Incidence of co-infections and superinfections in hospitalized patients with COVID-19: a retrospective cohort study

Disseminated histoplasmosis in an immunocompetent patient with COVID-19 pneumonia

Disseminated histoplasmosis is usually associated with immunosuppressive conditions like AIDS. People with respiratory distress syndrome secondary to SARS-CoV-2 pneumonia are vulnerable to bacterial infections. Additionally, coinfection with fungal pathogens should be considered as a differential diagnosis even in immunocompetent patients who remain on mechanical ventilation secondary to COVID-19. The case presents a 61-year-old immunocompetent man, admitted to the medical ward due to COVID-19 pneumonia. Despite appropriate therapy, the patient required transfer to the intensive care unit for invasive mechanical ventilation. He remained critically ill with worsening respiratory failure. Two weeks later, coinfection by disseminated histoplasmosis was detected. After immediate treatment with amphotericin B and itraconazole, the patient tolerated weaning from mechanical ventilation until extubation. Awareness of this possible fungal coinfection in immunocompetent patients is essential to reduce delays in diagnosis and treatment, and prevent severe illness and death.

Plasma cell-free RNA characteristics in COVID-19 patients

The pathogenesis of COVID-19 is still elusive, which impedes disease progression prediction, differential diagnosis, and targeted therapy. Plasma cell-free RNAs (cfRNAs) carry unique information from human tissue and thus could point to resourceful solutions for pathogenesis and host-pathogen interactions. Here, we performed a comparative analysis of cfRNA profiles between COVID-19 patients and healthy donors using serial plasma. Analyses of the cfRNA landscape, potential gene regulatory mechanisms, dynamic changes in tRNA pools upon infection, and microbial communities were performed. A total of 380 cfRNA molecules were up-regulated in all COVID-19 patients, of which seven could serve as potential biomarkers (AUC > 0.85) with great sensitivity and specificity. Antiviral (NFKB1A, IFITM3, and IFI27) and neutrophil activation (S100A8, CD68, and CD63)–related genes exhibited decreased expression levels during treatment in COVID-19 patients, which is in accordance with the dynamically enhanced inflammatory response in COVID-19 patients. Noncoding RNAs, including some microRNAs (let 7 family) and long noncoding RNAs (GJA9-MYCBP) targeting interleukin (IL6/IL6R), were differentially expressed between COVID-19 patients and healthy donors, which accounts for the potential core mechanism of cytokine storm syndromes; the tRNA pools change significantly between the COVID-19 and healthy group, leading to the accumulation of SARS-CoV-2 biased codons, which facilitate SARS-CoV-2 replication. Finally, several pneumonia-related microorganisms were detected in the plasma of COVID-19 patients, raising the possibility of simultaneously monitoring immune response regulation and microbial communities using cfRNA analysis. This study fills the knowledge gap in the plasma cfRNA landscape of COVID-19 patients and offers insight into the potential mechanisms of cfRNAs to explain COVID-19 pathogenesis.

Enhanced endocytosis elevated virulence and severity of SARS-CoV-2 due to hyperglycemia in type 2 diabetic patients

Diabetes mellitus is a metabolic disease that causes hyperglycemia. In COVID-19 patients the severity of the disease depends on myriad factors but diabetes mellitus is the most important comorbidity. The current review was conducted to investigate the virulence of SARS-CoV-2 and disease severity of COVID-19 in type 2 diabetes mellitus patients and relevant treatment. The literature published in PubMed, Scopus, Web of Science, and Google Scholar was reviewed up to September 2021. The keywords including SARS-CoV-2, type 2 diabetes mellitus in COVID-19, hyperglycemia in COVID-19, opportunistic infections in type 2 diabetes mellitus and COVID-19 were used in different combinations. Hyperglycemic individuals over-express ACE-2 receptors in the lungs thus increasing the SARS-CoV-2 susceptibility and replication. Although dipeptidyl peptidase-4 plays an important role in glucose homeostasis, additionally it also stimulates the production of proinflammatory cytokines such as IL-6 and TNF-α creating a cytokine storm. Cytokine storm might be responsible for respiratory insufficiency in severe COVID-19 patients. Type 2 diabetes mellitus is associated with immunosuppression and the patients are prone to get many opportunistic infections. Type 2 diabetes mellitus patients with severe COVID-19 have lymphopenia. Moreover, in type 2 diabetes mellitus patients the neutrophils exhibit decreased chemotaxis, hydrogen peroxide production, and phagocytosis. Reduction in lymphocyte count and defective neutrophil capacity renders them with COVID-19 susceptible to opportunistic bacterial and fungal infections increasing the mortality rate. The opportunistic bacterial infections in COVID-19 patients were due to Staphylococcus aureus, Streptococcus pneumonia, and coagulase-negative Staphylococci, E. coli, Pseudomonas aeruginosa, and Klebsiella sp. In COVID-19 patients with type 2 diabetes mellitus, mucormycosis was found to be the most common fungal infection with a higher predilection to males. Hyperglycemia in COVID-19 patients with type 2 diabetes mellitus enhances the SARS-CoV-2 replication with an adverse outcome. A strong correlation exists between the poor prognosis of COVID-19 and type 2 diabetes mellitus. Proper glycemic control in COVID-19 patients with diabetes mellitus might lessen the severity of the disease.

Pathogenesis of Respiratory Viral and Fungal Coinfections

Individuals suffering from severe viral respiratory tract infections have recently emerged as "at risk" groups for developing invasive fungal infections. Influenza virus is one of the most common causes of acute lower respiratory tract infections worldwide. Fungal infections complicating influenza pneumonia are associated with increased disease severity and mortality, with invasive pulmonary aspergillosis being the most common manifestation. Strikingly, similar observations have been made during the current coronavirus disease 2019 (COVID-19) pandemic. The copathogenesis of respiratory viral and fungal coinfections is complex and involves a dynamic interplay between the host immune defenses and the virulence of the microbes involved that often results in failure to return to homeostasis. In this review, we discuss the main mechanisms underlying susceptibility to invasive fungal disease following respiratory viral infections. A comprehensive understanding of these interactions will aid the development of therapeutic modalities against newly identified targets to prevent and treat these emerging coinfections.

Mucociliary Transport Deficiency and Disease Progression in Syrian Hamsters with SARS-CoV-2 Infection

Substantial clinical evidence supports the notion that ciliary function in the airways plays an important role in COVID-19 pathogenesis. Although ciliary damage has been observed in both in vitro and in vivo models, consequent impaired mucociliary transport (MCT) remains unknown for the intact MCT apparatus from an in vivo model of disease. Using golden Syrian hamsters, a common animal model that recapitulates human COVID-19, we quantitatively followed the time course of physiological, virological, and pathological changes upon SARS-CoV-2 infection, as well as the deficiency of the MCT apparatus using micro-optical coherence tomography, a novel method to visualize and simultaneously quantitate multiple aspects of the functional microanatomy of intact airways. Corresponding to progressive weight loss up to 7 days post-infection (dpi), viral detection and histopathological analysis in both the trachea and lung revealed steadily descending infection from the upper airways, as the main target of viral invasion, to lower airways and parenchymal lung, which are likely injured through indirect mechanisms. SARS-CoV-2 infection caused a 67% decrease in MCT rate as early as 2 dpi, largely due to diminished motile ciliation coverage, but not airway surface liquid depth, periciliary liquid depth, or cilia beat frequency of residual motile cilia. Further analysis indicated that the fewer motile cilia combined with abnormal ciliary motion of residual cilia contributed to the delayed MCT. The time course of physiological, virological, and pathological progression suggest that functional deficits of the MCT apparatus predispose to COVID-19 pathogenesis by extending viral retention and may be a risk factor for secondary infection. As a consequence, therapies directed towards the MCT apparatus deserve further investigation as a treatment modality.

COVID-19 vaccine prioritization based on district classification in Yogyakarta Province, Indonesia

Due to limited availability, Indonesia's coronavirus disease 2019 (COVID-19) vaccination will be done in 4 stages until herd immunity has been reached. Yogyakarta, an education and tourist destination, needs to get a specific, spatial estimation of the exact need for COVID-19 vaccination without delay. This study sheds light on identifying which districts should be prioritized at each vaccination phase. Secondary data collected from provincial, and county-level statistical agencies were quantitatively calculated by the Z-Score method. The results indicate that the first phase of vaccination should prioritize Pengasih and Sentolo districts in Kulon Progo Regency, which have a large number of health workers; the districts of Depok, Banguntapan, Piyungan, Sewon, Wonosari, Gamping, Mlati and Ngaglik should be done in the second phase based on the fact that these districts have many public service officials as well as elderly people; Umbulharjo and Depok districts will be approached in the third phase since they have more vulnerable groups and facilities that may promote COVID- 19 transmission during their daily activities; while the fourth phase should focus on the districts of Banguntapan, Sewon, Kasihan, Gamping, Mlati, Depok, and Ngaglik due to the intensity of COVID-19 clusters discovered there. Overall, vaccination would be given the priority in the districts with the largest number of people in need, i.e., public service officers, elderly people and those likely to be exposed to the coronavirus causing COVID-19.

COVID-19 findings in chest computed tomography

OBJECTIVE

The aim of this study was to describe chest computed tomography image findings in patients with COVID-19.

METHODS

The chest computed tomography scans of 453 hospitalized patients with confirmed COVID-19 were collected at two tertiary care Brazilian hospitals. Demographics and clinical data were extracted from the electronic record medical system.

RESULTS

The main chest computed tomography findings were ground-glass opacities (92.5%), consolidation (79.2%), crazy-paving pattern (23.9%), parenchymal bands (50%), septal thickening (43.5%), and inverted halo sign (3.5%). Of the 453 hospitalized patients, 136 (30%) died. In this group, ground-glass opacities (94.1%), consolidation (89.7%), septal thickening (58.1%), crazy-paving pattern (52.2%), and parenchymal bands (39.7%) were the most common imaging findings.

CONCLUSIONS

In a dynamic disease with a broad clinical spectrum such as COVID-19, radiologists can cooperate in a better patient management. On wisely indicated chest computed tomography scans, the fast identification of poor prognosis findings could advise patient management through hospital care facilities and clinical team decisions.

The landscape of antibiotic usage among COVID-19 patients in the early phase of pandemic: a Malaysian national perspective

Background

During the early phase of the COVID-19 pandemic, antibiotic usage among COVID-19 patients was noted to be high in many countries. The objective of this study was to determine the prevalence of antibiotic usage and factors affecting antibiotic usage among COVID-19 patients during the early phase of the COVID-19 pandemic in Malaysia.

Methods

This was a cross-sectional study that involved reviewing medical records of COVID-19 Malaysian patients aged 12 and above who were diagnosed with COVID-19 and received treatment in 18 COVID-19 hospitals from February to April 2020. A minimum sample of 375 patients was required. A binary logistic regression analysis was performed to determine factors associated with antibiotic usage. Variables with p < 0.05 were considered statistically significant.

Results

A total of 4043 cases were included for analysis. The majority of the patients (87.6%) were non-smokers, male (65.0%), and had at least one comorbidity (37.0%). The median age was 35 years (IQR: 38). The prevalence of antibiotic usage was 17.1%, with 5.5% of them being prescribed with two or more types of antibiotics. The most frequent antibiotics prescribed were amoxicillin/clavulanic acid (37.8%), ceftriaxone (12.3%), piperacillin/tazobactam (13.3%), azithromycin (8.3%), and meropenem (7.0%). Male patients (adjusted OR 1.53), who had a comorbidity (adjusted OR 1.36), associated with more severe stage of COVID-19 (adjusted OR 6.50–37.06), out-of-normal range inflammatory blood parameters for neutrophils, lymphocytes, and C-reactive protein (adjusted OR 2.04–3.93), corticosteroid use (adjusted OR 3.05), and ICU/HDU admission (adjusted OR 2.73) had higher odds of antibiotic use.

Conclusions

The prevalence of antibiotic usage in the early phase of the COVID-19 pandemic was low, with amoxicillin/clavulanic acid as the most common antibiotic of choice. The study showed that clinicians rationalized antibiotic usage based on clinical assessment, supported by relevant laboratory parameters.

Fungal Infections Other Than Invasive Aspergillosis in COVID-19 Patients

Invasive fungal disease (IFD) associated with Coronavirus Disease 2019 (COVID-19) has focussed predominantly on invasive pulmonary aspergillosis. However, increasingly emergent are non-Aspergillus fungal infections including candidiasis, mucormycosis, pneumocystosis, cryptococcosis, and endemic mycoses. These infections are associated with poor outcomes, and their management is challenged by delayed diagnosis due to similarities of presentation to aspergillosis or to non-specific features in already critically ill patients. There has been a variability in the incidence of different IFDs often related to heterogeneity in patient populations, diagnostic protocols, and definitions used to classify IFD. Here, we summarise and address knowledge gaps related to the epidemiology, risks, diagnosis, and management of COVID-19-associated fungal infections other than aspergillosis.

Combination of mycological criteria: a better surrogate to identify COVID-19 associated pulmonary aspergillosis patients and evaluate prognosis?

Diagnosis of coronavirus disease 2019 (COVID-19)-associated pulmonary aspergillosis (CAPA) remains unclear especially in nonimmunocompromised patients. The aim of this study was to evaluate seven mycological criteria and their combination in a large homogenous cohort of patients. All successive patients (n = 176) hospitalized for COVID-19 requiring mechanical ventilation and who clinically worsened despite appropriate standard of care were included over a 1-year period. Direct examination, culture, Aspergillus quantitative PCR (Af-qPCR), and galactomannan testing were performed on all respiratory samples (n = 350). Serum galactomannan, β-d-glucan, and plasma Af-qPCR were also assessed. The criteria were analyzed alone or in combination in relation to mortality rate. Mortality was significantly different in patients with 0, ≤2, and ≥3 positive criteria (log rank test, P = 0.04) with death rate of 43.1, 58.1, and 76.4%, respectively. Direct examination, plasma qPCR, and serum galactomannan were associated with a 100% mortality rate. Bronchoalveolar lavage (BAL) galactomannan and positive respiratory sample culture were often found as isolated markers (28.1 and 34.1%) and poorly repeatable when a second sample was obtained. Aspergillus DNA was detected in 13.1% of samples (46 of 350) with significantly lower quantitative cycle (Cq) when associated with at least one other criterion (30.2 versus 35.8) (P < 0.001). A combination of markers and/or blood biomarkers and/or direct respiratory sample examination seems more likely to identify patients with CAPA. Af-qPCR may help identifying false-positive results of BAL galactomannan testing and culture on respiratory samples while quantifying fungal burden accurately.

Hospital acquired infections in COVID-19 patients in sub intensive care unit: analysis of two waves of admissions

BACKGROUND AND AIM

The pandemic caused by SARS-COV-2 has increased Semi-Intensive Care Unit (SICU) admission, causing an increase in healthcare-associated infection (HAI). Mostly HAI reveals the same risk factors, but fewer studies have analyzed the possibility of multiple coinfections in these patients. The study aimed was to identify patterns of co-presence of different species describing at the same time the association between such patterns and patient demographics and, finally, comparing the patterns between the two cohorts of COVID-19 patients admitted at Policlinico during the first wave and the second one).

METHODS

All the patients admitted to SICUs during two COVID-19 waves, from March to June 2020 months and from October to December 2020, were screened following the local infection control surveillance program; whoever manifested fever has undergone on microbiological culture to detect bacterial species. Statistical analysis was performed to observe the existence of microbiological patterns through DBSCAN method.

RESULTS

246 patients were investigated and 83 patients were considered in our study because they presented infection symptoms with a mean age of 67 years and 33.7% of female patients. During the first and second waves were found respectively 10 and 8 bacterial clusters with no difference regarding the most frequent species.

CONCLUSIONS

The results show the importance of an analysis which considers the risk factors for the possibility of co- and superinfection (such as age and gender) to structure a good prognostic tool to predict which patients will encounter severe coinfections during hospitalization.

Non-typhoidal Salmonella Bacteremia in COVID-19 with Recrudescence of Fever After Corticosteroid Discontinuation: A case report

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Secondary bacterial infections occur in COVID-19 patients treated with corticosteroid.

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Rebound phenomenon is observed after the cessation of steroid treatment.

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Non-typhoidal Salmonella bacteremia is associated with immunosuppressive conditions.

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Blood cultures distinguish between secondary infections and rebound phenomena.

It is challenging for clinicians to determine the cause of occurrence of fever in COVID-19 patients after corticosteroid discontinuation. Blood cultures help us distinguish between secondary infections and rebound phenomena. We report a case of non-typhoidal Salmonella bacteremia in a 34-year-old male COVID-19 patient who developed fever after discontinuing corticosteroids.

Coronavirus disease 2019 (COVID-19): Secondary bacterial infections and the impact on antimicrobial resistance during the COVID-19 pandemic

Secondary bacterial infections and bacterial coinfections are an important complication of coronavirus disease 2019 (COVID-19), leading to antibiotic overuse and increased rates of antimicrobial resistance (AMR) during the COVID-19 pandemic. In this literature review, we summarize the reported rates of secondary bacterial infections and bacterial coinfections in patients with COVID-19, the impact on patient outcomes, the antibiotic treatment approaches employed, and the resistance patterns observed. The reported data suggest that although the incidence of secondary bacterial infections or bacterial coinfections is relatively low, they are associated with worse outcomes such as prolonged hospitalization, intensive care unit admission, mechanical ventilator use, and increased mortality. Interestingly, antibiotic prescription rates are typically higher than secondary bacterial and bacterial coinfection rates, and reports of AMR are common. These findings highlight the need for an improved understanding of secondary bacterial and bacterial coinfection in patients with COVID-19, as well as improved treatment options, to mitigate inappropriate antibiotic prescribing and AMR.

Unresolved issues in the epidemiology and diagnosis of bacteremia: an opinion paper

Bacteremia is an important cause of morbidity and mortality worldwide and, despite the diagnostic and therapeutic advances of the last decades, the evidence supporting many diagnostic aspects of bacteremia is scarce. Information on the epidemiological evolution of this entity is limited and many methodological aspects of blood culture collection and analysis are under discussion. Furthermore, the recommendations of the main scientific societies on many of these aspects are variable and, in many cases, have not been updated recently. In this scenario, we have arranged a series of questions on different aspects of bacteremia and reviewed the literature trying to find proper answers for them. We offer our opinion on the topics where the evidence was weak. The topics covered include epidemiological aspects of bacteremia, indications for blood culture extraction, methods for obtaining and incubating samples, or ways of transmitting results from the microbiology laboratory. We do not intend to summarize the current clinical practice guidelines, nor will we deal with the therapeutic management of this entity. The aim of this paper is to review the current perspective on the diagnosis of bacteremia with a critical approach, to point out the gaps in the literature, to offer the opinion of a team dedicated to infectious diseases and clinical microbiology, and to identify some areas of knowledge on which future studies should focus.

Leveraging antimicrobial stewardship programs in response to the coronavirus disease 2019 (COVID-19) public health emergency

The coronavirus disease 2019 (COVID-19) pandemic has strained antimicrobial stewardship programs (ASPs) but offered new opportunities. This review summarizes the impact of the COVID-19 pandemic on ASPs, review the contributions ASPs have made in the pandemic response, and highlight the potential role of ASPs in future pandemics.

Respiratory indications for ECMO: focus on COVID-19

Extracorporeal membrane oxygenation (ECMO) is increasingly being used for patients with severe respiratory failure and has received particular attention during the coronavirus disease 2019 (COVID-19) pandemic. Evidence from two key randomized controlled trials, a subsequent post hoc Bayesian analysis, and meta-analyses support the interpretation of a benefit of ECMO in combination with ultra-lung-protective ventilation for select patients with very severe forms of acute respiratory distress syndrome (ARDS). During the pandemic, new evidence has emerged helping to better define the role of ECMO for patients with COVID-19. Results from large cohorts suggest outcomes during the first wave of the pandemic were similar to those in non-COVID-19 cohorts. As the pandemic continued, mortality of patients supported with ECMO has increased. However, the precise reasons for this observation are unclear. Known risk factors for mortality in COVID-19 and non-COVID-19 patients are higher patient age, concomitant extra-pulmonary organ failures or malignancies, prolonged mechanical ventilation before ECMO, less experienced treatment teams and lower ECMO caseloads in the treating center. ECMO is a high resource-dependent support option; therefore, it should be used judiciously, and its availability may need to be constrained when resources are scarce. More evidence from high-quality research is required to better define the role and limitations of ECMO in patients with severe COVID-19.

Worldwide prevalence of microbial agents' coinfection among COVID-19 patients: A comprehensive updated systematic review and meta-analysis

BACKGROUND

To provide information about pathogens' coinfection prevalence with SARS-CoV-2 could be a real help to save patients' lives. This study aims to evaluate the pathogens' coinfection prevalence among COVID-19 patients.

METHOD

In order to find all of the relevant articles, we used systematic search approach. Research-based databases including PubMed, Web of Science, Embase, and Scopus, without language restrictions, were searched to identify the relevant bacterial, fungal, and viral coinfections among COVID-19 cases from December 1, 2019, to August 23, 2021. In order to dig deeper, other scientific repositories such as Medrxiv were probed.

RESULTS

A total of 13,023 studies were found through systematic search. After thorough analysis, only 64 studies with 61,547 patients were included in the study. The most common causative agents of coinfection among COVID-19 patients were bacteria (pooled prevalence: 20.97%; 95% CI: 15.95-26.46; I2 : 99.9%) and less frequent were virus coinfections (pooled prevalence: 12.58%; 95% CI: 7.31-18.96; I2 : 98.7%). The pooled prevalence of fungal coinfections was also 12.60% (95% CI: 7.84-17.36; I2 : 98.3%). Meta-regression analysis showed that the age sample size and WHO geographic region did not influenced heterogeneity.

CONCLUSION

We identified a high prevalence of pathogenic microorganism coinfection among COVID-19 patients. Because of this rate of coinfection empirical use of antibacterial, antifungal, and antiviral treatment are advisable specifically at the early stage of COVID-19 infection. We also suggest running simultaneously diagnostic tests to identify other microbiological agents' coinfection with SARS-CoV-2.

Procalcitonin for antimicrobial stewardship among cancer patients admitted with COVID-19

Background

Procalcitonin (PCT) has been used to guide antibiotic therapy in bacterial infections. We aimed to determine the role of PCT in decreasing the duration of empiric antibiotic therapy among cancer patients admitted with COVID-19.

Methods

This retrospective study included cancer patients admitted to our institution for COVID-19 between March 1, 2020, and June 28, 2021, with a PCT test done within 72 hr after admission. Patients were divided into two groups: PCT <0.25 ng/ml and PCT ≥0.25 ng/ml. We assessed pertinent cultures, antibacterial use, and duration of empiric antibacterial therapy.

Results

The study included 530 patients (median age, 62 years [range, 13-91]). All the patients had ≥1 culture test within 7 days following admission. Patients with PCT <0.25 ng/ml were less likely to have a positive culture than were those with PCT ≥0.25 ng/ml (6% [20/358] vs. 17% [30/172]; p<0.0001). PCT <0.25 ng/ml had a high negative predictive value for bacteremia and 30 day mortality. Patients with PCT <0.25 ng/ml were less likely to receive intravenous (IV) antibiotics for >72 hr than were patients with PCT ≥0.25 ng/ml (45% [162/358] vs. 69% [119/172]; p<0.0001). Among patients with PCT <0.25 ng/ml and negative cultures, 30 day mortality was similar between those who received IV antibiotics for ≥72 hr and those who received IV antibiotics for shorter durations (2% [2/111] vs. 3% [5/176], p=0.71).

Conclusions

Among cancer patients with COVID-19, PCT level <0.25 ng/ml is associated with lower likelihood of bacterial co-infection and greater likelihood of a shorter antibiotic course. In patients with PCT level <0.25 ng/ml and negative cultures, an antibiotic course of >72 hr may not be necessary. PCT could be useful in enhancing antimicrobial stewardship in cancer patients with COVID-19.

Funding

This research was supported by the National Institutes of Health/National Cancer Institute under award number P30CA016672, which supports MD Anderson Cancer Center's Clinical Trials Office.

OUP accepted manuscript

Studies demonstrated the impact of the COVID-19 pandemic in the prevalence and susceptibility profiles of bacterial and fungal organisms. We analyzed 4821 invasive fungal isolates collected during 2018, 2019, and 2020 in 48 hospitals worldwide to evaluate the impact of this event in the occurrence and susceptibility rates of common fungal species. Isolates were tested using the CLSI broth microdilution method. While the percentage of total isolates that were C. glabrata (n = 710 isolates) or C. krusei (n = 112) slightly increased in 2020, the percentage for C. parapsilosis (n = 542), A. fumigatus (n = 416), and C. lusitaniae (n = 84) significantly decreased (P < .05). Fluconazole resistance in C. glabrata decreased from 5.8% in 2018–2019 to 2.0% in 2020, mainly due to fewer hospitals in the US having these isolates (5 vs. 1 hospital). Conversely, higher fluconazole-resistance rates were noted for C. parapsilosis (13.9 vs. 9.8%) and C. tropicalis (3.5 vs. 0.7%; P < .05) during 2020. Voriconazole resistance also increased for these species. Echinocandin resistance was unchanged among Candida spp. Voriconazole susceptibility rates in A. fumigatus were similar in these two periods (91.7% in 2018 and 2019 vs. 93.0% in 2020). Changes were also noticed in the organisms with smaller numbers of collected isolates. We observed variations in the occurrence of organisms submitted to a global surveillance and the susceptibility patterns for some organism-antifungal combinations. As the COVID-19 pandemic is still ongoing, the impact of this event must continue to be monitored to guide treatment of patients affected by bacterial and fungal infections.

Antibiotic prescriptions in the context of suspected bacterial respiratory tract superinfections in the COVID-19 era: a retrospective quantitative analysis of antibiotic consumption and identification of antibiotic prescription drivers

This study aims to quantify antibiotic consumption for suspected respiratory tract superinfections in COVID-19 patients, while investigating the associated drivers of antibiotic prescribing in light of the current signs of antibiotic overuse. Adult patients with a positive COVID-19 diagnosis admitted to a Belgian 721-bed university hospital were analyzed retrospectively (March 11th-May 4th, 2020), excluding short-term admissions (< 24 h). Antibiotic prescriptions were analyzed and quantified, using Defined Daily Doses (DDD) per admission and per 100 bed days. Possible drivers of antibiotic prescribing were identified by means of mixed effects logistic modelling analysis with backwards selection. Of all included admissions (n = 429), 39% (n = 171) were prescribed antibiotics for (presumed) respiratory tract superinfection (3.6 DDD/admission; 31.5 DDD/100 bed days). Consumption of beta-lactamase inhibitor-penicillin combinations was the highest (2.55 DDD/admission; 23.3 DDD/100 bed days). Four drivers were identified: fever on admission (OR 2.97; 95% CI 1.42-6.22), lower SpO₂/FiO₂ ratio on admission (OR 0.96; 95% CI 0.92-0.99), underlying pulmonary disease (OR 3.04; 95% CI 1.12-8.27) and longer hospital stay (OR 1.09; 95% CI 1.03-1.16). We present detailed quantitative antibiotic data for presumed respiratory tract superinfections in hospitalized COVID-19 patients. In addition to knowledge on antibiotic consumption, we hope antimicrobial stewardship programs will be able to use the drivers identified in this study to optimize their interventions in COVID-19 wards.

Intensive care therapy during the pandemic in 2020 and beyond: Mnemonics can help

In a busy working environment, with a shortage of healthcare workers and increased workloads since the beginning of the COVID-19 pandemic, the implementation of an easy-to-remember mnemonic can significantly help anesthesiologists and clinicians in conducting intensive therapy. One of the first mnemonics in critical care therapy was implemented by Jean-Louis Vincent in 2005. FAST HUG concept reminds clinicians of crucial moments in therapy - nutritional support(F-feeding), analgesia and sedation (A - analgesia, S - sedation), thrombosis prophylaxis (T - thrombolytic prophylaxis), head elevation in bed (H - head of the elevated bed), antiulcer therapy (U - stress ulcer prevention) and glycemic control (G - glucose control). This acronym has been modified and tested in several studies over the years for the treatment of different patient types. This concept is widely utilized in intensive care units, it is characterized with easy implementation, and proved to be useful in ventilator-associated pneumonia prevention. Therapy of critically ill patients with COVID-19 is based on elements of general intensive care therapy with some specific therapeutic guidelines. With the intention to ease and improve therapy of patients with COVID-19 in intensive care units, a new and comprehensive acronym is proposed: One Fast Hug Bids COVID.

Evaluation of prevalance and risk factors for bloodstream infection in severe coronavirus disease 2019 (COVID-19) patients

Objectives:

In this study, we sought to determine the prevalence of bloodstream infection (BSI) in severe coronavirus disease 2019 (COVID-19) patients and to determine the risk factors of BSI in critical COVID-19 patients.

Design:

Retrospective, descriptive study between March 2020 and January 2021.

Setting:

An 1,007-bed university hospital.

Participants:

Patients who were hospitalized due to severe COVID-19 disease and had an aerobic blood culture taken at least once during hospitalization

Methods:

Case definitions were made according to National Institutes of Health clinical definitions. According to the blood culture results, the patients were grouped as with and without BSIs, and compared for BSIs risk factors.

Results:

In total, 195 patients were included in the study. Blood culture positivity was detected in 76 (39.0%) of 196 patients. Excluding blood culture positivity considered as contamination, the prevalence of BSI in all severe COVID-19 cases was 18.5% (n = 36). In intensive care unit patients the prevalence of BSI was 30.6% (n = 26). In multivariate analyses, central venous catheter (odds ratio [OR], 8.17; 95% confidence interval [CI], 2.46–27.1; P < .01) and hospitalization in the multibed intensive care unit (OR, 4.28; 95% CI, 1.28–14.3; P < .01) were risk factors associated with the acquisition of BSI.

Conclusion:

The prevalence of BSI in COVID-19 patients is particularly high in critically ill patients. The central venous catheter and multibed intensive care follow-up are risk factors for BSI. BSIs can be reduced by increasing compliance to infection control measures and central venous catheter insertion-care procedures. The use of single-bed intensive care units where compliance can be achieved more effectively is important for the prevention of BSIs.

Improving management and antimicrobial stewardship for bacterial and fungal infections in hospitalized patients with COVID-19

SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) infection is being one of the most significant challenges of health care systems worldwide. Bacterial and fungal infections in hospitalized patients with coronavirus disease 2019 (COVID-19) are uncommon but consumption of antibiotics and antifungals has increased dramatically during the ongoing pandemic resulting in increased selective pressure for global antimicrobial resistance. Nosocomial bacterial superinfections appear to be more frequent than community-acquired coinfections, particularly among patients admitted to the intensive care unit (ICU) and those receiving immunosuppressive treatment. Fungal infections associated with COVID-19 might be missed or misdiagnosed. Existing and new antimicrobial stewardship (AMS) programmes can be utilized directly in COVID-19 pandemic and are urgently needed to contain the high rates of misdiagnosis and antimicrobial prescription. The aim of this review is to describe the role of bacterial and fungal infections and possible strategies of AMS to use in daily practice for optimal management of COVID-19.

Recent Advancements on COVID-19: A Comprehensive Review

Over the last few decades, there have been several global outbreaks of severe respiratory infections. The causes of these outbreaks were coronaviruses that had infected birds, mammals and humans. The outbreaks predominantly caused respiratory tract and gastrointestinal tract symptoms and other mild to very severe clinical signs. The current coronavirus disease-2019 (COVID-19) outbreak, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a rapidly spreading illness affecting millions of people worldwide. Among the countries most affected by the disease are the United States of America (USA), India, Brazil, and Russia, with France recording the highest infection, morbidity, and mortality rates. Since early January 2021, thousands of articles have been published on COVID-19. Most of these articles were consistent with the reports on the mode of transmission, spread, duration, and severity of the sickness. Thus, this review comprehensively discusses the most critical aspects of COVID-19, including etiology, epidemiology, pathogenesis, clinical signs, transmission, pathological changes, diagnosis, treatment, prevention and control, and vaccination.

Promising Expectations for Pneumococcal Vaccination during COVID-19

The emergence of new viral infections has increased over the decades. The novel virus is one such pathogen liable for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, popularly known as coronavirus disease 2019 (COVID-19). Most fatalities during the past century's influenza pandemics have cooperated with bacterial co/secondary infections. Unfortunately, many reports have claimed that bacterial co-infection is also predominant in COVID-19 patients (COVID-19 associated co/secondary infection prevalence is up to 45.0%). In the COVID-19 pandemic, Streptococcus pneumoniae is the most common coinfecting pathogen. Half of the COVID-19 mortality cases showed co-infection, and pneumonia-related COVID-19 mortality in patients >65 years was 23%. The weakening of immune function caused by COVID-19 remains a high-risk factor for pneumococcal disease. Pneumococcal disease and COVID-19 also have similar risk factors. For example, underlying medical conditions on COVID-19 and pneumococcal diseases increase the risk for severe illness at any age; COVID-19 is now considered a primary risk factor for pneumococcal pneumonia and invasive pneumococcal disease. Thus, pneumococcal vaccination during the COVID-19 pandemic has become more critical than ever. This review presents positive studies of pneumococcal vaccination in patients with COVID-19 and other medical conditions and the correlational effects of pneumococcal disease with COVID-19 to prevent morbidity and mortality from co/secondary infections and superinfections. It also reports the importance and role of pneumococcal vaccination during the current COVID-19 pandemic era to strengthen the global health system.

Aftermath of COVID-19 and Critical Care in India

The coronavirus disease-2019 (COVID-19) pandemic had overwhelmed the healthcare system and forced many patients to be treated at home with oxygen, antibiotics, and steroids, particularly during the second wave. There was increased misuse of antimicrobials in hospitals as well as unguarded self-prescription of these medications among the common people. We are likely to see an increase in the incidence of antimicrobial resistance (AMR), change in the susceptibility pattern of the organisms causing community-acquired infections, and an increase in opportunistic bacterial, tubercular, viral, and fungal infections.

How to cite this article: Panda R, Hirolli D, Baidya DK. Aftermath of COVID-19 and Critical Care in India. Indian J Crit Care Med 2021; 25(10):1173–1175.

Global health emergencies during the pandemic and their solutions

In this review, we evaluated health care problems, which were not common before pandemic outbreak but have been common issues after its appereance and approaches to control pandemic considering its influences on people. We revised current health care developing approaches under the light of experience obtained throughout the pandemic so far. The aim is to be prepared in advance for possible upcoming pandemics. As in Covid 19 pandemics, such long lasting and widely affecting situations, durability is also very important together with flexibility and quickness. To provide durability, we need global policies taking the health to its center as well as health system policies.

COVID-19-Associated Pulmonary Aspergillosis in the Critical Care Setting

The first confirmed case of COVID-19 in the United States was reported on January 20, 2020. Most infected individuals experience a mild illness with loss of taste and smell, body aches, fatigue, cough, and fever. However, about 5% of patients become critically ill and experience more serious symptoms such as respiratory distress, pulmonary emboli, or even multisystem organ failure. Those who become critically ill with COVID-19 are at high risk for superinfections, including pulmonary, bloodstream, and urinary tract infections. Invasive aspergillosis is emerging as a serious secondary pulmonary infection in patients with COVID-19 who experience respiratory distress syndrome. If these patients are not accurately diagnosed and subsequently treated, the infection can be fatal. This case study describes COVID-19-associated pulmonary aspergillosis in the critically ill patient.

A High Frequency of Candida auris Blood Stream Infections in Coronavirus Disease 2019 Patients Admitted to Intensive Care Units, Northwestern India: A Case Control Study

Background

The ongoing pandemic of coronavirus disease 2019 (COVID-19) has overwhelmed healthcare facilities and raises an important novel concern of nosocomial transmission of Candida species in the intensive care units (ICUs).

Methods

We evaluated the incidence and risk factors for development of candidemia in 2384 COVID-19 patients admitted during August 2020–January 2021 in ICUs of 2 hospitals (Delhi and Jaipur) in India. A 1:2 case-control matching was used to identify COVID-19 patients who did not develop candidemia as controls.

Results

A total of 33 patients developed candidemia and accounted for an overall incidence of 1.4% over a median ICU stay of 24 days. A 2-fold increase in the incidence of candidemia in COVID-19 versus non-COVID-19 patients was observed with an incidence rate of 14 and 15/1000 admissions in 2 ICUs. Candida auris was the predominant species (42%) followed by Candida tropicalis. Multivariable regression analysis revealed the use of tocilizumab, duration of ICU stay (24 vs 14 days), and raised ferritin level as an independent predictor for the development of candidemia. Azole resistance was observed in C auris and C tropicalis harboring mutations in the azole target ERG11 gene. Multilocus sequence typing (MLST) identified identical genotypes of C tropicalis in COVID-19 patients, raising concern for nosocomial transmission of resistant strains.

Conclusions

Secondary bacterial infections have been a concern with the use of tocilizumab. In this cohort of critically ill COVID-19 patients, tocilizumab was associated with the development of candidemia. Surveillance of antifungal resistance is warranted to prevent transmission of multidrug-resistant strains of nosocomial yeasts in COVID-19 hospitalized patients.

Current pharmacotherapy for methicillin-resistant Staphylococcus aureus (MRSA) pneumonia

INTRODUCTION

Currently, several antibiotics are active against methicillin-resistant Staphylococcus aureus (MRSA) and can be used for the treatment of pneumonia. They show great variability in terms of antibiotic class, indication, pharmacodynamic/pharmacokinetic properties, type of available formulations, spectrum of activity against bacteria other than MRSA, and toxicity profile.

AREAS COVERED

In this narrative review, the authors discuss the characteristics of currently available agents for the treatment of MRSA pneumonia.

EXPERT OPINION

The availability of different agents with anti-MRSA activity, and approved for the treatment of pneumonia can allow a personalized approach for any given patient based on the severity of the disease, the setting of occurrence, the patient's baseline risk of toxicity and drug interactions, and the possibility of oral therapy whenever early discharge or outpatient treatment are possible. Although some gray areas still remain, like the lack of high certainty evidence on the efficacy of some old agents and on the precise role of companion agents with toxin inhibitory activity in the case of necrotizing pneumonia, the frequent availability of different treatment choices, each with peculiar characteristics, is already allowing an important step toward a precision medicine approach for the treatment of MRSA pneumonia.

Detection of bacteria via multiplex PCR in respiratory samples of critically ill COVID-19 patients with suspected HAP/VAP in the ICU

Background

Critically ill Coronavirus disease 2019 (COVID-19) patients have high rates of bacterial superinfection. Multiplex polymerase chain reaction panels may be able to provide useful information about the incidence and spectrum of bacteria causing superinfections.

Methods

In this retrospective observational study we included all COVID-19 positive patients admitted to our intensive care unit with suspected hospital-acquired pneumonia/ventilator-associated pneumonia (HAP/VAP) in whom the BioFire® Pneumonia Panel (PP) was performed from tracheal aspirate or bronchoalveolar lavage fluid for diagnostic purposes. The aim of our study was to analyze the spectrum of pathogens detected with the PP.

Results

In this study 60 patients with a median age of 62.5 years were included. Suspected VAP was the most frequent (48/60, 80%) indication for performing the PP. Tracheal aspirate was the predominant sample type (50/60, 83.3%).

The PP led to a negative, monomicrobial and polymicrobial result in 36.7%, 35% and 28.3% of the patients, respectively. The three most detected bacteria were Staphylococcus aureus (13/60, 21.7%), Klebsiella pneumoniae (12/60, 20%) and Haemophilus influenzae (9/60, 15%). Neither atypical bacteria nor resistance genes were detected.

Microbiological culture of respiratory specimens was performed in 36 (60%) patients concomitantly. The PP and microbiological culture yielded a non-concordant, partial concordant and completely concordant result in 13.9% (5/36), 30.6% (11/36) and 55.6% (20/36) of the analyzed samples, respectively.

Conclusion

In critically ill COVID-19 patients with suspected HAP/VAP results of the PP and microbiological culture methods were largely consistent. In our cohort, S. aureus and K. pneumoniae were the most frequently detected organisms. A higher diagnostic yield may be achieved if both methods are combined.

Extracorporeal membrane oxygenation support for SARS-CoV-2: a multi-centered, prospective, observational study in critically ill 92 patients in Saudi Arabia

BACKGROUND

Extracorporeal membrane oxygenation (ECMO) has been used as a rescue strategy in patients with severe with acute respiratory distress syndrome (ARDS) due to SARS-CoV-2 infection, but there has been little evidence of its efficacy.

OBJECTIVES

To describe the effect of ECMO rescue therapy on patient-important outcomes in patients with severe SARS-CoV-2.

METHODS

A case series study was conducted for the laboratory-confirmed SARS-CoV-2 patients who were admitted to the ICUs of 22 Saudi hospitals, between March 1, 2020, and October 30, 2020, by reviewing patient's medical records prospectively.

RESULTS

ECMO use was associated with higher in-hospital mortality (40.2% vs. 48.9%; p = 0.000); lower COVID-19 virological cure (41.3% vs 14.1%, p = 0.000); and longer hospitalization (20.2 days vs 29.1 days; p = 0.000), ICU stay (12.6 vs 26 days; p = 0.000) and mechanical ventilation use (14.2 days vs 22.4 days; p = 0.000) compared to non-ECMO group. Also, there was a high number of patients with septic shock (19.6%) and multiple organ failure (10.9%); and more complications occurred at any time during hospitalization [pneumothorax (5% vs 29.3%, p = 0.000), bleeding requiring blood transfusion (7.1% vs 38%, p = 0.000), pulmonary embolism (6.4% vs 15.2%, p = 0.016), and gastrointestinal bleeding (3.3% vs 8.7%, p = 0.017)] in the ECMO group. However, PaO2 was significantly higher in the 72-h post-ECMO initiation group and PCO2 was significantly lower in the 72-h post-ECMO start group than those in the 12-h pre-ECMO group (62.9 vs. 70 mmHg, p = 0.002 and 61.8 vs. 51 mmHg, p = 0.042, respectively).

CONCLUSION

Following the use of ECMO, the mortality rate of patients and length of ICU and hospital stay were not improved. However, these findings need to be carefully interpreted, as most of our cohort patients were relatively old and had multiple severe comorbidities. Future randomized trials, although challenging to conduct, are highly needed to confirm or dispute reported observations.

Pulmonary bacterial infections in adult patients hospitalized for COVID-19 in standard wards

OBJECTIVES

During the COVID-19 pandemic, antibiotic use was very common. However, bacterial co-/secondary infections with coronaviruses remain largely unknown in standard wards. We aimed to investigate the characteristics of pulmonary bacterial infections associated with COVID-19 in hospitalized patients.

METHODS

A retrospective monocentric observational study was conducted in Bichat hospital, France, between February 26 and April 22, 2020. All patients hospitalized in standard wards with COVID-19 (positive nasopharyngeal PCR and/or typical aspect on CT scan) and diagnosed with pulmonary bacterial infection (positive bacteriological samples) were included. Bacteriological and clinical data were collected from the microbiology laboratories and patient's medical records.

RESULTS

Twenty-three bacteriological samples from 22 patients were positive out of 2,075 screened samples (1.1%) from 784 patients (2.8%). Bacterial infection occurred within a median of 10 days after COVID-19 onset. Diagnosis of pulmonary bacterial infection was suspected on increase of oxygen requirements (20/22), productive cough or modification of sputum aspect (17/22), or fever (10/22). Positive samples included 13 sputum cultures, one FilmArray® assay on sputum samples, one bronchoalveolar lavage, six blood cultures, and two pneumococcal urinary antigen tests. The most frequent bacteria were Pseudomonas aeruginosa (6/23), Staphylococcus aureus (5/23), Streptococcus pneumoniae (4/23), Enterococcus faecalis (3/23), and Klebsiella aerogenes (3/23). No Legionella urinary antigen test was positive. Four out of 496 nasopharyngeal PCR tests (0.8%) were positive for intracellular bacteria (two Bordetella pertussis and two Mycoplasma pneumonia).

CONCLUSIONS

Pulmonary bacterial secondary infections and co-infections with SARS-CoV-2 are uncommon. Antibiotic use should remain limited in the management of COVID-19.

HSV-1 reactivation is associated with an increased risk of mortality and pneumonia in critically ill COVID-19 patients

BACKGROUND

Data in the literature about HSV reactivation in COVID-19 patients are scarce, and the association between HSV-1 reactivation and mortality remains to be determined. Our objectives were to evaluate the impact of Herpes simplex virus (HSV) reactivation in patients with severe SARS-CoV-2 infections primarily on mortality, and secondarily on hospital-acquired pneumonia/ventilator-associated pneumonia (HAP/VAP) and intensive care unit-bloodstream infection (ICU-BSI).

METHODS

We conducted an observational study using prospectively collected data and HSV-1 blood and respiratory samples from all critically ill COVID-19 patients in a large reference center who underwent HSV tests. Using multivariable Cox and cause-specific (cs) models, we investigated the association between HSV reactivation and mortality or healthcare-associated infections.

RESULTS

Of the 153 COVID-19 patients admitted for ≥ 48 h from Feb-2020 to Feb-2021, 40/153 (26.1%) patients had confirmed HSV-1 reactivation (19/61 (31.1%) with HSV-positive respiratory samples, and 36/146 (24.7%) with HSV-positive blood samples. Day-60 mortality was higher in patients with HSV-1 reactivation (57.5%) versus without (33.6%, p = 0.001). After adjustment for mortality risk factors, HSV-1 reactivation was associated with an increased mortality risk (hazard risk [HR] 2.05; 95% CI 1.16-3.62; p = 0.01). HAP/VAP occurred in 67/153 (43.8%) and ICU-BSI in 42/153 (27.5%) patients. In patients with HSV-1 reactivation, multivariable cause-specific models showed an increased risk of HAP/VAP (csHR 2.38, 95% CI 1.06-5.39, p = 0.037), but not of ICU-BSI.

CONCLUSIONS

HSV-1 reactivation in critically ill COVID-19 patients was associated with an increased risk of day-60 mortality and HAP/VAP.

Relationship between Pneumonia and the Thymus Gland in Children with COVID-19: A Volumetric Computed Tomography Study

Objective Many studies showed that less-severe disease symptoms and fewer mortality rates have been reported in pediatric novel coronavirus disease 2019 (COVID-19) patients. In this study, we aimed to reveal the relationship between the volume of thymus gland, which provides T lymphocyte maturation in children, with the severity of lung involvement and blood laboratory values in pediatric patients with COVID-19 infection.

Methods Thymus density and thymus and cardiac volumes were measured in pediatric COVID-19 patients and a control group that underwent thoracic tomography for reasons other than infection. Thymus/heart ratios were calculated to index the thymus volumes of the patients to their body dimensions. The severity of pneumonia was demonstrated by proportioning the involved lung parenchymal volume to the total lung volume in patients with typical involvement in thoracic tomography. The relationship between volumetric and blood laboratory values was statistically evaluated.

Results Thymus density (p = 0.015) and thymus/heart ratio (p = 0.04) significantly differed between patients with COVID-19 infection and the control group. A correlation was observed between the pneumonia involvement rate and C-reactive protein (CRP) (k: 0.451, p = 0.08) and white blood cell (WBC; k: 0.419, p = 0.015) values in the thoracic tomography of the COVID-19 group.

Conclusion The thymus gland is enlarged as an indicator of activation in COVID-19 infection. We hope that our study will guide new studies on the prognostic value of thymus size in lymphopenic patients with severe disease.

Root Causes of Fungal Coinfections in COVID-19 Infected Patients

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has infected over 200 million people, causing over 4 million deaths. COVID-19 infection has been shown to lead to hypoxia, immunosuppression, host iron depletion, hyperglycemia secondary to diabetes mellitus, as well as prolonged hospitalizations. These clinical manifestations provide favorable conditions for opportunistic fungal pathogens to infect hosts with COVID-19. Interventions such as treatment with corticosteroids and mechanical ventilation may further predispose COVID-19 patients to acquiring fungal coinfections. Our literature review found that fungal coinfections in COVID-19 infected patients were most commonly caused by Aspergillus, Candida species, Cryptococcus neoformans, and fungi of the Mucorales order. The distribution of these infections, particularly Mucormycosis, was found to be markedly skewed towards low- and middle-income countries. The purpose of this review is to identify possible explanations for the increase in fungal coinfections seen in COVID-19 infected patients so that physicians and healthcare providers can be conscious of factors that may predispose these patients to fungal coinfections in order to provide more favorable patient outcomes. After identifying risk factors for coinfections, measures should be taken to minimize the dosage and duration of drugs such as corticosteroids, immunosuppressants, and antibiotics.

Coronavirus Disease 2019: Clinics, Treatment, and Prevention

The coronavirus disease 2019 (COVID-19) pandemic, caused by a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), emerged at the end of 2019 in China and affected the entire world population, either by infection and its health consequences, or by restrictions in daily life as a consequence of hygiene measures and containment strategies. As of September 2021, more than 231,000.000 infections and 4,740.000 deaths due to COVID-19 have been reported. The infections present with varied clinical symptoms and severity, ranging from asymptomatic course to fatal outcome. Several risk factors for a severe course of the disease have been identified, the most important being age, gender, comorbidities, lifestyle, and genetics. While most patients recover within several weeks, some report persistent symptoms restricting their daily lives and activities, termed as post-COVID. Over the past 18months, we have acquired significant knowledge as reflected by an almost uncountable number of publications on the nature of the underlying virus and its evolution, host responses to infection, modes of transmission, and different clinical presentations of the disease. Along this line, new diagnostic tests and algorithms have been developed paralleled by the search for and clinical evaluation of specific treatments for the different stages of the disease. In addition, preventive non-pharmacological measures have been implemented to control the spread of infection in the community. While an effective antiviral therapy is not yet available, numerous vaccines including novel vaccine technologies have been developed, which show high protection from infection and specifically from a severe course or death from COVID-19. In this review, we tried to provide an up-to-date schematic of COVID-19, including aspects of epidemiology, virology, clinical presentation, diagnostics, therapy, and prevention.

Microbiological characteristics of bacteremias among COVID-19 hospitalized patients in a tertiary referral hospital in Northern Greece during the second epidemic wave

Northern Greece was struck by an intense second COVID-19 (coronavirus disease 2019) epidemic wave during the fall of 2020. Because of the coinciding silent epidemic of multidrug-resistant organisms, the handling of COVID-19 patients became even more challenging. In the present study, the microbiological characteristics of bacteremias in confirmed cases of hospitalized COVID-19 patients were determined. Data from 1165 patients hospitalized between September and December 2020 were reviewed regarding the frequency of bloodstream infections, the epidemiology and the antibiotic susceptibility profiles of the causative bacteria. The hospital's antibiotic susceptibility data for all major nosocomial pathogens isolated from bacteremias of COVID-19 patients between September and December 2020 versus those between September and December 2019 were also compared. Overall, 122 patients developed bacteremia (10.47%). The average of time interval between hospitalization date and development of bacteremia was 13.98 days. Admission to ICU occurred in 98 out of 122 patients with an average stay time of 15.85 days and 90.81% in-hospital mortality. In total, 166 pathogens were recovered including 114 Gram-negative bacteria and 52 Gram-positive cocci. Acinetobacter baumannii was the most frequent (n = 51) followed by Klebsiella pneumoniae (n = 45) and Enterococcus faecium (n = 31). Bacteremias in hospitalized COVID-19 patients were related with prolonged time of hospitalization and higher in-hospital mortality, and the isolated microorganisms represented the bacterial species that were present in our hospital before the COVID-19 pandemic. Worryingly, the antibiotic resistance rates were increased compared with the pre-pandemic era for all major opportunistic bacterial pathogens. The pandemic highlighted the need for continuous surveillance of patients with prolonged hospitalization.

Microbial coinfections and superinfections in critical COVID-19: a Kenyan retrospective cohort analysis

Objectives

The aim of our study was to outline the burden, risk factors, and outcomes for critical COVID-19 patients with coinfections or superinfections.

Methods

This was a retrospective descriptive study of adults who were admitted with critical COVID-19 for ≥ 24 hours. Data collected included demographic profiles and other baseline characteristics, laboratory and radiological investigations, medical interventions, and clinical outcomes. Outcomes of interest included the presence or absence of coinfections or superinfections, and in-hospital mortality. Differences between those with and without coinfections or superinfections were compared for statistical significance.

Results

In total, 321 patient records were reviewed. Baseline characteristics included a median age (IQR) of 61.4 (51.4-72.9) years, and a predominance of male (71.3%) and African/black (66.4%) patients. Death occurred in 132 (44.1%) patients, with a significant difference noted between those with added infections (58.2%) and those with none (36.6%) (p = 0.002, odds ratio (OR) = 2.41). One patient was coinfected with pulmonary tuberculosis. Approximately two-thirds of patients received broad-spectrum antimicrobial therapy.

Conclusion

Added infections in critically ill COVID-19 patients were relatively uncommon but, where present, were associated with higher mortality. Empiric use of broad-spectrum antimicrobials was common, and may have led to the selection of multidrug-resistant organisms. More robust local data on antimicrobial susceptibility patterns may help in appropriate antibiotic selection, in order to improve outcomes without driving up rates of drug-resistant pathogens.

The interface between COVID-19 and bacterial healthcare-associated infections

BACKGROUND

A wide range of bacterial infections occur in coronavirus disease 2019 (COVID-19) patients, particularly in those with severe coronaviral disease. Some of these are community-acquired co-infections.

OBJECTIVE

To review recent data that indicate the occurrence of hospital-onset bacterial infections, including with antibiotic-resistant isolates, in COVID-19 patients.

SOURCES

Using PubMed, the literature was searched using terms including: 'COVID-19'; 'SARS-CoV-2'; 'bacterial infection'; 'healthcare-associated infection'; 'antibiotic resistance'; 'antimicrobial resistance'; 'multi-drug resistance'; 'Streptococcus'; 'Staphylococcus'; 'Pseudomonas'; 'Escherichia'; 'Klebsiella'; 'Enterococcus'; 'Acinetobacter'; 'Haemophilus'; 'MRSA'; 'VRE'; 'ESBL'; 'NDM-CRE'; 'CR-Ab'; 'VRSA'; 'MDR'.

CONTENT

There is a growing number of reports of bacterial infections acquired by patients with severe COVID-19 after hospital admission. Antibiotic-resistant pathogens found to cause healthcare-associated infections (HAIs) in COVID-19 patients include methicillin-resistant Staphylococcus aureus, New Delhi metallo-β-lactamase-producing carbapenem-resistant Enterobacterales, carbapenem-resistant Acinetobacter baumannii, extended-spectrum β-lactamase Klebsiella pneumoniae and vancomycin-resistant enterococci. COVID-19 has impacted bacterial HAIs in a number of ways with an increase in the incidence of New Delhi metallo-β-lactamase-producing carbapenem-resistant Enterobacterales and carbapenem-resistant A. baumannii reported at some hospital sites compared with before the pandemic. Recommended guidelines for antimicrobial stewardship in COVID-19 patient treatment are discussed regarding minimization of empiric broad-spectrum antibiotic use. Other studies have reported a decrease in methicillin-resistant S. aureus and vancomycin-resistant enterococci cases, which has been attributed to enhanced infection prevention and control practices introduced to minimize intra-hospital spread of COVID-19.

IMPLICATIONS

Poorer outcomes have been observed in hospitalized COVID-19 patients with an antibiotic-resistant infection. Although heightened IPC measures have been accompanied by a reduction in some HAIs at specific sites, in other situations, COVID-19 has been associated with an increase in bacterial HAI incidence. Further research is needed to define the cost-benefit relationship of maintaining COVID-19-related infection prevention and control protocols beyond the pandemic to reduce the burden of HAIs. In addition, the longer-term impact of high usage of certain broad-spectrum antibiotics during the COVID-19 pandemic requires evaluation.

Outcomes of patients with severe and critical COVID-19 treated with dexamethasone: a prospective cohort study

Dexamethasone implementation for COVID-19 management represented a milestone but data regarding its impact and safety have not been consistently reproduced. We aimed to evaluate in-hospital mortality before and after the implementation of corticosteroid treatment (CS-T) for severe and critical COVID-19. We conducted a cohort study that included patients admitted with severe and critical COVID-19. The primary outcome was death during hospitalization. Secondary outcomes included the length of stay (LOS), need for invasive mechanical ventilation (IMV), time to IMV initiation, IMV duration, and development of hospital-acquired infections (HAIs). Bivariate, multivariate, and propensity-score matching analysis were performed. Among 1540 patients, 688 (45%) received CS-T. Death was less frequent in the CS-T group (18 vs 31%, p < .01). Among patients on IMV, death was also less frequent in the CS-T group (25 vs 55%, p < .01). The median time to IMV was longer in the CS-T group (5 vs 3 days, p < .01). HAIs occurred more frequently in the CS-T group (20 vs 10%, p < .01). LOS, IMV, and IMV duration were similar between groups. Multivariate analysis revealed an independent association between CS-T and lower mortality (aOR 0.26, 95% CI 0.19-0.36, p < .001). Propensity-score matching analysis revealed that CS-T was independently associated with lower mortality (aOR 0.33, 95% CI 0.22-0.50, p < .01). Treatment with corticosteroids was associated with reduced in-hospital mortality among patients with severe and critical COVID-19, including those on IMV.

Comparing efficacy and safety of different doses of dexamethasone in the treatment of COVID-19: a three-arm randomized clinical trial

Background and objectives

Corticosteroids are commonly used in the treatment of hospitalized patients with COVID-19. The goals of the present study were to compare the efficacy and safety of different doses of dexamethasone in the treatment of patients with a diagnosis of moderate to severe COVID-19.

Methods

Hospitalized patients with a diagnosis of moderate to severe COVID-19 were assigned to intravenous low-dose (8 mg once daily), intermediate-dose (8 mg twice daily) or high-dose (8 mg thrice daily) dexamethasone for up to 10 days or until hospital discharge. Clinical response, 60-day survival and adverse effects were the main outcomes of the study.

Results

In the competing risk survival analysis, patients in the low-dose group had a higher clinical response than the high-dose group when considering death as a competing risk (HR = 2.03, 95% CI: 1.23–3.33, p = 0.03). Also, the survival was significantly longer in the low-dose group than the high-dose group (HR = 0.36, 95% CI = 0.15–0.83, p = 0.02). Leukocytosis and hyperglycemia were the most common side effects of dexamethasone. Although the incidence was not significantly different between the groups, some adverse effects were numerically higher in the intermediate-dose and high-dose groups than in the low-dose group.

Conclusions

Higher doses of dexamethasone not only failed to improve efficacy but also resulted in an increase in the number of adverse events and worsen survival in hospitalized patients with moderate to severe COVID-19 compared to the low-dose dexamethasone. (IRCT20100228003449N31).

Supplementary Information

The online version contains supplementary material available at 10.1007/s43440-021-00341-0.

COVID-19 Pandemic as Risk Factors for Excessive Weight Gain in Pediatrics: The Role of Changes in Nutrition Behavior. A Narrative Review

During the coronavirus disease 2019 (COVID-19) pandemic, social isolation, semi-lockdown, and "stay at home" orders were imposed upon the population in the interest of infection control. This dramatically changes the daily routine of children and adolescents, with a large impact on lifestyle and wellbeing. Children with obesity have been shown to be at a higher risk of negative lifestyle changes and weight gain during lockdown. Obesity and COVID-19 negatively affect children and adolescents' wellbeing, with adverse effects on psychophysical health, due in large part to food choices, snacking between meals, and comfort eating. Moreover, a markable decrease in physical activity levels and an increase in sedentary behavior is associated with weight gain, especially in children with excessive weight. In addition, obesity is the most common comorbidity in severe cases of COVID-19, suggesting that immune dysregulation, metabolic unbalance, inadequate nutritional status, and dysbiosis are key factors in the complex mechanistic and clinical interplay between obesity and COVID-19. This narrative review aims to describe the most up-to-date evidence on the clinical characteristics of COVID-19 in children and adolescents, focusing on the role of excessive weight and weight gain in pediatrics. The COVID-19 pandemic has taught us that nutrition education interventions, access to healthy food, as well as family nutrition counselling should be covered by pediatric services to prevent obesity, which worsens disease outcomes related to COVID-19 infection.

COVID-19 associated infections in the ICU setting: A retrospective analysis in a tertiary-care hospital

Introduction

Our work describes the frequency of superinfections in COVID-19 ICU patients and identifies risk factors for its appearance. Second, we evaluated ICU length of stay, in-hospital mortality and analyzed a subgroup of multidrug-resistant microorganisms (MDROs) infections.

Methods

Retrospective study conducted between March and June 2020. Superinfections were defined as appeared ≥48 h. Bacterial and fungal infections were included, and sources were ventilator-associated lower respiratory tract infection (VA-LRTI), primary bloodstream infection (BSI), secondary BSI, and urinary tract infection (UTI). We performed a univariate analysis and a multivariate analysis of the risk factors.

Results

Two-hundred thirteen patients were included. We documented 174 episodes in 95 (44.6%) patients: 78 VA-LRTI, 66 primary BSI, 9 secondary BSI and 21 UTI. MDROs caused 29.3% of the episodes. The median time from admission to the first episode was 18 days and was longer in MDROs than in non-MDROs (28 vs. 16 days, p < 0.01). In multivariate analysis use of corticosteroids (OR 4.9, 95% CI 1.4–16.9, p 0.01), tocilizumab (OR 2.4, 95% CI 1.1–5.9, p 0.03) and broad-spectrum antibiotics within first 7 days of admission (OR 2.5, 95% CI 1.2–5.1, p < 0.01) were associated with superinfections. Patients with superinfections presented respect to controls prolonged ICU stay (35 vs. 12 days, p < 0.01) but not higher in-hospital mortality (45.3% vs. 39.7%, p 0.13).

Conclusions

Superinfections in ICU patients are frequent in late course of admission. Corticosteroids, tocilizumab, and previous broad-spectrum antibiotics are identified as risk factors for its development.

What have we learned from the first to the second wave of COVID-19 pandemic? An international survey from the ESCMID Study Group for Infection in the Elderly (ESGIE) group

The purpose of this survey is to explore changes in the management of COVID-19 during the first versus the second wave, with particular emphasis on therapies, antibiotic prescriptions, and elderly care. An internet-based questionnaire survey was distributed to European Society of Clinical Microbiology and Infectious Diseases (ESCMID) members. Therapeutic approach to patients with mild-to-moderate (PiO₂/FiO₂ 200–350) and severe (PiO₂/FiO₂ < 200) COVID-19, antibiotic use, and reasons for excluding patients from the intensive care unit (ICU) were investigated. A total of 463 from 21 countries participated in the study. Most representatives were infectious disease specialists (68.3%). During the second wave of pandemic, physicians abandoned the use of hydroxychloroquine, lopinavir/ritonavir, and azithromycin in favor of dexamethasone, low-molecular weight heparin (LMWH), and remdesivir in mild-to-moderate COVID-19. In critically ill patients, we detected an increased use of high-dose steroids (51%) and a decrease in tocilizumab use. The use of antibiotics at hospital admission decreased but remained high in the second wave. Age was reported to be a main consideration for exclusion of patients from ICU care by 25% of responders; a third reported that elderly were not candidates for ICU admission in their center. The decision to exclude patients from ICU care was based on the individual decision of an intensivist in 59.6% of cases. The approach of physicians to COVID-19 changed over time following evidence accumulation and guidelines. Antibiotic use at hospital admission and decision to exclude patients from ICU care remain critical aspects that should be better investigated and harmonized among clinicians.

Diagnosis and Treatment of Bacterial Pneumonia in Critically Ill Patients with COVID-19 Using a Multiplex PCR Assay: A Large Italian Hospital's Five-Month Experience

Bacterial pneumonia is a challenging coronavirus disease 2019 (COVID-19) complication for intensive care unit (ICU) clinicians. Upon its implementation, the FilmArray pneumonia plus (FA-PP) panel's practicability for both the diagnosis and antimicrobial therapy management of bacterial pneumonia was assessed in ICU patients with COVID-19. Respiratory samples were collected from patients who were mechanically ventilated at the time bacterial etiology and antimicrobial resistance were determined using both standard-of-care (culture and antimicrobial susceptibility testing [AST]) and FA-PP panel testing methods. Changes to targeted and/or appropriate antimicrobial therapy were reviewed. We tested 212 samples from 150 patients suspected of bacterial pneumonia. Etiologically, 120 samples were positive by both methods, two samples were culture positive but FA-PP negative (i.e., negative for on-panel organisms), and 90 were negative by both methods. FA-PP detected no culture-growing organisms (mostly Staphylococcus aureus or Pseudomonas aeruginosa) in 19 of 120 samples or antimicrobial resistance genes in two culture-negative samples for S. aureus organisms. Fifty-nine (27.8%) of 212 samples were from empirically treated patients. Antibiotics were discontinued in 5 (33.3%) of 15 patients with FA-PP-negative samples and were escalated/deescalated in 39 (88.6%) of 44 patients with FA-PP-positive samples. Overall, antibiotics were initiated in 87 (72.5%) of 120 pneumonia episodes and were not administered in 80 (87.0%) of 92 nonpneumonia episodes. Antimicrobial-resistant organisms caused 78 (60.0%) of 120 episodes. Excluding 19 colistin-resistant Acinetobacter baumannii episodes, AST confirmed appropriate antibiotic receipt in 101 (84.2%) of 120 episodes for one or more FA-PP-detected organisms. Compared to standard-of-care testing, the FA-PP panel may be of great value in the management of COVID-19 patients at risk of developing bacterial pneumonia in the ICU. IMPORTANCE Since bacterial pneumonia is relatively frequent, suspicion of it in COVID-19 patients may prompt ICU clinicians to overuse (broad-spectrum) antibiotics, particularly when empirical antibiotics do not cover the suspected pathogen. We showed that a PCR-based, culture-independent laboratory assay allows not only accurate diagnosis but also streamlining of antimicrobial therapy for bacterial pneumonia episodes. We report on the actual implementation of rapid diagnostics and its real-life impact on patient treatment, which is a gain over previously published studies on the topic. A better understanding of the role of that or similar PCR assays in routine ICU practice may lead us to appreciate the effectiveness of their implementation during the COVID-19 pandemic.

Snapshot of COVID-19 superinfections in Marseille hospitals: where are the common pathogens?

Episodes of bacterial superinfections have been well identified for several respiratory viruses, notably influenza. In this retrospective study, we compared the frequency of superinfections in COVID-19 patients to those found in influenza-positive patients, and to controls without viral infection. We included 42 468 patients who had been diagnosed with COVID-19 and 266 261 subjects who had tested COVID-19 negative between 26 February 2020 and 1 May 2021. In addition, 4059 patients were included who had tested positive for the influenza virus between 1 January 2017 and 31 December 2019. Bacterial infections in COVID-19 patients were more frequently healthcare-associated, and acquired in ICUs, were associated with longer ICU stays, and occurred in older and male patients when compared to controls and to influenza patients (P < 0.0001 for all). The most common pathogens proved to be less frequent in COVID-19 patients, including fewer cases of bacteraemia involving E. coli (P < 0.0001) and Klebsiella pneumoniae (P = 0.027) when compared to controls. In respiratory specimens Haemophilus influenzae (P < 0.0001) was more frequent in controls, while Streptococcus pneumoniae (P < 0.0001) was more frequent in influenza patients. Likewise, species associated with nosocomial transmission, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, were more frequent among COVID-19 patients. Finally, we observed a high frequency of Enterococcus faecalis bacteraemia among COVID-19 patients, which were mainly ICU-acquired and associated with a longer timescale to acquisition.