Bacterial superinfection in adults with COVID-19 hospitalized in two clinics in Medellín-Colombia, 2020

The burden of nosocomial superinfections in a retrospective cohort study of critically ill COVID-19 patients

OBJECTIVES

Viral respiratory infections can be complicated by bacterial superinfections. SARS-CoV-2 patients may suffer from superinfections, and negative effects of additional infections have been identified. When analysing hospital data, patients typically leave the facility of observation, due to discharge or death, which leads to changes in the study cohort over time. This may distort the estimate of the impact of superinfection. Therefore, it is essential for the statistical analysis of hospital data to acknowledge this change of the risk set over time. We analysed superinfections in a retrospective cohort study with 268 critically ill patients, taking into account discharge and death as competing risks in the statistical analysis.

METHODS

We evaluated bacterial respiratory infections and bloodstream infections and used multi-state statistical modelling to account for the different patient states. We calculated risks of superinfection, probability of discharge or death over time and analysed subgroups according to age and sex.

RESULTS

The observed pathogen spectrum was mainly composed of Enterobacterales, Nonfermenters but also Staphylococcus aureus. We identified an elevated mortality due to bacterial infection of the respiratory tract or bloodstream infection (adj. cause-specific HR 1.7, CI 1.15-2.52) as well as a reduced discharge rate (adj. cause-specific HR 0.51, CI 0.36-0.73). Female patients showed a tendency to have a reduced risk of acquiring a superinfection (adj. subdistribution HR 0.71, CI 0.48-1.04), and in case of infection a higher mortality compared to male patients (interaction effect HR 1.49, CI 0.67-3.30).

CONCLUSIONS

The study accounts for competing risks and quantifies the risk of death associated with bacterial superinfection in critically ill COVID-19 patients. We observed an increased risk of death for patients who developed a superinfection, with Enterobacterales being the predominant agent. The results emphasize the need for microbiological sampling in SARS-CoV-2-infected patients.

CLINICAL TRIAL NUMBER

German Clinical Trials Register number: DRKS00031367, registration date: 01.03.2023 ( https://drks.de/search/de/trial/DRKS00031367 ).

Genomic Characterization of NDM-1 Harboring Extensively-Drug Resistance Klebsiella pneumoniae Isolate From ICU-Admitted Patient With COVID-19

Currently, carbapenem-resistant Klebsiella pneumoniae (CR-KP) strains, particularly those producing New Delhi metallo-beta-lactamase (NDM), are increasingly recognized as a significant threat to global health. The present study aimed to conduct a genomic analysis of an NDM-1-producing CR-KP strain isolated from patients with coronavirus disease of 2019 (COVID-19) admitted to the intensive care unit (ICU). The K. pneumoniae isolate was obtained from the bronchoalveolar lavage fluid of a 68 year-old male patient hospitalized in the ICU with COVID-19 at Besat Hospital in Sanandaj, Iran. The minimum inhibitory concentrations (MICs) for 15 antibiotics were determined using the VITEK 2 system. Genomic analysis of the isolate was performed using whole genome sequencing. The CRKP-51 strain was identified as an extensively drug-resistant (XDR) strain, exhibiting resistance to all tested antibiotics except tigecycline (MIC = 2 μg/mL). The highest resistance values were recorded against sulfamethoxazole-trimethoprim (SXT), nitrofurantoin (NIT), and piperacillin-tazobactam (TZP), with MICs of ≥ 320, 256 μg/mL, and ≥ 128 μg/mL, respectively. Multilocus sequence typing revealed that CRKP-51 belonged to sequence type 15 (ST15). The IncHI1B replicon type associated with this strain harbored several resistance genes, including bla NDM-1 , armA, msrE, mphE, BRP (MBL), bla OXA-1, aadA2, dfrA12, qnrB1, bla CTX-M-15, and cat1. High-risk K. pneumoniae clones, such as ST15, are increasingly associated with antimicrobial resistance and the emergence of XDR strains in ICUs. Additionally, the global dissemination of the NDM enzyme occurs through various plasmid replicon types. Therefore, monitoring local epidemiology is essential for the effectiveness of antimicrobial stewardship programs.

Pathogenic and periodontal bacteria may contribute to the fatal outcome of critically ill elderly COVID-19 patients

Some studies suggest that the respiratory microbiome of COVID-19 patients differs from that of healthy individuals, infected patients may have reduced diversity and increased levels of opportunistic bacteria, however, the role of the microbiome in fatal SARS-CoV-2 infection remains poorly understood. Our study aimed to determine whether there are differences in the respiratory microbiome between patients who recovered from COVID-19 and those who died, by characterizing the bacterial communities of both groups. A total of 24 patients who recovered from COVID-19 and 24 who died were included in the study, patient data were analyzed for signs, symptoms and clinical variables. Airway samples were collected and the 16 S rRNA variable regions V3-V4 were amplified and sequenced using the Illumina MiSeq platform. Elevated levels of blood urea nitrogen, creatinine and lactate dehydrogenase, and higher frequencies of cardiovascular disease, diabetes mellitus and renal disease were observed in patients with a fatal outcome. Compared to patients who recovered from COVID-19, patients who died exhibited a microbiome enriched in periodontal and pathogenic bacteria such as Klebsiella pneumoniae. Our results highlighted a dual relationship between SARS CoV-2 infection and an exacerbated periodontopathogen-induced immune response.

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

Background

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

Methods

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

Results

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

Conclusions

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

Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications

SARS-CoV-2 infections, commonly referred to as COVID-19, remain a critical risk to both human life and global economies. Particularly, COVID-19 patients with weak immunity may suffer from different complications due to the bacterial co-infections/super-infections/secondary infections. Therefore, different variants of alternative antibacterial therapeutic agents are required to inhibit those infection-causing drug-resistant pathogenic bacteria. This study attempted to explore these bacterial pathogens and their inhibitors by using integrated statistical and bioinformatics approaches. By analyzing bacterial 16S rRNA sequence profiles, at first, we detected five bacterial genera and taxa (Bacteroides, Parabacteroides, Prevotella Clostridium, Atopobium, and Peptostreptococcus) based on differentially abundant bacteria between SARS-CoV-2 infection and control samples that are significantly enriched in 23 metabolic pathways. A total of 183 bacterial genes were found in the enriched pathways. Then, the top-ranked 10 bacterial genes (accB, ftsB, glyQ, hldD, lpxC, lptD, mlaA, ppsA, ppc, and tamB) were selected as the pathogenic bacterial key genes (bKGs) by their protein-protein interaction (PPI) network analysis. Then, we detected bKG-guided top-ranked eight drug molecules (Bemcentinib, Ledipasvir, Velpatasvir, Tirilazad, Acetyldigitoxin, Entreatinib, Digitoxin, and Elbasvir) by molecular docking. Finally, the binding stability of the top-ranked three drug molecules (Bemcentinib, Ledipasvir, and Velpatasvir) against three receptors (hldD, mlaA, and lptD) was investigated by computing their binding free energies with molecular dynamic (MD) simulation-based MM-PBSA techniques, respectively, and was found to be stable. Therefore, the findings of this study could be useful resources for developing a proper treatment plan against bacterial co-/super-/secondary-infection in SARS-CoV-2 infections.

Prevalence and Predictive Factors of Rhabdomyolysis in COVID-19 Patients: A Cross-sectional Study

Introduction

The aim of the present prospective observational study was to demonstrate the prevalence and predictive factors of rhabdomyolysis in coronavirus disease 2019 (COVID-19) patients.

Methods

The study was performed on reverse transcriptase-polymerase chain reaction (RT-PCR)-confirmed COVID-19 patients admitted to the emergency department between March 2020 and March 2021. Peak creatinine phosphokinase (CPK) levels were used to define rhabdomyolysis. A CPK level equal to or more than 1000 IU/L was defined as the presence of moderate to severe rhabdomyolysis. We developed a COVID-19-related Rhabdomyolysis Prognostic rule (CORP rule) using the independent predictors of rhabdomyolysis in COVID-19 patients.

Results

Five hundred and six confirmed COVID-19 patients (mean age 58.36 ± 17.83 years, 56.32% male) were studied. Rhabdomyolysis occurred in 44 (8.69%) cases throughout their hospitalization. Male gender (odds ratio [OR] = 2.78, 95% confidence interval [CI]: 1.28, 6.00), hyponatremia (OR = 2.46, 95% CI: 1.08, 5.59), myalgia (OR = 3.04, 95% CI: 1.41, 6.61), D-dimer >1000 (OR = 2.84, 95% CI: 1.27, 6.37), and elevated aspartate aminotransferase level (three times higher than normal range) (OR = 3.14, 95% CI: 1.52, 6.47) were the significant preliminary predictors of rhabdomyolysis. The area under the curve of the CORP rule was 0.75 (95% CI: 0.69, 0.81), indicating the fair performance of it in the prognosis of rhabdomyolysis following COVID-19 infection. The best cutoff of the CORP rule was 3, which had a sensitivity of 72.9% and a specificity of 72.7%.

Conclusion

This prospective study showed that 8.69% of patients developed rhabdomyolysis following COVID-19 infection. The CORP rule with optimal cutoff can correctly classify 72.8% of COVID-19 patients at risk of developing rhabdomyolysis.

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

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

Using risk factors and markers to predict bacterial respiratory co-/superinfections in COVID-19 patients: is the antibiotic steward's toolbox full or empty?

BACKGROUND

Adequate diagnosis of bacterial respiratory tract co-/superinfection (bRTI) in coronavirus disease (COVID-19) patients is challenging, as there is insufficient knowledge about the role of risk factors and (para)clinical parameters in the identification of bacterial co-/superinfection in the COVID-19 setting. Empirical antibiotic therapy is mainly based on COVID-19 severity and expert opinion, rather than on scientific evidence generated since the start of the pandemic.

PURPOSE

We report the best available evidence regarding the predictive value of risk factors and (para)clinical markers in the diagnosis of bRTI in COVID-19 patients.

METHODS

A multidisciplinary team identified different potential risk factors and (para)clinical predictors of bRTI in COVID-19 and formulated one or two research questions per topic. After a thorough literature search, research gaps were identified, and suggestions concerning further research were formulated. The quality of this narrative review was ensured by following the Scale for the Assessment of Narrative Review Articles.

RESULTS

Taking into account the scarcity of scientific evidence for markers and risk factors of bRTI in COVID-19 patients, to date, COVID-19 severity is the only parameter which can be associated with higher risk of developing bRTI.

CONCLUSIONS

Evidence on the usefulness of risk factors and (para)clinical factors as predictors of bRTI in COVID-19 patients is scarce. Robust studies are needed to optimise antibiotic prescribing and stewardship activities in the context of COVID-19.

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

INTRODUCTION

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Coinfections and Superinfections Associated with COVID-19 in Colombia: A Narrative Review

The COVID-19 pandemic has had significant impacts on healthcare systems around the world, including in Latin America. In Colombia, there have been over 23,000 confirmed cases and 100 deaths since 2022, with the highest number of cases occurring in females and the highest number of deaths in males. The elderly and those with comorbidities, such as arterial hypertension, diabetes mellitus, and respiratory diseases, have been particularly affected. Coinfections with other microorganisms, including dengue virus, Klebsiella pneumoniae, and Mycobacterium tuberculosis, have also been a significant factor in increasing morbidity and mortality rates in COVID-19 patients. It is important for surveillance systems to be improved and protocols to be established for the early detection and management of coinfections in COVID-19. In addition to traditional treatments, alternatives such as zinc supplementation and nanomedicine may have potential in the fight against COVID-19. It is also crucial to consider the social, labor, educational, psychological, and emotional costs of the pandemic and to address issues such as poverty and limited access to potable water in order to better prepare for future pandemics.

Description of pathogenic bacteria in patients with respiratory symptoms associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Colombia

Viral respiratory infections may predispose to co-infections with other pathogenic microorganisms. In this study, pathogenic respiratory bacteria were detected using commercial kit Allplex^™ Respiratory Panel 4 from nasopharyngeal samples from individuals suffering respiratory symptoms with and without severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Patients without respiratory symptoms were included as controls. Haemophilus influenzae and Streptococcus pneumoniae were detected from 12 patients (6%) in both, patients with respiratory symptoms (including hospitalized) (n = 6) and individual without symptoms (n = 6). Pathogenic bacteria possibly proliferate due to the limited immune response of patients with SARS-CoV-2, perhaps due to dysbiosis generated by the viral infection.

Antimicrobial Resistance and Antimicrobial Stewardship: Before, during and after the COVID-19 Pandemic

Antimicrobial resistance (AMR) is an ongoing phenomenon. It is a significant public health issue that has existed long before the coronavirus disease of 2019 (COVID-19) pandemic. It develops as microorganisms undergo genetic mutations that allow them to survive despite antimicrobial treatment. This process is highly associated with excessive and often unnecessary antimicrobial pharmacotherapy, which was often discussed during the COVID-19 pandemic. This article explores how the pandemic has affected antimicrobial stewardship by shifting the focus away from antimicrobial resistance, as well as the impact of enhanced antibiotic usage and measures such as lockdowns, mandatory testing and vaccination on antimicrobial resistance. Although these measures were regarded as successful in terms of limiting the pandemic, they have significantly contributed to an already escalating AMR issue. Outpatient methods in primary care and intensive care units aiming to prevent severe COVID-19 disease have contributed to the spread of multidrug-resistant bacteria, while laboratories burdened with COVID-19 testing have indirectly interrupted the detection of these bacteria. In this review, we summarize the pathogens whose AMRe has been greatly affected by COVID-19 measures and emphasize the importance of efficient antimicrobial stewardship in future pandemic and non-pandemic states to promote the responsible use of antibiotics and minimize AMR.

Antimicrobial Resistance of Staphylococcus aureus Isolated between 2017 and 2022 from Infections at a Tertiary Care Hospital in Romania

This study aimed to evaluate the frequency of isolation of Staphylococcus aureus from different pathological samples processed in the Microbiology Laboratory of the National Institute of Infectious Diseases "Prof. Dr. Matei Balș", Romania, between 1 January 2017 and 31 December 2022, aiming to establish the ratio of methicillin-resistant to methicillin-susceptible Staphylococcus aureus strains and the antibiotic resistance pattern of isolated microorganisms. The data of isolates originating from routine diagnostic tasks were analyzed retrospectively using laboratory data from the microbiology department. Up to 39.11% of Staphylococcus aureus strains were resistant to oxacillin (MRSA), with 49.97% resistance to erythromycin and 36.06% inducible resistance to clindamycin. Resistance rates to ciprofloxacin, rifampicin, gentamicin, and trimethoprim-sulfamethoxazole were 9.98%, 5.38%, 5.95%, and 0.96%, respectively. There was no resistance to vancomycin. Between 2017 and 2022, the percentage of MRSA strains decreased from 41.71% to 33.63%, sharply increasing to 42.42% in 2021 (the year of the COVID-19 pandemic, when the percentage of strains isolated from lower respiratory tract infections was higher than that of strains isolated from wounds or blood, as in previous years). This study showed a high percentage of MRSA strains (39.11% overall) with a higher proportion of these strains isolated from the blood (42.49%) compared to other clinical specimens.

Vaccines and therapeutics for immunocompromised patients with COVID-19

The COVID-19 pandemic has disproportionately impacted immunocompromised patients. This diverse group is at increased risk for impaired vaccine responses, progression to severe disease, prolonged hospitalizations and deaths. At particular risk are people with deficiencies in lymphocyte number or function such as transplant recipients and those with hematologic malignancies. Such patients' immune responses to vaccination and infection are frequently impaired leaving them more vulnerable to prolonged high viral loads and severe complications of COVID-19. Those in turn, have implications for disease progression and persistence, development of immune escape variants and transmission of infection. Data to guide vaccination and treatment approaches in immunocompromised people are generally lacking and extrapolated from other populations. The large clinical trials leading to authorisation and approval of SARS-CoV-2 vaccines and therapeutics included very few immunocompromised participants. While experience is accumulating, studies focused on the special circumstances of immunocompromised patients are needed to inform prevention and treatment approaches.

Leading Pathogens Involved in Co-Infection and Super-Infection with COVID-19: Forensic Medicine Considerations after a Systematic Review and Meta-Analysis

The COVID-19 pandemic raised concerns about the potential for co-infection or over-infection with other respiratory infections, as they can complicate the diagnosis, treatment and prognosis of the disease. This is also a challenge for forensic pathologists, who may come across cases where the presence of co-infection or over-infection is suspected or confirmed, and it is important that they take this into account when determining the cause of death. The aim of this systematic review is to analyse the prevalence of each specific pathogen co-infecting or over-infecting patients with SARS-CoV-2 infection. In total, 575 studies were selected from the Scopus and Pub-Med online databases and 8 studies were included in a meta-analysis. Male gender, advanced age and nursing home care are risk factors associated with the development of co-infection, whereas age, tachypnoea, hypoxaemia and bacterial infection are predictors of mortality. Overall, however, having a SARS-CoV-2 infection does not represent a real risk for the development of co-infections/super-infections.

A Retrospective Assessment of Sputum Samples and Antimicrobial Resistance in COVID-19 Patients

Data on bacterial or fungal pathogens and their impact on the mortality rates of Western Romanian COVID-19 patients are scarce. As a result, the purpose of this research was to determine the prevalence of bacterial and fungal co- and superinfections in Western Romanian adults with COVID-19, hospitalized in in-ward settings during the second half of the pandemic, and its distribution according to sociodemographic and clinical conditions. The unicentric retrospective observational study was conducted on 407 eligible patients. Expectorate sputum was selected as the sampling technique followed by routine microbiological investigations. A total of 31.5% of samples tested positive for Pseudomonas aeruginosa, followed by 26.2% having co-infections with Klebsiella pneumoniae among patients admitted with COVID-19. The third most common Pathogenic bacteria identified in the sputum samples was Escherichia coli, followed by Acinetobacter baumannii in 9.3% of samples. Commensal human pathogens caused respiratory infections in 67 patients, the most prevalent being Streptococcus penumoniae, followed by methicillin-sensitive and methicillin-resistant Staphylococcus aureus. A total of 53.4% of sputum samples tested positive for Candida spp., followed by 41.1% of samples with Aspergillus spp. growth. The three groups with positive microbial growth on sputum cultures had an equally proportional distribution of patients admitted to the ICU, with an average of 30%, compared with only 17.3% among hospitalized COVID-19 patients with negative sputum cultures (p = 0.003). More than 80% of all positive samples showed multidrug resistance. The high prevalence of bacterial and fungal co-infections and superinfections in COVID-19 patients mandates for strict and effective antimicrobial stewardship and infection control policies.

Respiratory Bacterial and Fungal Superinfections During the Third Surge of the COVID-19 Pandemic in Iran

Objective: We characterized bacterial and fungal superinfection and evaluated the antimicrobial resistance profile against the most common superinfection-causing pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, and Staphylococcus aureus). Methods: In a cross-sectional study, 192 respiratory samples were collected from patients with and without SARS-COV-2 admitted to a teaching hospital in Tehran. Superinfection proportions and the antibiotic resistance profile were assessed and compared with demographic, comorbidities, and other clinical factors. Results: Superinfection rate was 60% among COVID-19 patients (p = 0.629). Intensive care unit admission (p = 0.017), mortality rate (p ≤ 0.001), and antiviral and corticosteroid therapy (p ≤ 0.001) were significantly more common among patients with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2). The most common superinfections were caused by K. pneumoniae (42.7%, 82/192), A. baumannii (14.6%, 28/192), and S. aureus (13%, 25/192). A. baumannii isolates exhibited greater antibiotic resistance. Forty-four percent (11/25) of S. aureus isolates were cefoxitin resistant and also confirmed as methicillin-resistant S. aureus by PCR. Conclusion: The rise of difficult-to-treat infections with a high burden of antibiotic resistance, coupled with an increase in mortality rate of SARS-COV-2 superinfected individuals, illustrates the impact of the COVID-19 pandemic on antimicrobial resistance. Post-pandemic antimicrobial resistance crisis management requires precise microbiological diagnosis, drug susceptibility testing, and prescription of antimicrobials appropriate for the patient's condition.

Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis

BACKGROUND

Frequent use of antibiotics in patients with COVID-19 threatens to exacerbate antimicrobial resistance. We aimed to establish the prevalence and predictors of bacterial infections and antimicrobial resistance in patients with COVID-19.

METHODS

We did a systematic review and meta-analysis of studies of bacterial co-infections (identified within ≤48 h of presentation) and secondary infections (>48 h after presentation) in outpatients or hospitalised patients with COVID-19. We searched the WHO COVID-19 Research Database to identify cohort studies, case series, case-control trials, and randomised controlled trials with populations of at least 50 patients published in any language between Jan 1, 2019, and Dec 1, 2021. Reviews, editorials, letters, pre-prints, and conference proceedings were excluded, as were studies in which bacterial infection was not microbiologically confirmed (or confirmed via nasopharyngeal swab only). We screened titles and abstracts of papers identified by our search, and then assessed the full text of potentially relevant articles. We reported the pooled prevalence of bacterial infections and antimicrobial resistance by doing a random-effects meta-analysis and meta-regression. Our primary outcomes were the prevalence of bacterial co-infection and secondary infection, and the prevalence of antibiotic-resistant pathogens among patients with laboratory-confirmed COVID-19 and bacterial infections. The study protocol was registered with PROSPERO (CRD42021297344).

FINDINGS

We included 148 studies of 362  976 patients, which were done between December, 2019, and May, 2021. The prevalence of bacterial co-infection was 5·3% (95% CI 3·8-7·4), whereas the prevalence of secondary bacterial infection was 18·4% (14·0-23·7). 42 (28%) studies included comprehensive data for the prevalence of antimicrobial resistance among bacterial infections. Among people with bacterial infections, the proportion of infections that were resistant to antimicrobials was 60·8% (95% CI 38·6-79·3), and the proportion of isolates that were resistant was 37·5% (26·9-49·5). Heterogeneity in the reported prevalence of antimicrobial resistance in organisms was substantial (I2=95%).

INTERPRETATION

Although infrequently assessed, antimicrobial resistance is highly prevalent in patients with COVID-19 and bacterial infections. Future research and surveillance assessing the effect of COVID-19 on antimicrobial resistance at the patient and population level are urgently needed.

FUNDING

WHO.

The under investigated facet of the COVID-19 pandemic: Molecular analysis of secondary bacterial infections at a COVID dedicated intensive care unit within a tertiary care center in Lebanon

Background

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. Secondary bacterial infections are associated with unfavorable outcomes in respiratory viral infections. This study aimed at determining the prevalence of secondary bacterial infections in COVID-19 patients admitted at a tertiary medical center in Lebanon.

Methodology

From May till November, 2020, a total of 26 Gram-negative isolates were recovered from 16 patients during the course of their COVID-19 infection with Escherichia coli being the most prevalent. The isolates were assessed for their antimicrobial susceptibility by broth microdilution against 19 antimicrobial agents from different classes. Whole genome sequencing of 13 isolates allowed the mining of antimicrobial resistance (AMR) determinants as well as mobile genetic elements and sequence types (ST). Finally, broth microdilution with three different efflux pump inhibitors [theobromine, conessine and PheArg-β-naphthylamide (PAβN)] was done.

Results

Antimicrobial susceptibility testing showed that out of the 26 Gram-negative isolates, 1 (4%) was extensively drug resistant and 14 (54%) were multi-drug resistant (MDR). Whole genome sequencing results revealed a plethora of AMR determinants among the 13 sequenced isolates. Moreover, the 9 Enterobacterales and 4 Pseudomonas aeruginosa sequenced isolates belonged to 9 and 2 different ST, respectively. Using a variety of efflux pump inhibitors we demonstrated that only PAβN had a significant effect when combined with levofloxacin, and the latter regained its activity against two P. aeruginosa isolates.

Conclusion

The identification of carbapenem and colistin resistant Gram-negative bacilli causing secondary bacterial infections in critical patients diagnosed with COVID-19 should be of high concern. Additionally, it is crucial to monitor and track AMR, post-COVID pandemic, in order to better understand the effect of this disease on AMR exacerbation.

Serum procalcitonin level is independently associated with mechanical ventilation and case-fatality in hospitalized COVID-19-positive US veterans-A potential marker for disease severity

The Coronavirus-19 disease (COVID-19) has claimed over 6.8 million lives since first being reported in late 2019. The virus that causes COVID-19 disease is highly contagious and spreads rapidly. To date, there are no approved prognostic tools that could predict why some patients develop severe or fatal disease outcomes. Early COVID-19 studies found an association between procalcitonin (PCT) and hospitalization or duration of mechanical ventilation and death but were limited by the cohort sizes. Therefore, this study was designed to confirm the associations of PCT with COVID-19 disease severity outcomes in a large cohort. For this retrospective data analysis study, 27,154 COVID-19-positive US veterans with post-infection PCT laboratory test data and their disease severity outcomes were accessed using the VA electronic healthcare data. Cox regression models were used to test the association between serum PCT levels and disease outcomes while controlling for demographics and relevant confounding variables. The models demonstrated increasing disease severity (ventilation and death) with increasing PCT levels. For PCT serum levels above 0.20 ng/ml, the unadjusted risk increased nearly 2.3-fold for mechanical ventilation (hazard ratio, HR, 2.26, 95%CI: 2.11-2.42) and in-hospital death (HR, 2.28, 95%CI: 2.16-2.41). Even when adjusted for demographics, diabetes, pneumonia, antibiotic use, white blood cell count, and serum C-reactive protein levels, the risks remained relatively high for mechanical ventilation (HR, 1.80, 95%CI: 1.67-1.94) and death (HR, 1.76, 95%CI: 1.66-1.87). These data suggest that higher PCT levels have independent associations with ventilation and in-hospital death in veterans with COVID-19 disease, validating previous findings. The data suggested that serum PCT level may be a promising prognostic tool for COVID-19 severity assessment and should be further evaluated in a prospective clinical trial.

Bacterial profiles and their antibiotic resistance background in superinfections caused by multidrug-resistant bacteria among COVID-19 ICU patients from southwest Iran

This study investigated the bacterial causes of superinfections and their antibiotic resistance pattern in severe coronavirus disease 2019 (COVID-19) patients admitted to the intensive care unit (ICU) of Razi Hospital in Ahvaz, southwest Iran. In this cross-sectional study, endotracheal tube (ETT) secretion samples of 77 intubated COVID-19 patients, confirmed by reverse transcription-quantitative polymerase chain reaction, were investigated by standard microbiology test and analytical profile index kit. Antibiotic susceptibility testing was performed by disc diffusion. The presence of Haemophilus influenzae and Mycoplasma pneumoniae was investigated by the polymerase chain reaction (PCR). Using culture and PCR methods, 56 (72.7%) of the 77 COVID-19 patients (mean age of 55 years, 29 male and 27 female) had superinfections. Using culture, 67 isolates including 29 (43.2%) Gram-positive and 38 (56.7%) Gram-negative bacteria (GNB) were identified from 49 COVID-19 patients. The GNB were more predominant than the Gram-positive pathogens. Klebsiella pneumoniae (28.4%, n = 19/67) was the most common isolate followed by Staphylococcus aureus (22.4%, n = 15/67). Using PCR, 10.4% (8/77) and 11.7% (9/77) of ETT secretion specimens had H. influenzae and M. pneumoniae amplicons, respectively. Gram-positive and Gram-negative isolates showed high resistance rates (>70.0%) to majority of the tested antibiotics including fluoroquinolone, carbapenems, and cephalosporins and 68.7% (46/67) of isolates were multidrug-resistant (MDR). This study showed a high frequency rate of superinfections by MDR bacteria among COVID-19 patients in southwest Iran. The prevention of long-term consequences caused by COVID-19, demands continuous antibiotic surveillance particularly in management of bacterial superinfections.

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

Background

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

Materials and methods

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

Results

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

Conclusion

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

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

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

Bacterial and Fungal Superinfections in COVID-19 Patients Hospitalized in an Intensive Care Unit from Timișoara, Romania

PURPOSE

Critically ill patients hospitalized in the intensive care unit (ICU) have an increased infection risk. The aim of this study was to determine the bacterial and fungal superinfections rate in Coronavirus disease 2019 (COVID-19) patients stationed in the ICU, identify risk factors associated with their development and to determine whether superinfection plays a role in patients' outcome in this population.

PATIENTS AND METHODS

In this retrospective, non-interventional, single centre, cohort study, medical records of 302 consecutive patients with SARS-COV-2 pneumonia admitted into the COVID-19 ICU of the largest university hospital from Western Romania between October 2020 and May 2021, were reviewed, of whom 236 patients met the inclusion criteria.

RESULTS

One hundred and nineteen patients developed a superinfection ≥48 h after being admitted to the hospital. Superinfection rate in the ICU was 50.42%. Coagulase-negative Staphylococci (CoNS) and Enterococcus spp. were predominantly isolated from blood cultures, while Acinetobacter baumannii, Staphylococcus aureus and Candida spp. from tracheobronchial aspirates. Significant independent risk factors regarding bacterial/fungal superinfection in COVID-19 patients were obtained for the following variables: number of days of central venous catheter (HR = 1.13 [1.07-1.20], p < 0.001) and prior administration of corticosteroids (HR = 2.80 [1.33-5.93], p = 0.007). Four independent predictive risk factors were associated with unfavorable outcome: age (HR = 1.07 [95% CI 1.03-1.12], p = 0.001); Carmeli Score (HR = 6.09 [1.18-31.50], p = 0.031); body mass index (HR = 1.11 [1.02-1.21], p = 0.011) and the presence of a central venous catheter (HR = 6.49 [1.93-21.89], p = 0.003).

CONCLUSION

The superinfection rate in COVID-19 patients was high in this study group. Exogenous risk factors were associated with superinfection more than endogenous factors. Only a small percentage of uninfected COVID-19 patients were not prescribed antibiotics during their hospitalization, raising serious concerns regarding the judicious prescribing of antibiotics in viral infections.

Effect of asthma, COPD, and ACO on COVID-19: A systematic review and meta-analysis

INTRODUCTION

The prevalence of asthma, chronic obstructive pulmonary disease (COPD), and asthma-COPD overlap (ACO) in patients with COVID-19 varies, as well as their risks of mortality. The present study aimed to assess the prevalence of asthma, COPD, and ACO as comorbidities, and to determine their risks of mortality in patients with COVID-19 using a systematic review and meta-analysis.

METHODS

We systematically reviewed clinical studies that reported the comorbidities of asthma, COPD, and ACO in patients with COVID-19. We searched various databases including PubMed (from inception to 27 September 2021) for eligible studies written in English. A meta-analysis was performed using the random-effect model for measuring the prevalence of asthma, COPD, and ACO as comorbidities, and the mortality risk of asthma, COPD, and ACO in patients with COVID-19 was estimated. A stratified analysis was conducted according to country.

RESULTS

One hundred one studies were eligible, and 1,229,434 patients with COVID-19 were identified. Among them, the estimated prevalence of asthma, COPD, and ACO using a meta-analysis was 10.04% (95% confidence interval [CI], 8.79-11.30), 8.18% (95% CI, 7.01-9.35), and 3.70% (95% CI, 2.40-5.00), respectively. The odds ratio for mortality of pre-existing asthma in COVID-19 patients was 0.89 (95% CI, 0.55-1.4; p = 0.630), while that in pre-existing COPD in COVID-19 patients was 3.79 (95% CI, 2.74-5.24; p<0.001). France showed the highest prevalence of asthma followed by the UK, while that of COPD was highest in the Netherlands followed by India.

CONCLUSION

Pre-existing asthma and COPD are associated with the incidence of COVID-19. Having COPD significantly increases the risk of mortality in patients with COVID-19. These differences appear to be influenced by the difference of locations of disease pathophysiology and by the daily diagnosis and treatment policy of each country.

Coronavirus Lung Infection Impairs Host Immunity against Secondary Bacterial Infection by Promoting Lysosomal Dysfunction

Postviral bacterial infections are a major health care challenge in coronavirus infections, including COVID-19; however, the coronavirus-specific mechanisms of increased host susceptibility to secondary infections remain unknown. In humans, coronaviruses, including SARS-CoV-2, infect lung immune cells, including alveolar macrophages, a phenotype poorly replicated in mouse models of SARS-CoV-2. To overcome this, we used a mouse model of native murine β-coronavirus that infects both immune and structural cells to investigate coronavirus-enhanced susceptibility to bacterial infections. Our data show that coronavirus infection impairs the host ability to clear invading bacterial pathogens and potentiates lung tissue damage in mice. Mechanistically, coronavirus limits the bacterial killing ability of macrophages by impairing lysosomal acidification and fusion with engulfed bacteria. In addition, coronavirus-induced lysosomal dysfunction promotes pyroptotic cell death and the release of IL-1β. Inhibition of cathepsin B decreased cell death and IL-1β release and promoted bacterial clearance in mice with postcoronavirus bacterial infection.

Endotoxin removal therapy with Polymyxin B immobilized fiber column as a COVID-19-bedside strategy protocol for endotoxic shock

Endotoxin -induced sepsis is a leading cause of ICU mortality. From 1994 to the present, PMX-HP has been available as an adjuvant therapy for endotoxin removal and immunomodulation. The efficacy and usefulness of this therapy have been demonstrated for more than a quarter of a century and are partially supported by clinical studies. However, it appears that selected subgroups of patients with endotoxic shock and with appropriate timing could benefit. Endotoxemia may be involved in the pathophysiology of COVID-19, based on enterocyte dysfunction and malabsorptive syndrome. Due to the characteristics of the microbiota, Gram-negative bacteria or their fragments (i.e., endotoxin) may translocate into the systemic circulation leading to inflammatory activation, immune dysfunction, and sepsis. In addition, patients with severe forms of COVID-19 are at risk of superimposed infections. Endotoxemia can arise due to the translocation of Gram-negative bacteria or their fragments from the gut barrier. According to the most updated evidence available from large randomized trials, septic shock patients with MODS > 9 and EA levels ranging from 0.6 to 0.9 are those who may benefit the most from PMX-HP treatment in terms of improvement of survival. As shown in a previous publication, we believe that similarly to the source control, microbiological cultures, and antibiotics administration, EA evaluation at regular intervals, and the targeted use of PMX-HP could be lifesaving and adequate within the golden hour for the diagnosis and treatment of endotoxic shock. In our center, we applied a diagnostic-clinical flowchart also for endotoxic shock related to COVID-19.

Pathophysiology of Methicillin-Resistant Staphylococcus aureus Superinfection in COVID-19 Patients

The global spread of the coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has infected humans in all age groups, deteriorated host immune responses, and caused millions of deaths. The reasons for individuals succumbing to COVID-19 were not only the SARS-CoV-2 infection but also associated bacterial infections. Antibiotics were largely used to prevent bacterial infections during COVID-19 illness, and many bacteria became resistant to conventional antibiotics. Although COVID-19 was considered the main culprit behind the millions of deaths, bacterial coinfections and superinfections were the major factors that increased the mortality rate in hospitalized patients. In the present study, we assessed the pathophysiology of methicillin-resistant Staphylococcus aureus (MRSA) superinfection in COVID-19 patients in Pakistan. A total of 3492 COVID-19 hospitalized patients were screened among which 224 strain were resistant to methicillin; 110 strains were tazobactam-resistant; 53 strains were ciprofloxacin-resistant; 23 strains were gentamicin-resistant; 11 strains were azithromycin-resistant; 3 strains were vancomycin-resistant. A high frequency of MRSA was detected in patients aged ≥50 with a prevalence of 7.33%, followed by patients aged >65 with a prevalence of 5.48% and a 5.10% prevalence in patients aged <50. In addition, pneumonia was detected in the COVID-19-associated MRSA (COVID-MRSA) that showed decreased levels of lymphocytes and albumin and increased the mortality rate from 2.3% to 25.23%. Collectively, an MRSA superinfection was associated with increased mortality in COVID-19 after 12 to 18 days of hospitalization. The study assessed the prevalence of MRSA, mortality rate, pneumonia, and the emergence of antibiotic resistance as the main outcomes. The study summarized that COVID-MRSA aggravated the treatment and recovery of patients and suggested testing MRSA as critical for hospitalized patients.

Prospects on Repurposing a Live Attenuated Vaccine for the Control of Unrelated Infections

Live vaccines use attenuated microbes to acquire immunity against pathogens in a safe way. As live attenuated vaccines (LAVs) still maintain infectivity, the vaccination stimulates diverse immune responses by mimicking natural infection. Induction of pathogen-specific antibodies or cell-mediated cytotoxicity provides means of specific protection, but LAV can also elicit unintended off-target effects, termed non-specific effects. Such mechanisms as short-lived genetic interference and non-specific innate immune response or long-lasting trained immunity and heterologous immunity allow LAVs to develop resistance to subsequent microbial infections. Based on their safety and potential for interference, LAVs may be considered as an alternative for immediate mitigation and control of unexpected pandemic outbreaks before pathogen-specific therapeutic and prophylactic measures are deployed.

Immune Signature of COVID-19: In-Depth Reasons and Consequences of the Cytokine Storm

In the beginning of the third year of the fight against COVID-19, the virus remains at least still one step ahead in the pandemic "war". The key reasons are evolving lineages and mutations, resulting in an increase of transmissibility and ability to evade immune system. However, from the immunologic point of view, the cytokine storm (CS) remains a poorly understood and difficult to combat culprit of the extended number of in-hospital admissions and deaths. It is not fully clear whether the cytokine release is a harmful result of suppression of the immune system or a positive reaction necessary to clear the virus. To develop methods of appropriate treatment and therefore decrease the mortality of the so-called COVID-19-CS, we need to look deeply inside its pathogenesis, which is the purpose of this review.

COVID-19 Autopsies Reveal Underreporting of SARS-CoV-2 Infection and Scarcity of Co-infections

Coronavirus disease 2019 (COVID-19) mortality can be estimated based on reliable mortality data. Variable testing procedures and heterogeneous disease course suggest that a substantial number of COVID-19 deaths is undetected. To address this question, we screened an unselected autopsy cohort for the presence of SARS-CoV-2 and a panel of common respiratory pathogens. Lung tissues from 62 consecutive autopsies, conducted during the first and second COVID-19 pandemic waves in Switzerland, were analyzed for bacterial, viral and fungal respiratory pathogens including SARS-CoV-2. SARS-CoV-2 was detected in 28 lungs of 62 deceased patients (45%), although only 18 patients (29%) were reported to have COVID-19 at the time of death. In 23 patients (37% of all), the clinical cause of death and/or autopsy findings together with the presence of SARS-CoV-2 suggested death due to COVID-19. Our autopsy results reveal a 16% higher SARS-CoV-2 infection rate and an 8% higher SARS-CoV-2 related mortality rate than reported by clinicians before death. The majority of SARS-CoV-2 infected patients (75%) did not suffer from respiratory co-infections, as long as they were treated with antibiotics. In the lungs of 5 patients (8% of all), SARS-CoV-2 was found, yet without typical clinical and/or autopsy findings. Our findings suggest that underreporting of COVID-19 contributes substantially to excess mortality. The small percentage of co-infections in SARS-CoV-2 positive patients who died with typical COVID-19 symptoms strongly suggests that the majority of SARS-CoV-2 infected patients died from and not with the virus.

Methicillin-resistant Staphylococcus aureus lung infection in coronavirus disease 2019: how common?

PURPOSE OF REVIEW

Some patients with coronavirus disease 2019 (COVID-19) may develop pulmonary bacterial coinfection or superinfection, that could unfavorably impact their prognosis.

RECENT FINDINGS

The exact burden of methicillin-resistant Staphylococcus aureus (MRSA) lung infection in peculiar populations such as patients with COVID-19 remains somewhat elusive, possibly because of wide heterogeneity in methods and endpoints across studies.

SUMMARY

There was important heterogeneity in the retrieved literature on the epidemiology of MRSA lung infection in patients with COVID-19, both when considering all other bacteria as the denominator (relative prevalence ranging from 2% to 29%) and when considering only S. aureus as the denominator (relative prevalence ranging from 11% to 65%). Overall, MRSA is among the most frequent causative agents of pulmonary infection in patients with COVID-19. Improving our ability to rapidly reach etiological diagnosis of bacterial lung infection in COVID-19 patients remains fundamental if we are to improve the rates of appropriate antibiotic therapy in patients with COVID-19 and concomitant/superimposed MRSA infection, at the same time avoiding antibiotic overuse in line with antimicrobial stewardship principles.

The Microbial Profile and Resistance Pattern of Pathogens Isolated From Long COVID Pneumonia Patients and Their Correlation to Clinical Outcome: Our Experience From a Tertiary Care Hospital

Background

Coronavirus disease 2019 (COVID-19) patients with persistent symptoms for at least four weeks in spite of being reverse transcriptase-polymerase chain reaction (RTPCR) negative for COVID infection are defined as long COVID (wherein pulmonary involvement is seen in a significant proportion of cases). The history of prolonged use of corticosteroids, broad-spectrum antibiotics, and associated comorbid conditions in these patients increases the possibility of infection with multidrug-resistant microbial strains. It may lead to a grave prognosis, hence appropriate microbiological evaluation and management at the earliest can have a better outcome.

Methods

A retrospective observational study was carried out among long COVID patients admitted to the Kalinga Institute of Medical Sciences, Bhubaneswar, Odisha, India, a tertiary care hospital. Eighty-four patients admitted to the ICU or non-ICU ward in the hospital from April to October 2021 were included in the study. Antibiotics, as prescribed by our hospital antibiotic policy, were administered wherever required and were subsequently changed according to culture and sensitivity reports of the samples (sputum, endotracheal aspirates, or blood). An analysis of the antibiotic sensitivity patterns of the pathogens isolated was performed. The outcome after optimum medical management was assessed for survivors, discharge, or death.

Results

Out of the total of 84 patients, 41 samples (sputum, endotracheal aspirates or blood) were collected and sent for culture, of which 32 (78.1%) were found to be culture positive for pathogens. Among the pathogens isolated, there were 22 (69%) drug-resistant and 10 (31%) sensitive organisms. Among the 22 resistant pathogen isolates, 18 were Gram-negative species, the most common species being Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumanii; two were Gram-positive species, one each from Staphylococcus aureus and Enterococcus faecalis, and three were Candida tropicalis. Of five deaths reported among 22 cases with resistant isolates, extensively drug-resistant (XDR), multi-drug resistance (MDR), and pan drug resistance (PDR) strains were detected in three, one, and one cases, respectively, and were harboured by K. pneumoniae, P. aeruginosa, and A. baumanii. Of the total eight deaths, there were two deaths among the 43 patients who received an empiric antibiotic in the wards, and six deaths were reported in the ICU. Despite raised biomarkers of inflammation, comorbid illnesses, renal impairment, and immunocompromised states, there was 91% survival and discharge, which was statistically significant (p-value = 0.00).

Conclusion

To conclude, K. pneumoniae, P. aeruginosa, A. baumanii, C. tropicalis, S. aureus, and E. faecalis were the most commonly isolated organisms among long COVID pneumonia cases, of which some were MDR, PDR and XDR strains. Early microbiological evaluation with targeted, proper antimicrobial usage along with optimized medical management and, wherever needed, critical care support in the ICU may lead to a better prognostic outcome in those groups of patients.

Possible harm from glucocorticoid drugs misuse in the early phase of SARS-CoV-2 infection: a narrative review of the evidence

Since the publication of the RECOVERY trial, the use of glucocorticoid drugs (GC) has spread for the treatment of severe COVID-19 worldwide. However, the benefit of dexamethasone was largest in patients who received mechanical ventilation or supplemental oxygen therapy, while no benefit was found among patients without hypoxemia. In addition, a positive outcome was found in patients who received dexamethasone after several days of symptoms, while possible harm could exist if administered early. The right time interval for GC administration is still a matter of debate. Previous studies showed that an early GC use during the first phase of the disease, when viral replication peaks, may negatively affect the innate immune response through several mechanisms, such as the inhibition of pro-inflammatory and antiviral cytokine production and signaling pathway, including type I interferon, that is fundamental to counteract the virus and that was found to be impaired in several patients with life-threatening COVID-19. The GC misuse can lead to a more severe disease even in patients who do not have the established risk factors, such as obesity and cardiovascular diseases. In our focused review, we describe the role of immune response in viral infections, especially SARS-CoV-2, and discuss the potential harms of GC misuse in COVID-19.

RNA Sequencing in COVID-19 patients identifies neutrophil activation biomarkers as a promising diagnostic platform for infections

Infection with the SARS-CoV2 virus can vary from asymptomatic, or flu-like with moderate disease, up to critically severe. Severe disease, termed COVID-19, involves acute respiratory deterioration that is frequently fatal. To understand the highly variable presentation, and identify biomarkers for disease severity, blood RNA from COVID-19 patient in an intensive care unit was analyzed by whole transcriptome RNA sequencing. Both SARS-CoV2 infection and the severity of COVID-19 syndrome were associated with up to 25-fold increased expression of neutrophil-related transcripts, such as neutrophil defensin 1 (DEFA1), and 3-5-fold reductions in T cell related transcripts such as the T cell receptor (TCR). The DEFA1 RNA level detected SARS-CoV2 viremia with 95.5% sensitivity, when viremia was measured by ddPCR of whole blood RNA. Purified CD15+ neutrophils from COVID-19 patients were increased in abundance and showed striking increases in nuclear DNA staining by DAPI. Concurrently, they showed >10-fold higher elastase activity than normal controls, and correcting for their increased abundance, still showed 5-fold higher elastase activity per cell. Despite higher CD15+ neutrophil elastase activity, elastase activity was extremely low in plasma from the same patients. Collectively, the data supports the model that increased neutrophil and decreased T cell activity is associated with increased COVID-19 severity, and suggests that blood DEFA1 RNA levels and neutrophil elastase activity, both involved in neutrophil extracellular traps (NETs), may be informative biomarkers of host immune activity after viral infection.

COVID-19 Pulmonary Pathology, Ventilator-Induced Lung Injury (VILI), or Sepsis-Induced Acute Respiratory Distress Syndrome (ARDS)? Healthcare Considerations Arising From an Autopsy Case and Miny-Review

Acute respiratory distress syndrome (ARDS) caused by coronavirus disease (COVID-19) is a serious complication that requires early recognition. Autopsy reports or biopsies of the lungs in patients with COVID-19 revealed diffuse alveolar damage (DAD) at different stages; the fibrotic phase is usually associated with long-standing severe disease. Care management of hospitalized patients is not easy, given that the risk of incurring a ventilator-induced lung injury (VILI) is high. Additionally, if the patient develops nosocomial infections, sepsis-induced ARDS should be considered in the study of the pathophysiological processes. We present an autopsy case of a hospitalized patient whose death was linked to COVID-19 infection, with the histopathological pattern of advanced pulmonary fibrosis. After prolonged use of non-invasive and invasive ventilation, the patient developed polymicrobial superinfection oh the lungs. After analyzing the individual’s clinical history and pulmonary anatomopathological findings, we consider healthcare issues that should lead to an improvement in diagnosis and to more adequate standards of care management among health professionals.

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.

Tocilizumab in critically ill COVID-19 patients: An observational study

Tocilizumab decreases inflammatory response in the cytokine storm which is one of the mechanisms behind the development of ARDS in COVID-19 patients. The objective of our study was to determine response of tocilizumab in patients suffering from COVID-19 by analyzing clinical parameters and inflammatory markers. A single-arm observational retrospective study was conducted from March 15, 2020 to March 15, 2021. Clinical outcomes in terms of mortality, weaning from mechanical ventilator, improvement in laboratory parameters including inflammatory cytokines, and length of hospital stay were documented. Reduction in values of inflammatory markers, and patients discharged home in stable condition were defined as an improvement after tocilizumab administration. A total of 514 patients received tocilizumab, majority of whom were critically sick 333 (64.8%). Out of the total sample 363 (70.6%) patients were discharged home in stable condition. Overall mean length of stay was 11.50 ± 8.4 days. There was significant difference in length of stay of patients who required invasive mechanical ventilation as compared to those who were kept only on supplemental oxygen (p < 0.05). Patients who were discharged home showed significant improvement in inflammatory markers and neutrophil to lymphocyte ratio as compared to those who expired (p < 0.05). A total of 21 (4.1%) patients had positive blood culture while 57 (11.1%) had positive culture of tracheal aspirate. Hence, tocilizumab is found to be a reasonable therapeutic option for worsening COVID-19 pneumonia by decreasing the need for mechanical ventilation. However, it is associated with adverse events including bacterial and fungal infections.

Bacterial and fungal growth in sputum cultures from 165 COVID-19 pneumonia patients requiring intubation: evidence for antimicrobial resistance development and analysis of risk factors

BACKGROUND

Coronavirus SARS-CoV-2 causes COVID-19 illness which can progress to severe pneumonia. Empiric antibacterials are often employed though frequency of bacterial coinfection superinfection is debated and concerns raised about selection of bacterial antimicrobial resistance. We evaluated sputum bacterial and fungal growth from 165 intubated COVID-19 pneumonia patients. Objectives were to determine frequency of culture positivity, risk factors for and outcomes of positive cultures, and timing of antimicrobial resistance development.

METHODS

Retrospective reviews were conducted of COVID-19 pneumonia patients requiring intubation admitted to a 1058-bed four community hospital system on the east coast United States, March 1 to May 1, 2020. Length of stay (LOS) was expressed as mean (standard deviation); 95% confidence interval (95% CI) was computed for overall mortality rate using the exact binomial method, and overall mortality was compared across each level of a potential risk factor using a Chi-Square Test of Independence. All tests were two-sided, and significance level was set to 0.05.

RESULTS

Average patient age was 68.7 years and LOS 19.9 days. Eighty-three patients (50.3% of total) originated from home, 10 from group homes (6.1% of total), and 72 from nursing facilities (43.6% of total). Mortality was 62.4%, highest for nursing home residents (80.6%). Findings from 253 sputum cultures overall did not suggest acute bacterial or fungal infection in 73 (45%) of 165 individuals sampled within 24 h of intubation. Cultures ≥ 1 week following intubation did grow potential pathogens in 72 (64.9%) of 111 cases with 70.8% consistent with late pneumonia and 29.2% suggesting colonization. Twelve (10.8% of total) of these late post-intubation cultures revealed worsened antimicrobial resistance predominantly in Pseudomonas, Enterobacter, or Staphylococcus aureus.

CONCLUSIONS

In severe COVID-19 pneumonia, a radiographic ground glass interstitial pattern and lack of purulent sputum prior to/around the time of intubation correlated with no culture growth or recovery of normal oral flora ± yeast. Discontinuation of empiric antibacterials should be considered in these patients aided by other clinical findings, history of prior antimicrobials, laboratory testing, and overall clinical course. Continuing longterm hospitalisation and antibiotics are associated with sputum cultures reflective of hospital-acquired microbes and increasing antimicrobial resistance.

TRIAL REGISTRATION

Not applicable as this was a retrospective chart review study without interventional arm.