Bacterial and Fungal Coinfection in Individuals With Coronavirus: A Rapid Review To Support COVID-19 Antimicrobial Prescribing

Clinical evaluation of a multiplex droplet digital PCR for pathogen detection in critically ill COVID-19 patients with bloodstream infections

BACKGROUND

Nosocomial bloodstream infections (nBSI) have emerged as a clinical concern for physicians treating COVID-19 patients. In this study, we aimed to evaluate the effectiveness of a multiplex ddPCR in detecting bacterial pathogens in the blood of COVID-19 critically ill patients.

METHODS

This prospective diagnostic study included RT-PCR-confirmed COVID-19 patients admitted to our hospital from December 2022 to February 2023. A multiplex ddPCR assay was used to detect common bacterial pathogens and AMR genes in blood samples of the patients, along with antimicrobial susceptibility testing (AST). The diagnostic performance of the ddPCR assay was evaluated by comparing the results with those obtained through blood culture and clinical diagnosis. Additionally, the ability of ddPCR in detecting bacterial resistance was compared with the AST results.

RESULTS

Of the 200 blood samples collected from 184 patients, 45 (22.5%) were positive using blood culture, while 113 (56.5%) were positive for bacterial targets using the ddPCR assay. The ddPCR assay outperformed blood culture in pathogen detection rate, mixed infection detection rate, and fungal detection rate. Acinetobacter baumannii and Klebsiella pneumoniae were the most commonly detected pathogens in COVID-19 critically ill patients, followed by Enterococcus and Streptococcus. Compared to blood culture, ddPCR achieved a sensitivity of 75.5%, specificity of 51.0%, PPV of 30.9%, and NPV of 87.8%, respectively. However, there were significant differences in sensitivity among different bacterial species, where Gram-negative bacteria have the highest sensitivity of 90.3%. When evaluated on the ground of clinical diagnosis, the sensitivity, specificity, PPV and NPV of ddPCR were 78.1%, 90.5%, 94.7%, and 65.5%, respectively. In addition, the ddPCR assay detected 23 cases of blaKPC, which shown a better consistent with clinical test results than other detected AMR genes. Compared to blaKPC, there were few other AMR genes detected, indicating that the application of other AMR gene detection in the COVID-19 critically ill patients was limited.

CONCLUSION

The multiplex ddPCR assay had a significantly higher pathogen detection positivity than the blood culture, which could be an effective diagnostic tool for BSIs in COVID-19 patients and to improve patient outcomes and reduce the burden of sepsis on the healthcare system, though there is room for optimization of the panels used.- Adjusting the targets to include E. faecalis and E. faecium as well as Candida albicans and Candida glabrata could improve the ddPCR' s effectiveness. However, further research is needed to explore the potential of ddPCR in predicting bacterial resistance through AMR gene detection.

The vacuolar fusion regulated by HOPS complex promotes hyphal initiation and penetration in Candida albicans

The transition between yeast and hyphae is crucial for regulating the commensalism and pathogenicity in Candida albicans. The mechanisms that affect the invasion of hyphae in solid media, whose deficiency is more related to the pathogenicity of C. albicans, have not been elucidated. Here, we found that the disruption of VAM6 or VPS41 which are components of the homotypic vacuolar fusion and protein sorting (HOPS) complex, or the Rab GTPase YPT72, all responsible for vacuole fusion, led to defects in hyphal growth in both liquid and solid media, but more pronounced on solid agar. The phenotypes of vac8Δ/Δ and GTR1OE-vam6Δ/Δ mutants indicated that these deficiencies are mainly caused by the reduced mechanical forces that drive agar and organs penetration, and confirmed that large vacuoles are required for hyphal mechanical penetration. In summary, our study revealed that large vacuoles generated by vacuolar fusion support hyphal penetration and provided a perspective to refocus attention on the role of solid agar in evaluating C. albicans invasion.

Antimicrobial resistance in intensive care patients hospitalized with SEPSIS: a comparison between the COVID-19 pandemic and pre-pandemic era

Introduction

Coronavirus disease 2019 (COVID-19) is a highly contagious viral illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has had a dramatic effect on the world, resulting in millions of deaths worldwide and causing drastic changes in daily life. A study reported that septic complications were associated with high mortality in COVID-19 patients. This study aimed to evaluate how the COVID-19 pandemic changed the pre-pandemic and post-pandemic prevalence of sepsis in ICUs and to evaluate the different risk factors associated with mortality and the different diffusion of microorganisms and their resistance.

Materials and methods

We conducted a single-center retrospective observational clinical study, observing all patients in the ICU of the SS Annunziata Hospital in Chieti (Italy) who were diagnosed with sepsis and had a bacterial isolate from their blood culture. Sepsis was diagnosed by SEPSIIS III criteria. We enrolled all in-patients in the ICU from January 2018 to December 2021. We divided the patients into three groups: (1) non-pandemic period (Np) hospitalized in 2018-2019, (2) pandemic period (Pp)-COVID hospitalized in 2020-2021 with a diagnosis of COVID-19, and (3) Pp-non-COVID patients hospitalized in 2020-2021 without a diagnosis of COVID-19.

Results

From January 2018 to December 2021, 1,559 patients were admitted to the ICU, of which 211 patients [36 (17.1%) in 2018, 52 (24.6%) in 2019, 73 (34.6%) in 2020, and 50 (23.7%) in 2021, respectively] met the selection criteria: 88 patients in period Np, 67 patients in Pp without COVID-19, and 56 patients Pp with COVID-19. The overall mortality of these patients was high (65.9% at 30 days in Np), but decreased during the Pp (60.9%): Pp-non-COVID was 56.7% vs. Pp-COVID 66.1%, with a statistically significant association with APACHE III score (OR 1.08, 95%CI 1.04-1.12, p < 0.001), SOFA score (OR 1.12, 95%CI 1.03-1.22, p = 0.004), and age (OR 1.04, 95%CI 1.02-1.07, p < 0.0001). Between the Np vs. Pp periods, we observed an increase in a few Gram-positive bacteria such as S. capitis (1 pt. -0.9% vs. 14 pt. -7.65%- p = 0.008), S. epidermidis, Streptococcus spp., and E. faecalis, as well as a decrease in a case of blood culture positive for S. aureus, S. hominis, and E. faecium. In Gram-negative bacteria, we observed an increase in cases of Acinetobacter spp. (Np 6 pt. -5.1%- vs. Pp 20 pt. -10.9%, p = 0.082), and Serratia spp., while cases of sepsis decreased from E. faecium (Np 11 pt. -9.4%- vs. Pp 7 pt. -3.8%, p = 0.047), and Enterobacter spp., S. haemolyticus, S. maltophilia, Proteus spp., and P. aeruginosa have not changed. Finally, we found that resistance to OXA-48 (p = 0.040), ESBL (p = 0.002), carbapenems (p = 0.050), and colistin (p = 0.003) decreased with time from Np to Pp, particularly in Pp-COVID.

Conclusion

This study demonstrated how the COVID-19 pandemic changed the prevalence of sepsis in the ICU. It emerged that the risk factors associated with mortality were APACHE and SOFA scores, age, and, above all, the presence of ESBL-producing bacteria. Despite this, during the pandemic phase, we have observed a significant reduction in the emergence of resistant germs compared to the pre-pandemic phase.

The human microbiota is a beneficial reservoir for SARS-CoV-2 mutations

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations are rapidly emerging. In particular, beneficial mutations in the spike (S) protein, which can either make a person more infectious or enable immunological escape, are providing a significant obstacle to the prevention and treatment of pandemics. However, how the virus acquires a high number of beneficial mutations in a short time remains a mystery. We demonstrate here that variations of concern may be mutated due in part to the influence of the human microbiome. We searched the National Center for Biotechnology Information database for homologous fragments (HFs) after finding a mutation and the six neighboring amino acids in a viral mutation fragment. Among the approximate 8,000 HFs obtained, 61 mutations in S and other outer membrane proteins were found in bacteria, accounting for 62% of all mutation sources, which is 12-fold higher than the natural variable proportion. A significant proportion of these bacterial species-roughly 70%-come from the human microbiota, are mainly found in the lung or gut, and share a composition pattern with COVID-19 patients. Importantly, SARS-CoV-2 RNA-dependent RNA polymerase replicates corresponding bacterial mRNAs harboring mutations, producing chimeric RNAs. SARS-CoV-2 may collectively pick up mutations from the human microbiota that change the original virus's binding sites or antigenic determinants. Our study clarifies the evolving mutational mechanisms of SARS-CoV-2.

IMPORTANCE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations are rapidly emerging, in particular advantageous mutations in the spike (S) protein, which either increase transmissibility or lead to immune escape and are posing a major challenge to pandemic prevention and treatment. However, how the virus acquires a high number of advantageous mutations in a short time remains a mystery. Here, we provide evidence that the human microbiota is a reservoir of advantageous mutations and aids mutational evolution and host adaptation of SARS-CoV-2. Our findings demonstrate a conceptual breakthrough on the mutational evolution mechanisms of SARS-CoV-2 for human adaptation. SARS-CoV-2 may grab advantageous mutations from the widely existing microorganisms in the host, which is undoubtedly an "efficient" manner. Our study might open a new perspective to understand the evolution of virus mutation, which has enormous implications for comprehending the trajectory of the COVID-19 pandemic.

Fungal melanin suppresses airway epithelial chemokine secretion through blockade of calcium fluxing

Respiratory infections caused by the human fungal pathogen Aspergillus fumigatus are a major cause of mortality for immunocompromised patients. Exposure to these pathogens occurs through inhalation, although the role of the respiratory epithelium in disease pathogenesis has not been fully defined. Employing a primary human airway epithelial model, we demonstrate that fungal melanins potently block the post-translational secretion of the chemokines CXCL1 and CXCL8 independent of transcription or the requirement of melanin to be phagocytosed, leading to a significant reduction in neutrophil recruitment to the apical airway both in vitro and in vivo . Aspergillus -derived melanin, a major constituent of the fungal cell wall, dampened airway epithelial chemokine secretion in response to fungi, bacteria, and exogenous cytokines. Furthermore, melanin muted pathogen-mediated calcium fluxing and hindered actin filamentation. Taken together, our results reveal a critical role for melanin interaction with airway epithelium in shaping the host response to fungal and bacterial pathogens.

Predictors and patterns of empirical antibiotic therapy and associated outcomes in COVID-19 patients: a retrospective study in a tertiary care facility in South India

BACKGROUND

The coronavirus disease (COVID-19) led to a global health crisis. Inappropriate use of antibiotics in COVID-19 patients has been a concern, leading to antimicrobial resistance. This study evaluated the patterns and predictors of empirical antibiotic therapy in COVID-19 patients and associated outcomes.

METHODS

A hospital-based retrospective study was conducted with 525 patients admitted to Kasturba Hospital, Manipal, India, with moderate and severe COVID-19 from 1 March to 1 August 2021. They were divided based on empirical therapy, and predictors of antibiotic usage were assessed by logistic regression.

RESULTS

Four hundred and eighty (91.4%) COVID-19 patients received at least one course of antibiotics, with 440 (83.8%) initiating empirical therapy. Patients with severe COVID-19 manifestations were more likely to be prescribed empirical antibiotics. Multivariable analysis showed that patients initiated on empirical antibiotics had significantly elevated levels of procalcitonin [OR: 3.91 (95% CI: 1.66-9.16) (p = 0.001)], invasive ventilation [OR: 3.93 (95% CI: 1.70-9.09) (p = 0.001)], shortness of breath [OR: 2.25 (95% CI: 1.30-3.89) (p = 0.003)] and higher CRP levels [OR: 1.01 (95% CI: 1.00-1.01) (p = 0.005)]. Most antibiotics (65.9%) were prescribed from the 'Watch' group, the highest being ceftriaxone. Only 23.8% of the patients had microbiologically confirmed infections.

CONCLUSION

The study identified predictors for initiating empirical antibacterial therapy in our setting.

Meropenem population pharmacokinetics and model-based dosing optimisation in patients with serious bacterial infection

OBJECTIVES

The objective of this study was to develop a population pharmacokinetic model of meropenem in a heterogeneous population of patients with a serious bacterial infection in order to propose dosing optimisation leading to improved achievement of the pharmacokinetic/pharmacodynamic (PK/PD) target.

METHODS

A total of 174 meropenem serum levels obtained from 144 patients during therapeutic drug monitoring were analysed using a non-linear mixed-effects modelling approach and Monte Carlo simulation was then used to compare various dosing regimens in order to optimise PK/PD target attainment.

RESULTS

The meropenem volume of distribution of the patient population was 54.95 L, while clearance started at 3.27 L/hour and increased by 0.91 L/hour with each 1 mL/s/1.73 m2 of estimated glomerular filtration rate. Meropenem clearance was also 0.31 L/hour higher in postoperative patients with central nervous system infection. Meropenem administration by continuous infusion showed a significantly higher probability of attaining the PK/PD target than a standard 30 min infusion (95.3% vs 49.5%).

CONCLUSIONS

A daily meropenem dose of 3 g, 6 g and 10.5 g administered by continuous infusion was shown to be accurate for patients with moderate to severe renal impairment, normal renal function to mild renal impairment and augmented renal clearance, respectively.

Trends in decision-making by primary care physicians regarding common infectious complaints

BACKGROUND

Primary care physicians played an important role in the global response during the COVID-19 pandemic, but with the absence of laboratory and diagnostics services, the move to telehealth and the focus on respiratory assessment, they faced increased uncertainty when making clinical decisions.

OBJECTIVES

This paper aims to examine the impact of the pandemic on decisions made by primary care physicians, as measured by referrals to chest X-ray and laboratory tests and by prescriptions of antibiotics.

METHODS

We conducted a retrospective study of all visits recorded with fever or cough, presenting to 209 community clinics in Southern Israel during the years 2018-2022. We describe changes in outcome rates across time and use multivariate generalised linear mixed effects model to compare the odds of referrals and prescriptions between periods, while accounting for gender, age, clinic sector, visit type, diagnosis, and season.

RESULTS

In total, 609,823 visits to primary care physicians complied with the cohort definitions. Social restrictions were associated with a decline in all measured outcomes for primary care physician decisions, most prominently among ages 20-59, for throat culture referral during the first lockdown (OR = 0.46) and for cephalosporine prescription during the second lockdown (OR = 0.55). This trend persisted following the cancellation of the restrictions.

CONCLUSIONS

Despite higher uncertainty during the COVID-19 social restrictions, the overall course of clinical decision-making processes was maintained, and was associated with a reduction in the use of auxiliary resources, which can improve the quality of patient care by lowering costs and supporting prevention of future antibiotics resistance.

Community antibiotic prescribing in patients with COVID-19 across three pandemic waves: a population-based study in Scotland, UK

OBJECTIVES

This study aims to examine community antibiotic prescribing across a complete geographical area for people with a positive COVID-19 test across three pandemic waves, and to examine health and demographic factors associated with antibiotic prescribing.

DESIGN

A population-based study using administrative data.

SETTING

A complete geographical region within Scotland, UK.

PARTICIPANTS

Residents of two National Health Service Scotland health boards with SARS-CoV-2 virus test results from 1 February 2020 to 31 March 2022 (n=184 954). Individuals with a positive test result (n=16 025) had data linked to prescription and hospital admission data ±28 days of the test, general practice data for high-risk comorbidities and demographic data.

OUTCOME MEASURES

The associations between patient factors and the odds of antibiotic prescription in COVID-19 episodes across three pandemic waves from multivariate binary logistic regression.

RESULTS

Data included 768 206 tests for 184 954 individuals, identifying 16 240 COVID-19 episodes involving 16 025 individuals. There were 3263 antibiotic prescriptions ±28 days for 2395 episodes. 35.6% of episodes had a prescription only before the test date, 52.3% of episodes after and 12.1% before and after. Antibiotic prescribing reduced over time: 20.4% of episodes in wave 1, 17.7% in wave 2 and 12.0% in wave 3. In multivariate logistic regression, being female (OR 1.31, 95% CI 1.19 to 1.45), older (OR 3.02, 95% CI 2.50 to 3.68 75+ vs <25 years), having a high-risk comorbidity (OR 1.45, 95% CI 1.31 to 1.61), a hospital admission ±28 days of an episode (OR 1.58, 95% CI 1.42 to 1.77) and health board region (OR 1.14, 95% CI 1.03 to 1.25, board B vs A) increased the odds of receiving an antibiotic.

CONCLUSION

Community antibiotic prescriptions in COVID-19 episodes were uncommon in this population and likelihood was associated with patient factors. The reduction over pandemic waves may represent increased knowledge regarding COVID-19 treatment and/or evolving symptomatology.

Infection with the multidrug-resistant Klebsiella pneumoniae New Delhi metallo-B-lactamase strain in patients with COVID-19: Nec Hercules contra plures?

Background

During the coronavirus disease 2019 (COVID-19) pandemic, in patients treated for SARS-CoV-2 infection, infections with the Klebsiella pneumoniae bacteria producing New Delhi metallo-B-lactamase (NDM) carbapenemase in the USA, Brazil, Mexico, and Italy were observed, especially in intensive care units (ICUs). This study aimed to assess the impact of Klebsiella pneumoniae NDM infection and other bacterial infections on mortality in patients treated in ICUs due to COVID-19.

Methods

The 160 patients who qualified for the study were hospitalized in ICUs due to COVID-19. Three groups were distinguished: patients with COVID-19 infection only (N = 72), patients with COVID-19 infection and infection caused by Klebsiella pneumoniae NDM (N = 30), and patients with COVID-19 infection and infection of bacterial etiology other than Klebsiella pneumoniae NDM (N = 58). Mortality in the groups and chosen demographic data; biochemical parameters analyzed on days 1, 3, 5, and 7; comorbidities; and ICU scores were analyzed.

Results

Bacterial infection, including with Klebsiella pneumoniae NDM type, did not elevate mortality rates. In the group of patients who survived the acute phase of COVID-19 the prolonged survival time was demonstrated: the median overall survival time was 13 days in the NDM bacterial infection group, 14 days in the other bacterial infection group, and 7 days in the COVID-19 only group. Comparing the COVID-19 with NDM infection and COVID-19 only groups, the adjusted model estimated a statistically significant hazard ratio of 0.28 (p = 0.002). Multivariate analysis revealed that age, APACHE II score, and CRP were predictors of mortality in all the patient groups.

Conclusion

In patients treated for SARS-CoV-2 infection acquiring a bacterial infection due to prolonged hospitalization associated with the treatment of COVID-19 did not elevate mortality rates. The data suggests that in severe COVID-19 patients who survived beyond the first week of hospitalization, bacterial infections, particularly Klebsiella pneumoniae NDM, do not significantly impact mortality. Multivariate analysis revealed that age, APACHE II score, and CRP were predictors of mortality in all the patient groups.

Evolutionary trends in antifungal resistance: a meta-analysis

The present paper includes a meta-analysis of literature data on 318 species of fungi belonging to 34 orders in their response to 8 antifungal agents (amphotericin B, caspofungin, fluconazole, itraconazole, ketoconazole, posaconazole, terbinafine, and voriconazole). Main trends of MIC results at the ordinal level were visualized. European Committee on Antimicrobial Susceptibility Testing and Clinical & Laboratory Standards Institute (CLSI) clinical breakpoints were used as the staff gauge to evaluate MIC values ranging from resistance to susceptibility, which were subsequently compared with a phylogenetic tree of the fungal kingdom. Several orders (Hypocreales, Microascales, and Mucorales) invariably showed resistance. Also the basidiomycetous orders Agaricales, Polyporales, Sporidiales, Tremellales, and Trichosporonales showed relatively high degrees of azole multi-resistance, while elsewhere in the fungal kingdom, including orders with numerous pathogenic and opportunistic species, that is, Onygenales, Chaetothyiales, Sordariales, and Malasseziales, in general were susceptible to azoles. In most cases, resistance vs susceptibility was consistently associated with phylogenetic distance, members of the same order showing similar behavior.

IMPORTANCE

A kingdom-wide the largest set of published wild-type antifungal data comparison were analyzed. Trends in resistance in taxonomic groups (monophyletic clades) can be compared with the phylogeny of the fungal kingdom, eventual relationships between fungus-drug interaction and evolution can be described.

Bacterial co-infections, secondary infections and antimicrobial use among hospitalized COVID-19 patients in the sixth wave in Pakistan: findings and implications

INTRODUCTION

Previous studies in Pakistan have shown considerable over prescribing of antibiotics in patients hospitalized with COVID-19 despite very low prevalence of bacterial infections. Irrational use of antibiotics will worsen antimicrobial resistance (AMR).

METHODS

Retrospective analysis of medical records of patients in the COVID-19 wards of three tertiary care hospitals to assess antibiotic use during the sixth COVID-19 wave.

RESULTS

A total of 284 patients were included, most were male (66.9%), aged 30-50 years (50.7%) with diabetes mellitus the most common comorbidity. The most common symptoms at presentation were cough (47.9%) and arthralgia-myalgia (41.5%). Around 3% were asymptomatic, 34.9% had mild, 30.3% moderate, and 23.6% had severe disease, with 8.1% critical. Chest X-ray abnormalities were seen in 43.3% of patients and 37% had elevated white cell counts, with 35.2% having elevated C-reactive protein levels. Around 91% COVID-19 patients were prescribed antibiotics during their hospital stay, with only a few with proven bacterial co-infections or secondary bacterial infections. Most antibiotics were from the 'Watch' category (90.8%) followed by the 'Reserve' category (4.8%), similar to previous COVID-19 waves.

CONCLUSION

There continued to be excessive antibiotics use among hospitalized COVID-19 patients in Pakistan. Urgent measures are needed to address inappropriate prescribing including greater prescribing of Access antibiotics where pertinent.

A dynamic nomogram to predict invasive fungal super-infection during healthcare-associated bacterial infection in intensive care unit patients: an ambispective cohort study in China

Objectives

Invasive fungal super-infection (IFSI) is an added diagnostic and therapeutic dilemma. We aimed to develop and assess a nomogram of IFSI in patients with healthcare-associated bacterial infection (HABI).

Methods

An ambispective cohort study was conducted in ICU patients with HABI from a tertiary hospital of China. Predictors of IFSI were selected by both the least absolute shrinkage and selection operator (LASSO) method and the two-way stepwise method. The predictive performance of two models built by logistic regression was internal-validated and compared. Then external validity was assessed and a web-based nomogram was deployed.

Results

Between Jan 1, 2019 and June 30, 2023, 12,305 patients with HABI were screened in 14 ICUs, of whom 372 (3.0%) developed IFSI. Among the fungal strains causing IFSI, the most common was C.albicans (34.7%) with a decreasing proportion, followed by C.tropicalis (30.9%), A.fumigatus (13.9%) and C.glabrata (10.1%) with increasing proportions year by year. Compared with LASSO-model that included five predictors (combination of priority antimicrobials, immunosuppressant, MDRO, aCCI and S.aureus), the discriminability of stepwise-model was improved by 6.8% after adding two more predictors of COVID-19 and microbiological test before antibiotics use (P<0.01).And the stepwise-model showed similar discriminability in the derivation (the area under curve, AUC=0.87) and external validation cohorts (AUC=0.84, P=0.46). No significant gaps existed between the proportion of actual diagnosed IFSI and the frequency of IFSI predicted by both two models in derivation cohort and by stepwise-model in external validation cohort (P=0.16, 0.30 and 0.35, respectively).

Conclusion

The incidence of IFSI in ICU patients with HABI appeared to be a temporal rising, and our externally validated nomogram will facilitate the development of targeted and timely prevention and control measures based on specific risks of IFSI.

Antibiotic resistance: a global crisis, problems and solutions

Healthy state is priority in today's world which can be achieved using effective medicines. But due to overuse and misuse of antibiotics, a menace of resistance has increased in pathogenic microbes. World Health Organization (WHO) has announced ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) as the top priority pathogens as these have developed resistance against certain antibiotics. To combat such a global issue, it is utmost important to identify novel therapeutic strategies/agents as an alternate to such antibiotics. To name certain antibiotic adjuvants including: inhibitors of beta-lactamase, efflux pumps and permeabilizers for outer membrane can potentially solve the antibiotic resistance problems. In this regard, inhibitors of lytic domain of lytic transglycosylases provide a novel way to not only act as an alternate to antibiotics but also capable of restoring the efficiency of previously resistant antibiotics. Further, use of bacteriophages is another promising strategy to deal with antibiotic resistant pathogens. Taking in consideration the alternatives of antibiotics, a green synthesis nanoparticle-based therapy exemplifies a good option to combat microbial resistance. As horizontal gene transfer (HGT) in bacteria facilitates the evolution of new resistance strains, therefore identifying the mechanism of resistance and development of inhibitors against it can be a novel approach to combat such problems. In our perspective, host-directed therapy (HDT) represents another promising strategy in combating antimicrobial resistance (AMR). This approach involves targeting specific factors within host cells that pathogens rely on for their survival, either through replication or persistence. As many new drugs are under clinical trials it is advisable that more clinical data and antimicrobial stewardship programs should be conducted to fully assess the clinical efficacy and safety of new therapeutic agents.

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.

Community-acquired and hospital-acquired bacterial co-infections in patients hospitalized with Covid-19 or influenza: a retrospective cohort study

BACKGROUND

Bacterial co-infections are believed to be less frequent in patients with Covid-19 than influenza, but frequencies varied between studies.

METHODS

This single-center retrospective, propensity score-matched analysis included adult patients with Covid-19 or influenza admitted to normal-care wards between 02/2014 and 12/2021. Covid-19 cases were propensity score matched to influenza cases at a 2:1 ratio. Community-acquired and hospital-acquired bacterial co-infections were defined as positive blood or respiratory cultures ≤ 48 h or > 48 h after hospital admission, respectively. The primary outcome was comparison of community-acquired and hospital-acquired bacterial infections between patients with Covid-19 and influenza in the propensity score-matched cohort. Secondary outcomes included frequency of early and late microbiological testing.

RESULTS

A total of 1337 patients were included in the overall analysis, of which 360 patients with Covid-19 were matched to 180 patients with influenza. Early (≤ 48 h) microbiological sampling was performed in 138 (38.3%) patients with Covid-19 and 75 (41.7%) patients with influenza. Community-acquired bacterial co-infections were found in 14 (3.9%) of 360 patients with Covid-19 and 7 (3.9%) of 180 patients with influenza (OR 1.0, 95% CI 0.3-2.7). Late (> 48 h) microbiological sampling was performed in 129 (35.8%) patients with Covid-19 and 74 (41.1%) patients with influenza. Hospital-acquired bacterial co-infections were found in 40 (11.1%) of 360 patients with Covid-19 and 20 (11.1%) of 180 patients with influenza (OR 1.0, 95% CI 0.5-1.8).

CONCLUSION

The rate of community-acquired and hospital-acquired bacterial co-infections was similar in hospitalized Covid-19 and influenza patients. These findings contrast previous literature reporting that bacterial co-infections are less common in Covid-19 than influenza.

Characterization of Coinfections in Patients with COVID-19

Background

Little is known about coinfections in patients with COVID-19, with antibiotics often initiated empirically.

Objectives

To determine the rates and characteristics of early and late coinfections in COVID-19 patients and to characterize the use of anti-infective agents, especially antibiotics.

Methods

This retrospective chart review involved patients with COVID-19 who were admitted to Lions Gate Hospital (Vancouver, British Columbia) between January 1 and June 30, 2020. Data were extracted from electronic medical records, and descriptive statistics were used to analyze the data.

Results

Of the 48 patients admitted during the study period, 10 (21%) were determined to have coinfections: 3 (6%) had early coinfections and 7 (15%) had late coinfections. Early empiric use of antibiotics was observed in 32 (67%) patients; for 29 (91%) of these 32 patients, the therapy was deemed inappropriate. Patients with coinfections had longer hospital stays and more complications.

Conclusions

Despite low rates of early coinfection, empiric antibiotics were started for a majority of the patients. Most late coinfections occurred in patients in the intensive care unit who required mechanical ventilation. Patients with coinfections had poorer outcomes than those without coinfections.

Systematic review of ceftaroline fosamil in the management of patients with methicillin-resistant Staphylococcus aureus pneumonia

Methicillin-resistant Staphylococcus aureus (MRSA) is responsible for an array of problematic community- and healthcare-acquired infections, including pneumonia, and is frequently associated with severe disease and high mortality rates. Standard recommended treatments for empiric and targeted coverage of suspected MRSA in patients with community-acquired pneumonia (CAP) and hospital-acquired pneumonia (HAP), including ventilator-associated pneumonia (VAP), are vancomycin and linezolid. However, adverse events such as acute kidney injury and Clostridium difficile infection have been associated with these antibiotics. Ceftaroline fosamil is a β-lactam/extended-spectrum cephalosporin approved for the treatment of adults and children with CAP and complicated skin and soft tissue infections. Ceftaroline has in vitro activity against a range of common Gram-positive bacteria and is distinct among the β-lactams in retaining activity against MRSA. Due to the design of the pivotal randomised controlled trials of ceftaroline fosamil, outcomes in patients with MRSA CAP were not evaluated. However, various reports of real-world outcomes with ceftaroline fosamil for pneumonia caused by MRSA, including CAP and HAP/VAP, been published since its approval. A systematic literature review and qualitative analysis of relevant publications was undertaken to collate and summarise relevant published data on the efficacy and safety of ceftaroline fosamil in patients with MRSA pneumonia. While relatively few real-world outcomes studies are available, the available data suggest that ceftaroline fosamil is a possible alternative to linezolid and vancomycin for MRSA pneumonia. Specific scenarios in which ceftaroline fosamil might be considered include bacteraemia and complicating factors such as empyema.

The impact of the COVID-19 pandemic on blood culture practices and bloodstream infections

IMPORTANCE

Bacterial infections are a significant cause of morbidity and mortality worldwide. In the wake of the COVID-19 pandemic, previous studies have demonstrated pandemic-related shifts in the epidemiology of bacterial bloodstream infections (BSIs) in the general population and in specific hospital systems. Our study uses a large, comprehensive data set stratified by setting [community, long-term care (LTC), and hospital] to uniquely demonstrate how the effect of the COVID-19 pandemic on BSIs and testing practices varies by healthcare setting. We showed that, while the number of false-positive blood culture results generally increased during the pandemic, this effect did not apply to hospitalized patients. We also found that many infections were likely under-recognized in patients in the community and in LTC, demonstrating the importance of maintaining healthcare for these groups during crises. Last, we found a decrease in infections caused by certain pathogens in the community, suggesting some secondary benefits of pandemic-related public health measures.

Impact of SARS-CoV2 infection on gut microbiota dysbiosis

The composition and function of the gut microbiota constantly influence health. Disruptions in this delicate balance, termed gut microbiota dysbiosis, have been implicated in various adverse health events. As the largest global epidemic since 1918, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had devastating consequences. While the primary impact of Corona Virus Disease 2019 (COVID-19) has been on the respiratory system, a growing body of research has unveiled the significant involvement of the gastrointestinal tract as well. Emerging evidence underscores notable alterations in the gut microbiome of COVID-19 patients. In addition, the gut microbiome is also characterized by an abundance of opportunistic pathogens, which is related to disease manifestations of COVID-19 patients. The intricate bidirectional interaction between the respiratory mucosa and the gut microbiota, known as the gut-lung axis, emerges as a crucial player in the pathological immune response triggered by SARS-CoV-2. Here, we discuss microbiota-based gut characteristics of COVID-19 patients and the long-term consequences of gut microbiota dysregulation. These insights could potentially transform the development of long-term interventions for COVID-19, offering hope for improved outcomes and enhanced patient recovery.

Coronavirus disease 2019 (COVID-19)-associated brain abscesses caused by Pseudomonas aeruginosa and Aspergillus fumigatus: two case and a review of the literature

BACKGROUND

Bacterial and fungal superinfections are commonly reported in patients with coronavirus disease 2019.

CASE PRESENTATION

We report the first case of brain and intramedullary abscesses caused by Pseudomonas aeruginosa and a rare case of brain abscesses caused by Aspergillus fumigatus in two post-coronavirus disease 2019 patients. The first patient-34-year-old Iranian woman-presented with weakness of the left upper limb, headaches, and lower limb paresthesia. She had a history of undiagnosed diabetes and had received corticosteroid therapy. The second patient-45-year-old Iranian man-presented with right-sided weakness and had a history of intensive care unit admission. Both patients passed away despite appropriate medical therapy.

CONCLUSION

The immune dysregulation induced by coronavirus disease 2019 and its' treatments can predispose patients, especially immunosuppressed ones, to bacterial and fungal infections with unusual and opportunistic pathogens in the central nervous system. Pseudomonas aeruginosa and Aspergillus fumigatus should be considered as potential causes of brain infection in any coronavirus disease 2019 patient presenting with neurological symptoms and evidence of brain abscess in imaging, regardless of sinonasal involvement. These patients should get started on appropriate antimicrobial therapy as soon as possible, as any delay in diagnosis or treatment can be associated with adverse outcomes.

Mapping the spread and mobility of antibiotic resistance in wastewater due to COVID-19 surge

Large amounts of antibiotics have been discharged into wastewater during the COVID-19 pandemic due to overuse and misuse of antibiotics to treat patients. Wastewater-based surveillance can be used as an early warning for antibiotic resistance (AR) emergence. The present study analyzed municipal wastewater corresponding to the major pandemic waves (WW1, WW2, and WW3) in India along with hospital wastewater (Ho) taken as a benchmark for AR. Commonly prescribed antibiotics during a pandemic, azithromycin and cefixime residues, were found in the range of 2.1-2.6 μg/L in Ho and WW2. Total residual antibiotic concentration was less in WW2; however, the total antibiotic resistance gene (ARG) count was 1065.6 ppm compared to 85.2 ppm in Ho. Metagenome and RT-qPCR analysis indicated a positive correlation between antibiotics and non-corresponding ARGs (blaOXA, aadA, cat, aph3, and ere), where 7.2-7.5% was carried by plasmid in the bacterial community of WW1 and WW2. Moreover, as the abundance of the dfrA and int1 genes varied most among municipal wastewater, they can be suggested as AR markers for the pandemic. The common pathogens Streptococcus, Escherichia, Shigella, and Aeromonas were putative ARG hosts in metagenome-assembled genomes. The ARG profile and antibiotic levels varied between municipal wastewaters but were fairly similar for WW2 and Ho, suggesting the impact of the pandemic in shaping the resistome pattern. The study provides insights into the resistome dynamic, AR markers, and host-ARG association in wastewater during the COVID-19 surge. Continued surveillance and identification of intervention points for AR beyond the pandemic are essential to curbing the environmental spread of ARGs in the near future.

The Role of Procalcitonin/Albumin Ratio and CRP/Albumin Ratio in Predicting In-hospital Mortality in COVID-19 Patients

Background

Hospitalized coronavirus disease 2019 (COVID-19) patients have higher mortality rates. Parameters to predict mortality are needed. Therefore, we investigated the power of procalcitonin/albumin ratio (PAR) and C-reactive protein/albumin ratio (CAR) to predict in-hospital mortality in hospitalized COVID-19 patients.

Methods

In this study, 855 patients were included. Patients' PAR and CAR values were recorded from the hospital information management system. The patients were evaluated in two groups according to their in-hospital mortality status.

Results

In-hospital mortality was observed in 163 patients (19.1%). The median PAR and CAR values of patients in the non-survivor group were statistically significantly higher than those of patients in the survivor group, PAR (median: 0.07, interquartile range [IQR]: 0.03-0.33 vs. median: 0.02, IQR: 0.01-0.04, respectively; p < 0.001); CAR (median: 27.60, IQR: 12.49-44.91 vs. median: 7.47, IQR: 2.66-18.93, respectively; p < 0.001). The area under the curve (AUC) and odds ratio (OR) values obtained by PAR to predict in-hospital mortality were higher than the values obtained by procalcitonin, CAR, albumin, and CRP (AUCs of PAR, procalcitonin, CAR, albumin, and CRP: 0.804, 0.792, 0.762, 0.755, and 0.748, respectively; OR: PAR > 0.04, procalcitonin > 0.14, CAR > 20.59, albumin < 4.02, and CRP > 63; 8.215, 7.134, 5.842, 6.073, and 5.07, respectively). Patients with concurrent PAR > 0.04 and CAR > 20.59 had an OR of 15.681 compared to patients with concurrent PAR < 0.04 and CAR < 20.59.

Conclusions

In this study, PAR was found to be more valuable for predicting in-hospital COVID-19 mortality than all other parameters. In addition, concurrent high levels of PAR and CAR were found to be more valuable than a high level of PAR or CAR alone.

Microbiological profile of multidrug resistant bacteria before and during COVID-19 in CHU Mohammed VI

Background and Objectives

A new type of corona virus has caused Corona virus disease-19 and, subsequently, a global pandemic. All individuals are prone to the disease, so drastic measures were taken to prevent its spread. This study aimed to evaluate the impact of COVID-19 on the progression of the antimicrobial resistance rate by comparing two periods: before and during COVID-19.

Materials and Methods

We used a cross-sectional design to investigate the Antimicrobial Resistance (AMR) rate before (03/2019 to 03/2020) and during COVID-19 (03/2020 to 03/2021) in a University Hospital in Marrakech. The data were analyzed using SPSS Version 25.0.

Results

Among the 7106 specimens, there was a significant increase in the multidrug-resistant bacterial from 27.38% to 35.87% during COVID-19 (p<0.001), particularly in blood culture, cerebrospinal fluid, catheter, and pus. However, there was a non-significant change in puncture fluid, expectoration, protected distal sampling, joint fluid, stool culture, and genital sampling. A decrease in Multidrug-resistant bacteria (MDRB) was observed only in cytobacteriological urine tests (p<0.05). According to species, there was an increase in extended-spectrum beta-lactamase-producing Enterobacteriaceae, carbapenem-resistant Enterobacteriaceae, and methicillin-resistant Staphylococcus aureus.

Conclusion

In our study, it is particularly noticeable that the MDRB has increased. These results highlight the importance that the pandemic has not been able to slow the progression.

Update of antimicrobial resistance in level III and IV health institutions in Colombia between January 2018 and December 2021

Introduction

Antimicrobial resistance surveillance is a fundamental tool for the development, improvement, and adjustment of antimicrobial stewardship programs, therapeutic guidelines, and universal precautions to limit the cross-transmission of resistant bacteria between patients. Since the beginning of 2020, the SARS-CoV-2 pandemic profoundly challenged the health system and, according to some reports, increased the rates of antimicrobial resistance.

Objective

To describe the behavior of antimicrobial resistance of the most frequent bacterial pathogens in twenty Colombian hospitals from January 2018 to December 2021.

Materials and methods

We conducted a descriptive study based on the microbiological information recorded from January 2018 to December 2021 in twenty levels III and IV health institutions in twelve Colombian cities. We identified the species of the ten most frequent bacteria along with their resistance profile to the antibiotic markers after analyzing the data through WHONET.

Results

We found no statistically significant changes in most pathogens’ resistance profiles from January 2018 to December 2021. Only Pseudomonas aeruginosa had a statistically significant increase in its resistance profile, particularly to piperacillin/tazobactam and carbapenems.

Conclusions

The changes in antimicrobial resistance in these four years were not statistically significant except for P. aeruginosa to piperacillin/tazobactam and carbapenems.

COVID-19 therapeutics: stewardship in England and considerations for antimicrobial resistance

The COVID-19 pandemic saw unprecedented resources and funds driven into research for the development, and subsequent rapid distribution, of vaccines, diagnostics and directly acting antivirals (DAAs). DAAs have undeniably prevented progression and life-threatening conditions in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, there are concerns of antimicrobial resistance (AMR), antiviral resistance specifically, for DAAs. To preserve activity of DAAs for COVID-19 therapy, as well as detect possible mutations conferring resistance, antimicrobial stewardship and surveillance were rapidly implemented in England. This paper expands on the ubiquitous ongoing public health activities carried out in England, including epidemiologic, virologic and genomic surveillance, to support the stewardship of DAAs and assess the deployment, safety, effectiveness and resistance potential of these novel and repurposed therapeutics.

The impact of immunosuppressive therapy on secondary infections and antimicrobial use in COVID-19 inpatients: a retrospective cohort study

BACKGROUND

Immunosuppressive therapies have become a cornerstone of the management of severe COVID-19. The impact of these therapies on secondary infections and antimicrobial prescribing remains unclear. We sought to assess antimicrobial use and the incidence of bacterial and fungal infections in patients with severe COVID-19, and to explore their associations with receipt of immunosuppressive therapies.

METHODS

Our retrospective cohort study included 715 hospitalised, adult patients with severe COVID-19 admitted to St George's Hospital, London, UK, during the first UK pandemic wave (1st March-10th June 2020). Co-infections (occurring within 48 h of admission) and secondary infections (≥ 48 h) were defined as a positive microbiological culture with supporting clinical, radiological or laboratory data to suggest true infection. Cox regression models with time-dependent covariates were used to explore the association between immunosuppressant use and secondary infection.

RESULTS

Microbiologically confirmed co-infection occurred in 4.2% (n = 30) and secondary infection in 9.3% (n = 66) of the cohort (n = 715) and were associated with in-hospital mortality (48% vs 35%, OR 1.8, 95%CI 1.1-2.7, p = 0.01). Respiratory (n = 41, 39%) and bloodstream infections (n = 38, 36%) predominated, with primarily Gram-negative pathogens. 606 (84.7%) patients received an antimicrobial, amounting to 742 days of therapy per 1000 patient-days (DOTs). In multivariable models, receipt of high-dose steroids (≥ 30 mg prednisolone or equivalent) or tocilizumab was significantly associated with increased antimicrobial consumption (+ 5.5 DOTs, 95%CI 3.4-7.7 days) but not secondary infection (HR 0.56, 95%CI 0.26-1.18).

CONCLUSIONS

Bacterial and fungal infections in severe COVID-19 were uncommon. Receipt of steroids or tocilizumab was independently associated with antimicrobial consumption despite its lack of association with secondary infection. These findings should galvanise efforts to promote antimicrobial stewardship in patients with COVID-19.

Ventilator-associated pneumonia in Polish intensive care unit dedicated to COVID-19 patients

BACKGROUND

Healthcare-Associated Infections (HAI) are most frequently associated with patients in the Intensive Care Unit (ICU). Coronavirus disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), led to ICU hospitalization for some patients.

METHODS

The study was conducted in 2020 and 2021 at a hospital in southern Poland. The Healthcare-Associated Infections Surveillance Network (HAI-Net) of the European Centre for Disease Prevention and Control (ECDC) was used for HAI diagnosis. The aim of this case-control study was to retrospectively assess the epidemiology of HAIs in ICU patients, distinguishing between COVID-19 and non-COVID-19 cases.

RESULTS

The study included 416 ICU patients: 125 (30%) with COVID-19 and 291 (70%) without COVID-19, p < 0.05. The mortality rate was 80 (64%) for COVID-19 patients and 45 (16%) for non-COVID-19 patients, p < 0.001. Ventilator-Associated Pneumonia (VAP) occurred in 40 cases, with an incidence rate density of 6.3/1000 patient-days (pds): 14.1/1000 pds for COVID-19 patients vs. 3.6/1000 pds for non-COVID-19 patients. Odds Ratio (OR) was 2.297, p < 0.01. Acinetobacter baumannii was the most often isolated microorganism in VAP, with 25 cases (incidence rate 8.5%): 16 (18.2%) in COVID-19 patients vs. 9 (4.4%) in non-COVID-19 patients. OR was 4.814 (1.084-4.806), p < 0.001.

CONCLUSIONS

Patients treated in the ICU for COVID-19 faced twice the risk of VAP compared to non-COVID-19 patients. The predominant microorganism in VAP cases was Acinetobacter baumannii.

Assessment of Medication Prescribing Pattern in COVID-19 Admitted Patients by Using WHO Prescribing Indicators at Eka Kotebe General Hospital, Addis Ababa, Ethiopia; Retrospective Cross-Sectional Study

Introduction

Drug therapy is a crucial component of health care and plays a vital role in preserving life. However, the irrational utilization of medications is a worldwide issue, particularly in developing nations.

Objective

To assess the prescription patterns of medications based on the World Health Organization's prescribing indicator among patients who were admitted with COVID-19 to Eka Kotebe General Hospital in Addis Ababa, Ethiopia, in June 2021.

Methods

A retrospective cross-sectional analysis was conducted to evaluate the prescription patterns of medications in patients admitted with COVID-19 at Eka Kotebe General Hospital from June 2021 to September 15, 2021. The data were extracted using card review formats and prescription assessment questionnaires, and a systematic random sampling procedure was employed to collect the data. Finally, the data were coded and analyzed using SPSS version 26 to meet the study's objectives. Descriptive statistics were employed to determine the frequency and prevalence, and the results were presented using tables and figures.

Results and Discussion

The average number of medications prescribed per encounter was 2.64, which is above the WHO standard. The percentage of encounters in which antibiotics and injections were prescribed was 80.20% and 99.2%, which exceeds the upper limit of WHO standard range (20-26.8%) and (13.4-24.1%), respectively. All medications were prescribed using generic names and were included in Eka Kotebe General Hospital's essential drug list, which is in line with WHO standards.

Conclusion

The degree of polypharmacy and the prescription practices for antibiotics and injections at Eka Kotebe General Hospital deviated from the World Health Organization's standards. As a result, there is a need to enhance medical education programs to rationalize the prescription of antibiotics and injection use.

A systematic review of the clinical characteristics of influenza-COVID-19 co-infection

COVID-19 has impacted populations across the globe and has been a major cause of morbidity and mortality. Influenza is another potentially deadly respiratory infection that affects people worldwide. While both of these infections pose major health threats, little is currently understood regarding the clinical aspects of influenza and COVID-19 co-infection. Our objective was to therefore provide a systematic review of the clinical characteristics, treatments, and outcomes for patients who are co-infected with influenza and COVID-19. Our review, which was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, involved searching for literature in seven different databases. Studies were eligible for inclusion if they included at least one co-infected patient, were available in English, and described clinical characteristics for the patients. Data were pooled after extraction. Study quality was assessed using the Joanna Brigg's Institute Checklists. Searches produced a total of 5096 studies, and of those, 64 were eligible for inclusion. A total of 6086 co-infected patients were included, 54.1% of whom were male; the mean age of patients was 55.9 years (SD = 12.3). 73.6% of cases were of influenza A and 25.1% were influenza B. 15.7% of co-infected patients had a poor outcome (death/deterioration). The most common symptoms were fever, cough, and dyspnea, with the most frequent complications being pneumonia, linear atelectasis, and acute respiratory distress syndrome. Oseltamivir, supplemental oxygen, arbidol, and vasopressors were the most common treatments provided to patients. Having comorbidities, and being unvaccinated for influenza, were shown to be important risk factors. Co-infected patients show symptoms that are similar to those who are infected with COVID-19 or influenza only. However, co-infected patients have been shown to be at an elevated risk for poor outcomes compared to mono-infected COVID-19 patients. Screening for influenza in high-risk COVID-19 patients is recommended. There is also a clear need to improve patient outcomes with more effective treatment regimens, better testing, and higher rates of vaccination.

Activities of a broad-spectrum antimicrobial peptide analogue SAMP-A4-C8 and its combat against pneumonia in Staphylococcus aureus-infected mice

Antimicrobial peptides and their analogues have become substitutes for antibiotics in recent years. The antimicrobial peptide analogue SAMP-A4-C8 (n-octanoic-VRLLRRRI) with high antimicrobial activity was found in our lab. We speculate that it may kill pathogens by some lethal mechanism of action. In the present investigation, the microbicidal activities of SAMP-A4-C8 and its mechanism of action were investigated. The results demonstrated that SAMP-A4-C8 had lethal activities against Staphylococcus aureus and Candida albicans by cell disruption. Based on its microbicidal activities, we believe that it is worth further research for its potential as drug candidate. The results showed that SAMP-A4-C8, with low propensity to induce the resistance of S. aureus and C. albicans, could kill the persister cells of S. aureus and C. albicans, exhibited biofilm forming inhibition activity and preformed biofilm eradication ability against S. aureus and C. albicans, and displayed therapeutic potential on pneumonia in S. aureus-infected mice by reducing lung inflammation. The present study provided a promising drug candidate in the war against multidrug resistance.

Eco-Friendly Cellulose-Based Nonionic Antimicrobial Polymers with Excellent Biocompatibility, Nonleachability, and Polymer Miscibility

This study aims to prepare natural biomass-based nonionic antimicrobial polymers with excellent biocompatibility, nonleachability, antimicrobial activity, and polymer miscibility. Two new cellulose-based nonionic antimicrobial polymers (MIPA and MICA) containing many terminal indole groups were synthesized using a sustainable one-pot method. The structures and properties of the nonionic antimicrobial polymers were characterized using nuclear magnetic resonance hydrogen spectroscopy (1H NMR), infrared spectroscopy (FTIR), wide-angle X-ray diffractometry (XRD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), scanning electron microscopy (SEM), gel chromatography (GPC), and other analytical techniques. The results showed that microcrystalline cellulose (MCC) molecules combined with indole derivatives through an esterification reaction to produce MICA and MIPA. The crystallinity of the prepared MICA and MIPA molecules decreased after MCC modification; their morphological structure changed from short fibrous to granular and showed better thermal stability and solubility. The paper diffusion method showed that both nonionic polymers had good bactericidal effects against the two common pathogenic bacteria Escherichia coli (E. coli, inhibition zone diameters >22 mm) and Staphylococcus aureus (S. aureus, inhibition zone diameters >38 mm). Moreover, MICA and MIPA showed good miscibility with biodegradable poly(vinyl alcohol) (PVA), and the miscible cellulose-based composite films (PVA-MICA and PVA-MIPA) showed good phase compatibility, light transmission, thermal stability (maximum thermal decomposition temperature >300 °C), biocompatibility, biological cell activity (no cytotoxicity), nonleachability, antimicrobial activity, and mechanical properties (maximum fracture elongation at >390%).

Evaluation of pulmonary abnormalities in recipients of hematopoietic cell transplants and cellular therapies

Hematopoietic cell transplant (HCT) and chimeric antigen receptor T-cell (CAR-T) therapy recipients are susceptible to multiple pulmonary complications that are caused by infectious and noninfectious processes. Numerous variables can be associated with specific pulmonary diseases including time from transplantation, presence of graft versus host disease (GVHD), underlying disease, and prolonged neutropenia and lymphocytopenia. Most pulmonary complications are infectious in origin, with bacterial pneumonia remaining the most common pulmonary infection, particularly before neutrophil engraftment. Invasive fungal infections continue to affect this patient population even when antifungal prophylaxis is used. Noninfectious pulmonary complications include a wide differential of pathologies in this population, and as clinical presentations of these various pulmonary disorders often overlap, clinicians frequently will use a multidisciplinary approach in diagnosing these abnormalities. Radiography, particularly with chest computed tomography (CT) imaging, is an essential tool in identifying pulmonary pathology and potential sources. While standard microbiological cultures of respiratory specimens are still utilized, their role is limited by low sensitivity and diagnostic yield. The likelihood of obtaining a diagnosis can be improved by using other microbiological assays, including fungal antigen tests and molecular diagnostic methods, particularly if specimens are collected via bronchoscopy. This review will highlight the more common causes of pulmonary diseases encountered after HCT and CAR-T and will examine the different methods in their diagnosis.

Use of RT-PCR in conjunction with a respiratory pathogen assay to concurrently determine the prevalence of bacteria and SARS-CoV-2 from the nasopharynx of outpatients

Introduction

COVID-19 has emerged as a highly contagious and debilitating disease caused by the SARS-CoV-2 virus and has claimed the lives of over 7.7 million people worldwide. Bacterial co-infections are one of many co-morbidities that have been suggested to impact the outcome of COVID-19 in patients. The goals of this study are to elucidate the presence of bacteria in the nasopharynx of SARS-CoV-2 positive and negative patients and to describe demographic categories that may be associated with the detection of these organisms during one of the initial waves of the COVID-19 pandemic.

Methods

To this end, we investigated SARS-CoV-2 and bacterial co-detection from outpatient RT-PCR testing in Texas.

Results

The results indicate that Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae were the most frequently detected bacteria in both SARS-CoV-2 positive and SARS-CoV-2 negative patients and that these bacteria were present in these two patient populations at similar proportions. We also detected Staphylococcus aureus in a significantly larger proportion of males relative to females and people under 65 years of age relative to those 65 and over. Finally, we observed that SARS-CoV-2 was more commonly detected in Hispanics compared to non-Hispanics; however, low disclosure rates make volunteer bias a concern when interpreting the effects of demographic variables.

Discussion

This study describes the bacteria present in the nasopharynx of SARS-CoV-2 positive and negative patients, highlights associations between patient demographics and SARS-CoV-2 as well as bacterial co-detection. In addition, this study highlights RT-PCR based molecular testing as a tool to detect bacteria simultaneously when SARS-CoV-2 tests are performed.

Coinfection of SARS-CoV-2 with other respiratory pathogens in outpatients from Ecuador

Worldwide, the COVID-19 pandemic caused by SARS-CoV-2 has enormously impacted healthcare systems, especially in low and middle-income countries. Coinfections with respiratory pathogens in COVID-19 patients may contribute to worse outcomes. This study identified the presence of 12 viral coinfections and pneumococcal carriers among individuals with SARS-CoV-2 infection in outpatient and community settings in Ecuador. From January 2020 to November 2021, 215 nasopharyngeal and nasal swabs were taken from individuals who reported symptoms of COVID-19 or had known exposure to someone with confirmed or suspected COVID-19. One hundred fifty-eight tested positive for SARS-CoV-2 by RT-qPCR and coinfections were detected in 12% (19/158) of SARS-CoV-2-positive patients; the most frequent coinfection was with influenza A virus at 4.4% (7/158; 95% CI: 1.2-7.6), followed by respiratory syncytial virus with 3.1% (5/158; 95% CI: 0.4-5.8), and finally rhinovirus and human coronavirus NL63 with 1.2% (2/158). Pneumococcal carriage was detected in 3.7% (6/158; 95% CI: 0.76-6.64) of SARS-CoV-2 cases. Influenza B, adenovirus, human metapneumovirus (HMPV), parainfluenza virus types 1, 2, and 3, and human coronavirus HKU1 were undetected. To our knowledge, this is the first study of coinfection of SARS-CoV-2 and respiratory pathogens performed on outpatients in Latin America. The high proportion of outpatients with viral coinfections reported in our cohort allows us to suggest that testing for SARS-CoV-2 and other common respiratory pathogens should be carried out to ensure accurate diagnoses, prompt patient treatment, and appropriate isolation.

A Review of Antibiotic Efficacy in COVID-19 Control

Severe acute respiratory disease is associated with chronic secondary infections that exacerbate symptoms and mortality. So far, many drugs have been introduced to treat this disease, none of which effectively control the coronavirus. Numerous studies have shown that mitochondria, as the center of cell biogenesis, are vulnerable to drugs, especially antibiotics. Antibiotics were widely prescribed during the early phase of the pandemic. We performed a literature review to assess the reasons, evidence, and practices on the use of antibiotics in coronavirus disease 2019 (COVID-19) in- and outpatients. The current research found widespread usage of antibiotics, mostly in an empirical context, among COVID-19 hospitalized patients. The effectiveness of this approach has not been established. Given the high death rate linked with secondary infections in COVID-19 patients and the developing antimicrobial resistance, further study is urgently needed to identify the most appropriate rationale for antibiotic therapy in these patients.

Overprescription of antibiotics for treating hospitalized COVID-19 patients: A systematic review & meta-analysis

Background

Empirical use of antibiotics was reported throughout the coronavirus disease of 2019 (COVID-19) pandemic; however, evidence of bacterial coinfection or secondary bacterial infection among COVID-19 patients was sparse. Antibiotic overprescription for COVID-19 patients without confirmed bacterial coinfection can increase antimicrobial resistance (AMR). The objective of this study is to assess the appropriateness of antibiotic use during COVID-19 by summarizing the frequency of antibiotic use among hospitalized COVID-19 and the frequency of antibiotic use in patients with COVID-19.

Methods

A systematic search was conducted of the Embase, Medline, Web of Science, and Cochrane Library databases by generating search terms using the concepts of "COVID-19," "Bacterial Coinfection," "Secondary bacterial infection," and "Antimicrobial resistance" to identify studies reporting antibiotic prescription for hospitalized COVID-19 patients with or without bacterial coinfection. We excluded studies on outpatients, studies informed infection due to mechanical ventilation, and randomized controlled trials. The pooled estimate of the percentage of the total and confirmed appropriate antibiotic prescriptions provided to hospitalized COVID-19 patients was generated using a random effect meta-analysis with inverse variance weighting. The study protocol registration DOI is osf.io/d3fpm.

Results

Of 157,623 participants from 29 studies (11 countries, 45 % women) included in our review, antibiotics were prescribed to 67 % of participants (CI 64 %-71 %, P < 0·001), of which 80 % (CI 76 %-83 %, P < 0·001) of prescriptions were for COVID-19 patients without confirmed bacterial coinfections. Antibiotic overprescription varied during different periods of the pandemic and between High-Income and Upper and Lower Middle-Income Countries. We found heterogeneity among the studies (I2 = 100 %). The risk of bias analysis showed that 100 % of the included studies had the proper sample framing, and we are at low risk of bias due to sampling.

Discussion

We find greater than expected use of antibiotics to treat hospitalized COVID-19 patients without bacterial coinfections, which may contribute to AMR globally. Concrete guidelines for using antibiotics to treat COVID-19 patients, strict monitoring, and administering Antimicrobial Stewardship are needed to prevent overprescription.

A brief overview of SARS-CoV-2 infection and its management strategies: a recent update

The COVID-19 pandemic has become a global health crisis, inflicting substantial morbidity and mortality worldwide. A diverse range of symptoms, including fever, cough, dyspnea, and fatigue, characterizes COVID-19. A cytokine surge can exacerbate the disease's severity. This phenomenon involves an increased immune response, marked by the excessive release of inflammatory cytokines like IL-6, IL-8, TNF-α, and IFNγ, leading to tissue damage and organ dysfunction. Efforts to reduce the cytokine surge and its associated complications have garnered significant attention. Standardized management protocols have incorporated treatment strategies, with corticosteroids, chloroquine, and intravenous immunoglobulin taking the forefront. The recent therapeutic intervention has also assisted in novel strategies like repurposing existing medications and the utilization of in vitro drug screening methods to choose effective molecules against viral infections. Beyond acute management, the significance of comprehensive post-COVID-19 management strategies, like remedial measures including nutritional guidance, multidisciplinary care, and follow-up, has become increasingly evident. As the understanding of COVID-19 pathogenesis deepens, it is becoming increasingly evident that a tailored approach to therapy is imperative. This review focuses on effective treatment measures aimed at mitigating COVID-19 severity and highlights the significance of comprehensive COVID-19 management strategies that show promise in the battle against COVID-19.

Identification and targeting of microbial putrescine acetylation in bloodstream infections

The growth of antimicrobial resistance (AMR) has highlighted an urgent need to identify bacterial pathogenic functions that may be targets for clinical intervention. Although severe bacterial infections profoundly alter host metabolism, prior studies have largely ignored alterations in microbial metabolism in this context. Performing metabolomics on patient and mouse plasma samples, we identify elevated levels of bacterially-derived N-acetylputrescine during gram-negative bloodstream infections (BSI), with higher levels associated with worse clinical outcomes. We discover that SpeG is the bacterial enzyme responsible for acetylating putrescine and show that blocking its activity reduces bacterial proliferation and slows pathogenesis. Reduction of SpeG activity enhances bacterial membrane permeability and results in increased intracellular accumulation of antibiotics, allowing us to overcome AMR of clinical isolates both in culture and in vivo. This study highlights how studying pathogen metabolism in the natural context of infection can reveal new therapeutic strategies for addressing challenging infections.

The impact of the COVID-19 pandemic on the treatment of common infections in primary care and the change to antibiotic prescribing in England

BACKGROUND

There is concern that the COVID-19 pandemic altered the management of common infections in primary care. This study aimed to evaluate infection-coded consultation rates and antibiotic use during the pandemic and how any change may have affected clinical outcomes.

METHODS

With the approval of NHS England, a retrospective cohort study using the OpenSAFELY platform analysed routinely collected electronic health data from GP practices in England between January 2019 and December 2021. Infection coded consultations and antibiotic prescriptions were used estimate multiple measures over calendar months, including age-sex adjusted prescribing rates, prescribing by infection and antibiotic type, infection consultation rates, coding quality and rate of same-day antibiotic prescribing for COVID-19 infections. Interrupted time series (ITS) estimated the effect of COVID-19 pandemic on infection-coded consultation rates. The impact of the pandemic on non- COVID-19 infection-related hospitalisations was also estimated.

RESULTS

Records from 24 million patients were included. The rate of infection-related consultations fell for all infections (mean reduction of 39% in 2020 compared to 2019 mean rate), except for UTI which remained stable. Modelling infection-related consultation rates highlighted this with an incidence rate ratio of 0.44 (95% CI 0.36-0.53) for incident consultations and 0.43 (95% CI 0.33-0.54) for prevalent consultations. Lower respiratory tract infections (LRTI) saw the largest reduction of 0.11 (95% CI 0.07-0.17). Antibiotic prescribing rates fell with a mean reduction of 118.4 items per 1000 patients in 2020, returning to pre-pandemic rates by summer 2021. Prescribing for LRTI decreased 20% and URTI increased 15.9%. Over 60% of antibiotics were issued without an associated same-day infection code, which increased during the pandemic. Infection-related hospitalisations reduced (by 62%), with the largest reduction observed for pneumonia infections (72.9%). Same-day antibiotic prescribing for COVID-19 infection increased from 1 to 10.5% between the second and third national lockdowns and rose again during 2022.

CONCLUSIONS

Changes to consultations and hospital admissions may be driven by reduced transmission of non-COVID-19 infections due to reduced social mixing and lockdowns. Inconsistencies in coding practice emphasises the need for improvement to inform new antibiotic stewardship policies and prevent resistance to novel infections.

Leveraging the COVID-19 pandemic as a natural experiment to assess changes in antibiotic use and antibiotic-resistant E. coli carriage in semi-rural Ecuador

The coronavirus 2019 (COVID-19) pandemic has had significant impacts on health systems, population dynamics, public health awareness, and antibiotic stewardship, which could affect antibiotic resistant bacteria (ARB) emergence and transmission. In this study, we aimed to compare knowledge, attitudes, and practices (KAP) of antibiotic use and ARB carriage in Ecuadorian communities before versus after the COVID-19 pandemic began. We leveraged data collected for a repeated measures observational study of third-generation cephalosporin-resistant E. coli (3GCR-EC) carriage among children in semi-rural communities in Quito, Ecuador between July 2018 and September 2021. We included 241 households that participated in surveys and child stool sample collection in 2019, before the pandemic, and in 2021, after the pandemic began. We estimated adjusted Prevalence Ratios (aPR) and 95% Confidence Intervals (CI) using logistic and Poisson regression models. Child antibiotic use in the last 3 months declined from 17% pre-pandemic to 5% in 2021 (aPR: 0.30; 95% CI 0.15, 0.61) and 3GCR-EC carriage among children declined from 40 to 23% (aPR: 0.48; 95% CI 0.32, 0.73). Multi-drug resistance declined from 86 to 70% (aPR: 0.32; 95% CI 0.13; 0.79), the average number of antibiotic resistance genes (ARGs) per 3GCR-EC isolate declined from 9.9 to 7.8 (aPR of 0.79; 95% CI 0.65, 0.96), and the diversity of ARGs was lower in 2021. In the context of Ecuador, where COVID-19 prevention and control measures were strictly enforced after its major cities experienced some of the world's the highest mortality rates from SARS-CoV-2 infections, antibiotic use and ARB carriage declined in semi-rural communities of Quito from 2019 to 2021.

The impact of the COVID-19 pandemic on antibiotic consumption and prevalence of pathogens in primary and secondary healthcare settings in Northern Ireland

AIM

To evaluate the impact of the COVID-19 pandemic on the patterns of antimicrobial use and the incidence of pathogens in primary and secondary healthcare settings in Northern Ireland.

METHODS

Data were collected on antibiotic use and Gram-positive and Gram-negative pathogens from primary and secondary healthcare settings in Northern Ireland for the period before (January 2015-March 2020) and during (April 2020-December 2021) the pandemic. Time series intervention analysis methods were utilized.

RESULTS

In the hospital setting, the mean total hospital antibiotic consumption during the pandemic was 1864.5 defined daily doses (DDDs) per 1000 occupied-bed days (OBD), showing no significant change from pre-pandemic (P = .7365). During the pandemic, the use of second-generation cephalosporins, third-generation cephalosporins, co-amoxiclav and levofloxacin increased, there was a decrease in the percentage use of the hospital Access group (P = .0083) and an increase in the percentage use of Watch group (P = .0040), and the number of hospital Klebsiella oxytoca and methicillin-susceptible Staphylococcus aureus cases increased. In primary care, the mean total antibiotic consumption during the COVID-19 pandemic was 20.53 DDDs per 1000 inhabitants per day (DID), compared to 25.56 DID before the COVID-19 pandemic (P = .0071). During the pandemic, there was a decrease in the use of several antibiotic classes, an increase in the percentage use of the Reserve group (P = .0032) and an increase in the number of community-onset Pseudomonas aeruginosa cases.

CONCLUSION

This study provides details of both changes in antibiotic consumption and the prevalence of infections in hospitals and primary care before and during the COVID-19 pandemic that emphasize the importance of antimicrobial stewardship in pandemic situations.

Acute invasive fungal rhinosinusitis (AIFRS) - A histopathological analysis of expanding spectrum of fungal infections in backdrop of COVID-19 pandemic

Context

Acute invasive fungal rhinosinusitis (AIFRS) is an aggressive infection affecting immunocompromised patients and carries a high morbidity and mortality. It is commonly seen in immunocompromised patients, mainly in uncontrolled diabetes, malignancy, acquired immunodeficiency syndrome, and so on. However, there has been an exponential increase in the incidence of AIFRS in relation to recent coronavirus disease 2019 (COVID-19) infection.

Aims

We present this study to assess histomorphological features of fungal infections in the background of COVID-19 era.

Materials and Methods

The study includes interpretation of 34 biopsies of suspected AIFRS in post COVID-19 patients. The demographic details like patients age, sex, diabetic status, COVID-19 status, and history of steroid intake were collected. All specimens were stained with hematoxylin and eosin and PAS stain. Detailed microscopic examination including the presence of fungal hyphae in the tissue, characterization of inflammatory response, presence of tissue invasion, angioinvasion, and necrosis was noted for each case.

Results

Thirty-four biopsy specimens from various sites - nasal cavity, maxillary sinus, ethmoid sinus, and so on - were studied. The mean age of the patients with AIFRS was 52.68 years. The dominant fungi were Mucorales in 31 (91.3%), Aspergillus and Mucorales in 1 (2.9%), a combination of Mucorales and Candida identified in 1 (2.9%) case, and Candida alone in 1 case (2.9%). Bony invasion and perineural invasion were observed in 5 cases (14.7%) and 1 (2.9%) case, respectively.

Conclusion

Histopathological examination plays an essential role in the diagnosis and appropriate management of the patients. Histopathological features including characterization of fungi, angioinvasion, and bone invasion may provide information on rare dreaded infections in post-COVID-19 patients for possible prognostic characteristics on histology.

Use of antibiotics in hospitalized patients with COVID-19: evolving concepts in a highly dynamic antimicrobial stewardship scenario

INTRODUCTION

Excessive use of antibiotics has been frequently reported in hospitalized patients with COVID-19 worldwide, compared to the actual number of bacterial co-infections or super-infections.

AREAS COVERED

In this perspective, we discuss the current literature on the use of antibiotics and antimicrobial stewardship interventions in hospitalized patients with COVID-19. A search was conducted in PubMed up to March 2023.

EXPERT OPINION

The COVID-19 pandemic has witnessed an excessive use of antibiotics in hospitals worldwide, especially before the advent of COVID-19 vaccination, although according to the most recent data there is still an important disproportion between the prevalence of antibiotic use and that of proven bacterial coinfection or superinfections. An important reduction in the prevalence of antibiotic use in COVID-19 patients reported in the literature, from 70-100% to 50-60%, has been observed after successful vaccination campaigns, likely related to the reduced median disease severity of hospitalized COVID-19 patients and some successful interventions of antimicrobial and diagnostic stewardship. However, the disproportion between antibiotic use and the prevalence of bacterial infections (4-6%) is still uncomfortable from an antimicrobial stewardship perspective and requires further attention.

Procalcitonin-Guided Antibiotic Prescription in Patients With COVID-19: A Multicenter Observational Cohort Study

BACKGROUND

Despite the low rate of bacterial coinfection, antibiotics are very commonly prescribed in hospitalized patients with COVID-19.

RESEARCH QUESTION

Does the use of a procalcitonin (PCT)-guided antibiotic protocol safely reduce the use of antibiotics in patients with a COVID-19 infection?

STUDY DESIGN AND METHODS

In this multicenter cohort, three groups of patients with COVID-19 were compared in terms of antibiotic consumption, namely one group treated based on a PCT-algorithm in one hospital (n = 216) and two control groups, consisting of patients from the same hospital (n = 57) and of patients from three similar hospitals (n = 486) without PCT measurements during the same period. The primary end point was antibiotic prescription in the first week of admission.

RESULTS

Antibiotic prescription during the first 7 days was 26.8% in the PCT group, 43.9% in the non-PCT group in the same hospital, and 44.7% in the non-PCT group in other hospitals. Patients in the PCT group had lower odds of receiving antibiotics in the first 7 days of admission (OR, 0.33; 95% CI, 0.16-0.66 compared with the same hospital; OR, 0.42; 95% CI, 0.28-0.62 compared with the other hospitals). The proportion of patients receiving antibiotic prescription during the total admission was 35.2%, 43.9%, and 54.5%, respectively. The PCT group had lower odds of receiving antibiotics during the total admission only when compared with the other hospitals (OR, 0.23; 95% CI, 0.08-0.63). There were no significant differences in other secondary end points, except for readmission in the PCT group vs the other hospitals group.

INTERPRETATION

PCT-guided antibiotic prescription reduces antibiotic prescription rates in hospitalized patients with COVID-19, without major safety concerns.

Coinfection and superinfection in ICU critically ill patients with severe COVID-19 pneumonia and influenza pneumonia: are the pictures different?

Background

Similar to influenza, coinfections and superinfections are common and might result in poor prognosis. Our study aimed to compare the characteristics and risks of coinfections and superinfections in severe COVID-19 and influenza virus pneumonia.

Methods

The data of patients with COVID-19 and influenza admitted to the intensive care unit (ICU) were retrospectively analyzed. The primary outcome was to describe the prevalence and pathogenic distribution of coinfections/ICU-acquired superinfections in the study population. The secondary outcome was to evaluate the independent risk factors for coinfections/ICU-acquired superinfections at ICU admission. Multivariate analysis of survivors and non-survivors was performed to investigate whether coinfections/ICU-acquired superinfections was an independent prognostic factor.

Results

In the COVID-19 (n = 123) and influenza (n = 145) cohorts, the incidence of coinfections/ICU-acquired superinfections was 33.3%/43.9 and 35.2%/52.4%, respectively. The most common bacteria identified in coinfection cases were Enterococcus faecium, Pseudomonas aeruginosa, and Acinetobacter baumannii (COVID-19 cohort) and A. baumannii, P. aeruginosa, and Klebsiella pneumoniae (influenza cohort). A significant higher proportion of coinfection events was sustained by Aspergillus spp. [(22/123, 17.9% in COVID-19) and (18/145, 12.4% in influenza)]. The COVID-19 group had more cases of ICU-acquired A. baumannii, Corynebacterium striatum and K. pneumoniae. A. baumannii, P. aeruginosa, and K. pneumoniae were the three most prevalent pathogens in the influenza cases with ICU-acquired superinfections. Patients with APACHE II ≥18, CD8+ T cells ≤90/μL, and 50 < age ≤ 70 years were more susceptible to coinfections; while those with CD8+ T cells ≤90/μL, CRP ≥120 mg/L, IL-8 ≥ 20 pg./mL, blood glucose ≥10 mmol/L, hypertension, and smoking might had a higher risk of ICU-acquired superinfections in the COVID-19 group. ICU-acquired superinfection, corticosteroid administration for COVID-19 treatment before ICU admission, and SOFA score ≥ 7 were independent prognostic factors in patients with COVID-19.

Conclusion

Patients with COVID-19 or influenza had a high incidence of coinfections and ICU-acquired superinfections. The represent agents of coinfection in ICU patients were different from those in the general ward. These high-risk patients should be closely monitored and empirically treated with effective antibiotics according to the pathogen.

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.