from 2017 to 2023

Background: Antimicrobial consumption (AMC) patterns, besides prescribing behaviors, reflect the changing epidemiology of infectious diseases. Routine surveillance data have been used to investigate the development of AMC from 2017 to 2023 and the impact of COVID-19 within the context of the framing time periods. Methods: Data from 112 hospitals, continuously participating from 2017 to 2023 in the national surveillance system of hospital antimicrobial consumption based at the Robert Koch Institute, were analyzed according to the WHO ATC (Anatomical Therapeutic Chemical)/DDD (Defined Daily Dose) method and categorized according to the WHO AWaRe-classification. AMC was quantified by consumption density (CD) expressed in DDD/100 patient days (PD) and DDD/100 admissions (AD). The time period was subdivided into three phases: pre-pandemic phase (2017-2019), main pandemic phase (2020-2021) and transition phase (2022-2023). Linear regression models have been used to determine the presence of an overall trend, the change in intra-phasic trends and phase-specific mean consumption levels over time. Results: From 2017 to 2023 total antibiotic consumption decreased by 7% from 57.1 to 52.9 DDD/100 PD. Four main kinetic patterns emerged across different antibiotic classes: Pattern 1 displays a decreasing pre-pandemic trend, which slowed down throughout the pandemic and transition phase and was exhibited by second-generation cephalosporins and fluoroquinolones. Pattern 2 reveals a rising pre-pandemic trend, which decelerated in the pandemic phase and accelerated again in the transition phase and was expressed by aminopenicillins/beta-lactamase inhibitors, beta-lactamase sensitive pencillins, azithromycin and first-generation cephalosporins. Pattern 3 shows elevated mean consumption levels in the pandemic phase exhibited by carbapenems, glycopeptides, linezolid and third-generation cephalosporins. Pattern 4 reveals a rising trend throughout the pre-pandemic and pandemic phase, which reversed in the transition phase without achieving pre-pandemic levels and was expressed by beta-lactamase resistant penicillins, daptomycin, fosfomycin (parenteral) and ceftazidime/avibactam. Conclusions: Kinetic consumption patterns across different antibiotic classes might reflect COVID-19-related effects and associated changes in the epidemiology of co-circulating pathogens and health care supply. Broad-spectrum antibiotics with persisting elevated consumption levels throughout the transition phase require special attention and focused antimicrobial stewardship activities.

Poor Prognosis of Pneumococcal Co-Infection in Hospitalized Patients with COVID-19: A Propensity Score-Matched Analysis

The impact of Streptococcus pneumoniae coinfection on coronavirus disease 2019 (COVID-19) prognosis remains uncertain. We conducted a retrospective analysis of patients hospitalized with COVID-19 who underwent a pneumococcal urinary antigen (PUA) test to assess its clinical utility. Results showed that PUA-positive patients required more oxygen support, high-flow nasal cannula, and dexamethasone compared to PUA-negative patients. Furthermore, the significantly higher incidence of a National Early Warning Score ≥5 in the PUA-positive group (P<0.001) suggests that a positive PUA test is associated with a severe disease course. However, no significant difference in mortality was observed between the two groups, and antibiotics were used in almost all patients (96.2%). While the PUA test may help guide antibiotic use in COVID-19 patients, its interpretation should be approached with caution.

Investigating the Prevalence of Bacterial Infections in Patients with Coronavirus Disease 2019 Hospitalized in Intensive Care Unit and Determining their Antibiotic Resistance Patterns

BACKGROUND

COVID-19 patient hospitalization, particularly in intensive care units, exposes them to bacterial and fungi co-infections, which can have very serious consequences, including increased mortality. In addition, antibiotic resistance among pathogens is a hidden threat behind COVID-19.

METHODS

In the period from 2020 September to 2021 August, bacterial isolates from COVID- 19 patients admitted to the ICU of Sina Hospital in Hamadan, Iran, were collected and identified based on standard biochemical tests. COVID-19 cases were confirmed based on clinical symptoms, computed tomography, and polymerase chain reaction. Antimicrobial susceptibility tests were conducted using disc diffusion and broth microdilution methods.

RESULTS

In total, 207 bacterial isolates were collected, with Klebsiella pneumoniae accounting for 69 (33.33%) and Acinetobacter baumannii accounting for 59 (28.15%). The frequency and percentage of isolated bacteria were as follows: Alcaligenes species 28 (13.59%), Staphylococcus aureus 18 (8.73%), Pseudomonas aeruginosa 15 (7.28%), Escherichia coli 11 (5.33%), Stenotrophomonas maltophilia 3 (1.45%), Enterococcus species 3 (1.45%), and Serratia species 1 (0.48%). About 95.38% resistance to ceftazidime and cefotaxime and 92.31% resistance to ciprofloxacin and cefepime were found in K. pneumoniae isolates. A. baumannii isolates were 100% resistant to cefotaxime, ceftriaxone, and cefepime. About 22.22% resistance to vancomycin and 66.67% resistance to clindamycin, erythromycin, and cefoxitin were seen in S. aureus isolates.

CONCLUSION

Knowledge of bacterial co-infections and their antibiotic resistance pattern in COVID-19 patients can help in choosing effective antibiotics for the treatment and prevention of antibiotic resistance.

An Observational Study to Determine the Prevalence of COVID-19 Among Hospitalized Patients With Multidrug-Resistant Enterobacterales Infections and Clinical Outcomes, 10 US Sites, 2020--2022

Background

We investigated hospitalized carbapenem-resistant Enterobacterales (CRE) and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) cases with and without COVID-19, as identified through Emerging Infections Program surveillance in 10 sites from 2020 to 2022.

Methods

We defined a CRE case as the first isolation of Escherichia coli, Enterobacter cloacae complex, Klebsiella aerogenes, K oxytoca, K pneumoniae, or K variicola resistant to any carbapenem. We defined an ESBL-E case as the first isolation of E coli, K pneumoniae, or K oxytoca resistant to any third-generation cephalosporin and nonresistant to all carbapenems tested. Specimens were drawn from a normally sterile site or urine among hospitalized residents of the surveillance area in a 30-day period. We defined COVID-19 as a positive SARS-CoV-2 test result (SC2+) within 14 days before CRE or ESBL-E specimen collection and performed multivariable logistic regression analyses.

Results

Of 1595 CRE and 1866 ESBL-E hospitalized cases, 38 (2.4%) and 60 (3.2%), respectively, had a SC2+. Among these cases, a SC2+ was associated with intensive care unit admission (adjusted odds ratio [aOR], 1.69 [95% CI, 1.14-2.50]; aOR, 1.48 [95% CI, 1.03-2.12]) and 30-day mortality (aOR, 1.79 [95% CI, 1.22-2.64]; aOR, 1.94 [95% CI, 1.39-2.70]).

Conclusions

CRE and ESBL-E infections among hospitalized patients with preceding COVID-19 were uncommon but had worse outcomes when compared with cases without COVID-19. COVID-19 prevention in patients at risk of CRE and ESBL-E infections is needed, as well as continued infection control measures and antibiotic stewardship for patients with COVID-19.

Outcomes of patients hospitalized in ward settings for COVID-19 pneumonia with or without early empirical antibiotics

BACKGROUND

During the first pandemic of COVID-19, early empirical antibiotic use rates for pneumonia varied widely. The benefit remains hypothetical.

METHODS

We assessed the benefit of empirical antibiotic use at admission in patients hospitalized with COVID-19 pneumonia. We enrolled all adults admitted from 1 March to 30 April 2020 with symptoms for ≤14 days, a positive nasopharyngeal PCR or a highly suggestive CT scan. The primary outcome was mortality at Day 28. The secondary outcomes were transfer to the ICU, mechanical ventilation and length of hospital stay. To handle confounding-by-indication bias, we used a propensity score analysis, expressing the outcomes in the original and overlap weighted populations.

RESULTS

Among 616 analysed patients, 402 (65%) received antibiotics. At Day 28, 102 patients (17%) had died, 90 (15%) had been transferred to the ICU and 24 (4%) had required mechanical ventilation. Mortality in patients who received antibiotics was higher before but not after weighting (OR 2.7, 95% CI 1.5-5.0, P < 0.001 and OR 1.4, 95% CI 0.8-2.5, P = 0.28, respectively. Antibiotic use had no benefit on: transfer to ICU before and after weighting (OR 1.3, 95% CI 0.8-2.3, P = 0.30 and OR 1.1, 95% CI 0.6-1.9, P = 0.78, respectively); mechanical ventilation before and after weighting (OR 0.5, 95% CI 0.2-1.1, P = 0.079 and OR 0.75, 95% CI 0.3-2.0, P = 0.55, respectively); and length of hospital stay before and after weighting (mean difference -0.02 ± 0.5 days, P = 0.97 and mean difference 0.54 ± 0.75 days, P = 0.48, respectively).

CONCLUSIONS

We did not find any benefit of antibiotic use in patients hospitalized with COVID-19 pneumonia.

Increased 30-day all-cause mortality associated with Gram-negative bloodstream infections in England during the COVID-19 pandemic

BACKGROUND

Our aim was to assess the impact of COVID-19 pandemic on mortality in patients hospitalised with Gram-negative bloodstream infections (GNBSIs).

METHODS

A retrospective cohort study including cases of Escherichia coli, Klebsiella species and Pseudomonas aeruginosa in England (January 2015-December 2021) reported to UKHSA's Second Generation Surveillance System. The outcome was 30-day all-cause mortality. Multivariable logistic regression models were built, and adjusted Odds Ratios (ORs) with 95% confidence intervals were reported.

RESULTS

Total E. coli, Klebsiella spp. and P. aeruginosa infections were 206,030, 53,819 and 21,129, respectively. Compared to the pre-pandemic period, odds of death during the pandemic (March 2020 onwards) in E. coli, Klebsiella spp. and P. aeruginosa infections with no COVID-19 infection within 28-days of onset were 1.13 (1.08-1.18), 1.15 (1.07-1.25) and 1.09 (0.97-1.22), while odds in GNBSIs with an associated COVID-19 infection were 2.45 (2.26-2.66), 2.96 (2.62-3.34) and 3.15 (2.61-3.80), respectively. Asian patients with an associated COVID-19 infection were more likely to die during the pandemic compared to White patients (E. coli: OR 1.28 (0.95-1.71); Klebsiella spp. OR 1.59 (1.20-2.11); P. aeruginosa: OR 2.02 (1.23-3.31)).

CONCLUSIONS

Patients suffering from a GNBSI had increased risk of death during the pandemic, with the risk higher in patients with an associated COVID-19 infection.

Cell-free plasma next-generation sequencing assists in the evaluation of secondary pneumonia in patients with COVID-19: a case series

Secondary pneumonia occurs in 8-24% of patients with Coronavirus 2019 (COVID-19) infection and is associated with increased morbidity and mortality. Diagnosis of secondary pneumonia can be challenging. The purpose of this study was to evaluate the use of plasma microbial cell free DNA sequencing (mcfNGS) in the evaluation of secondary pneumonia after COVID-19. We performed a single-center case series of patients with COVID-19 who underwent mcfNGS to evaluate secondary pneumonia and reported the organisms identified, concordance with available tests, clinical utility, and outcomes. In 8/13 (61%) cases, mcfNGS detected 1-6 organisms, with clinically significant organisms identified in 4 cases, including Pneumocystis jirovecii, and Legionella spp. Management was changed in 85% (11/13) of patients based on results, including initiation of targeted therapy, de-escalation of empiric antimicrobials, and avoiding contingent escalation of antifungals. mcfNGS may be helpful to identify pathogens causing secondary pneumonia, including opportunistic pathogens in immunocompromised patients with COVID-19. However, providers need to carefully interpret this test within the clinical context.

Investigation of microbial coinfection in 453 septic COVID-19 patients admitted to hospital; a retrospective study

Aim

We evaluated the rate of COVID-19 microbial coinfection in an Iranian population.

Methods

In this single-center, retrospective observational study, we evaluated 453 septic COVID-19 patients for possible coinfection in an Iranian hospital.

Results

Overall, 211 (46.57%) cases died due to COVID-19 complications. Positive respiratory secretion and blood cultures were reported in 99 (21.9%) and 19 (4.2%) cases. Klebsiella species were the most commonly isolated microorganisms in respiratory (n = 50, 50.5%) and blood (n = 10, 52.6%) specimens. After adjustment for underlying disorders, positive respiratory microbial cultures significantly increase the odds of developing death, intubation, and ICU admission and negatively impact healthy discharge (P < 0.05).

Conclusion

Coinfections with bacteria and fungi independently contribute to poor outcomes in septic COVID-19 patients.

A meta-meta-analysis of co-infection, secondary infections, and antimicrobial resistance in COVID-19 patients

The newly discovered coronavirus SARS-CoV-2 has sparked a worldwide pandemic of COVID-19, which has caused havoc on medical infrastructures, economies, and cultures around the world. Determining the whole scenario is essential since SARS-CoV-2 variants and sub-variants keep appearing after vaccinations and booster doses. The objective of this secondary meta-analysis is to analysis co-infection, secondary infections, and antimicrobial resistance (AMR) in COVID-19 patients. This study used five significant databases to conduct a systematic review and an overlap meta-analysis to evaluate the pooled estimates of co-infections and secondary infections. The summary of the meta-analysis showed an overall co-infection effect of 26.19% (95% confidence intervals CI: 21.39-31.01, I2 =98.78, n = 14 meta-analysis) among patients with COVID-19. A coinfection effect of 11.13% (95% CI: 9.7-12.56, I2 =99.14, n = 11 meta-analysis) for bacteria; 9.69% (95% CI: 1.21-7.90, I2 =98.33) for fungal and 3.48% (95% CI: 2.15-4.81, I2 =95.84) for viruses. A secondary infection effect of 19.03% (95% CI: 9.53-28.54, I2 =85.65) was pooled from 2 meta-analyses (Ave: 82 primary studies). This is the first study that compiles the results of all the previous three years meta-analyses into a single source and offers strong proof of co-infections and secondary infections in COVID-19 patients. Early detection of co-infection and AMR is crucial for COVID-19 patients in order to effective treatment.

SARS-CoV-2 suppresses TLR4-induced immunity by dendritic cells via C-type lectin receptor DC-SIGN

SARS-CoV-2 causes COVID-19, an infectious disease with symptoms ranging from a mild cold to severe pneumonia, inflammation, and even death. Although strong inflammatory responses are a major factor in causing morbidity and mortality, superinfections with bacteria during severe COVID-19 often cause pneumonia, bacteremia and sepsis. Aberrant immune responses might underlie increased sensitivity to bacteria during COVID-19 but the mechanisms remain unclear. Here we investigated whether SARS-CoV-2 directly suppresses immune responses to bacteria. We studied the functionality of human dendritic cells (DCs) towards a variety of bacterial triggers after exposure to SARS-CoV-2 Spike (S) protein and SARS-CoV-2 primary isolate (hCoV-19/Italy). Notably, pre-exposure of DCs to either SARS-CoV-2 S protein or a SARS-CoV-2 isolate led to reduced type I interferon (IFN) and cytokine responses in response to Toll-like receptor (TLR)4 agonist lipopolysaccharide (LPS), whereas other TLR agonists were not affected. SARS-CoV-2 S protein interacted with the C-type lectin receptor DC-SIGN and, notably, blocking DC-SIGN with antibodies restored type I IFN and cytokine responses to LPS. Moreover, blocking the kinase Raf-1 by a small molecule inhibitor restored immune responses to LPS. These results suggest that SARS-CoV-2 modulates DC function upon TLR4 triggering via DC-SIGN-induced Raf-1 pathway. These data imply that SARS-CoV-2 actively suppresses DC function via DC-SIGN, which might account for the higher mortality rates observed in patients with COVID-19 and bacterial superinfections.

Reduced Reliability of Procalcitonin (PCT) as a Biomarker of Bacterial Superinfection: Concerns about PCT-Driven Antibiotic Stewardship in Critically Ill COVID-19 Patients-Results from a Retrospective Observational Study in Intensive Care Units

BACKGROUND

The aim of this study was to assess whether procalcitonin levels is a diagnostic tool capable of accurately identifying sepsis and ventilator-associated pneumonia (VAP) even in critically ill COVID-19 patients.

METHODS

In this retrospective, observational study, all critically ill COVID-19 patients who survived for ≥2 days in a single university hospital and had at least one serum procalcitonin (PCT) value and associated blood culture and/or culture from a lower respiratory tract specimen available were eligible for the study.

RESULTS

Over the research period, 184 patients were recruited; 67 VAP/BSI occurred, with an incidence rate of 21.82 episodes of VAP/BSI (95% CI: 17.18-27.73) per 1000 patient-days among patients who were included. At the time of a positive microbiological culture, an average PCT level of 1.25-3.2 ng/mL was found. Moreover, also in subjects without positive cultures, PCT was altered in 21.7% of determinations, with an average value of 1.04-5.5 ng/mL. Both PCT and PCT-72 h were not linked to a diagnosis of VAP/BSI in COVID-19 patients, according to the multivariable GEE models (aOR 1.13, 95% CI 0.51-2.52 for PCT; aOR 1.32, 95% CI 0.66-2.64 for PCT-72 h).

CONCLUSION

Elevated PCT levels might not always indicate bacterial superinfections or coinfections in a severe COVID-19 setting.

Respiratory co-infections in COVID-19-positive patients

BACKGROUND

Opportunistic respiratory infections may complicate critically ill patients with COVID-19. Early detection of co-infections helps to administrate the appropriate antimicrobial agent, to guard against patient deterioration. This study aimed at estimating co-infections in COVID-19-positive patients.

METHODS

Eighty-nine COVID-19-positive patients confirmed by SARS-COV-2 PCR were tested for post-COVID-19 lower respiratory tract co-infections through bacterial culture, fungal culture and galactomannan (GM) testing.

RESULTS

Fourteen patients showed positive coinfection with Klebsiella, nine with Acinetobacter, six with Pseudomonas and three with E. coli. As for fungal infections, nine showed coinfection with Aspergillus, two with Zygomycetes and four with Candida. Galactomannan was positive among one patient with Aspergillus coinfection, one with Zygomycetes coinfection and three with Candida, 13 samples with negative fungal culture were positive for GM. Ten samples showed positive fungal growth, however, GM test was negative.

CONCLUSION

In our study, SARS-COV-2 respiratory coinfections were mainly implicated by bacterial pathogens; most commonly Klebsiella species (spp.), Aspergillus spp. were the most common cause of fungal coinfections, GM test showed low positive predictive value for fungal infection. Respiratory coinfections may complicate SARS-COV-2 probably due to the prolonged intensive care units (ICU) hospitalization, extensive empiric antimicrobial therapy, steroid therapy, mechanical ventilation during the COVID-19 outbreak. Antimicrobial stewardship programs are required so that antibiotics are prescribed judiciously according to the culture results.

Coronavirus and co-infections: A Saudi Arabian perspective

Mortality due to infectious diseases continues to rise globally, despite advances in antimicrobial therapy and supportive care. This is evident with the occurrence of coronavirus disease 2019 (COVID-19) pandemic, instigated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Saudi Arabia, an eminent country within the Arab region, has had significant impact during global pandemics, concomitant with the fact that millions of Muslims travel to Saudi Arabia for pilgrimages every year. Herein, we discuss the significance of SARS-CoV-1, SARS-CoV-2, as well as the Middle East respiratory syndrome coronavirus (MERS-CoV) in Saudi Arabia with particular reference to global transmission and/or emergence of new variants due to genetic mixing of different strains. Furthermore, we also discuss the role of Saudi Arabia with reference to novel emerging infectious diseases and re-emerging infections, such as Ebola, zika, and monkeypox, as well as in the context on coinfections. Future strategies to limit the spread of viral infections and the pivotal role of Saudi Arabia, are deliberated upon.

Prevalence of secondary infections and association with mortality rates of hospitalized COVID-19 patients

BACKGROUND

ICU and other patients hospitalized with corona-virus disease 2019 (COVID-19) are more susceptible to secondary infections. Undetected secondary infections tend to have a severe clinical impact, associated with prolonged hospitalization and higher rates of inpatient mortality.

OBJECTIVES

Estimate the prevalence of secondary infections, determine the frequency of microbial species detected at different body sites, and measure the association between secondary infections and outcomes among hospitalized COVID-19 patients.

DESIGN

Cross-sectional analytical study.

SETTING

Tertiary care center in Riyadh PATIENTS AND METHODS: Data were collected through retrospective chart review of hospitalized COVID-19 patients >18 years old from March 2020 until May 2022 at King Saud University Medical City (27 months). Rates of secondary infections among hospitalized COVID-19 patients were described and data on clinical outcomes (intensive care admission, invasive management procedures and mortality) was collected.

MAIN OUTCOME MEASURES

Features and rates of infection and mortality.

SAMPLE SIZE

260 RESULTS: In total, 24.2% of the study population had secondary infections. However, only 68.8% of patients had secondary infection testing, from which 35.2% had a confirmed secondary infection. These patients had a significantly higher prevalence of diabetes mellitus (P<.0001) and cardiovascular diseases (P=.001). The odds of ICU admissions (63.3%) among secondarily infected patients was 8.4 times higher compared to patients with only COVID-19 infection (17.3%). Secondarily infected patients were more likely to receive invasive procedures (OR=5.068) and had a longer duration of hospital stay compared to COVID-19 only patients. Overall mortality was 16.2%, with a predominantly higher proportion among those secondarily infected (47.6% vs 6.1%) (OR=14.015). Bacteria were the most commonly isolated organisms, primarily from blood (23.3%), followed by fungal isolates, which were mostly detected in urine (17.2%). The most detected organism was Candida albicans (17.2%), followed by Escherichia coli (9.2%), Klebsiella pneumoniae (9.2%) and Pseudomonas aeruginosa (9.2%).

CONCLUSION

Secondary infections were prevalent among hospitalized COVID-19 patients. Secondarily infected patients had longer hospital stay, higher odds of ICU admission, mortality, and invasive procedures.

LIMITATION

Single-center study, retrospective design and small sample size.

CONFLICT OF INTEREST

None.

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

Patients with viral infections are at higher risk to acquire bacterial and fungal superinfections associated with a worse prognosis. We explored this critical point in the setting of patients with severe COVID-19 disease. The study included 1911 patients admitted to intensive care unit (ICU) during a 2-year study period (March 2020-March 2022). Of them, 713 (37.3%) were infected with SARS-CoV-2 and 1198 were negative (62.7%). Regression analysis was performed to determine risk factors associated with the presence of bacterial and/or fungal superinfections in SARS-CoV-2 patients and to evaluate predictors of ICU mortality. Of the 713 patients with SARS-CoV-2 infection, 473 (66.3%) had respiratory and/or bloodstream bacterial and/or fungal superinfections, while of the 1198 COVID-19-negative patients, only 369 (30%) showed respiratory and/or bloodstream bacterial and/or fungal superinfections (p < 0.0001). Baseline characteristics of COVID-19 patients included a median age of 66 (interquartile range [IQR], 58-73), a predominance of males (72.7%), and the presence of a BMI higher than 24 (median 26; IQR, 24.5-30.4). Seventy-four percent (527, 73.9%) had one or more comorbidities and 135 (18.9%) of them had received previous antibiotic therapy. Furthermore, most of them (473, 66.3%) exhibited severe radiological pictures and needed invasive mechanical ventilation. Multivariate logistic regression analysis showed that 1 unit increment in BMI rises the risk of bacterial and/or fungal superinfections acquisition by 3% and 1-day increment in ICU stays rises the risk of bacterial and/or fungal superinfections acquisition by 11%. Furthermore, 1-day increment in mechanical ventilation rises the risk of bacterial and/or fungal superinfection acquisition by 2.7 times. Furthermore, patients with both bacterial and fungal infections had a significantly higher mortality rate than patients without superinfections (45.8% vs. 26.2%, p < 0.0001). Therefore, bacterial and fungal superinfections are frequent in COVID-19 patients admitted to ICU and their presence is associated with a worse outcome. This is an important consideration for targeted therapies in critically ill SARS-CoV-2 infected patients to improve their clinical course.

Early Bacterial Coinfections in Patients Admitted to the ICU With COVID-19 or Influenza: A Retrospective Cohort Study

Previous findings suggest that bacterial coinfections are less common in ICU patients with COVID-19 than with influenza, but evidence is limited.

OBJECTIVES

This study aimed to compare the rate of early bacterial coinfections in ICU patients with COVID-19 or influenza.

DESIGN SETTING AND PARTICIPANTS

Retrospective propensity score matched cohort study. We included patients admitted to ICUs of a single academic center with COVID-19 or influenza (January 2015 to April 2022).

MAIN OUTCOMES AND MEASURES

The primary outcome was early bacterial coinfection (i.e., positive blood or respiratory culture within 2 d of ICU admission) in the propensity score matched cohort. Key secondary outcomes included frequency of early microbiological testing, antibiotic use, and 30-day all-cause mortality.

RESULTS

Out of 289 patients with COVID-19 and 39 patients with influenza, 117 (n = 78 vs 39) were included in the matched analysis. In the matched cohort, the rate of early bacterial coinfections was similar between COVID-19 and influenza (18/78 [23%] vs 8/39 [21%]; odds ratio, 1.16; 95% CI, 0.42-3.45; p = 0.82). The frequency of early microbiological testing and antibiotic use was similar between the two groups. Within the overall COVID-19 group, early bacterial coinfections were associated with a statistically significant increase in 30-day all-cause mortality (21/68 [30.9%] vs 40/221 [18.1%]; hazard ratio, 1.84; 95% CI, 1.01-3.32).

CONCLUSIONS AND RELEVANCE

Our data suggest similar rates of early bacterial coinfections in ICU patients with COVID-19 and influenza. In addition, early bacterial coinfections were significantly associated with an increased 30-day mortality in patients with COVID-19.

Fatal cases after Omicron BA.1 and BA.2 infection: Results of an autopsy study

OBJECTIVES

Omicron lineages BA.1/2 are considered to cause mild clinical courses. Nevertheless, fatal cases after those infections are recognized but little is known about risk factors.

METHODS

A total of 23 full and three partial autopsies in deceased with known Omicron BA.1/2 infections have been consecutively performed. The investigations included histology, blood analyses, and molecular virus detection.

RESULTS

COVID-19-associated diffuse alveolar damage was found in only eight cases (31%). This rate is significantly lower compared with previous studies, including non-Omicron variants, where rates between 69% and 92% were observed. Neither vaccination nor known risk factors were significantly associated with a direct cause of death by COVID-19. Only those patients who were admitted to the clinic because of COVID-19 but not for other reasons had a significant association with a direct COVID-19 -caused death (P >0.001).

CONCLUSION

Diffuse alveolar damage still occurred in the Omicron BA.1/BA.2 era but at a considerably lower frequency than seen with previous variants of concern. None of the known risk factors discriminated the cases with COVID-19-caused death from those that died because of a different disease. Therefore, the host's genomics might play a key role in this regard. Further studies should elucidate the existence of such a genomic risk factor.

A beacon in the dark: COVID-19 course in CVID patients from two European countries: Different approaches, similar outcomes

BACKGROUND

CVID patients present an increased risk of prolonged SARS-CoV-2 infection and re-infection and a higher COVID-19-related morbidity and mortality compared to the general population. Since 2021, different therapeutic and prophylactic strategies have been employed in vulnerable groups (vaccination, SARS-CoV-2 monoclonal antibodies and antivirals). The impact of treatments over the last 2 years has not been explored in international studies considering the emergence of viral variants and different management between countries.

METHODS

A multicenter retrospective/prospective real-life study comparing the prevalence and outcomes of SARS-CoV-2 infection between a CVID cohort from four Italian Centers (IT-C) and one cohort from the Netherlands (NL-C), recruiting 773 patients.

RESULTS

329 of 773 CVID patients were found positive for SARS-CoV-2 infection between March 1st, 2020 and September 1st 2022. The proportion of CVID patients infected was comparable in both national sub-cohorts. During all waves, chronic lung disease, "complicated" phenotype, chronic immunosuppressive treatment and cardiovascular comorbidities impacted on hospitalization, whereas risk factors for mortality were older age, chronic lung disease, and bacterial superinfections. IT-C patients were significantly more often treated, both with antivirals and mAbs, than NL-C patients. Outpatient treatment, available only in Italy, started from the Delta wave. Despite this, no significant difference was found for COVID-19 severity between the two cohorts. However, pooling together specific SARS-CoV-2 outpatient treatments (mAbs and antivirals), we found a significant effect on the risk of hospitalization starting from Delta wave. Vaccination with ≥ 3 doses shortened RT-PCR positivity, with an additional effect only in patients receiving antivirals.

CONCLUSIONS

The two sub-cohorts had similar COVID-19 outcomes despite different treatment approaches. This points out that specific treatment should now be reserved for selected subgroups of CVID patients, based on pre-existing conditions.

Impact of viral co-infection on clinical outcomes and mortality of COVID-19 patients: a study from Saudi Arabia

Background

In COVID-19 patients undetected co-infections may have severe clinical implications associated with prolonged hospitalization, ICU admission, and mortality. Therefore, we aimed to investigate the impact of viral coinfections on the outcomes of hospitalized patients with COVID-19 in a large tertiary Saudi Arabian Hospital.

Methods

A total of 178 adult patients with confirmed SARS-CoV-2 who were hospitalized at the Armed Forces Hospital Southern Region (AFHSR), Saudi Arabia, from March 1^st to June 30^th 2022, were enrolled. Real-time PCR for the detection of viral co‑infections was carried out. Cases (SARS-CoV-2 with viral coinfections) and control (SARS-CoV-2 mono-infection) groups were compared.

Results

12/178 (7%) of enrolled COVID-19 patients had viral coinfections. 82/178 (46%) of patients were males. 58% of patients had comorbidities. During the study period, 4/12 (33%) and 21/166 (13%) cases and control patients died, p=0.047, respectively. Duration of hospitalization was the only significant independent factor associated with SARS-CoV-2 coinfections, OR 1.140, 95% CI 1.020-1.274, p=0.021.

Conclusions

The findings of this study from a large tertiary Saudi Arabian Center revealed a prevalence of 7% for SARS-CoV-2 viral coinfections. SARS-CoV-2 coinfected patients had a significantly prolonged duration of hospitalization and higher mortality than those with SARS-CoV-2 alone. Future studies are needed.

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.

Incidence and clinical outcomes of bacterial superinfections in critically ill patients with COVID-19

Background

Bacterial superinfection is not uncommon in critically ill patients with coronavirus disease (COVID-19) pneumonia requiring intensive care unit (ICU) treatment. However, there is still a lack of evidence related to bacterial superinfection and their clinical significance in critically ill patients with COVID-19. Therefore, we assessed the incidence of bacterial superinfections and their effects on clinical outcomes in critically ill patients with COVID-19.

Materials and methods

This single-center retrospective cohort study analyzed critically ill patients with COVID-19 admitted to the ICU at a tertiary academic hospital between February 2020 and December 2021. We reviewed data including patient demographics, clinical and microbiological characteristics, and outcomes.

Results

During the study period, 106 patients (median [IQR] age, 67 [58-75] years) were included, of which 32 (30%) were diagnosed with bacterial superinfections. Of these, 12 cases (38%) were associated with multidrug-resistant pathogens. Klebsiella aerogenes (6 cases [19%]) and Klebsiella pneumoniae (6 cases [19%]) were the most common pathogens associated with superinfections. The median time to bacterial superinfection was 13 (IQR, 9-20) days after ICU admission. Patients with bacterial superinfections had significantly fewer ventilator-free days on day 28 (0 [IQR, 0-0] days) than those without bacterial superinfections (19 [IQR, 0-22] days) (p < 0.001). Patients with bacterial superinfections had a longer ICU length of stay (32 [IQR, 9-53] days) than those without bacterial superinfections (11 [IQR, 7-18] days) (p < 0.001). Additionally, they had a longer hospital length of stay after ICU admission (39 [IQR, 18-62] days) than those without bacterial superinfections (18 [IQR, 12-37] days) (p = 0.001). There were no differences in ICU mortality or in-hospital mortality between the two groups. In the multivariable analysis, higher SAPS II score (OR, 2.697; 95% CI, 1.086-6.695) and thrombocytopenia (OR, 3.318; 95% CI, 1.355-8.123) were identified as risk factors for development of bacterial superinfection.

Conclusion

In critically ill patients with COVID-19, bacterial superinfections were common, and more than one-third of the bacterial superinfection cases were caused by multidrug-resistant pathogens. As patients with bacterial superinfections had worse clinical outcomes, the development of bacterial superinfections should be actively monitored.

Clinical Performance Evaluation of the NeuMoDx Flu A-B/RSV/SARS-CoV-2 Vantage Assay

SARS-CoV-2 infections may present with various symptoms that are similar to those of other respiratory diseases. For this reason, the need for simultaneous detection of at least RSV and influenza viruses together with SARS-CoV-2 was evident from the early stages of the pandemic. In the present study, we evaluated the clinical performance of the NeuMoDx™ Flu A-B/RSV/SARS-CoV-2 Vantage Assay against the conventional low-plex PCR utilized to detect influenza A-B, RSV, and SARS-CoV-2. There were 115 known positive clinical samples and 35 negative controls obtained from asymptomatic health-care workers included in the study; 25 samples were positive for influenza viruses, 46 for RSV, and 44 for SARS-CoV-2. The sensitivity, specificity, positive predictive value, and negative predictive value of the evaluated method for influenza and SARS-CoV-2 were 100%. The Spearman correlation coefficient was 0.586 (p < 0.05) for influenza and 0.893 (p < 0.05) for SARS-CoV-2. The sensitivity of the aforementioned assay for RSV was 93.47%; the specificity and the positive predictive value were 100%, and the negative predictive value was 92.10%, while the Spearman correlation coefficient was not applicable for the RSV. Overall, the assay under evaluation was shown to be a reliable alternative for the simultaneous detection of influenza viruses, RSV and SARS-CoV-2.

A Total of 207 Days of Veno-Venous Extracorporeal Membrane Oxygenation Support for Severe COVID-19 Prior to Successful Lung Transplantation: A Case Report

Veno-venous extracorporeal membrane oxygenation (VV-ECMO) is a life-saving treatment for respiratory failure that may serve as a bridge to patient recovery or lung transplantation. In COVID-19, recovery is somewhat unpredictable and occasionally occurs after >100 days on VV-ECMO support. Thus, determining therapy cessation may be difficult. We report the case of a 59-year-old male without specific risk factors admitted to a tertiary center for rapidly progressive respiratory failure due to severe COVID-19, despite aggressive mechanical ventilatory support. Immediate insertion of VV-ECMO was associated with prompt resolution of hypoxemia and hypercapnia; however, all therapeutic efforts to wean the patient from VV-ECMO failed. During the prolonged hospitalization on VV-ECMO, sepsis was the most life-threatening complication. The patient overcame roughly 40 superinfections, predominantly affecting the respiratory tract, and spent 183 days on antimicrobial treatment. Although the function of other organ systems was generally stable, gradually progressive right ventricular dysfunction due to precapillary pulmonary hypertension required increasing doses of inotropes. A successful lung transplantation was performed after 207 days of VV-ECMO support. The present case provides evidence for prolonged VV-ECMO therapy as a bridge to lung transplantation in severe COVID-19 despite numerous, predominantly infectious complications.

Examining the Determinants of COVID-19 Severity: A Cohort Study in Morocco of 915 Patients

INTRODUCTION

Coronavirus disease 2019 (COVID-19) is unpredictable and it varies from mild to severe and critical forms that are associated with a higher mortality rate. Risk factors associated with severe forms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have been investigated worldwide. We aimed to evaluate the clinical course of severe COVID-19 patients and to compare them with the non-severe patients concerning clinical and epidemiological characteristics, biological parameters and outcomes and thus, highlight the factors associated with severe forms of COVID-19 in our country.

METHODS

This is a single-center, ambidirectional cohort study, conducted in Tangier's COVID-19 care premises. We included diagnosed COVID-19 patients between August 2020 and October 2021. Sampling was performed through stratification according to clinical forms. All patients were followed-up throughout disease evolution, until remission for mild to moderate forms and 30 days after discharge for hospitalized patient's group (severe to critical forms). Data were collected using the WHO International Severe Acute Respiratory and Emerging Infection (ISARIC) case report form (CRF) and extracted from medical records alongside with interviews with patients and their relatives.

RESULTS

Among 915 included COVID-19 patients in Tangier, the non-severe group comprised 344 (37.6%) patients and the severe group comprised 571 (62.4%) patients. Some 514 were males (56.2%) and 401 were females (43.8%) and the mean age was 56.01 years (±16.76). The mean delay from onset of symptoms to diagnosis was 6.65 days ±4.68 in the severe group and 5.4 days ±4.57 in the non-severe group (p<0.001). Among the severe patient's group, 230 (40.3%) patients were admitted to the resuscitation unit, 258 (45.2%) patients were deceased during hospitalization, 313 (54.8%) were discharged alive, and 16 deaths occurred after discharge. Demographic, clinical, and biological characteristics showed significant differences between non-severe group and severe group. Multivariable logistic regression analysis showed increased odds of severity with male gender (adjusted odds ratio, aOR=2.91, p<0.003), age over 65 years old (aOR=2.68, p<0.001), diabetes (aOR=2.18, p<0.03), elevated D-dimers (>1 mg/mL) (aOR=6.09, p<0.001), superinfection (aOR=3.78, p<0.001), and baseline lymphopenia < 1000c/mm3 (aOR=8.66, p<0.001).

CONCLUSION

The high-risk factors for developing severe COVID-19 are age > 65 years, male gender, diabetes, elevated D-dimers, baseline lymphopenia, and superinfection. To predict severe and fatal COVID-19, factors identified may be used in the development of prediction tools for COVID-19 prognosis and risk stratification. Recalling the importance of considering at-risk populations, the management of epidemics must be planned in conjunction with the specificity of each community. Findings from our study may serve for health economic analyses and research in order to assist public health decisions in the future and should be integrated into health emergency preparedness and response strategies ensuring a resilient health system.

Characteristics and Outcomes of Critically Ill Pregnant/Postpartum Women with COVID-19 Pneumonia in Western Balkans, The Republic of Srpska Report

Background and Objectives: Coronavirus disease 2019 (COVID-19) is a novel infectious disease that has spread worldwide. As of 5 March 2020, the COVID-19 pandemic has resulted in approximately 111,767 cases and 6338 deaths in the Republic of Srpska and 375,554 cases and 15,718 deaths in Bosnia and Herzegovina. Our objective in the present study was to determine the characteristics and outcomes of critically ill pregnant/postpartum women with COVID-19 in the Republic of Srpska. Materials and Methods: The retrospective observational study of prospectively collected data included all critically ill pregnant/postpartum women with COVID-19 in a university-affiliated hospital between 1 April 2020 and 1 April 2022. Infection was confirmed by real-time reverse transcriptase polymerase chain reaction (RT-PCR) from nasopharyngeal swab specimens and respiratory secretions. Patients' demographics, clinical and laboratory data, pharmacotherapy, and neonatal outcomes were analysed. Results: Out of the 153 registered pregnant women with COVID-19 treated at the gynaecology department of the University Clinical Centre of the Republic of Srpska, 19 (12.41%) critically ill pregnant/postpartum women (median age of 36 (IQR, 29-38) years) were admitted to the medical intensive care unit (MICU). The mortality rate was 21.05% (four patients) during the study period. Of all patients (19), 14 gave birth (73.68%), and 4 (21.05%) were treated with veno-venous extracorporeal membrane oxygenation (vvECMO). Conclusions: Fourteen infants were born prematurely and none of them died during hospitalisation. A high mortality rate was detected among the critically ill pregnant/postpartum patients treated with mechanical ventilation and vvECMO in the MICU. The preterm birth rate was high in patients who required a higher level of life support (vvECMO and ventilatory support).

EEG background frequency is associated with discharge outcomes in non-ICU hospitalized patients with COVID-19

Objective

To assess risk factors for encephalopathy in non-ICU hospitalized patients with COVID-19 and the effect of encephalopathy on short-term outcomes.

Methods

We collected clinical and electrophysiological characteristics of fifty patients with COVID-19 infection admitted to a ward service and who had an electroencephalogram (EEG) performed. Associations with short-term outcomes including hospital length of stay and discharge disposition were determined from univariate and multivariate statistical analysis.

Results

Clinical delirium was associated with encephalopathy on EEG, cefepime use was associated with increased length of stay, and of all factors analyzed, background frequency on EEG alone was correlated with discharge disposition.

Conclusion

Encephalopathy is one of the major determinants of short-term outcomes in hospitalized non-ICU patients with COVID-19.