Co-infections: potentially lethal and unexplored in COVID-19

Elongasome core proteins and class A PBP1a display zonal, processive movement at the midcell of Streptococcus pneumoniae

Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus), have two spatially separated peptidoglycan (PG) synthase nanomachines that locate zonally to the midcell of dividing cells. The septal PG synthase bPBP2x:FtsW closes the septum of dividing pneumococcal cells, whereas the elongasome located on the outer edge of the septal annulus synthesizes peripheral PG outward. We showed previously by sm-TIRFm that the septal PG synthase moves circumferentially at midcell, driven by PG synthesis and not by FtsZ treadmilling. The pneumococcal elongasome consists of the PG synthase bPBP2b:RodA, regulators MreC, MreD, and RodZ, but not MreB, and genetically associated proteins Class A aPBP1a and muramidase MpgA. Given its zonal location separate from FtsZ, it was of considerable interest to determine the dynamics of proteins in the pneumococcal elongasome. We found that bPBP2b, RodA, and MreC move circumferentially with the same velocities and durations at midcell, driven by PG synthesis. However, outside of the midcell zone, the majority of these elongasome proteins move diffusively over the entire surface of cells. Depletion of MreC resulted in loss of circumferential movement of bPBP2b, and bPBP2b and RodA require each other for localization and circumferential movement. Notably, a fraction of aPBP1a molecules also moved circumferentially at midcell with velocities similar to those of components of the core elongasome, but for shorter durations. Other aPBP1a molecules were static at midcell or diffusing over cell bodies. Last, MpgA displayed non-processive, subdiffusive motion that was largely confined to the midcell region and less frequently detected over the cell body.

Respiratory syncytial virus: A new era

Respiratory syncytial virus (RSV) is a major public health problem that has undergone significant changes in recent years. First of all, it has become easier to diagnose with highly reliable and rapidly available confirmatory tests. This has led to a better understanding of its epidemiology and RSV has gone from being a disease of the pediatric age group, severe only in infants and immunosuppressed children, to being a common disease in people of all ages, particularly important in patients of advanced age or with immunosuppressive diseases. Recent therapeutic and prophylactic advances, both with long-lasting monoclonal antibodies and vaccines, are another reason for satisfaction. For these reasons, the COVID and Emerging Pathogens Committee of the Illustrious Official College of Physicians of Madrid (ICOMEM) has considered it pertinent to review this subject in the light of new knowledge and new resources for dealing with this infection. We have formulated a series of questions that we believe will be of interest not only to members of the College but also to any non-expert in this subject, with a particular focus on the situation of RSV infection in Spain.

Device-Associated Infections in COVID-19 Patients: Frequency of Resistant Bacteria, Predictors and Mortality in Medellín, Colombia

INTRODUCTION

Increased antimicrobial use during the COVID-19 pandemic has raised concerns about the spread of resistant bacteria. This study analyzed the frequency of device-associated infections (DAI) caused by resistant bacteria, the predictors of these infections, and 30-day all-cause mortality in patients with and without COVID-19.

METHODS

A retrospective cohort study was conducted on DAI patients admitted to the ICU (intensive care unit) in 20 hospitals in Medellin, Colombia (2020-2021). The exposure assessed was the COVID-19 diagnosis, and outcomes analyzed were resistant bacterial infections and 30-day mortality. Clinical and microbiological information was collected from surveillance databases. Statistical analysis included generalized linear mixed-effects models.

RESULTS

Of the 1521 patients included, 1033 (67.9%) were COVID-19-positive and 1665 DAI were presented. Carbapenem-resistant Enterobacteriaceae (CRE) infections predominated during the study (n = 98; 9.9%). The patients with COVID-19 had a higher frequency of metallo-beta-lactamase-producing CRE infections (n = 15; 33.3%) compared to patients without the disease (n = 3; 13.0%). Long-stay in the ICU (RR: 2.09; 95% CI: 1.39-3.16), diabetes (RR: 1.73; 95% CI: 1.21-2.49), and mechanical ventilation (RR: 2.13; 95% CI: 1.01-4.51) were CRE infection predictors in COVID-19 patients, with a mortality rate of 60.3%.

CONCLUSION

CRE infections were predominant in COVID-19 patients. In pandemic situations, the strategies to control DAI should be maintained to avoid infections caused by resistant bacteria, such as length of stay in the ICU and duration of mechanical ventilation.

Bacterial co-infections and secondary infections and their antimicrobial resistance in Covid-19 patients during the second pandemic wave

Background

COVID-19 pneumonia with an unusual outbreak is considered a new, global public health threat. Microbiological characterization of co-infections in patients with COVID-19 is important, and antimicrobial use is high. We aimed to describe microbiologically confirmed co-infections and the antimicrobial resistance of the causative pathogens.

Method

From January to December 2020, we tested 1,301 patients who were COVID-19 positive. We received clinical samples (blood, respiratory and sterile body fluids) of COVID-19 patients who were suspected to have bacterial co-infections. Samples were processed and antimicrobial susceptibility testing was performed based on the CLSI recommendation. Demographic, clinical, laboratory and outcome data of those with positive cultures were collected.

Result

A total of 1301 COVID-19 patients (568 from the COVID ward and 733 from ICU) were admitted to the Covid care ward of a tertiary care hospital. 363 samples were sent for culturing and testing antibiotic susceptibility, of which 131 (36%) were found to be culture-positive (90 from ICUs, 41 from wards). Out of the 143 total isolates thus obtained from 131 samples, the majority (62.2%) were Gram-negative bacteria, and most of them were (70.8%) multidrug resistant.

Discussion

Bacterial co-infection in patients with COVID-19 is more commonly reported in the severely ill hospitalized individuals (58%), particularly in the ICU (73.3%) setting. In terms of mortality, almost half of co-infected patients died (51.1%). In most of them, the cause of death was found to be sepsis with post-COVID ARDS (58%).

Conclusion

Co-infection in COVID-19 patients may affect the outcome in terms of increasing the hospital stay.

Treatment and Management of Acinetobacter Pneumonia: Lessons Learned from Recent World Event

Acinetobacter pneumonia is a significant healthcare-associated infection that poses a considerable challenge to clinicians due to its multidrug-resistant nature. Recent world events, such as the COVID-19 pandemic, have highlighted the need for effective treatment and management strategies for Acinetobacter pneumonia. In this review, we discuss lessons learned from recent world events, particularly the COVID-19 pandemic, in the context of the treatment and management of Acinetobacter pneumonia. We performed an extensive literature review to uncover studies and information pertinent to the topic. The COVID-19 pandemic underscored the importance of infection control measures in healthcare settings, including proper hand hygiene, isolation protocols, and personal protective equipment use, to prevent the spread of multidrug-resistant pathogens like Acinetobacter. Additionally, the pandemic highlighted the crucial role of antimicrobial stewardship programs in optimizing antibiotic use and curbing the emergence of resistance. Advances in diagnostic techniques, such as rapid molecular testing, have also proven valuable in identifying Acinetobacter infections promptly. Furthermore, due to the limited availability of antibiotics for treating infections caused A. baumannii, alternative strategies are needed like the use of antimicrobial peptides, bacteriophages and their enzymes, nanoparticles, photodynamic and chelate therapy. Recent world events, particularly the COVID-19 pandemic, have provided valuable insights into the treatment and management of Acinetobacter pneumonia. These lessons emphasize the significance of infection control, antimicrobial stewardship, and early diagnostics in combating this challenging infection.

Nanotechnology-based fungal detection and treatment: current status and future perspective

Fungal infections impose a significant impact on global health and encompass major expenditures in medical treatments. Human mycoses, a fungal co-infection associated with SARS-CoV-2, is caused by opportunistic fungal pathogens and is often overlooked or misdiagnosed. Recently, there is increasing threat about spread of antimicrobial resistance in fungus, mostly in hospitals and other healthcare facilities. The diagnosis and treatment of fungal infections are associated with several issues, including tedious and non-selective detection methods, the growth of drug-resistant bacteria, severe side effects, and ineffective drug delivery. Thus, a rapid and sensitive diagnostic method and a high-efficacy and low-toxicity therapeutic approach are needed. Nanomedicine has emerged as a viable option for overcoming these limitations. Due to the unique physicochemical and optical properties of nanomaterials and newer biosensing techniques, nanodiagnostics play an important role in the accurate and prompt differentiation and detection of fungal diseases. Additionally, nano-based drug delivery techniques can increase drug permeability, reduce adverse effects, and extend systemic circulation time and drug half-life. This review paper is aimed at highlighting recent, promising, and unique trends in nanotechnology to design and develop diagnostics and treatment methods for fungal diseases.

Reduction in the incidence of invasive infections caused by encapsulated bacteria after the onset of the COVID-19 pandemic

Interaction between severe acute respiratory coronavirus 2 (SARS-CoV-2) and IIEB remains under investigation. Objective: to compare IIEB incidence before and during COVID-19 pandemic, and assess incidence of coinfection with COVID-19 and case fatality. A cross-sectional study was performed on data from a centralized microbiology laboratory serving a network of healthcare centers comprising 713 pediatric and adult inpatient beds, expanded by 20% during the pandemic. Three periods were evaluated: (1) pre-pandemic: March 1, 2019-February 29, 2020; (2) pandemic year 1: March 1, 2020-February 28, 2021; (3) pandemic year 2: March 1, 2021-July 31, 2021. Descriptive statistical analysis was performed. 56 502 samples (96% blood cultures) from 27224 patients were analyzed. Of these, 54 samples (from 54 patients) were positive for encapsulated bacteria. IIEB incidence was: 167.4, 32.6, and 50.4 per 100000 samples for periods 1, 2, and 3, respectively. Twelve IIEB episodes occurred during the pandemic period: 10 Streptococcus pneumoniae, and 2 Haemophilus influenzae, of which 7 were SARS-CoV-2/S. pneumoniae coinfections, with an incidence of 5.68 per 10000 COVID-19-related hospitalizations (0.056%). IIEB case fatality was 31%, 29%, and 60% for each period, respectively, 3/7 patients with coinfection died (43%). Case fatality for invasive pneumococcal disease (IPD) in patients without COVID-19, was 32.5%. Significant reduction in IIEB incidence was observed during the pandemic, coinciding with implementation of containment measures. The incidence of SARS-CoV-2/S. pneumoniae coinfection was low, with higher case fatality than IPD patients without COVID-19.

Unveiling the Clinical Spectrum of Post-COVID-19 Conditions: Assessment and Recommended Strategies

SARS-CoV-2 caused the pandemic of the rapidly evolving COVID-19. As of December 6, 2023, there were 765,152,854 COVID-19-recovering cases. Long-term consequences known as "long COVID" and "post-COVID-19 conditions" (PCCs) or "post-acute COVID-19 syndrome" are being reported more frequently in a subset of recovering patients. Systemic, neuropsychiatric, cardio-respiratory, and gastrointestinal symptoms are the most prevalent. The management of PCCs poses unique challenges due to the lack of official guidelines and the complex nature of the illness. This abstract highlights key principles derived from recent reviews and expert recommendations to provide healthcare professionals with a comprehensive approach to manage post-COVID-19 patients. Preventive medicine plays a crucial role in managing PCCs. While no specific medications are available for treatment, preventive measures such as COVID-19 vaccination, adherence to precautionary measures, regular consultations with medical professionals, monitoring symptoms and progress, and seeking information on symptom management are essential to assist patients in their recovery and improve their quality of life. Medical management requires transparent goal-setting and collaborative decision-making based on the patient's symptoms, comorbidities, and treatment objectives. Treatment plans for post-COVID-19 patients should focus on patient education, using registries and calendars to track symptoms and triggers, providing support and reassurance, and offering holistic support through peer networks and supportive psychotherapy techniques. Symptomatic and rehabilitative care, including well-established symptom management techniques, physical rehabilitation programs, and addressing mental health and well-being, are vital components of post-COVID-19 management. Lifestyle factors such as stress reduction, nutrition, and sleep should be incorporated into managing underlying medical conditions in post-COVID-19 patients. Regular follow-up visits and referrals to specialists are recommended to monitor the patient's progress and address specific organ system involvement or additional care needs. In summary, for the effective management of PCCs, a holistic approach should include preventive measures, patient education, supportive psychotherapy, symptomatic and rehabilitative care, medical management, counseling on lifestyle elements, and appropriate follow-up plans. However, it is crucial to stay updated with evolving guidelines and recommendations from healthcare authorities to provide the most effective and evidence-based care to post-COVID-19 patients.

Impact of SARS-CoV2 infection on gut microbiota dysbiosis

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

Adverse events during the COVID-19 pandemic in Ecuador: high frequency of healthcare-associated infections and increasing hospital stay and costs

Background

The COVID-19 pandemic generated high workloads given the high volume of seriously ill patients; conditions that could increase the risk of adverse events (AE). This study analyzed the frequency of AE in patients with COVID-19 and their effect on mortality, hospital stay and costs.

Methods

This retrospective cohort study included in-patients with COVID-19 at a single hospital between March 2020-June 2021. Exposure was the occurrence of at least one AE. Hospital stay, costs and death were considered outcomes. Clinical information and direct costs were obtained from medical and billing records. Generalized linear models were used to estimate the association measures.

Results

405 patients were included, 55.8% (n=226) men, median age 56 years (IQR: 41.0-70.0) and with a history of hypertension (26.2%; n=106), diabetes mellitus (13.8%; n=56) and obesity (13.8%; n=56). The incidence of AE was 13.3% (n=54), 29 patients presented more than one AE, for a total of 70 events. Most events (74.3%; n=52) were preventable and the most frequent were healthcare-associated infections (50%; n=35), phlebitis (14.3%; n=10) and pressure ulcers (12.9%; n=9). AE prolonged hospital stay (change rate: 1.57; 95%CI: 1.26-1.95; P=0.001) and increased direct healthcare costs (change rate: 1.20; 95% CI: 1.03-1.39, P=0.019). Likewise, the risk of death was 56% higher in patients with AE.

Conclusion

Pandemics are unexpected events that present challenges to safe healthcare. Improving quality policies, monitoring compliance with protocols and providing ongoing education are strategies to prevent AE such as healthcare-associated infections, which increase hospital costs and stay.

Antibiotics and nano-antibiotics in treatment of lung infection: In management of COVID-19

The world has witnessed the cruelty of COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The association of COVID-19 with other secondary and bacterial co-infections has tremendously contributed to lung infections. An increased probability of having a secondary lung infection was observed among the post-COVID patients. The treatment of antibiotics has ameliorated the mortality rate. However, the stewardship of antibiotic treatment was linked to increased organ failure. Therefore, the paper discusses the interactions between the virus and host through the ACE2 receptors that contribute to COVID-19 development. Furthermore, the paper provides an invaluable compendium history of SARS-CoV-2 genomic composition. It revolves around most classes of antibiotics used to treat COVID-19 disease and post-COVID lung infections with the complete mechanism. This binds with the exertion of the antibiotics for bacterial infection associated with COVID-19 patients and how beneficial and effective responses have been recorded for the treatment. The application of nanotechnology and possible approaches of nanomedicines is also discussed to its potential usage.

Evaluation of Acinetobacter baumannii, Klebsiella pneumoniae, and Staphylococcus aureus respiratory tract superinfections among patients with COVID-19 at a tertiary-care hospital in Tehran, Iran

BACKGROUND

The emergence of healthcare-associated infections (HAIs) or superinfections in COVID-19 patients has resulted in poor prognosis and increased mortality.

METHODS

In a cross-sectional study, 101 respiratory samples were collected from ICU-admitted COVID-19 patients. The HAI rate, demographics, and antibiotic resistance were assessed.

RESULTS

The HAI rate was 83.16% (76.62% bacterial and 6.54% fungal). The prevalence of 3 major HAI-causing organisms included Klebsiella pneumoniae (41.5%), Acinetobacter baumannii (20.8%), and Staphylococcus aureus (4.9%). Mortality and intubation ventilation proportions of 90% (p = 0.027) and 92.2% (p = 0.02) were significant among patients with superinfection, respectively. Multiple logistic regression analysis showed SpO2 pressure (odds ratio 0.842; 95% CI 0.750-0.945; p = 0.004) as a predictive factor in the association between antibiotic usage and mortality. More than 50% of patients received carbapenems. The resistance rates to at least one antibiotic of third-generation cephalosporins, aminoglycosides, quinolones/fluoroquinolones, tetracyclines, and β-lactam inhibitors were 95.2%, 95.2%, 90%, 57.1%, and 100% among A. baumannii isolates and 71.4%, 55%, 69%, 61.9%, and 59.5% among K. pneumoniae isolates, respectively. A proportion of 60% was recorded for methicillin-resistant S. aureus isolates.

CONCLUSION

As a result, antibiotic treatment should be administered following the microbial resistance profile. Contact isolation and infection control measures should be implemented as needed.

Negative regulation of MurZ and MurA underlies the essentiality of GpsB- and StkP-mediated protein phosphorylation in Streptococcus pneumoniae D39

GpsB links peptidoglycan synthases to other proteins that determine the shape of the respiratory pathogen Streptococcus pneumoniae (pneumococcus; Spn) and other low-GC Gram-positive bacteria. GpsB is also required for phosphorylation of proteins by the essential StkP(Spn) Ser/Thr protein kinase. Here we report three classes of frequently arising chromosomal duplications (≈21-176 genes) containing murZ (MurZ-family homolog of MurA) or murA that suppress ΔgpsB or ΔstkP. These duplications arose from three different repeated sequences and demonstrate the facility of pneumococcus to modulate gene dosage of numerous genes. Overproduction of MurZ or MurA alone or overproduction of MurZ caused by ΔkhpAB mutations suppressed ΔgpsB or ΔstkP phenotypes to varying extents. ΔgpsB and ΔstkP were also suppressed by MurZ amino-acid changes distant from the active site, including one in commonly studied laboratory strains, and by truncation or deletion of the homolog of IreB(ReoM). Unlike in other Gram-positive bacteria, MurZ is predominant to MurA in pneumococcal cells. However, ΔgpsB and ΔstkP were not suppressed by ΔclpCP, which did not alter MurZ or MurA amounts. These results support a model in which regulation of MurZ and MurA activity, likely by IreB(Spn), is the only essential requirement for StkP-mediated protein phosphorylation in exponentially growing D39 pneumococcal cells.

Description of the colonizing mycobiota of endotracheal tubes from patients admitted to two intensive care units in Bogotá, Colombia

Introduction. Medical device colonization by pathogenic microorganisms is a risk factor for increasing infections associated with health care and, consequently, the morbidity and mortality of intubated patients. In Colombia, fungal colonization of endotracheal tubes has not been described, and this information could lead to new therapeutic options for the benefit of patients. Objective. To describe the colonizing fungi of the endotracheal tubes from patients in the intensive care unit, along with its antifungal sensitivity profile. Materials and methods. We conducted a descriptive, observational study in two health centers for 12 months. Endotracheal tubes were collected from patients in intensive care units. Samples were processed for culture, fungi identification, and antifungal sensitivity profile assessment. Results. A total of 121 endotracheal tubes, obtained from 113 patients, were analyzed: 41.32 % of the tubes were colonized by Candida albicans (64.62%), C. non‑albicans (30.77%), Cryptococcus spp. (3.08%) or molds (1.54%). All fungi evaluated showed a high sensitivity to antifungals, with a mean of 91%. Conclusion. Fungal colonization was found in the endotracheal tubes of patients under invasive mechanical ventilation. The antifungal sensitivity profile in these patients was favorable. A clinical study is required to find possible correlations between the colonizing microorganisms and infectivity.

Antibiotic-Resistant ESKAPE Pathogens and COVID-19: The Pandemic beyond the Pandemic

Antibacterial resistance is a renewed public health plague in modern times, and the COVID-19 pandemic has rekindled this problem. Changes in antibiotic prescribing behavior, misinformation, financial hardship, environmental impact, and governance gaps have generally enhanced the misuse and improper access to antibiotics during the COVID-19 pandemic. These determinants, intersected with antibacterial resistance in the current pandemic, may amplify the potential for a future antibacterial resistance pandemic. The occurrence of infections with multidrug-resistant (MDR), extensively drug-resistant (XDR), difficult-to-treat drug-resistant (DTR), carbapenem-resistant (CR), and pan-drug-resistant (PDR) bacteria is still increasing. The aim of this review is to highlight the state of the art of antibacterial resistance worldwide, focusing on the most important pathogens, namely Enterobacterales, Acinetobacter baumannii, and Klebsiella pneumoniae, and their resistance to the most common antibiotics.

Microbial Landscape and Antibiotic-Susceptibility Profiles of Microorganisms in Patients with Bacterial Pneumonia: A Comparative Cross-Sectional Study of COVID-19 and Non-COVID-19 Cases in Aktobe, Kazakhstan

This cross-sectional study investigated the microbial landscape and antibiotic-resistance patterns in patients with bacterial pneumonia, with a focus on the impact of COVID-19. Sputum samples from individuals with bacterial pneumonia, including coronavirus disease 2019-positive polymerase chain reaction (COVID-19-PCR+), COVID-19-PCR- and non-COVID-19 patients, were analyzed. Surprisingly, the classic etiological factor of bacterial pneumonia, Streptococcus pneumoniae, was rarely isolated from the sputum samples. Furthermore, the frequency of multidrug-resistant pathogens was found to be higher in non-COVID-19 patients, highlighting the potential impact of the pandemic on antimicrobial resistance. Strains obtained from COVID-19-PCR+ patients exhibited significant resistance to commonly used antibiotics, including fluoroquinolones and cephalosporins. Notably, the ESKAPE pathogens, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, and Enterobacter aerogenes, were identified among the isolated microorganisms. Our findings underscore the urgent need for infection control measures and responsible antibiotic use in healthcare settings, as well as the importance of enhancing pneumonia diagnostics and implementing standardized laboratory protocols.

Impact of COVID-19 on the distribution of pathogenic bacteria in the lower respiratory tract of the elderly

BACKGROUND

To investigate the distribution of bacterial pathogens of lower respiratory tract infection (LRTI) in hospitalized elderly patients during the COVID-19 epidemic and to explore the influence of COVID-19 on the distribution of bacterial pathogens, to provide guidance for clinical diagnosis.

METHODS

Specimens of sputum from elderly LRTIs patients at Fuding Hospital of China were consecutively collected from October 2022 to January 2023. Cultures and identification were done, and RT-PCR was employed to detect SARS-Cov-2 nucleic acid.

RESULTS

A total of 195 isolates were characterized in 163 sputum samples of consecutive hospitalized elderly patients, of which 11.3% were Gram-positive bacteria and 88.7% were Gram-negative. The top of frequently isolated pathogens was Klebsiella pneumonia (30.3%), Pseudomonas aeruginosa (19.0%), Acinetobacter baumannii (12.8%), Stenotrophomonas maltophili, (7.7%), Escherichia coli (7.2%). According to the results of novel coronavirus nucleic acid detection, the 163 patients were divided into COVID-19 group and non-COVID control (CNT) group. The comparison of bacterial distribution between the groups revealed that Stenotrophomonas maltophilia was lower in the COVID-19 than in the CNT group, while A. baumannii was higher in the COVID-19 group, and the difference was statistically significant (p < .05).

CONCLUSION

The major bacteria identified in sputum culture of hospitalized elderly patients were K. pneumonia, P. aeruginosa, A. baumannii, S. maltophilia, and E. coli. Furthermore, the distribution of S. maltophilia and A. baumannii between the COVID-19 and CNT groups was found to be significantly different (p < .05), while there were no significant differences in the distribution of other bacteria.

Symptoms, Treatment, and Outcomes of COVID-19 Patients Coinfected with Clostridioides difficile: Single-Center Study from NE Romania during the COVID-19 Pandemic

The Coronavirus disease 2019 (COVID-19) pandemic has brought new challenges across medical disciplines, particularly in infectious disease medicine. In Romania, the incidence of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) infection increased dramatically since March 2020 until March 2022. Antibiotic administration for pulmonary superinfections in COVID-19 intensified and, consequently, increased rates of Clostridioides difficile infection (CDI) were hypothesized. We conducted a single-center, retrospective, observational study on patients from North-Eastern Romania to assess clinical characteristics and outcomes of COVID-19 and Clostridioides difficile (CD) coinfection, and to identify risk factors for CDI in COVID-19 patients. The study enrolled eighty-six CDI and COVID-19 coinfected patients admitted during March 2020-February 2021 (mean age 59.14 years, 53.49% men, 67.44% urban residents) and a group of eighty-six COVID-19 patients. On admission, symptoms were more severe in mono-infected patients, while coinfected patients associated a more intense acute inflammatory syndrome. The main risk factors for severe COVID-19 were smoking, diabetes mellitus, and antibiotic administration. Third generation cephalosporins (55%) and carbapenems (24%) were the main antibiotics used, and carbapenems were significantly associated with severe COVID-19 in patients coinfected with CD during hospitalization. Coinfection resulted in longer hospitalization and poorer outcomes. The extensive use of antibiotics in COVID-19, particularly carbapenems, contributed substantially to CD coinfection.

Potential interaction between the oral microbiota and COVID-19: a meta-analysis and bioinformatics prediction

Objectives

The purpose of this study was to evaluate available evidence on the association between the human oral microbiota and coronavirus disease 2019 (COVID-19) and summarize relevant data obtained during the pandemic.

Methods

We searched EMBASE, PubMed, and the Cochrane Library for human studies published up to October 2022. The main outcomes of the study were the differences in the diversity (α and β) and composition of the oral microbiota at the phylum and genus levels between patients with laboratory-confirmed SARS-CoV-2 infection (CPs) and healthy controls (HCs). We used the Human Protein Atlas (HPA), Gene Expression Profiling Interactive Analysis (GEPIA) database, Protein-protein interaction (PPI) network (STRING) and Gene enrichment analysis (Metascape) to evaluate the expression of dipeptidyl peptidase 4 (DPP4) (which is the cell receptor of SARS CoV-2) in oral tissues and evaluate its correlation with viral genes or changes in the oral microbiota.

Results

Out of 706 studies, a meta-analysis of 9 studies revealed a significantly lower alpha diversity (Shannon index) in CPs than in HCs (standardized mean difference (SMD): -0.53, 95% confidence intervals (95% CI): -0.97 to -0.09). Subgroup meta-analysis revealed a significantly lower alpha diversity (Shannon index) in older than younger individuals (SMD: -0.54, 95% CI: -0.86 to -0.23/SMD: -0.52, 95% CI: -1.18 to 0.14). At the genus level, the most significant changes were in Streptococcus and Neisseria, which had abundances that were significantly higher and lower in CPs than in HCs based on data obtained from six out of eleven and five out of eleven studies, respectively. DPP4 mRNA expression in the oral salivary gland was significantly lower in elderly individuals than in young individuals. Spearman correlation analysis showed that DPP4 expression was negatively correlated with the expression of viral genes. Gene enrichment analysis showed that DPP4-associated proteins were mainly enriched in biological processes, such as regulation of receptor-mediated endocytosis of viruses by host cells and bacterial invasion of epithelial cells.

Conclusion

The oral microbial composition in COVID-19 patients was significantly different from that in healthy individuals, especially among elderly individuals. DPP4 may be related to viral infection and dysbiosis of the oral microbiome in elderly individuals.

Outcomes of patients with coronavirus disease versus other lung infections requiring venovenous extracorporeal membrane oxygenation

Background

Patients with Coronavirus Disease (COVID-19) often develop severe acute respiratory distress syndrome (ARDS) requiring prolonged mechanical ventilation (MV), and venovenous extracorporeal membrane oxygenation (V-V ECMO).Mortality in COVID-19 patients on V-V ECMO was exceptionally high; therefore, whether survival can be ameliorated should be investigated.

Methods

We collected data from 85 patients with severe ARDS who required ECMO support at the University Hospital Magdeburg from 2014 to 2021. The patients were divided into the COVID-19 group (52 patients) and the non-COVID-19 group (33 patients). Demographic and pre-, intra-, and post-ECMO data were retrospectively recorded. The parameters of mechanical ventilation, laboratory data before using ECMO, and during ECMO were compared.

Results

There was a significant difference between the two groups regarding survival: 38.5% of COVID-19 patients and 63.6% of non-COVID-19 patients survived 60 days (p = 0.024). COVID-19 patients required V-V ECMO after 6.5 days of MV, while non-COVID-19 patients required V-V ECMO after 2.0 days of MV (p = 0.048). The COVID-19 group had a greater proportion of patients with ischemic heart disease (21.2% vs 3%, p = 0.019). The rates of most complications were comparable in both groups, whereas the COVID-19 group showed a significantly higher rate of cerebral bleeding (23.1 vs 6.1%, p = 0.039) and lung bacterial superinfection (53.8% vs 9.1%, p = <0.001).

Conclusion

The higher 60-days mortality among patients with COVID-19 with severe ARDS was attributable to superinfection, a higher risk of intracerebral bleeding, and the pre-existing ischemic heart disease.

Using system biology and bioinformatics to identify the influences of COVID-19 co-infection with influenza virus on COPD

Coronavirus disease 2019 (COVID-19) has speedily increased mortality globally. Although they are risk factors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), less is known about the common molecular mechanisms behind COVID-19, influenza virus A (IAV), and chronic obstructive pulmonary disease (COPD). This research used bioinformatics and systems biology to find possible medications for treating COVID-19, IAV, and COPD via identifying differentially expressed genes (DEGs) from gene expression datasets (GSE171110, GSE76925, GSE106986, and GSE185576). A total of 78 DEGs were subjected to functional enrichment, pathway analysis, protein-protein interaction (PPI) network construct, hub gene extraction, and other potentially relevant disorders. Then, DEGs were discovered in networks including transcription factor (TF)-gene connections, protein-drug interactions, and DEG-microRNA (miRNA) coregulatory networks by using NetworkAnalyst. The top 12 hub genes were MPO, MMP9, CD8A, HP, ELANE, CD5, CR2, PLA2G7, PIK3R1, SLAMF1, PEX3, and TNFRSF17. We found that 44 TFs-genes, as well as 118 miRNAs, are directly linked to hub genes. Additionally, we searched the Drug Signatures Database (DSigDB) and identified 10 drugs that could potentially treat COVID-19, IAV, and COPD. Therefore, we evaluated the top 12 hub genes that could be promising DEGs for targeted therapy for SARS-CoV-2 and identified several prospective medications that may benefit COPD patients with COVID-19 and IAV co-infection.

ESKAPE and Beyond: The Burden of Coinfections in the COVID-19 Pandemic

The ESKAPE group constitute a threat to public health, since these microorganisms are associated with severe infections in hospitals and have a direct relationship with high mortality rates. The presence of these bacteria in hospitals had a direct impact on the incidence of healthcare-associated coinfections in the SARS-CoV-2 pandemic. In recent years, these pathogens have shown resistance to multiple antibiotic families. The presence of high-risk clones within this group of bacteria contributes to the spread of resistance mechanisms worldwide. In the pandemic, these pathogens were implicated in coinfections in severely ill COVID-19 patients. The aim of this review is to describe the main microorganisms of the ESKAPE group involved in coinfections in COVID-19 patients, addressing mainly antimicrobial resistance mechanisms, epidemiology, and high-risk clones.

Impact of COVID-19 Outbreak on Influenza and Pneumococcal Vaccination Uptake: A Multi-Center Retrospective Study

During the coronavirus disease 2019 (COVID-19) pandemic, global vaccination efforts declined due to the burden on health systems and community resistance to epidemic control measures. Influenza and pneumococcal vaccines have been recommended for vulnerable populations to prevent severe pneumonia. We investigated community response towards influenza and pneumococcal vaccines (pneumococcal conjugate vaccine and pneumococcal polysaccharide vaccine) after the COVID-19 outbreak in Taiwan. We retrospectively included adults who visited Chang Gung Memorial Hospital (CGMH) institutions for influenza or pneumococcal vaccination from January 2018 to December 2021. The first case of COVID-19 in Taiwan was detected in January 2020; therefore, in this study, hospitalized cases from January 2018 to December 2019 were defined as "before COVID-19 outbreak," and hospitalized cases from January 2020 to December 2021 were defined as "after COVID-19 outbreak". A total of 105,386 adults were enrolled in the study. An increase in influenza vaccination (n = 33,139 vs. n = 62,634) and pneumococcal vaccination (n = 3035 vs. n = 4260) were observed after the COVID-19 outbreak. In addition, there was an increased willingness to receive both influenza and pneumococcal vaccinations among women, adults without underlying disease and younger adults. The COVID-19 pandemic may have increased awareness of the importance of vaccination in Taiwan.

Invasive Pulmonary Aspergillosis in Coronavirus Disease 2019 Patients Lights and Shadows in the Current Landscape

Invasive pulmonary aspergillosis (IPA) presents a known risk to critically ill patients with SARS-CoV-2; quantifying the global burden of IPA in SARS-CoV-2 is extremely challenging. The true incidence of COVID-19-associated pulmonary aspergillosis (CAPA) and the impact on mortality is difficult to define because of indiscriminate clinical signs, low culture sensitivity and specificity and variability in clinical practice between centers. While positive cultures of upper airway samples are considered indicative for the diagnosis of probable CAPA, conventional microscopic examination and qualitative culture of respiratory tract samples have quite low sensitivity and specificity. Thus, the diagnosis should be confirmed with serum and BAL GM test or positive BAL culture to mitigate the risk of overdiagnosis and over-treatment. Bronchoscopy has a limited role in these patients and should only be considered when diagnosis confirmation would significantly change clinical management. Varying diagnostic performance, availability, and time-to-results turnaround time are important limitations of currently approved biomarkers and molecular assays for the diagnosis of IA. The use of CT scans for diagnostic purposes is controversial due to practical concerns and the complex character of lesions presented in SARS-CoV-2 patients. The key objective of management is to improve survival by avoiding misdiagnosis and by initiating early, targeted antifungal treatment. The main factors that should be considered upon selection of treatment options include the severity of the infection, concomitant renal or hepatic injury, possible drug interactions, requirement for therapeutic drug monitoring, and cost of therapy. The optimal duration of antifungal therapy for CAPA is still under debate.

Development of a novel, entirely herbal-based mouthwash effective against common oral bacteria and SARS-CoV-2

BACKGROUND

Parallel to the growth of the oral healthcare market, there is a constantly increasing demand for natural products as well. Many customers prefer products that contain fewer toxic agents, therefore providing an environmentally friendly solution with the benefit of smaller risk to the user. Medieval and early modern medicinal knowledge might be useful when looking for natural, herbal-based components to develop modern products. Along with these considerations we created, tested, and compared an entirely natural mouthwash, named Herba Dei.

METHODS

The manufacturing procedure was standardized, and the created tincture was evaluated by GC/MS analysis for active compounds, experimentally tested in cell-based cytotoxicity, salivary protein integrity, cell-free antioxidant activity, anti-bacterial and anti-viral assays, and compared with three market-leading mouthwashes.

RESULTS

Our tincture did not show significant damage in the cytotoxicity assays to keratinocyte and Vero E6 cells and did not disrupt the low molecular weight salivary proteins. Its radical scavenging capacity surpassed that of two tested, partly natural, and synthetic mouthwashes, while its antibacterial activity was comparable to the tested products, or higher in the bacterial aerobic respiratory assay. The active compounds responsible for the effects include naturally occurring phenylpropanoids, terpenes, and terpenoids. Our mouthwash proved to be effective in vitro in lowering the copy number of SARS-CoV-2 in circumstances mimicking the salivary environment.

CONCLUSIONS

The developed product might be a useful tool to impede the transmission and spread of SARS-CoV-2 in interpersonal contact and aerosol-generating conditions. Our mouthwash can help reduce the oral bacterial flora and has an antioxidant activity that facilitates wound healing and prevents adverse effects of smoke in the oral cavity.

Creating anti-viral high-touch surfaces using photocatalytic transparent films

Antimicrobial and self-cleaning surface coatings are promising tools to combat the growing global threat of infectious diseases and related healthcare-associated infections (HAIs). Although many engineered TiO₂-based coating technologies are reporting antibacterial performance, the antiviral performance of these coatings has not been explored. Furthermore, previous studies have underscored the importance of the "transparency" of the coating for surfaces such as the touch screens of medical devices. Hence, in this study, we fabricated a variety of nanoscale TiO₂-based transparent thin films (anatase TiO₂, anatase/rutile mixed phase TiO₂, silver-anatase TiO₂ composite, and carbon nanotube-anatase TiO₂ composite) via dipping and airbrush spray coating technologies and evaluated their antiviral performance (Bacteriophage MS2 as the model) under dark and illuminated conditions. The thin films showed high surface coverage (ranging from 40 to 85%), low surface roughness (maximum average roughness 70 nm), super-hydrophilicity (water contact angle 6-38.4°), and high transparency (70-80% transmittance under visible light). Antiviral performance of the coatings revealed that silver-anatase TiO₂ composite (nAg/nTiO₂) coated samples achieved the highest antiviral efficacy (5-6 log reduction) while the other TiO₂ coated samples showed fair antiviral results (1.5-3.5 log reduction) after 90 min LED irradiation at 365 nm. Those findings indicate that TiO₂-based composite coatings are effective in creating antiviral high-touch surfaces with the potential to control infectious diseases and HAIs.

Clinical and treatment factors associated with the mortality of COVID-19 patients admitted to a referral hospital in Indonesia

Background

Indonesia had the second-highest number of COVID-19 cases and deaths in South-East Asia. We aimed to determine the factors associated with this mortality and the effect of the recommended COVID-19 treatment regimen during the first 10 months of the epidemic.

Methods

This was a retrospective cohort study using secondary data from medical records. In total, 689 adult COVID-19 inpatients hospitalized between March and December 2020 were enrolled. Clinical characteristics, laboratory parameters, and treatments were analyzed by survival outcome. Kaplan-Meier statistics were used to estimate survival.

Findings

Of the 689 patients enrolled, 103 (14.9%) died. Disease severity was highly associated with mortality (hazard ratio [HR]: 7.69, p < 0.001). Other clinical factors associated with mortality were older age and comorbidities. Based on laboratory parameters, higher procalcitonin and C-reactive protein contents and a neutrophil-to-lymphocyte ratio >3.53 were also linked to mortality. Favipiravir was associated with lower mortality, with adjusted HRs of 0.24 (0.11-0.54) and 0.40 (0.17-0.98) among the mild/moderate and severe cases, respectively. Among patients with severe disease, steroids showed some beneficial effects in the early days of hospitalization.

Interpretation

Older age and comorbidities were associated with disease severity and, consequently, higher mortality. Higher mortality after the second week of hospitalization may be related to secondary bacterial infection. Favipiravir showed significant benefit for COVID-19 survival, while steroids showed benefit only in the early days of admission among patients with severe disease.

Funding

This research did not receive a specific grant from any funding agency in the public, commercial, or not-for-profit sectors.

Chromosomal Duplications of MurZ (MurA2) or MurA (MurA1), Amino Acid Substitutions in MurZ (MurA2), and Absence of KhpAB Obviate the Requirement for Protein Phosphorylation in Streptococcus pneumoniae D39

GpsB links peptidoglycan synthases to other proteins that determine the shape of the respiratory pathogen Streptococcus pneumoniae (pneumococcus; Spn ) and other low-GC Gram-positive bacteria. GpsB is also required for phosphorylation of proteins by the essential StkP( Spn ) Ser/Thr protein kinase. Here we report three classes of frequently arising chromosomal duplications (≈21-176 genes) containing murZ (MurZ-family homolog of MurA) or murA that suppress Δ gpsB or Δ stkP . These duplications arose from three different repeated sequences and demonstrate the facility of pneumococcus to modulate gene dosage of numerous genes. Overproduction of MurZ or MurA alone or overexpression of MurZ caused by Δ khpAB mutations suppressed Δ gpsB or Δ stkP phenotypes to varying extents. Δ gpsB and Δ stkP were also suppressed by MurZ amino-acid changes distant from the active site, including one in commonly studied laboratory strains, and by truncation or deletion of the homolog of IreB(ReoM). Unlike in other Gram-positive bacteria, MurZ is predominant to MurA in pneumococcal cells. However, Δ gpsB and Δ stkP were not suppressed by Δ clpCP , which did not alter MurZ or MurA amounts. These results support a model in which regulation of MurZ and MurA activity, likely by IreB( Spn ), is the only essential requirement for protein phosphorylation in exponentially growing D39 pneumococcal cells.

Heat-Treated Lysozyme Hydrochloride: A Study on Its Structural Modifications and Anti-SARS-CoV-2 Activity

Lysozyme (E.C. 3.2.1.17), an about 14 kDa protein and pI 11, widely spread in nature, is present in humans mainly in milk, saliva, and intestinal mucus as a part of innate defense mechanisms. It is endowed with antimicrobial activity due to its action as an N-acetylmuramidase, cleaving the 1-4β glycosidic linkage in the peptidoglycan layer of Gram-positive bacteria. This antimicrobial activity is exerted only against a limited number of Gram-negative bacteria. Different action mechanisms are proposed to explain its activity against Gram-negative bacteria, viruses, and fungi. The antiviral activity prompted the study of a possible application of lysozyme in the treatment of SARS-CoV-2 infections. Among the different sources of lysozyme, the chicken egg albumen was chosen, being the richest source of this protein (c-type lysozyme, 129 amino acids). Interestingly, the activity of lysozyme hydrochloride against SARS-CoV-2 was related to the heating (to about 100 °C) of this molecule. A chemical-physical characterization was required to investigate the possible modifications of native lysozyme hydrochloride by heat treatment. The FTIR analysis of the two preparations of lysozyme hydrochloride showed appreciable differences in the secondary structure of the two protein chains. HPLC and NMR analyses, as well as the enzymatic activity determination, did not show significant modifications.

Evaluation of the Diagnostic Performance of a SARS-CoV-2 and Influenza A/B Combo Rapid Antigen Test in Respiratory Samples

This study aimed to evaluate the performance characteristics of a rapid antigen test developed to detect SARS-CoV-2 (COVID-19), influenza A virus (IAV), and influenza B virus (IBV) (flu) compared with those of the real-time reverse transcription-polymerase chain reaction (rRT-PCR) method. One hundred SARS-CoV-2, one hundred IAV, and twenty-four IBV patients whose diagnoses were confirmed by clinical and laboratory methods were included in the patient group. Seventy-six patients, who were negative for all respiratory tract viruses, were included as the control group. The Panbio™ COVID-19/Flu A&B Rapid Panel test kit was used in the assays. The sensitivity values of the kit were 97.5%, 97.9%, and 33.33% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load below 20 Ct values. The sensitivity values of the kit were 16.7%, 36.5%, and 11.11% for SARS-CoV-2, IAV, and IBV, respectively, in samples with a viral load above 20 Ct. The kit's specificity was 100%. In conclusion, this kit demonstrated high sensitivity to SARS-CoV-2 and IAV for viral loads below 20 Ct values, but the sensitivity values were not compatible with PCR positivity for lower viral loads over 20 Ct values. Rapid antigen tests may be preferred as a routine screening tool in communal environments, especially in symptomatic individuals, when diagnosing SARS-CoV-2, IAV, and IBV with high caution.

Surge of mucormycosis during the COVID-19 pandemic

Patients with respiratory viral infections are more likely to develop co-infections leading to increased fatality. Mucormycosis is an epidemic amidst the COVID-19 pandemic that conveys a 'double threat' to the global health fraternity. Mucormycosis is caused by the Mucorales group of fungi and exhibits acute angioinvasion generally in immunocompromised patients. The most familiar foci of infections are sinuses (39%), lungs (24%), and skin tissues (19%) where the overall dissemination occurs in 23% of cases. The mortality rate in the case of disseminated mucormycosis is found to be 96%. Symptoms are mostly nonspecific and often resemble other common bacterial or fungal infections. Currently, COVID-19-associated mucormycosis (CAM) is being reported from a number of countries such as the USA, Turkey, France, Mexico, Iran, Austria, UK, Brazil, and Italy, while India is the hotspot for this deadly co-infection, accounting for approximately 28,252 cases up to June 8, 2021. It strikes patients within 12-18 days after COVID-19 recovery, and nearly 80% require surgery. Nevertheless, the mortality rate can reach 94% if the diagnosis is delayed or remains untreated. Sometimes COVID-19 is the sole predisposing factor for CAM. Therefore, this study may provide a comprehensive resource for clinicians and researchers dealing with fungal infections, intending to link the potential translational knowledge and prospective therapeutic challenges to counter this opportunistic pathogen.

Understanding Drivers of Vaccine Hesitancy During the COVID-19 Pandemic Among Older Adults in Jiangsu Province, China: Cross-sectional Survey

BACKGROUND

Older adults are particularly at risk from infectious diseases, including serve complications, hospitalization, and death.

OBJECTIVE

This study aimed to explore the drivers of vaccine hesitancy among older adults based on the "3Cs" (confidence, complacency, and convenience) framework, where socioeconomic status and vaccination history played the role of moderators.

METHODS

A cross-sectional questionnaire survey was conducted in Jiangsu Province, China, between June 1 and July 20, 2021. Older adults (aged ≥60 years) were recruited using a stratified sampling method. Vaccine hesitancy was influenced by the 3Cs in the model. Socioeconomic status and vaccination history processed through the item parceling method were used to moderate associations between the 3Cs and hesitancy. Hierarchical regression analyses and structural equation modeling were used to test the validity of the new framework. We performed 5000 trials of bootstrapping to calculate the 95% CI of the pathway's coefficients.

RESULTS

A total of 1341 older adults participated. The mean age was 71.3 (SD 5.4) years, and 44.7% (599/1341) of participants were men. Confidence (b=0.967; 95% CI 0.759-1.201; P=.002), convenience (b=0.458; 95% CI 0.333-0.590; P=.002), and less complacency (b=0.301; 95% CI 0.187-0.408; P=.002) were positively associated with less vaccine hesitancy. Socioeconomic status weakened the positive effect of low complacency (b=-0.065; P=.03) on low vaccine hesitancy. COVID-19 vaccination history negatively moderated the positive association between confidence (b=-0.071; P=.02) and lower vaccine hesitancy.

CONCLUSIONS

Our study identified that confidence was the more influential dimension in reducing vaccine hesitancy among older adults. COVID-19 vaccination history, as well as confidence, had a positive association with less vaccine hesitancy and could weaken the role of confidence in vaccine hesitancy. Socioeconomic status had a substitution relationship with less complacency, which suggested a competitive positive association between them on less vaccine hesitancy.

Peripheral Blood Genes Crosstalk between COVID-19 and Sepsis

Severe coronavirus disease 2019 (COVID-19) has led to a rapid increase in death rates all over the world. Sepsis is a life-threatening disease associated with a dysregulated host immune response. It has been shown that COVID-19 shares many similarities with sepsis in many aspects. However, the molecular mechanisms underlying sepsis and COVID-19 are not well understood. The aim of this study was to identify common transcriptional signatures, regulators, and pathways between COVID-19 and sepsis, which may provide a new direction for the treatment of COVID-19 and sepsis. First, COVID-19 blood gene expression profile (GSE179850) data and sepsis blood expression profile (GSE134347) data were obtained from GEO. Then, we intersected the differentially expressed genes (DEG) from these two datasets to obtain common DEGs. Finally, the common DEGs were used for functional enrichment analysis, transcription factor and miRNA prediction, pathway analysis, and candidate drug analysis. A total of 307 common DEGs were identified between the sepsis and COVID-19 datasets. Protein-protein interactions (PPIs) were constructed using the STRING database. Subsequently, hub genes were identified based on PPI networks. In addition, we performed GO functional analysis and KEGG pathway analysis of common DEGs, and found a common association between sepsis and COVID-19. Finally, we identified transcription factor-gene interaction, DEGs-miRNA co-regulatory networks, and protein-drug interaction, respectively. Through ROC analysis, we identified 10 central hub genes as potential biomarkers. In this study, we identified SARS-CoV-2 infection as a high risk factor for sepsis. Our study may provide a potential therapeutic direction for the treatment of COVID-19 patients suffering from sepsis.

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.

Bacterial Superinfection and Antibiotic Management in Patients with COVID-19 Admitted to Intensive Care Medicine in Central Iran: A Follow-Up Study

Background

Bacterial superinfections are one of the crucial challenges in patients with coronavirus disease 2019 (COVID-19) that are associated with a high mortality rate. The current study was designed to assess bacterial superinfections and antibiotic management in COVID-19 patients admitted to intensive care unit (ICU).

Material and Methods

Seventy-three adult intubated patients with COVID-19 were included in a cross-sectional study. The lung aspirate samples were collected in two stages and assessed for bacterial growth by standard methods. Antimicrobial susceptibility testing was performed using the Kirby-Bauer method as recommended by the Clinical Laboratory Standard Institute guideline (2021 edition). Also, demographic and clinical data were collected. The statistical analysis was done by chisquare test and Student's t-test, and a P value <0.05 was considered significant.

Results

Forty men and thirty-three women with a mean age of 64.78 ± 13.90 have included in our study. The mean length of hospitalization and stay in ICU were 18.77 ± 12.94 and 13.51 ± 9.83 days, respectively; 84.9% of cases died. Thirty-three patients had a bacterial superinfection mainly caused by Klebsiella spp and Acinetobacter spp; 21.2% of piperacillin/tazobactam consumers' patients survived that; the differences were significant (p = 0.034). A significant relationship was seen between superinfection and length of hospital stay until intubation (p = 0.033).

Conclusion

Bacterial superinfection and mortality rates were relatively high in COVID-19 patients admitted to ICU. According to the results, using beta-lactam/beta-lactamase inhibitors antibiotics in hospitalized patients in ICU can effectively control superinfection.

Association between severity of COVID-19, Periodontal health and disease in Riyadh subpopulation

Background

Periodontitis and coronavirus disease (COVID-19) both exhibit an exaggerated inflammatory response as common traits. Given that periodontal diseases have been linked to respiratory illnesses like pneumonia, it is quite possible that periodontitis and COVID-19 are related. Therefore, the purpose of the current study was to ascertain whether the severity of COVID-19 and periodontal disease are related.

Methods

A retrospective study was done using the 3 years of patients' medical and dental records in the University Hospital. A telephone interview was employed to estimate the severity of symptoms got through COVID-19 infection. The data obtained were subjected to statistical analysis. The Chi-square test, with statistical significance set at 0.05, was used to determine the relationship between the severity of periodontal disease and the severity of COVID-19.

Results

It was seen that there was a strong relationship between the severities of COVID-19 disease and periodontal disease. The mildest gingivitis cases (63%), Stage 1 periodontitis (62.9%), were associated with the COVID-19-negative group, whereas the most severe gingivitis cases (85.7%), Stage 4 periodontitis group (66.66%), were associated with COVID-19-positive group. In comparison to those without periodontitis, patients with periodontitis had a 1.54 times higher risk of COVID-19 complications (P = 0.048). Patients who had comorbidities were 2.49 times to have COVID-19 complications (P = 0.02).

Conclusion

The observations presented above lead to the conclusion that COVID-19 and periodontal disease severities are related. Understanding the potential association between periodontitis and COVID-19 through systemic inflammation could be a means of achieving a high-quality medical care. To validate the findings, additional research with larger samples is required.

Coinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus during the COVID-19 pandemic

The prevalence of coinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus among referred patients in Hamadan province, Iran, from November 2, 2021, to January 30, 2022, was evaluated. Samples were obtained from 14,116 individuals with COVID-19 symptoms and screened for SARS-CoV-2 and influenza viruses using a multiplex real-time PCR panel assay. Of these patients, 14.19%, 17.11%, and 1.35% were infected with influenza virus, SARS-CoV-2, and both viruses, respectively. The majority of the coinfected patients were female outpatients aged 19-60 years.

COVID-19-associated pulmonary aspergillosis (CAPA) in Iranian patients admitted with severe COVID-19 pneumonia

PURPOSE

Bacterial or virus co-infections with SARS-CoV-2 have been reported in many studies; however, the knowledge on Aspergillus co-infection among patients with COVID-19 was limited. This study was conducted to identify and isolate fungal agents and to evaluate the prevalence of pulmonary aspergillosis (CAPA) as well as antifungal susceptibility patterns of Aspergillus species in patients with COVID-19 admitted to Shahid Beheshti Hospital, Kashan, Iran.

METHODS

The study involved 119 patients with severe COVID-19 pneumonia referred to the Shahid Beheshti Hospital, Kashan, Iran. A total of 17 Aspergillus spp. that were isolated from COVID-19 patients suspected of CAPA were enrolled in the study. CAPA was defined using ECMM/ISHAM consensus criteria. The PCR amplification of the β-tubulin gene was used to identify the species. The antifungal activities of fluconazole, itraconazole, voriconazole, amphotericin B against Aspergillus spp. were evaluated according to the Clinical and Laboratory Standards Institute manual (M38-A3).

RESULTS

From the 119 patients with severe COVID-19 pneumonia, CAPA was confirmed in 17 cases (14.3%). Of these, 12 (70.6%) were males and 5 (29.4%) were females; the mean age at presentation was 73.8 years (range: 45-88 years; median = 77; IQR = 18). Aspergillus fumigatus (9/17; 52.9%), Aspergillus flavus (5/17; 29.4%), Aspergillus oryzae (3/17, 17.6%), were identified as etiologic agents of CAPA, using the molecular techniques. Voriconazole and amphotericin B showed more activity against all isolates. Moreover, the MIC of fluconazole, itraconazole varied with the tested isolates. For 3 clinical isolates of A. fumigatus, 2 isolate of A. flavus and 3 A. oryzae, the MIC of fluconazole and itraconazole were ≥ 16 µg/mL.

CONCLUSIONS

We observed a high incidence (14.3%) of probable aspergillosis in 119 patients with COVID-19, which might indicate the risk for developing IPA in COVID-19 patients. When comparing patients with and without CAPA regarding baseline characteristics, CAPA patients were older (p =0 .024), had received more frequent systemic corticosteroids (p = 0.024), and had a higher mortality rate (p = 0.018). The outcome of CAPA is usually poor, thus emphasis shall be given to screening and/or prophylaxis in COVID-19 patients with any risk of developing CAPA.

The Impact of Clostridioides Difficile Infection in Hospitalized Patients: What Changed during the Pandemic?

(1) Background: Clostridioides difficile (C. difficile) and SARS-CoV-2 coronavirus represent significant health threats. Our study focused on the impact of concurrent infections on patient outcomes against the backdrop of changes imposed by the pandemic. (2) Materials and methods. We performed a retrospective analysis and included patients diagnosed with CDI who were admitted in our hospital before and during the pandemic. We compared patient exposure to risk factors for CDI in both groups and patient negative outcomes: need for ICU care, prolonged hospitalization, organ failure, toxic megacolon, and death. (3) Results. Overall, 188 patients were included, of which 100 had CDI (the pre-pandemic group), and 88 patients presented both CDI and COVID-19 (the pandemic group). Patients in the pandemic group were significantly older, with a higher Charlson Comorbidity Index (CCI) and a greater exposure to antibiotics and corticosteroids, and were more likely to develop organ dysfunction, to require ICU care and have prolonged hospitalization. The severity of COVID-19, leukocytosis and increased D-dimer levels were indicators of poor prognosis in the pandemic group. Higher CCI scores and leukocytosis increased the risk for negative outcomes in CDI alone patients. (4) Conclusions. The study highlights the negative impact of associated infections on patient outcome. The severity of COVID-19 directly influences the prognosis of patients with concurrent infections.

The impact of the secondary infections in ICU patients affected by COVID-19 during three different phases of the SARS-CoV-2 pandemic

Microbial secondary infections can contribute to an increase in the risk of mortality in COVID-19 patients, particularly in case of severe diseases. In this study, we collected and evaluated the clinical, laboratory and microbiological data of COVID-19 critical ill patients requiring intensive care (ICU) to evaluate the significance and the prognostic value of these parameters. One hundred seventy-eight ICU patients with severe COVID-19, hospitalized at the S. Francesco Hospital of Nuoro (Italy) in the period from March 2020 to May 2021, were enrolled in this study. Clinical data and microbiological results were collected. Blood chemistry parameters, relative to three different time points, were analyzed through multivariate and univariate statistical approaches. Seventy-four percent of the ICU COVID-19 patients had a negative outcome, while 26% had a favorable prognosis. A correlation between the laboratory parameters and days of hospitalization of the patients was observed with significant differences between the two groups. Moreover, Staphylococcus aureus, Enterococcus faecalis, Candida spp, Pseudomonas aeruginosa and Klebsiella pneumoniae were the most frequently isolated microorganisms from all clinical specimens. Secondary infections play an important role in the clinical outcome. The analysis of the blood chemistry tests was found useful in monitoring the progression of COVID-19.

Long-Term Lactulose Administration Improves Dysbiosis Induced by Antibiotic and C. difficile in the PathoGutTM SHIME Model

Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and an important nosocomial infection with different severity degrees. Disruption of the gut microbiota by broad-spectrum antibiotics creates a proper environment for C. difficile colonization, proliferation, and clinical disease onset. Restoration of the gut microbial ecosystem through prebiotic interventions can constitute an effective complementary treatment of CDI. Using an adapted simulator of the human gut microbial ecosystem, the PathoGutTM SHIME, the effect of different long-term and repeated dose lactulose treatments was tested on C. difficile germination and growth in antibiotic-induced dysbiotic gut microbiota environments. The results showed that lactulose reduced the growth of viable C. difficile cells following clindamycin treatment, shifted the antibiotic-induced dysbiotic microbial community, and stimulated the production of health-promoting metabolites (especially butyrate). Recovery of the gut microenvironment by long-term lactulose administration following CDI was also linked to lactate production, decrease in pH and modulation of bile salt metabolism. At a structural level, lactulose showed a significant bifidogenic potential and restored key commensal members of the gut ecosystem such as Lactobacillaceae, Veillonellaceae and Lachnospiraceae. These results support further human intervention studies aiming to validate the in vitro beneficial effects of lactulose on gut microbiome recovery during antibiotic exposure and CDI.

Potential Original Drug for Aspergillosis: In Vitro and In Vivo Effects of 1-N,N-Dimethylamino-5-Isocyanonaphthalene (DIMICAN) on Aspergillus fumigatus

As the recent outbreak of coronavirus disease 2019 (COVID-19) has shown, viral infections are prone to secondary complications like invasive aspergillosis with a high mortality rate, and therefore the development of novel, effective antifungals is of paramount importance. We have previously demonstrated that 1-amino-5-isocyanonaphthalene (ICAN) derivatives are promising original drug candidates against Candida strains (Patent pending), even against fluconazole resistant C. albicans. Consequently, in this study ICANs were tested on Aspergillus fumigatus, an opportunistic pathogen, which is the leading cause of invasive and systematic pulmonary aspergillosis in immunosuppressed, transplanted and cancer- or COVID-19 treated patients. We have tested several N-alkylated ICANs, a well as 1,5-naphthalene-diisocyanide (DIN) with the microdilution method against Aspergillus fumigatus strains. The results revealed that the diisocyanide (DIN) was the most effective with a minimum inhibitory concentration (MIC) value as low as 0.6 µg mL⁻¹ (3.4 µM); however, its practical applicability is limited by its poor water solubility, which needs to be overcome by proper formulation. The other alkylated derivatives also have in vitro and in vivo anti-Aspergillus fumigatus effects. For animal experiments the second most effective derivative 1-N, N-dimethylamino-5-isocyanonaphthalene (DIMICAN, MIC: 7–8 µg mL⁻¹, 36–41 µM) was selected, toxicity tests were made with mice, and then the antifungal effect of DIMICAN was tested in a neutropenic aspergillosis murine model. Compared to amphotericin B (AMB), a well-known antifungal, the antifungal effect of DIMICAN in vivo turned out to be much better (40% vs. 90% survival after eight days), indicating its potential as a clinical drug candidate.

Invasiveness of Ventilation Therapy Is Associated to Prevalence of Secondary Bacterial and Fungal Infections in Critically Ill COVID-19 Patients

Superinfections are a fundamental critical care problem, and their significance in severe COVID-19 cases needs to be determined. This study analyzed data from the Lean European Open Survey on SARS-CoV-2-Infected Patients (LEOSS) cohort focusing on intensive care patients. A retrospective analysis of patient data from 840 cases of COVID-19 with critical courses demonstrated that co-infections were frequently present and were primarily of nosocomial origin. Furthermore, our analysis showed that invasive therapy procedures accompanied an increased risk for healthcare-associated infections. Non-ventilated ICU patients were rarely affected by secondary infections. The risk of infection, however, increased even when non-invasive ventilation was used. A further, significant increase in infection rates was seen with the use of invasive ventilation and even more so with extracorporeal membrane oxygenation (ECMO) therapy. The marked differences among ICU techniques used for the treatment of COVID-19-induced respiratory failure in terms of secondary infection risk profile should be taken into account for the optimal management of critically ill COVID-19 patients, as well as for adequate antimicrobial therapy.

Multiplex PCR in the empirical antibiotic treatment of patients with SARS-CoV-2 and bacterial respiratory superinfection

Background

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic led to overuse of antimicrobials, which increased concerns regarding antimicrobial resistance.

Objective

To measure the impact of a multiplex polymerase chain reaction (PCR) pneumonia panel on empirical antibiotic treatment for patients with critical coronavirus disease 2019 (COVID-19) with suspected bacterial respiratory superinfection.

Methods

This descriptive, prospective study was undertaken in a 36-bed intensive care unit from June 2020 to July 2021. Patients with severe COVID-19 who were ventilated and under suspicion of bacterial respiratory superinfection were included in the study. The intervention was a semi-quantitative multiplex PCR alongside concurrent standard cultures. When PCR panel results were expected to be obtained within 3 h of sampling, empirical antibiotic treatment was not administered while awaiting the results. Otherwise, empirical treatment was initiated. Patients classified as 'avoided empirical treatment' avoided 48-72 h of empirical antibiotic therapy. For those patients who received empirical treatment, the PCR panel results were used to decide whether treatment should be escalated, de-escalated, maintained or stopped. Positive and negative predictive values, and 'avoided empirical treatment' were calculated. Medical conduct and panel results were analysed for patients who received empirical treatment.

Results

Eighty-two patients (71% male, 29% female) were included in this study. The mean age was 57.5 years, and the mean APACHE II score was 16. Ninety PCR panels were performed, and the negative and positive predictive values were 99.9% and 66.7%, respectively. Empirical treatment was avoided in 61% of episodes. Of those patients who were receiving antibiotics when the PCR panel was performed, treatment was de-escalated in 71%, escalated in 14%, stopped in 9% and maintained in 6%. A diagnosis of bacterial respiratory superinfection was ruled out in 19% of cases.

Conclusions

PCR panels prevented the initiation of empirical antibiotic treatment in two-thirds of patients, and led to de-escalation in more than two-thirds of those who had started empirical antibiotic treatment. The high negative predictive value of the PCR panel allowed the diagnosis of bacterial respiratory superinfection to be ruled out. This tool represents a significant contribution to diagnostic stewardship in order to avoid the unnecessary use of antibiotics.

COVID-19 patients share common, corticosteroid-independent features of impaired host immunity to pathogenic molds

Patients suffering from coronavirus disease-2019 (COVID-19) are susceptible to deadly secondary fungal infections such as COVID-19-associated pulmonary aspergillosis and COVID-19-associated mucormycosis. Despite this clinical observation, direct experimental evidence for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2)-driven alterations of antifungal immunity is scarce. Using an ex-vivo whole blood stimulation assay, we challenged blood from twelve COVID-19 patients with Aspergillus fumigatus and Rhizopus arrhizus antigens and studied the expression of activation, maturation, and exhaustion markers, as well as cytokine secretion. Compared to healthy controls, T-helper cells from COVID-19 patients displayed increased expression levels of the exhaustion marker PD-1 and weakened A. fumigatus- and R. arrhizus-induced activation. While baseline secretion of proinflammatory cytokines was massively elevated, whole blood from COVID-19 patients elicited diminished release of T-cellular (e.g., IFN-γ, IL-2) and innate immune cell-derived (e.g., CXCL9, CXCL10) cytokines in response to A. fumigatus and R. arrhizus antigens. Additionally, samples from COVID-19 patients showed deficient granulocyte activation by mold antigens and reduced fungal killing capacity of neutrophils. These features of weakened anti-mold immune responses were largely decoupled from COVID-19 severity, the time elapsed since diagnosis of COVID-19, and recent corticosteroid uptake, suggesting that impaired anti-mold defense is a common denominator of the underlying SARS-CoV-2 infection. Taken together, these results expand our understanding of the immune predisposition to post-viral mold infections and could inform future studies of immunotherapeutic strategies to prevent and treat fungal superinfections in COVID-19 patients.

Role of Intracellular Pulmonary Pathogens during SARS-CoV-2 Infection in the First Pandemic Wave of COVID-19: Clinical and Prognostic Significance in a Case Series of 1200 Patients

Background: Since 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) has caused millions of deaths worldwide and is the second most serious pandemic after the Spanish flu. Despite SARS-CoV-2 infection having a dominant effect on morbidity and life-threatening outcomes, the role of bacterial co-infection in patients with COVID-19 is poorly understood. The present study aimed to verify the existence of bacterial co-infections and their possible role as cofactors worsening COVID-19-related clinical manifestations. Methods: All patients with suspected SARS-CoV-infection, hospitalised in COVID-19 wards at the Sant'Anna University Hospital of Ferrara, were retrospectively included in this single-centre study and their specific bacterial serologies were assessed. Univariate and logistic regression analyses were performed. Results: A total of 1204 individual records were retrieved. Among them, 959 were excluded because of a negative nasopharyngeal swab or missing data; of the eligible 245 patients, 51 were co-infected. Compared to patients with SARS-CoV-2 infection alone, those with Chlamydia pneumoniae or Mycoplasma pneumoniae co-infections had worse respiratory/radiological features and more intensive care unit admissions. However, the co-infection did not result in a higher mortality rate. Conclusions: The present study, comparing clinical, laboratory and radiological findings between patients with COVID-19 vs. those with co-infections (C. pneumoniae or M. pneumoniae) showed that, on admission, these features were worse in co-infected patients, although the mortality rate did not differ between the two groups.

Modeling the crossover behavior of the bacterial infection with the COVID-19 epidemics

To explore the crossover linkage of the bacterial infections resulting from the viral infection, within the host body, a computational framework is developed. It analyzes the additional pathogenic effect of Streptococcus pneumonia, one of the bacteria that can trigger the super-infection mechanism in the COVID-19 syndrome and the physiological effects of innate immunity for the control or eradication of this bacterial infection. The computational framework, in a novel manner, takes into account the action of pro-inflammatory and anti-inflammatory cytokines in response to the function of macrophages. A hypothetical model is created and is transformed to a system of non-dimensional mathematical equations. The dynamics of three main parameters (macrophages sensitivity κ , sensitivity to cytokines η and bacterial sensitivity ϵ ), analyzes a "threshold value" termed as the basic reproduction number R 0 which is based on a sub-model of the inflammatory state. Piece-wise differentiation approach is used and dynamical analysis for the inflammatory response of macrophages is studied in detail. The results shows that the inflamatory response, with high probability in bacterial super-infection, is concomitant with the COVID-19 infection. The mechanism of action of the anti-inflammatory cytokines is discussed during this research and it is observed that these cytokines do not prevent inflammation chronic, but only reduce its level while increasing the activation threshold of macrophages. The results of the model quantifies the probable deficit of the biological mechanisms linked with the anti-inflammatory cytokines. The numerical results shows that for such mechanisms, a minimal action of the pathogens is strongly amplified, resulting in the "chronicity" of the inflammatory process.

Bacterial Co-Infection in Patients with COVID-19 Hospitalized (ICU and Not ICU): Review and Meta-Analysis

The prevalence of patients hospitalized in ICUs with COVID-19 and co-infected by pathogenic bacteria is relevant in this study, considering the integrality of treatment. This systematic review assesses the prevalence of co-infection in patients admitted to ICUs with SARS-CoV-2 infection, using the PRISMA guidelines. We examined the results of the PubMed, Embase, and SciELO databases, searching for published English literature from December 2019 to December 2021. A total of 542 rec ords were identified, but only 38 were eligible and, and of these only 10 were included. The tabulated studies represented a sample group of 1394 co-infected patients. In total, 35%/138 of the patients were co-infected with Enterobacter spp., 27% (17/63) were co-infected with methicillin-sensitive Staphylococ cus aureus, 21% (84/404) were co-infected with Klebsiella spp., 16% (47/678) of patients were co-infected with coagulase-negative Staphylococcus, 13% (10/80) co-infected with Escherichia coli (ESBL), and 3% (30/1030) of patients were co-infected with Pseudomonas aeruginosa. The most common co-infections were related to blood flow; although in the urinary and respiratory tracts of patients Streptococcus pneumoniae was found in 57% (12/21) of patients, coagulase negative Staphylococcus in 44% (7/16) of patients, and Escherichia coli was found in 37% (11/29) of patients. The present research demonstrated that co-infections caused by bacteria in patients with COVID-19 are a concern.