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

High Prevalence of Antibiotic Resistance among Opportunistic Pathogens Isolated from Patients with COVID-19 under Mechanical Ventilation: Results of a Single-Center Study

The effect of the COVID-19 pandemic on antibiotic resistance diffusion in healthcare settings has not been fully investigated. In this study we evaluated the prevalence of antibiotic resistance among opportunistic pathogens isolated from patients with COVID-19 under mechanical ventilation. An observational, retrospective, analysis was performed on confirmed cases of COVID-19 patients who were admitted to the ICU department of San Salvatore Hospital in Pesaro, Italy, from 1 February 2021 to 31 May 2021. We considered all consecutive patients aged ≥ 18, under mechanical ventilation for longer than 24 h. Eighty-nine patients, 66 (74.1%) men and 23 (25.9%) women, with a median age of 67.1 years, were recruited. Sixty-eight patients (76.4%) had at least one infection, and 11 patients (12.3%) were colonized, while in the remaining 10 patients (11.2%) neither colonization nor infection occurred. In total, 173 microorganisms were isolated. There were 73 isolates (42.2%) causing bacterial or fungal infections while the remaining 100 isolates (57.8%) were colonizers. Among Gram-negative bacteria, E. coli, A. baumannii and K. pneumoniae were the most common species. Among Gram-positive bacteria, S. aureus and E. faecalis were the most common species. Overall, there were 58/105 (55.2%) and 22/59 (37.2%) MDR isolates among Gram-negative and Gram-positive bacteria, respectively. The prevalence of an MDR microorganism was significantly higher in those patients who had been exposed to empiric antibiotic treatment before ICU admission. In conclusion, we found a high prevalence of antibiotic resistance among opportunistic pathogens isolated from patients with COVID-19 under mechanical ventilation.

Viral Coinfection among COVID-19 Patient Groups: An Update Systematic Review and Meta-Analysis

BACKGROUND

Coinfections have a potential role in increased morbidity and mortality rates during pandemics. Our investigation is aimed at evaluating the viral coinfection prevalence in COVID-19 patients.

METHODS

We systematically searched scientific databases, including Medline, Scopus, WOS, and Embase, from December 1, 2019, to December 30, 2020. Preprint servers such as medRxiv were also scanned to find other related preprint papers. All types of studies evaluating the viral coinfection prevalence in COVID-19 patients were considered. We applied the random effects model to pool all of the related studies.

RESULTS

Thirty-three studies including 10484 patients were identified. The viral coinfection estimated pooled prevalence was 12.58%; 95% CI: 7.31 to 18.96). Blood viruses (pooled prevalence: 12.48%; 95% CI: 8.57 to 16.93) had the most frequent viral coinfection, and respiratory viruses (pooled prevalence: 4.32%; 95% CI: 2.78 to 6.15) had less frequent viral coinfection. The herpesvirus pooled prevalence was 11.71% (95% CI: 3.02 to 24.80). Also, the maximum and minimum of viral coinfection pooled prevalence were in AMRO and EMRO with 15.63% (95% CI: 3.78 to 33.31) and 7.05% (95% CI: 3.84 to 11.07), respectively.

CONCLUSION

The lowest rate of coinfection belonged to respiratory viruses. Blood-borne viruses had the highest coinfection rate. Our results provide important data about the prevalence of blood-borne viruses among COVID-19 patients which can be critical when it comes to their treatment procedure.

COVID-19 and Co-infection in Children: The Indian Perspectives

BACKGROUND AND OBJECTIVES

Assessing the co-infections with COVID-19 is crucial to delineate its true clinical impact. Pediatric information in this aspect is limited. Our study aims to analyze the spectrum of co-infections in pediatric COVID-19 patients and determine the clinical as well as laboratory parameters predicting co-infection.

METHODOLOGY

In this prospective observational study conducted from June to December 2020 in a single tertiary care institution, data pertaining to demographic, illness and treatment-related variables were analyzed among two subsets of pediatric patients of age 1 month-12 years with RT-PCR-confirmed COVID-19 infection-Group A: those with confirmed co-infection and Group B: moderate to severe disease without co-infection. Among Group A, etiology of co-infection was characterized through relevant microbiological examination within 48 h admission.

RESULT

Among our study population, 15.03% and 20.6% had co-infections and moderate to severe disease respectively. Among those with confirmed co-infection, 32.5%, 11.6% and 6.97% recorded blood culture, respiratory secretion and CSF growth, respectively, the picture being dominated by Methicillin resistant and sensitive Staphylococcus aureus. Serum serology demonstrated Scrub typhus infection to be most prevalent. Concurrent respiratory viral infections were seen in 11.6%. Children with co-infection had significantly higher morbidity and need for supportive therapy. Predictors of co-infection were localization of infection, Neutrophil count ≥10×109, age-specific lymphopenia, CRP > 100 mg/dl and hyperferritinemia.

CONCLUSION

Co-infections are an important factor prognosticating pediatric COVID infection. Their early detection, prompt and appropriate treatment is of paramount importance.

Evaluation of serum procalcitonin level as a biomarker for disease severity in COVID-19 patients

The pandemic of coronavirus disease 2019 (COVID-19) has infected millions of individuals around the globe. Forecasting the COVID-19 severity is essential, and various biomarkers could be used to evaluate it. The current study was therefore aimed to evaluate the serum pro-calcitonin (PCT) level as a biomarker for bacterial co-infection and disease severity in COVID-19 patients. A total of 430 COVID-19 positive individuals were examined, in which 332 (77.2%) were male individuals while 98 (22.8%) were female individuals. Among the examined samples, 281 were classified as moderate (PCT value 0.07 ± 0.06 ng/mL), 95 were severe (PCT value 0.5 ± 0.4 ng/mL), and 54 were classified as critical (PCT value > 1 ng/mL) individuals. The increase in the total serum level of PCT was observed with the severity of the disease (p < 0.05). The statistical analysis represented no association of PCT value with gender (p 0.9650) while revealed a significant association (p < 0.001) with the age and PCT value in COVID-19 patients. It can be concluded that the serial PCT measurement could determine the prognosis of the disease and the presence of bacterial co-infection in COVID-19 patients. Further exploration of the topic is needed to evaluate the effect of different therapies on the PCT level and to prescribe specific treatment options for coinfection.

Candidemia in COVID-19 treated with corticosteroids and tocilizumab

COVID-19 patients treated with anti-inflammatory drugs are rarely complicated by candidemia. Since immunosuppressive therapy can blunt inflammatory reactions, clinicians should actively survey latent candidemia during severe COVID-19 treatment.

Bacterial coinfection among coronavirus disease 2019 patient groups: an updated systematic review and meta-analysis

The pandemic of severe acute respiratory syndrome coronavirus 2 raised the attention towards bacterial coinfection and its role in coronavirus disease 2019 (COVID-19) disease. This study aims to systematically review and identify the pooled prevalence of bacterial coinfection in the related articles. A comprehensive search was conducted in international databases, including MEDLINE, Scopus, Web of Science, and Embase, to identify the articles on the prevalence of bacterial coinfections in COIVD-19 patients from 1 December 2019 until 30 December 2020. All observational epidemiological studies that evaluated the prevalence of bacterial coinfections in patients with COVID-19 were included without any restriction. Forty-two studies including a total sample size of 54,695 were included in the analysis. The pooled estimate for the prevalence of bacterial coinfections was 20.97% (95% CI: 15.95-26.46), and the pooled prevalence of bacterial coinfections was 5.20% (95% CI: 2.39-8.91) for respiratory subtype and 4.79% (95% CI: 0.11-14.61) for the gastrointestinal subtype. The pooled prevalence for Eastern Mediterranean Regional Office and South-East Asia Regional Office was 100% (95% CI: 82.35-100.00) and 2.61% (95% CI: 1.74-3.62). This rate of coinfection poses a great danger towards patients, especially those in critical condition. Although there are multiple complications and adverse effects related to extensive use of antibiotics to treat patients with COVID-19, it seems there is no other option except applying them, and it needs to be done carefully.

Impact of COVID-19 on Lung Allograft and Clinical Outcomes in Lung Transplant Recipients: A Case-control Study

BACKGROUND

The impacts of COVID-19 on lung allograft function, rejection, secondary infection, and clinical outcomes in lung transplant recipients (LTRs) remain unknown.

METHODS

A 1:2 matched case-control study was performed to evaluate rehospitalization, lung allograft function, and secondary infections up to 90 d after COVID-19 diagnosis (or index dates for controls).

RESULTS

Twenty-four LTRs with COVID-19 (cases) and 48 controls were identified. Cases and controls had similar baseline characteristics and lung allograft function. LTRs with COVID-19 had higher incidence of secondary bacterial infection (29.2% versus 6.3%, P = 0.008), readmission (29.2% versus 10.4%, P = 0.04), and for-cause bronchoscopy (33.3% versus 12.5%, P = 0.04) compared with controls. At d 90, mortality in cases versus controls was 8.3% versus 2.1% (P = 0.21), incidence of invasive fungal infections in cases versus controls was 20.8% versus 8.3% (P = 0.13) and forced expiratory volume in 1 s (FEV1) decline ≥10% from baseline occurred in 19% of cases versus 12.2% of controls (P = 0.46). No acute cellular rejection, acute antibody-mediated rejection, or new donor-specific anti-HLA antibodies were observed among cases or controls within 90 d post index date.

CONCLUSIONS

We found LTRs with COVID-19 were at risk to develop secondary infections and rehospitalization post COVID-19, compared with controls. While we did not observe post viral acute cellular rejection or antibody-mediated rejection, further studies are needed to understand if LTRs with COVID-19 who did not recover baseline lung function within 90 d have developed chronic lung allograft dysfunction stage progression.

Co-infection of SARS-CoV-2 and influenza viruses: A systematic review and meta-analysis

We conducted this meta-analysis to determine the proportion of co-infection with influenza viruses in SARS-CoV-2 positive patients and to investigate the severity of COVID-19 in these patients. We included studies with SARS-CoV-2 infection confirmed by qRT-PCR and influenza virus infection (A and/or B) by nucleic acid tests. The proportion of co-infection was compared between children and adults, and between critically ill or deceased patients compared to overall patients. Fifty-four articles were included. The overall proportion of co-infection was 0.7%, 95%CI = [0.4 – 1.3]. Most influenza co-infections were due to the influenza A virus (74.4%). The proportion of co-infection with influenza viruses among children (3.2%, 95% CI = [0.9 – 10.9]) was significantly higher than that in adult patients (0.3%, 95% CI = [0.1 – 1.2]), p-value <0.01. The proportion of co-infection with influenza viruses among critically ill patients tended to be higher than that in overall patients (2.2%, 95% CI = [0.3 – 22.4] versus 0.6%, 95% CI = [0.3 – 1.2], respectively, p-value = 0.22). Screening for pathogens in co-infection, particularly influenza viruses in patients infected with SARS-CoV-2, is necessary. This warrants close surveillance and investigation of the co-incidences and interactions of SARS-CoV-2 and other respiratory viruses, which is facilitated by the expansion of syndromic diagnosis approaches through the use of multiplex PCR assays.

Dynamics of SARS-CoV2 Infection and Multi-Drug Resistant Bacteria Superinfection in Patients With Assisted Mechanical Ventilation

Objective

To investigate the presence of bacteria and fungi in bronchial aspirate (BA) samples from 43 mechanically ventilated patients with severe COVID-19 disease.

Methods

Detection of SARS-CoV-2 was performed using Allplex 2019-nCoV assay kits. Isolation and characterisation of bacteria and fungi were carried out in BA specimens treated with 1X dithiothreitol 1% for 30 min at room temperature, using standard culture procedures.

Results

Bacterial and/or fungal superinfection was detected in 25 out of 43 mechanically ventilated patients, generally after 7 days of hospitalisation in an intensive care unit (ICU). Microbial colonisation (colony forming units (CFU) <1000 colonies/ml) in BA samples was observed in 11 out of 43 patients, whereas only 7 patients did not show any signs of bacterial or fungal growth. Pseudomonas aeruginosa was identified in 17 patients. Interestingly, 11 out of these 17 isolates also showed carbapenem resistance. The molecular analysis demonstrated that resistance to carbapenems was primarily related to OprD mutation or deletion. Klebsiella pneumoniae was the second most isolated pathogen found in 13 samples, of which 8 were carbapenemase-producer strains.

Conclusion

These data demonstrate the detection of bacterial superinfection and antimicrobial resistance in severe SARS-CoV-2-infected patients and suggest that bacteria may play an important role in COVID-19 evolution. A prospective study is needed to verify the incidence of bacterial and fungal infections and their influence on the health outcomes of COVID-19 patients.

Viral and Bacterial Co-Infections in the Lungs: Dangerous Liaisons

Respiratory tract infections constitute a significant public health problem, with a therapeutic arsenal that remains relatively limited and that is threatened by the emergence of antiviral and/or antibiotic resistance. Viral–bacterial co-infections are very often associated with the severity of these respiratory infections and have been explored mainly in the context of bacterial superinfections following primary influenza infection. This review summarizes our current knowledge of the mechanisms underlying these co-infections between respiratory viruses (influenza viruses, RSV, and SARS-CoV-2) and bacteria, at both the physiological and immunological levels. This review also explores the importance of the microbiome and the pathological context in the evolution of these respiratory tract co-infections and presents the different in vitro and in vivo experimental models available. A better understanding of the complex functional interactions between viruses/bacteria and host cells will allow the development of new, specific, and more effective diagnostic and therapeutic approaches.

Immunometabolic signatures predict risk of progression to sepsis in COVID-19

Viral sepsis has been proposed as an accurate term to describe all multisystemic dysregulations and clinical findings in severe and critically ill COVID-19 patients. The adoption of this term may help the implementation of more accurate strategies of early diagnosis, prognosis, and in-hospital treatment. We accurately quantified 110 metabolites using targeted metabolomics, and 13 cytokines/chemokines in plasma samples of 121 COVID-19 patients with different levels of severity, and 37 non-COVID-19 individuals. Analyses revealed an integrated host-dependent dysregulation of inflammatory cytokines, neutrophil activation chemokines, glycolysis, mitochondrial metabolism, amino acid metabolism, polyamine synthesis, and lipid metabolism typical of sepsis processes distinctive of a mild disease. Dysregulated metabolites and cytokines/chemokines showed differential correlation patterns in mild and critically ill patients, indicating a crosstalk between metabolism and hyperinflammation. Using multivariate analysis, powerful models for diagnosis and prognosis of COVID-19 induced sepsis were generated, as well as for mortality prediction among septic patients. A metabolite panel made of kynurenine/tryptophan ratio, IL-6, LysoPC a C18:2, and phenylalanine discriminated non-COVID-19 from sepsis patients with an area under the curve (AUC (95%CI)) of 0.991 (0.986-0.995), with sensitivity of 0.978 (0.963-0.992) and specificity of 0.920 (0.890-0.949). The panel that included C10:2, IL-6, NLR, and C5 discriminated mild patients from sepsis patients with an AUC (95%CI) of 0.965 (0.952-0.977), with sensitivity of 0.993(0.984-1.000) and specificity of 0.851 (0.815-0.887). The panel with citric acid, LysoPC a C28:1, neutrophil-lymphocyte ratio (NLR) and kynurenine/tryptophan ratio discriminated severe patients from sepsis patients with an AUC (95%CI) of 0.829 (0.800-0.858), with sensitivity of 0.738 (0.695-0.781) and specificity of 0.781 (0.735-0.827). Septic patients who survived were different from those that did not survive with a model consisting of hippuric acid, along with the presence of Type II diabetes, with an AUC (95%CI) of 0.831 (0.788-0.874), with sensitivity of 0.765 (0.697-0.832) and specificity of 0.817 (0.770-0.865).

Pan-drug resistant Providencia rettgeri contributing to a fatal case of COVID-19

Following prolonged hospitalization that included broad-spectrum antibiotic exposure, a strain of Providencia rettgeri was cultured from the blood of a patient undergoing extracorporeal membrane oxygenation treatment for hypoxic respiratory failure due to COVID-19. The strain was resistant to all antimicrobials tested including the novel siderophore cephalosporin, cefiderocol. Whole genome sequencing detected ten antimicrobial resistance genes, including the metallo-β-lactamase bla _NDM-1, the extended-spectrum β-lactamase bla _PER-1, and the rare 16S methyltransferase rmtB2.

Evaluation of procalcitonin-guided antimicrobial stewardship in patients admitted to hospital with COVID-19 pneumonia

Background

Procalcitonin is a biomarker that may be able to identify patients with COVID-19 pneumonia who do not require antimicrobials for bacterial respiratory tract co-infections.

Objectives

To evaluate the safety and effectiveness of a procalcitonin-guided algorithm in rationalizing empirical antimicrobial prescriptions in non-critically ill patients with COVID-19 pneumonia.

Methods

Retrospective, single-site, cohort study in adults hospitalized with confirmed or suspected COVID-19 pneumonia and receiving empirical antimicrobials for potential bacterial respiratory tract co-infection. Regression models were used to compare the following outcomes in patients with and without procalcitonin testing within 72 h of starting antimicrobials: antimicrobial consumption (DDD); antimicrobial duration; a composite safety outcome of death, admission to HDU/ICU or readmission to hospital within 30 days; and length of admission. Procalcitonin levels of ≤0.25 ng/L were interpreted as negatively predictive of bacterial co-infection. Effects were expressed as ratios of means (ROM) or prevalence ratios (PR) accordingly.

Results

259 patients were included in the final analysis. Antimicrobial use was lower in patients who had procalcitonin measured within 72 h of starting antimicrobials: mean antimicrobial duration 4.4 versus 5.4 days, adjusted ROM 0.7 (95% CI 0.6-0.9); mean antimicrobial consumption 6.8 versus 8.4 DDD, adjusted ROM 0.7 (95% CI 0.6-0.8). Both groups had similar composite safety outcomes (adjusted PR 0.9; 95% CI 0.6-1.3) and lengths of admission (adjusted ROM 1.3; 95% CI 0.9-1.6).

Conclusions

A procalcitonin-guided algorithm may allow for the safe reduction of antimicrobial usage in hospitalized non-critically ill patients with COVID-19 pneumonia.

Incidence, Risk Factors and Impact on Clinical Outcomes of Bloodstream Infections in Patients Hospitalised with COVID-19: A Prospective Cohort Study

With the aim of describing the burden and epidemiology of community-acquired/healthcare-associated and hospital-acquired bloodstream infections (CA/HCA-BSIs and HA-BSIs) in patients hospitalised with COVID-19, and evaluating the risk factors for BSIs and their relative impact on mortality, an observational cohort study was performed on patients hospitalised with COVID-19 at San Paolo Hospital in Milan, Italy from 24 February to 30 November 2020. Among 1351 consecutive patients hospitalised with COVID-19, 18 (1.3%) had CA/HCA-BSI and 51 (3.8%) HA-BSI for a total of 82 episodes of BSI. The overall incidence of HA-BSI was 3.3/1000 patient-days (95% CI 2.4-4.2). Patients with HA-BSI had a longer hospital stay compared to CA/HCA-BSI and no-BSI groups (27 (IQR 21-35) vs. 12 (7-29) vs. 9 (5-17) median-days, p < 0.001) but a similar in-hospital mortality (31% vs. 33% vs. 25%, p = 0.421). BSI was not associated with an increased risk of mortality (CA/HCA-BSI vs. non-BSI aOR 1.27 95% CI 0.41-3.90, p = 0.681; HA-BSI vs. non-BSI aOR 1.29 95% CI 0.65-2.54, p = 0.463). Upon multivariate analysis, NIMV/CPAP (aOR 2.09, 95% CI 1.06-4.12, p = 0.034), IMV (aOR 5.13, 95% CI 2.08-12.65, p < 0.001) and corticosteroid treatment (aOR 2.11, 95% CI 1.06-4.19, p = 0.032) were confirmed as independent factors associated with HA-BSI. Development of HA-BSI did not significantly affect mortality. Patients treated with corticosteroid therapy had double the risk of developing BSI.

The microbiota-related coinfections in COVID-19 patients: a real challenge

BACKGROUND

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of ongoing global pandemic of coronavirus disease 2019 (COVID-19), has infected millions of people around the world, especially the elderly and immunocompromised individuals. The infection transmission rate is considered more rapid than other deadly pandemics and severe epidemics encountered earlier, such as Ebola, Zika, Influenza, Marburg, SARS, and MERS. The public health situation therefore is really at a challenging crossroads.

MAIN BODY

The internal and external and resident microbiota community is crucial in human health and is essential for immune responses. This community tends to be altered due to pathogenic infections which would lead to severity of the disease as it progresses. Few of these resident microflora become negatively active during infectious diseases leading to coinfection, especially the opportunistic pathogens. Once such a condition sets in, it is difficult to diagnose, treat, and manage COVID-19 in a patient.

CONCLUSION

This review highlights the various reported possible coinfections that arise in COVID-19 patients vis-à-vis other serious pathological conditions. The local immunity in lungs, nasal passages, oral cavity, and salivary glands are involved with different aspects of COVID-19 transmission and pathology. Also, the role of adaptive immune system is discussed at the site of infection to control the infection along with the proinflammatory cytokine therapy.

Multi-Drug Resistance Bacterial Infections in Critically Ill Patients Admitted with COVID-19

Introduction. It is known that bacterial infections represent a common complication during viral respiratory tract infections such as influenza, with a concomitant increase in morbidity and mortality. Nevertheless, the prevalence of bacterial co-infections and secondary infections in critically ill patients affected by coronavirus disease 2019 (COVID-19) is not well understood yet. We performed a review of the literature currently available to examine the incidence of bacterial secondary infections acquired during hospital stay and the risk factors associated with multidrug resistance. Most of the studies, mainly retrospective and single-centered, highlighted that the incidence of co-infections is low, affecting about 3.5% of hospitalized patients, while the majority are hospital acquired infections, developed later, generally 10–15 days after ICU admission. The prolonged ICU hospitalization and the extensive use of broad-spectrum antimicrobial drugs during the COVID-19 outbreak might have contributed to the selection of pathogens with different profiles of resistance. Consequently, the reported incidence of MDR bacterial infections in critically ill COVID-19 patients is high, ranging between 32% to 50%. MDR infections are linked to a higher length of stay in ICU but not to a higher risk of death. The only risk factor independently associated with MDR secondary infections reported was invasive mechanical ventilation (OR 1.062; 95% CI 1.012–1.114), but also steroid therapy and prolonged length of ICU stay may play a pivotal role. The empiric antimicrobial therapy for a ventilated patient with suspected or proven bacterial co-infection at ICU admission should be prescribed judiciously and managed according to a stewardship program in order to interrupt or adjust it on the basis of culture results.

Nosocomial infections among COVID-19 patients: an analysis of intensive care unit surveillance data

Surveillance of nosocomial infections, like catheter-associated urinary tract infection (CAUTI), central line-associated bloodstream infection, possible ventilator-associated pneumonia and secondary bloodstream infections were observed to study the impact of COVID-19 outbreak in ICUs from Tan Tock Seng Hospital and National Centre for Infectious Diseases, Singapore between February and June 2020. Higher nosocomial infection rates were observed in COVID-19 patients, although it was not statistically significant. Moreover, COVID-19 patients seem to be more predisposed to CAUTI despite a higher proportion of non-COVID-19 patients having urinary catheters. Thus, continued vigilance to ensure adherence to IPC measures is needed.

Characterization of Secondary Bacterial Infections and Antibiotic Use in Mechanically Ventilated Patients With COVID-19 Induced Acute Respiratory Distress Syndrome

Background:

COVID-19 has a widely variable clinical syndrome that is difficult to distinguish from bacterial sepsis, leading to high rates of antibiotic use. Early studies indicate low rates of secondary bacterial infections (SBIs) but have included heterogeneous patient populations. Here, we catalogue all SBIs and antibiotic prescription practices in a population of mechanically ventilated patients with COVID-19 induced acute respiratory distress syndrome (ARDS).

Methods:

This was a retrospective cohort study of all patients with COVID-19 ARDS requiring mechanical ventilation from 3 Seattle, Washington hospitals in 2020. Data were obtained via electronic and manual review of the electronic medical record. We report the incidence and site of SBIs, mortality, and antibiotics per day using descriptive statistics.

Results:

We identified 126 patients with COVID-19 induced ARDS during the study period. Of these patients, 61% developed clinical infection confirmed by bacterial culture. Ventilator associated pneumonia was confirmed in 55% of patients, bacteremia in 20%, and urinary tract infection (UTI) in 17%. Staphylococcus aureus was the most commonly isolated bacterial species. A total of 97% of patients received antibiotics during their hospitalization, and patients received nearly one antibiotic per day during their hospital stay.

Conclusions:

Mechanically ventilated patients with COVID-19 induced ARDS are at high risk for secondary bacterial infections and have extensive antibiotic exposure.

Paradigm Shift in Antimicrobial Resistance Pattern of Bacterial Isolates during the COVID-19 Pandemic

Antimicrobial resistance (AMR) is an emerging public health problem in modern times and the current COVID-19 pandemic has further exaggerated this problem. Due to bacterial co-infection in COVID-19 cases, an irrational consumption of antibiotics has occurred during the pandemic. This study aimed to observe the COVID-19 patients hospitalized from 1 March 2019 to 31 December 2020 and to evaluate the AMR pattern of bacterial agents isolated. This was a single-center study comprising 494 bacterial isolates (blood and urine) that were obtained from patients with SARS-CoV-2 admitted to the ICU and investigated in the Department of Microbiology of a tertiary care hospital in Delhi, India. Out of the total bacterial isolates, 55.46% were gram negative and 44.53% were gram positive pathogens. Of the blood samples processed, the most common isolates were CoNS (Coagulase Negative Staphylococcus) and Staphylococcus aureus. Amongst the urinary isolates, most common pathogens were Escherichia coli and Staphylococcus aureus. A total of 60% MRSA was observed in urine and blood isolates. Up to 40% increase in AMR was observed amongst these isolates obtained during COVID-19 period compared to pre-COVID-19 times. The overuse of antibiotics gave abundant opportunity for the bacterial pathogens to gradually develop mechanisms and to acquire resistance. Since the dynamics of SARS-COV-2 are unpredictable, a compromise on hospital antibiotic policy may ultimately escalate the burden of drug resistant pathogens in hospitals. A shortage of trained staff during COVID-19 pandemic renders it impossible to maintain these records in places where the entire hospital staff is struggling to save lives. This study highlights the extensive rise in the use of antibiotics for respiratory illness due to COVID-19 compared to antibiotic use prior to COVID-19 in ICUs. The regular prescription audit followed by a constant surveillance of hospital infection control practices by the dedicated teams and training of clinicians can improve the quality of medications in the long run and help to fight the menace of AMR.

Contemporary narrative review of treatment options for COVID-19

The coronavirus disease 2019 (COVID-19) pandemic is ongoing and many drugs have been studied in clinical trials. From a pathophysiological perspective, anti-viral drugs may be more effective in the early stage while immunomodulators may be more effective in severe patients in later stages of infection. While drugs such as lopinavir-ritonavir, hydroxychloroquine and azithromycin have proved to be ineffective in randomized controlled trials, corticosteroids, neutralizing monoclonal antibodies, remdesivir, tocilizumab and baricitinib have been reported to benefit certain groups of patients with COVID-19. In this review, we will present the key clinical evidence and progress in promising COVID-19 therapeutics, as well as summarize the experience and lessons learned from the development of the current therapeutics.

Host factors facilitating SARS-CoV-2 virus infection and replication in the lungs

SARS-CoV-2 is the virus causing the major pandemic facing the world today. Although, SARS-CoV-2 primarily causes lung infection, a variety of symptoms have proven a systemic impact on the body. SARS-CoV-2 has spread in the community quickly infecting humans from all age, ethnicities and gender. However, fatal outcomes have been linked to specific host factors and co-morbidities such as age, hypertension, immuno-deficiencies, chronic lung diseases or metabolic disorders. A major shift in the microbiome of patients suffering of the coronavirus disease 2019 (COVID-19) have also been observed and is linked to a worst outcome of the disease. As many co-morbidities are already known to be associated with a dysbiosis of the microbiome such as hypertension, diabetes and metabolic disorders. Host factors and microbiome changes are believed to be involved as a network in the acquisition of the infection and the development of the diseases. We will review in detail in this manuscript, the immune response toward SARS-CoV-2 infection as well as the host factors involved in the facilitation and worsening of the infection. We will also address the impact of COVID-19 on the host's microbiome and secondary infection which also worsen the disease.

Predisposition of COVID-19 patients to secondary infections: set in stone or subject to change?

PURPOSE OF REVIEW

There likely are several predisposing factors to secondary infections in patients with Coronavirus disease 2019 (COVID-19), some of which may be preventable. The aim of this review is to explore the literature, summarize potential predisposing factors to secondary infections and their incidence. It also summarizes a variety of healthcare scenarios in which different kinds of secondary infections occur.

RECENT FINDINGS

Apart from immune dysregulation, severe resource limitations in healthcare settings have made COVID-19 units conducive to a variety of secondary infections. Long-term effect of excess antibiotic use in COVID-19 patients is yet to be studied. Very few studies have assessed secondary infections as the primary outcome measure making it difficult to know the true incidence. Mortality attributable to secondary infections in COVID-19 patients is also unclear.

SUMMARY

Incidence of secondary infections in COVID-19 patients is likely higher than what is reported in the literature. Well designed studies are needed to understand the incidence and impact of secondary infections in this patient population. Many of these may be preventable especially now, as personal protective equipment and other healthcare resources are recovering. Infection prevention and control (IPC) and antimicrobial stewardship programmes (ASP) must reassess current situation to correct any breaches that could potentially cause more harm in these already vulnerable patients as we brace for a future surge with another pandemic wave.

Antimicrobial stewardship in the ICU in COVID times: the known unknowns

Since the start of the COVID-19 pandemic, there has been concern about the concomitant rise of antimicrobial resistance. While bacterial co-infections seem rare in COVID-19 patients admitted to hospital wards and intensive care units (ICUs), an increase in empirical antibiotic use has been described. In the ICU setting, where antibiotics are already abundantly—and often inappropriately—prescribed, the need for an ICU-specific antimicrobial stewardship programme is widely advocated. Apart from essentially warning against the use of antibacterial drugs for the treatment of a viral infection, other aspects of ICU antimicrobial stewardship need to be considered in view of the clinical course and characteristics of COVID-19. First, the distinction between infectious and non-infectious (inflammatory) causes of respiratory deterioration during an ICU stay is difficult, and the much-debated relevance of fungal and viral co-infections adds to the complexity of empirical antimicrobial prescribing. Biomarkers such as procalcitonin for the decision to start antibacterial therapy for ICU nosocomial infections seem to be more promising in COVID-19 than non-COVID-19 patients. In COVID-19 patients, cytomegalovirus reactivation is an important factor to consider when assessing patients infected with SARS-CoV-2 as it may have a role in modulating the patient immune response. The diagnosis of COVID-19-associated invasive aspergillosis is challenging because of the lack of sensitivity and specificity of the available tests. Furthermore, altered pharmacokinetic/pharmacodynamic properties need to be taken into account when prescribing antimicrobial therapy. Future research should now further explore the ‘known unknowns’, ideally with robust prospective study designs.

Risk factors and outcomes associated with community-onset and hospital-acquired coinfection in patients hospitalized for coronavirus disease 2019 (COVID-19): A multihospital cohort study

Background:

We sought to determine the incidence of community-onset and hospital-acquired coinfection in patients hospitalized with coronavirus disease 2019 (COVID-19) and to evaluate associated predictors and outcomes.

Methods:

In this multicenter retrospective cohort study of patients hospitalized for COVID-19 from March 2020 to August 2020 across 38 Michigan hospitals, we assessed prevalence, predictors, and outcomes of community-onset and hospital-acquired coinfections. In-hospital and 60-day mortality, readmission, discharge to long-term care facility (LTCF), and mechanical ventilation duration were assessed for patients with versus without coinfection.

Results:

Of 2,205 patients with COVID-19, 141 (6.4%) had a coinfection: 3.0% community onset and 3.4% hospital acquired. Of patients without coinfection, 64.9% received antibiotics. Community-onset coinfection predictors included admission from an LTCF (OR, 3.98; 95% CI, 2.34–6.76; P < .001) and admission to intensive care (OR, 4.34; 95% CI, 2.87–6.55; P < .001). Hospital-acquired coinfection predictors included fever (OR, 2.46; 95% CI, 1.15–5.27; P = .02) and advanced respiratory support (OR, 40.72; 95% CI, 13.49–122.93; P < .001). Patients with (vs without) community-onset coinfection had longer mechanical ventilation (OR, 3.31; 95% CI, 1.67–6.56; P = .001) and higher in-hospital mortality (OR, 1.90; 95% CI, 1.06–3.40; P = .03) and 60-day mortality (OR, 1.86; 95% CI, 1.05–3.29; P = .03). Patients with (vs without) hospital-acquired coinfection had higher discharge to LTCF (OR, 8.48; 95% CI, 3.30–21.76; P < .001), in-hospital mortality (OR, 4.17; 95% CI, 2.37–7.33; P ≤ .001), and 60-day mortality (OR, 3.66; 95% CI, 2.11–6.33; P ≤ .001).

Conclusion:

Despite community-onset and hospital-acquired coinfection being uncommon, most patients hospitalized with COVID-19 received antibiotics. Admission from LTCF and to ICU were associated with increased risk of community-onset coinfection. Future studies should prospectively validate predictors of COVID-19 coinfection to facilitate the reduction of antibiotic use.

Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.

AIM

To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.

METHODS

The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients' records and the microbiology laboratory data to identify patients' demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.

RESULTS

The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.

CONCLUSION

Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.

Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.

AIM

To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.

METHODS

The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients’ records and the microbiology laboratory data to identify patients’ demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.

RESULTS

The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.

CONCLUSION

Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.

Co-infections and superinfections complicating COVID-19 in cancer patients: A multicentre, international study

Background

We aimed to describe the epidemiology, risk factors, and clinical outcomes of co-infections and superinfections in onco-hematological patients with COVID-19.

Methods

International, multicentre cohort study of cancer patients with COVID-19. All patients were included in the analysis of co-infections at diagnosis, while only patients admitted at least 48 h were included in the analysis of superinfections.

Results

684 patients were included (384 with solid tumors and 300 with hematological malignancies). Co-infections and superinfections were documented in 7.8% (54/684) and 19.1% (113/590) of patients, respectively. Lower respiratory tract infections were the most frequent infectious complications, most often caused by Streptococcus pneumoniae and Pseudomonas aeruginosa. Only seven patients developed opportunistic infections. Compared to patients without infectious complications, those with infections had worse outcomes, with high rates of acute respiratory distress syndrome, intensive care unit (ICU) admission, and case-fatality rates. Neutropenia, ICU admission and high levels of C-reactive protein (CRP) were independent risk factors for infections.

Conclusions

Infectious complications in cancer patients with COVID-19 were lower than expected, affecting mainly neutropenic patients with high levels of CRP and/or ICU admission. The rate of opportunistic infections was unexpectedly low. The use of empiric antimicrobials in cancer patients with COVID-19 needs to be optimized.

Tackling Antimicrobial Resistance in the Shadow of COVID-19

The coronavirus disease 2019 (COVID-19) pandemic is a challenge for ongoing efforts to combat antimicrobial-resistant (AMR) bacterial infections. As we learn more about COVID-19 disease and drug stewardship evolves, there is likely to be a lasting impact of increased use of antimicrobial agents and antibiotics, as well as a lack of consistent access to health care across many populations. Sexually transmitted infections have been underreported during the pandemic and are often caused by some of the most drug-resistant pathogens. In their recent article in mBio, Parzych et al. (E. M. Parzych, S. Gulati, B. Zheng, M. A. Bah, et al., mBio 12:e00242-21, 2021, https://doi.org/10.1128/mBio.00242-21) focus on protection against Neisseria gonorrhoeae infection via in vivo delivery of an antigonococcal DNA-encoded antibody that has been modified for increased complement activation. Nucleic acid approaches are highly adaptable and could be tremendously beneficial for personalized strategies to combat AMR pathogens.

Association between Early Antibiotic Therapy and In-Hospital Mortality among Older Patients with SARS-CoV-2 Pneumonia

Background

It is uncertain whether antibiotic therapy should be started in SARS CoV-2 pneumonia. We aimed to investigate the association between early antibiotic therapy and the risk of in-hospital mortality in older patients.

Methods

We performed a retrospective international cohort study (ANTIBIOVID) in five COVID-19 geriatric units in France and Switzerland. Among 1,357 consecutive patients aged 75 or more hospitalised and testing positive for SARS-CoV-2, 1072 had a radiologically confirmed pneumonia, of which 914 patients were still alive and hospitalized at 48 hours. To adjust for confounders, a propensity score for treatment was created, and stabilized inverse probability of treatment weighting (SIPTW) was applied. To assess the association between early antibiotic therapy and in-hospital 30-day mortality, SIPTW-adjusted Kaplan-Meier and Cox proportional hazards regression analyses were performed.

Results

Of the 914 patients with SARS-CoV-2 pneumonia, median age of 86, 428 (46.8%) received antibiotics in the first 48 hours after diagnosis. Among these patients, 147 (34.3%) died in hospital within one month vs 118 patients (24.3%) with no early antibiotic treatment. After SIPTW, early antibiotic treatment was not significantly associated with mortality (adjusted hazard ratio, 1.23; 95% CI, 0.92-1.63; P = .160). Microbiologically confirmed superinfections occurred rarely in both groups (bacterial pneumonia: 2.5% vs 1.5%, P = .220; blood stream infection: 8.2% vs 5.2%, P = .120; Clostridioides difficile colitis: 2.4% vs 1.0%, P = .222).

Conclusions

In a large multicentre cohort of older inpatients with SARS-CoV-2 pneumonia, early antibiotic treatment did not appear to be associated with an improved prognosis.

SARS-CoV-2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance

Understanding how SARS-CoV-2 spreads within the respiratory tract is important to define the parameters controlling the severity of COVID-19. Here we examine the functional and structural consequences of SARS-CoV-2 infection in a reconstructed human bronchial epithelium model. SARS-CoV-2 replication causes a transient decrease in epithelial barrier function and disruption of tight junctions, though viral particle crossing remains limited. Rather, SARS-CoV-2 replication leads to a rapid loss of the ciliary layer, characterized at the ultrastructural level by axoneme loss and misorientation of remaining basal bodies. Downregulation of the master regulator of ciliogenesis Foxj1 occurs prior to extensive cilia loss, implicating this transcription factor in the dedifferentiation of ciliated cells. Motile cilia function is compromised by SARS-CoV-2 infection, as measured in a mucociliary clearance assay. Epithelial defense mechanisms, including basal cell mobilization and interferon-lambda induction, ramp up only after the initiation of cilia damage. Analysis of SARS-CoV-2 infection in Syrian hamsters further demonstrates the loss of motile cilia in vivo. This study identifies cilia damage as a pathogenic mechanism that could facilitate SARS-CoV-2 spread to the deeper lung parenchyma.

Application of an evidence-based, out-patient treatment strategy for COVID-19: Multidisciplinary medical practice principles to prevent severe disease

The COVID-19 pandemic has devastated individuals, families, and institutions throughout the world. Despite the breakneck speed of vaccine development, the human population remains at risk of further devastation. The decision to not become vaccinated, the protracted rollout of available vaccine, vaccine failure, mutational forms of the SARS virus, which may exhibit mounting resistance to our molecular strike at only one form of the viral family, and the rapid ability of the virus(es) to hitch a ride on our global transportation systems, means that we are will likely continue to confront an invisible, yet devastating foe. The enemy targets one of our human physiology's most important and vulnerable life-preserving body tissues, our broncho-alveolar gas exchange apparatus. Notwithstanding the fear and the fury of this microbe's potential to raise existential questions across the entire spectrum of human endeavor, the application of an early treatment intervention initiative may represent a crucial tool in our defensive strategy. This strategy is driven by evidence-based medical practice principles, those not likely to become antiquated, given the molecular diversity and mutational evolution of this very clever "world traveler".

Bacterial infections in critically ill patients with SARS-2-COVID-19 infection: results of a prospective observational multicenter study

Purpose

To investigate the prevalence, incidence and characteristics of bacterial infections and their impact on outcome in critically ill patients infected with COVID-19.

Methods

We conducted a prospective observational study in eight Italian ICUs from February to May 2020; data were collected through an interactive electronic database. Kaplan–Meier analysis (limit product method) was used to identify the occurrence of infections and risk of acquisition.

Results

During the study period 248 patients were recruited in the eight participating ICUs. Ninety (36.3%) patients developed at least one episode of secondary infection. An ICU length of stay between 7 and 14 days was characterized by a higher occurrence of infectious complications, with ventilator-associated pneumonia being the most frequent. At least one course of antibiotic therapy was given to 161 (64.9%) patients. Overall ICU and hospital mortality were 33.9% and 42.9%, respectively. Patients developing bacteremia had a higher risk of ICU mortality [45.9% vs. 31.6%, odds ratio 1.8 (95% CI 0.9–3.7), p = 0.069] and hospital mortality [56.8% vs. 40.3%, odds ratio 1.9 (95% CI 1.1–3.9), p = 0.04].

Conclusion

In critically ill patients infected with COVID-19 the incidence of bacterial infections is high and associated with worse outcomes. Regular microbiological surveillance and strict infection control measures are mandated.

Supplementary Information

The online version contains supplementary material available at 10.1007/s15010-021-01661-2.

COVID-19 and invasive fungal coinfections: A case series at a Brazilian referral hospital

Background

COVID-19 co-infections have been described with different pathogens, including filamentous and yeast fungi.

Methodology

A retrospective case series study conducted from February to December 2020, at a Brazilian university hospital. Data were collected from two hospital surveillance systems: Invasive fungal infection (IFI) surveillance (Mycosis Resistance Program - MIRE) and COVID-19 surveillance. Data from both surveillance systems were cross-checked to identify individuals diagnosed with SARS-CoV-2 (by positive polymerase chain reaction (PCR)) and IFI during hospital stays within the study period.

Results

During the study period, 716 inpatients with COVID-19 and 55 cases of IFI were identified. Fungal co-infection with SARS-CoV-2 was observed in eight (1%) patients: three cases of aspergillosis; four candidemia and one cryptococcosis. The median age of patients was 66 years (IQR 58-71 years; range of 28-77 years) and 62.5% were men. Diagnosis of IFI occurred a median of 11.5 days (IQR 4.5-23 days) after admission and 11 days (IQR 6.5-16 days) after a positive PCR result for SARS-CoV-2. In 75% of cases, IFI was diagnosed in the intensive care unit (ICU). Cases of aspergillosis emerged earlier than those of candidemia: an average of 8.6 and 28.6 days after a positive PCR for SARS-CoV-2, respectively. All the patients with both infections ultimately died.

Conclusion

A low rate of COVID-19 co-infection with IFI was observed, with high mortality. Most cases were diagnosed in ICU patients. Aspergillosis diagnosis is highly complex in this context and requires different criteria.

Antifungal Drug Susceptibility and Genetic Characterization of Fungi Recovered from COVID-19 Patients

Fungal infections are common complications of respiratory viral infections and are associated with the increased need for intensive care and elevated mortality. Data regarding microbiological and molecular characteristics of such infections in COVID-19 patients are scarce. Here, we performed a comprehensive analysis, including species identification, antifungal susceptibility testing, molecular resistance determinants analysis, typing, and retrospective clinical data review, of fungal isolates recovered from 19 COVID-19 patients, who were hospitalized at the Hackensack University Medical Center (HUMC) in Hackensack, New Jersey, USA, in the initial phase of the pandemic from April–May 2020. In total, 17 Candida albicans, two C. parapsilosis, and two Aspergillus fumigatus were analyzed. All Candida spp. isolates were susceptible to micafungin and azole drugs (fluconazole, voriconazole, posaconazole, itraconazole, isavuconazole). A. fumigatus isolates were susceptible to micafungin and all triazole drugs except fluconazole (intrinsic resistance). Multilocus sequence typing (MLST) of C. albicans isolates revealed 15 different sequence types (STs), which clustered below the clade-defining limit of p-distance < 0.04. Pulsed-field gel electrophoresis (PFGE) karyotyping revealed no chromosomal rearrangements in these isolates. A. fumigatus isolates were of different, non-related genotypes. We speculate that virus- and drug-induced immunosuppression (94.7% of the patients received corticosteroids), together with prolonged hospital stay (median duration of 29 days) and mechanical ventilation (median duration of 24 days) likely increased the susceptibility to secondary respiratory and bloodstream infections in the studied patient population. The presence of fungi in blood or respiratory tract fluid was a prognosticator for poor clinical outcome, which presented as an 89.5% 30-day mortality in our patient cohort.

Immunomodulatory therapy, risk factors and outcomes of hospital-acquired bloodstream infection in patients with severe COVID-19 pneumonia: a Spanish case-control matched multicentre study (BACTCOVID)

Objectives

The effect of the use of immunomodulatory drugs on the risk of developing hospital-acquired bloodstream infection (BSI) in patients with COVID-19 has not been specifically assessed. We aim to identify risk factors for, and outcomes of, BSI among hospitalized patients with severe COVID-19 pneumonia.

Methods

We performed a severity matched case–control study (1:1 ratio) nested in a large multicentre prospective cohort of hospitalized adults with COVID-19. Cases with BSI were identified from the cohort database. Controls were matched for age, sex and acute respiratory distress syndrome. A Cox proportional hazard ratio model was performed.

Results

Of 2005 patients, 100 (4.98%) presented 142 episodes of BSI, mainly caused by coagulase-negative staphylococci, Enterococcus faecalis and Pseudomonas aeruginosa. Polymicrobial infection accounted for 23 episodes. The median time from admission to the first episode of BSI was 15 days (IQR 9–20), and the most frequent source was catheter-related infection. The characteristics of patients with and without BSI were similar, including the use of tocilizumab, corticosteroids, and combinations. In the multivariate analysis, the use of these immunomodulatory drugs was not associated with an increased risk of BSI. A Cox proportional hazard ratio (HR) model showed that after adjusting for the time factor, BSI was associated with a higher in-hospital mortality risk (HR 2.59; 1.65–4.07; p < 0.001).

Discussion

Hospital-acquired BSI in patients with severe COVID-19 pneumonia was uncommon and the use of immunomodulatory drugs was not associated with its development. When adjusting for the time factor, BSI was associated with a higher mortality risk.

Microbial co-infections in COVID-19: Associated microbiota and underlying mechanisms of pathogenesis

The novel coronavirus infectious disease-2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has traumatized the whole world with the ongoing devastating pandemic. A plethora of microbial domains including viruses (other than SARS-CoV-2), bacteria, archaea and fungi have evolved together, and interact in complex molecular pathogenesis along with SARS-CoV-2. However, the involvement of other microbial co-pathogens and underlying molecular mechanisms leading to extortionate ailment in critically ill COVID-19 patients has yet not been extensively reviewed. Although, the incidence of co-infections could be up to 94.2% in laboratory-confirmed COVID-19 cases, the fate of co-infections among SARS-CoV-2 infected hosts often depends on the balance between the host's protective immunity and immunopathology. Predominantly identified co-pathogens of SARS-CoV-2 are bacteria such as Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, Acinetobacter baumannii, Legionella pneumophila and Clamydia pneumoniae followed by viruses including influenza, coronavirus, rhinovirus/enterovirus, parainfluenza, metapneumovirus, influenza B virus, and human immunodeficiency virus. The cross-talk between co-pathogens (especially lung microbiomes), SARS-CoV-2 and host is an important factor that ultimately increases the difficulty of diagnosis, treatment, and prognosis of COVID-19. Simultaneously, co-infecting microbiotas may use new strategies to escape host defense mechanisms by altering both innate and adaptive immune responses to further aggravate SARS-CoV-2 pathogenesis. Better understanding of co-infections in COVID-19 is critical for the effective patient management, treatment and containment of SARS-CoV-2. This review therefore necessitates the comprehensive investigation of commonly reported microbial co-pathogens amid COVID-19, their transmission pattern along with the possible mechanism of co-infections and outcomes. Thus, identifying the possible co-pathogens and their underlying molecular mechanisms during SARS-CoV-2 pathogenesis may shed light in developing diagnostics, appropriate curative and preventive interventions for suspected SARS-CoV-2 respiratory infections in the current pandemic.

Pharmacotherapy in Coronavirus Disease 2019 and Risk of Secondary Infections: A Single-Center Case Series and Narrative Review

Since the onset of the coronavirus disease 2019 pandemic, immune modulators have been considered front-line candidates for the management of patients presenting with clinical symptoms secondary to severe acute respiratory syndrome coronavirus 2 infection. Although heavy emphasis has been placed on early clinical efficacy, we sought to evaluate the impact of pharmacologic approach to coronavirus disease 2019 within the ICU on secondary infections and clinical outcomes.

DATA SOURCES

PubMed (inception to March 2021) database search and manual selection of bibliographies from selected articles.

STUDY SELECTION AND DATA EXTRACTION

Articles relevant to coronavirus disease 2019, management of severe acute respiratory syndrome coronavirus 2-associated respiratory failure, and prevalence of secondary infections with pharmacotherapies were selected. The MeSH terms "COVID-19," "secondary infection," "SARS-CoV-2," "tocilizumab," and "corticosteroids" were used for article identification. Articles were narratively synthesized for this review.

DATA SYNTHESIS

Current data surrounding the use of tocilizumab and/or corticosteroids for coronavirus disease 2019 management are limited given the short follow-up period and conflicting results between studies. Further complicating the understanding of immune modulator role is the lack of definitive understanding of clinical impact of the immune response in coronavirus disease 2019.

CONCLUSIONS

Based on the current available literature, we suggest prolonged trials and follow-up intervals for those patients managed with immune modulating agents for the management of coronavirus disease 2019.

Compassionate mesenchymal stem cell treatment in a severe COVID-19 patient: a case report

COVID-19 presentations range from cold-like symptoms to severe symptoms with the development of acute respiratory distress syndrome (ARDS). We report on a severe COVID-19 patient who was mechanically ventilated and who developed ARDS and bacterial infection. Because of rapid clinical deterioration and the exhaustion of other treatment options, the family and attending physicians requested a compassionate use of adult allogeneic bone marrow-derived mesenchymal stem cells (MSC) in addition to commonly used immunosuppressive, antiviral, and supportive therapy. The clinical course is discussed thoroughly, with a special emphasis on the safety and effect of MSC therapy. Compassionate MSC treatment, given in three rounds, affected ARDS regression. The patient was discharged from the intensive care unit after 31 days and from hospital after 49 days in a good general condition. MSC treatment was not associated with any side effects and was well tolerated in a three-week period; therefore, it should be studied in larger trials and considered for compassionate use.

COVID-19 in Solid Organ Transplant Recipients: a Review of the Current Literature

Purpose of review

The approach to ongoing organ transplantation and management of COVID-19 in solid organ transplant recipients (SOTR) has evolved tremendously since the pandemic’s beginning. We summarize the current literature surrounding the virology of SARS-CoV-2, epidemiology of COVID-19 in transplant recipients, review the clinical features and complications of COVID-19 in SOTR, and discuss the safety and efficacy of current therapies and candidate vaccines in this population.

Recent findings

Despite initial suspensions in organ transplantation during early 2020, routine donor testing and de-crowding of hospitals have allowed transplant activity to resume at pre-pandemic rates. COVID-19-associated mortality in SOTR is similar to that of the general population, and lower than that of patients with end-organ disease awaiting transplant. The optimal approach to immunosuppression in SOTR with COVID-19 is unknown and disease severity may influence management decisions. Many vaccines in development are likely to be safe for immunocompromised hosts, though post-marketing investigations will be required to determine the efficacy in the SOTR.

Summary

Though there are multiple unique considerations in the care of SOTR with COVID-19, immunosuppression does not appear to have a detrimental impact on overall outcome. Organ transplantation remains a lifesaving intervention and can be safely performed despite a global pandemic.

The Clinical Significance of Procalcitonin Elevation in Patients over 75 Years Old Admitted for COVID-19 Pneumonia

Aim

To investigate the clinical significance of procalcitonin (PCT) elevation on hospital admission for coronavirus disease-19 (COVID-19) and its association with mortality in oldest old patients (age > 75 years).

Methods

The clinical records of 1074 patients with chest high-resolution computed-tomography (HRCT) positive for interstitial pneumonia and symptoms compatible for COVID-19, hospitalized in medical wards during the first pandemic wave in a single academic center in Northern Italy, were retrospectively analyzed. All patients had serum PCT testing performed within six hours from admission. Information on COVID-19-related symptoms, comorbidities, drugs, autonomy in daily activities, respiratory exchanges, other routine lab tests, and outcomes were collected. Clinical characteristics were compared across different admission PCT levels and ages. The association of admission PCT with mortality was tested separately in participants aged > 75 and ≤75 years old by stepwise multivariate Cox regression model with forward selection.

Results

With increasing classes of PCT levels (<0.05, 0.05-0.49, 0.5-1.99, and ≥2 ng/ml), there was a significant trend (P < 0.0001) towards older age, male gender, wider extension of lung involvement on HRCT, worse respiratory exchanges, and several other laboratory abnormalities. Each incremental PCT class was associated with increased risk of hospital death at multivariate models in subjects older than 75 (hazard ratio for PCT ≥ 2 vs. <0.05 ng/ml: 30.629, 95% confidence interval 4.176-224.645, P = 0.001), but not in subjects aged 75 or younger.

Conclusions

In patients admitted for COVID-19, PCT elevation was associated with several clinical, radiological, and laboratory characteristics of disease severity. However, PCT elevation was strongly associated with hospital mortality only in oldest old subjects (age > 75).

Multidrug-resistant Acinetobacter baumannii infections in COVID-19 patients hospitalized in intensive care unit

Objectives

Superinfections in patients hospitalized in intensive care unit (ICU) are an important and challenging complication, also in COVID-19. However, no definitive data are available about the role of multidrug-resistant Acinetobacter baumannii (MDR-AB) in COVID-19.

Methods

This was a single-center, cross-sectional study including patients with MDR-AB infections admitted to ICU with or without COVID-19, between January 2019 and January 2021. The primary objective of the study was to evaluate risk factor for MDR-AB infections in ICU patients hospitalized for COVID-19 or other etiology. The secondary endpoints were 30-days mortality in all study population and risk factors associated with development of bloodstream infection (BSI).

Results

During the study period 32 adults with COVID-19 were enrolled and compared with 115 patients admitted in the same ICU for other reasons. We observed a total of 114 deaths, with a survival rate of 29.3%: 18.8% in COVID-19 and 32.2% in control group. Relative risk for MDR-AB infection in COVID-19 showed that serum lactate levels mmol/l > 2, Acinetobacter baumannii colonization, BSI and steroid therapy were observed more frequently in COVID-19 patients. Cox regression analysis showed that serum lactate levels > 2 mmol/l, Acinetobacter baumannii colonization, BSI, and steroid therapy were associated with 30-days mortality. Finally, patients with COVID-19, white blood cells count > 11,000 mm³, serum lactate levels > 2 mmol/l, infections at time of ICU admission, Acinetobacter baumannii colonization, and steroid therapy were independently associated with development of BSI.

Conclusions

Our data highlight the impact of BSI on outcome, the role of Acinetobacter baumannii colonization and the use of steroids on the risk to develop MDR-AB infections also during COVID-19.

Increase of Antimicrobial Consumption in a Tertiary Care Hospital during the First Phase of the COVID-19 Pandemic

Background: The COVID-19 pandemic poses novel challenges in antimicrobial consumption metrics and stewardship strategies. COVID-19 patients became the major cause of hospital admission during the first wave of the pandemic, often leading to an antimicrobial prescription upon admission or treatment for superinfections. The aim of this study was to understand how antimicrobial consumption was impacted at the beginning of the pandemic in a tertiary care hospital, a reference center for COVID-19. Materials and Methods: A retrospective before-and-after study was done. Descriptive statistics of discharges, patient-days, and antimicrobial use indicators (defined daily doses (DDD)/100 discharges, DDD/100 patient-days) for various groups were calculated for the first three months of the pandemic (March, April, and May 2020) as a quarterly value, and for each year in 2011–2019, and their annual percentage changes were used to estimate 95% confidence intervals. The indicators were compared to patient type (medical/surgical), type of admission (urgent/elective), and age groups using Spearman’s correlation coefficient. Results: Statistically significant increases occurred in 2020 for total antibacterials, macrolides, cephalosporins, amoxicillin/clavulanic acid, carbapenems, meropenem, and third-generation cephalosporins, while a reduction was seen in cefazolin/cefoxitin. A correlation was found between antibacterial consumption and patient or admission type. In 2020, unlike in pre-pandemic years, there was a different impact in DDD/100 discharges and DDD/100 patient-days due to increased lengths-of-stay and longer antimicrobial therapy. Conclusions: The COVID-19 pandemic led to an increase in antimicrobial consumption with a different impact in DDD/100 discharges and DDD/100 patient-days. This highlights the need to use both indicators simultaneously to better understand the causes of antimicrobial consumption variation and improve the design of effective antimicrobial stewardship interventions.

Coinfections with Bacteria, Fungi, and Respiratory Viruses in Patients with SARS-CoV-2: A Systematic Review and Meta-Analysis

Background: Coinfection with bacteria, fungi, and respiratory viruses in SARS-CoV-2 is of particular importance due to the possibility of increased morbidity and mortality. In this meta-analysis, we calculated the prevalence of such coinfections. Methods: Electronic databases were searched from 1 December 2019 to 31 March 2021. Effect sizes of prevalence were pooled with 95% confidence intervals (CIs). To minimize heterogeneity, we performed sub-group analyses. Results: Of the 6189 papers that were identified, 72 articles were included in the systematic review (40 case series and 32 cohort studies) and 68 articles (38 case series and 30 cohort studies) were included in the meta-analysis. Of the 31,953 SARS-CoV-2 patients included in the meta-analysis, the overall pooled proportion who had a laboratory-confirmed bacterial infection was 15.9% (95% CI 13.6–18.2, n = 1940, 49 studies, I² = 99%, p < 0.00001), while 3.7% (95% CI 2.6–4.8, n = 177, 16 studies, I² = 93%, p < 0.00001) had fungal infections and 6.6% (95% CI 5.5–7.6, n = 737, 44 studies, I² = 96%, p < 0.00001) had other respiratory viruses. SARS-CoV-2 patients in the ICU had higher co-infections compared to ICU and non-ICU patients as follows: bacterial (22.2%, 95% CI 16.1–28.4, I² = 88% versus 14.8%, 95% CI 12.4–17.3, I² = 99%), and fungal (9.6%, 95% CI 6.8–12.4, I² = 74% versus 2.7%, 95% CI 0.0–3.8, I² = 95%); however, there was an identical other respiratory viral co-infection proportion between all SARS-CoV-2 patients [(ICU and non-ICU) and the ICU only] (6.6%, 95% CI 0.0–11.3, I² = 58% versus 6.6%, 95% CI 5.5–7.7, I² = 96%). Funnel plots for possible publication bias for the pooled effect sizes of the prevalence of coinfections was asymmetrical on visual inspection, and Egger’s tests confirmed asymmetry (p values < 0.05). Conclusion: Bacterial co-infection is relatively high in hospitalized patients with SARS-CoV-2, with little evidence of S. aureus playing a major role. Knowledge of the prevalence and type of co-infections in SARS-CoV-2 patients may have diagnostic and management implications.

Antimicrobial Use in COVID-19 Patients in the First Phase of the SARS-CoV-2 Pandemic: A Scoping Review

This scoping review provides new evidence on the prevalence and patterns of global antimicrobial use in the treatment of COVID-19 patients; identifies the most commonly used antibiotics and clinical scenarios associated with antibiotic prescribing in the first phase of the pandemic; and explores the impact of documented antibiotic prescribing on treatment outcomes in COVID-19 patients. The review complies with PRISMA guidelines for Scoping Reviews and the protocol is registered with the Open Science Framework. In the first six months of the pandemic, there was a similar mean antibiotic prescribing rate between patients with severe or critical illness (75.4%) and patients with mild or moderate illness (75.1%). The proportion of patients prescribed antibiotics without clinical justification was 51.5% vs. 41.9% for patients with mild or moderate illness and those with severe or critical illness. Comparison of patients who were provided antibiotics with a clinical justification with those who were given antibiotics without clinical justification showed lower mortality rates (9.5% vs. 13.1%), higher discharge rates (80.9% vs. 69.3%), and shorter length of hospital stay (9.3 days vs. 12.2 days). In the first 6 months of the pandemic, antibiotics were prescribed for COVID-19 patients regardless of severity of illness. A large proportion of antibiotic prescribing for mild and moderate COVID-19 patients did not have clinical evidence of a bacterial co-infection. Antibiotics may not be beneficial to COVID-19 patients without clinical evidence of a bacterial co-infection.

Distinct clinical and immunological profiles of patients with evidence of SARS-CoV-2 infection in sub-Saharan Africa

Although the COVID-19 pandemic has left no country untouched there has been limited research to understand clinical and immunological responses in African populations. Here we characterise patients hospitalised with suspected (PCR-negative/IgG-positive) or confirmed (PCR-positive) COVID-19, and healthy community controls (PCR-negative/IgG-negative). PCR-positive COVID-19 participants were more likely to receive dexamethasone and a beta-lactam antibiotic, and survive to hospital discharge than PCR-negative/IgG-positive and PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants exhibited a nasal and systemic cytokine signature analogous to PCR-positive COVID-19 participants, predominated by chemokines and neutrophils and distinct from PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants had increased propensity for Staphylococcus aureus and Streptococcus pneumoniae colonisation. PCR-negative/IgG-positive individuals with high COVID-19 clinical suspicion had inflammatory profiles analogous to PCR-confirmed disease and potentially represent a target population for COVID-19 treatment strategies.

Impact of Inflammatory Response Modifiers on the Incidence of Hospital-Acquired Infections in Patients with COVID-19

Introduction

The study aim was to assess the influence of inflammatory response modifiers, including anti-interleukin-6 (IL-6) biologics and corticosteroids, on the incidence of hospital-acquired infections in patients with coronavirus disease 2019 (COVID-19).

Methods

Case–control study performed at a university hospital from February 26 to May 26, 2020. Cases were defined as patients with COVID-19 who developed hospital-acquired infections. For each case, two controls were selected among patients without infections. Cases and controls were matched obeying three criteria in a hierarchical sequence: length of hospital stay up until the first infection; comorbidity; and need for Intensive care unit (ICU) admission. Conditional logistic regression analysis was used to estimate the association of exposures with being a case.

Results

A total of 71 cases and 142 controls were included. Independent predictors for acquiring a hospital infection were chronic liver disease [odds ratio (OR) 16.56, 95% CI 1.87–146.5, p = 0.012], morbid obesity (OR 6.11, 95% CI 1.06–35.4, p = 0.043), current or past smoking (OR 4.15, 95% CI 1.45–11.88, p = 0.008), exposure to hydroxychloroquine (OR 0.2, 95% CI 0.041–1, p = 0.053), and invasive mechanical ventilation (OR 61.5, 95% CI 11.08–341, p ≤ 0.0001).

Conclusions

Inflammatory response modifiers had no influence on acquisition of nosocomial infections in admitted patients with COVID-19. Hospital-acquired infections primarily occurred in the critically ill and invasive mechanical ventilation was the main exposure conferring risk.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40121-021-00477-9.

Staphylococcus aureus ventilator-associated pneumonia in patients with COVID-19: clinical features and potential inference with lung dysbiosis

Background

Hospitalized patients with COVID-19 admitted to the intensive care unit (ICU) and requiring mechanical ventilation are at risk of ventilator-associated bacterial infections secondary to SARS-CoV-2 infection. Our study aimed to investigate clinical features of Staphylococcus aureus ventilator-associated pneumonia (SA-VAP) and, if bronchoalveolar lavage samples were available, lung bacterial community features in ICU patients with or without COVID-19.

Methods

We prospectively included hospitalized patients with COVID-19 across two medical ICUs of the Fondazione Policlinico Universitario A. Gemelli IRCCS (Rome, Italy), who developed SA-VAP between 20 March 2020 and 30 October 2020 (thereafter referred to as cases). After 1:2 matching based on the simplified acute physiology score II (SAPS II) and the sequential organ failure assessment (SOFA) score, cases were compared with SA-VAP patients without COVID-19 (controls). Clinical, microbiological, and lung microbiota data were analyzed.

Results

We studied two groups of patients (40 COVID-19 and 80 non-COVID-19). COVID-19 patients had a higher rate of late-onset (87.5% versus 63.8%; p = 0.01), methicillin-resistant (65.0% vs 27.5%; p < 0.01) or bacteremic (47.5% vs 6.3%; p < 0.01) infections compared with non-COVID-19 patients. No statistically significant differences between the patient groups were observed in ICU mortality (p = 0.12), clinical cure (p = 0.20) and microbiological eradication (p = 0.31). On multivariable logistic regression analysis, SAPS II and initial inappropriate antimicrobial therapy were independently associated with ICU mortality. Then, lung microbiota characterization in 10 COVID-19 and 16 non-COVID-19 patients revealed that the overall microbial community composition was significantly different between the patient groups (unweighted UniFrac distance, R² 0.15349; p < 0.01). Species diversity was lower in COVID-19 than in non COVID-19 patients (94.4 ± 44.9 vs 152.5 ± 41.8; p < 0.01). Interestingly, we found that S. aureus (log₂ fold change, 29.5), Streptococcus anginosus subspecies anginosus (log₂ fold change, 24.9), and Olsenella (log₂ fold change, 25.7) were significantly enriched in the COVID-19 group compared to the non–COVID-19 group of SA-VAP patients.

Conclusions

In our study population, COVID-19 seemed to significantly affect microbiological and clinical features of SA-VAP as well as to be associated with a peculiar lung microbiota composition.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13054-021-03623-4.