The role of co-infections and secondary infections in patients with COVID-19

Increased serum ferritin is associated with severity of orbital disease in COVID-19-associated rhino-orbito-cerebral mucormycosis: A quantitative analysis

CONTEXT

Effect of serum ferritin on severity of coronavirus disease 2019 (COVID-19)-associated rhino-orbito-cerebral mucormycosis.

PURPOSE

To study the association between increased serum ferritin and severity of orbital disease in COVID-19-associated rhino-orbito-cerebral mucormycosis.

SETTINGS AND DESIGN

A cross-sectional study.

METHODS

Hundred ( n ) out of 155 treatment-naive patients of COVID-19 infection presenting with the signs and symptoms of rhino-orbito-cerebral mucormycosis were enrolled in study. Based on the classification proposed by Honavar, the study patients were classified into four stages: Stage 1: involvement of the nasal mucosa ( n = 11), Stage 2: involvement of paranasal sinuses ( n = 14), Stage 3: involvement of the orbit ( n = 37), Stage 4: involvement of the central nervous system ( n = 38). Stage 3 was further divided into four substages: 3a: nasolacrimal duct, medial orbit, vision unaffected ( n = 4); 3b: diffuse orbital involvement (>1 quadrant or >2 structures), vision unaffected ( n = 15); 3c: central retinal artery occlusion or ophthalmic artery occlusion, superior ophthalmic vein thrombosis, involvement of superior orbital fissure, inferior orbital fissure, orbital apex, diminution or loss of vision ( n = 13); 3d: bilateral orbital involvement ( n = 5). Fasting blood sugar (FBS), postprandial blood sugar (PPBS), and inflammatory markers (serum ferritin, interleukin-6, C-reactive protein, and D-dimer) were assessed. Serum level of ferritin was analyzed by using chemiluminescence immunoassay method.

RESULTS

Mean FBS (mg/dl) was 165.03 ± 70.43 for stage 1, 185.67 ± 64.82 for stage 2, 159.05 ± 68.60 for stage 3, and 158.20 ± 62.05 for stage 4. Mean PPBS (mg/dl) was 238.70 ± 141.29 for stage 1, 252 ± 103.69 for stage 2, 257.09 ± 103.48 for stage 3, and 229.53 ± 76.81 for stage 4. Mean serum ferritin (μg/l) was 302.67 ± 266.95 in stage 1, 444.19 ± 116.36 in stage 2, 504.85 ± 205.99 in stage 3, and 825.95 ± 777.30 in stage 4. A statistically significant increase in serum ferritin levels with severity of disease ( P = 0.005) was noted. Similar trend was observed in substages of stage 3. Pearson correlation analysis showed a positive correlation between serum ferritin and severity of disease ( P = 0.0007).

CONCLUSION

Increased serum ferritin was significantly independently associated with severity of orbital disease in COVID-19-associated rhino-orbito-cerebral mucormycosis.

Epidemiology of bacterial respiratory tract infections during the pre-pandemic, COVID-19 pandemic and post-pandemic era: A retrospective study of hospitalized adults in northern Greece between 2018 and 2023

INTRODUCTION

The COVID-19 pandemic has had impact on global healthcare and respiratory disease patterns. The aim was to evaluate the changes in positive respiratory cultures during the pandemic.

METHODS

A retrospective analysis of respiratory specimens in Papanikolaou Hospital during 2018-2023 was performed. In total, 18,852 samples (12,277 males, 6575 females) of respiratory samples were recorded.

RESULTS

During 2018-2019, 684 BAL samples were received, of which 12.3 % were positive. Positive pharyngeal smears constituted 24.8 %, compared to 18.5 % in pandemic years, and 29.6 % in 2023. In PTC, pre-pandemic, positives were 12.3 %, while in 2021 the maximum percentage of positives (21.9 %) was observed. Positive levels remained high in 2023 (18.3 %). Concerning bronchial secretions, there was an increase (55.3 % in 2022 vs 47.0 % in 2019). The predominant bacteria were Acinetobacter spp, Klebsiella spp and Pseudomonas spp.

CONCLUSION

Except for the bronchial secretions, the rest of the respiratory specimens do not exhibit any definite trends.

Lethal Synergistic Infections by Two Concurrent Respiratory Pathogens

Lethal synergistic infections by concurrent pathogens have occurred in humans, including human immunodeficiency virus and Mycobacterium tuberculosis infections, or in animal or human models of influenza virus, or bacteria, e.g., Streptococcus pneumoniae, concurrent with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the intracellular synergistic interaction possibilities between two respiratory viral pathogens, or between viral and fungal pathogens, merits additional examination. The requirements for synergistic concurrent pathogen infections are: a) relatively little detrimental interference between two pathogens, b) one pathogen having the capability of directly or indirectly assisting the second pathogen by direct immuno-manipulation or indirect provision of infection opportunities and/or metabolic assistance, c) substantial human or environmental prevalence, possibly including a prevalence in any type of health-care facilities or other locations having congregations of potentially infected human or animal vectors and d) substantial transmissibility of the pathogens, which would make their concurrent pathogen infections much more probable. A new definition of pathogen synergy is proposed: "pathogen synergy is an interaction of two or more pathogens during concurrent infections causing an increased infection severity compared to mono-infections by the individual pathogens." Non-respiratory pathogens can also concurrently infect organs besides the lungs. However, the air-transmissible respiratory pathogens, particularly the RNA viruses, can enable highly widespread and synergistic concurrent infections. For instance, certain strains of coronaviruses, influenza viruses and similar respiratory viruses, are highly transmissible and/or widely prevalent in various vectors for transmission to humans and have numerous capabilities for altering lung immune defenses.

Microbial Dynamics in COVID-19: Unraveling the Impact of Human Microbiome on Disease Susceptibility and Therapeutic Strategies

This review explores the bidirectional relationship between the human microbiome and SARS-CoV-2 infection, elucidating its implications for COVID-19 susceptibility, severity, and therapeutic strategies. Metagenomic analyses reveal notable alterations in microbiome composition associated with SARS-CoV-2 infection, impacting disease severity and clinical outcomes. Dysbiosis within the respiratory, gastrointestinal, oral, and skin microbiomes exacerbates COVID-19 pathology through immune dysregulation and inflammatory pathways. Understanding these microbial shifts is pivotal for devising targeted therapeutic interventions. Notably, co-infection of oral pathogens with SARS-CoV-2 worsens lung pathology, while gut microbiome dysbiosis influences viral susceptibility and severity. Potential therapeutic approaches targeting the microbiome include probiotics, antimicrobial agents, and immunomodulatory strategies. This review underscores the importance of elucidating host-microbiota interactions to advance precision medicine and public health initiatives in combating COVID-19 and other infectious diseases.

A Case of Autoimmune Hemolytic Anemia Following COVID-19 Infection Accompanied by Acute Tubulointerstitial Nephritis in a Kidney Transplant Recipient

BACKGROUND

Acute tubular injury is one of the main causes of acute tubular injury (acute kidney injury ) in patients with COVID-19 infection. Autoimmune hemolytic anemia (AIHA) is also one of the autoimmune complications of COVID-19. However, AIHA accompanied by acute tubulointerstitial nephritis (ATIN) caused by SARS-CoV-2 is rarely reported. Here, we report a kidney transplant recipient who underwent graftectomy owing to ATIN accompanied by AIHA, possibly exacerbated by COVID-19 infection.

CASE PRESENTATION

A 32-year-old male renal allograft recipient owing to immunoglobulin A nephropathy visited the emergency department owing to dyspnea and general weakness. Three weeks earlier, the patient had been transplanted with deceased-donor kidney with full HLA-A, -B, -DR match, and had been on tacrolimus, prednisolone, and mycophenolate since then. At the time of the visit, laboratory findings revealed hemoglobin of 2.4 g/dL, reticulocyte of 21.7%, total bilirubin of 1.9 mg/dL, direct bilirubin of 0.3 mg/dL, lactate dehydrogenase of 946 U/L, haptoglobin of <10 mg/dL, and severe red cell agglutination on peripheral blood smear, which suggested AIHA. In addition, his SARS-CoV-2 real-time polymerase chain reaction test was positive. During steroid treatment for AIHA, a sudden decrease in urine volume, estimated glomerular filtration rate (from 64.9 to 35.1 mL/min/1.73 m2) and increase of creatinine (from 1.42 to 2.36 mg/dL) indicated renal function deterioration, so steroid was increased to 500 mg. On the third day of renal function deterioration, dialysis was started owing to anuria and fluid retention. On renal biopsy, C4d was absent; however, ATIN with eosinophilic infiltration was observed. On renal ultrasound examination, a severely enlarged kidney with edema was observed. At the same time, the patient had a high fever with increased C-reactive protein and procalcitonin. Graftectomy was performed to prevent secondary infection. The postgraftectomy renal biopsy showed renal parenchymal and hilar inflammatory change, endotheliitis, and lymphocytic infiltration of peripheral nerve fibers. After graftectomy, dialysis was maintained and AIHA had ameliorated.

CONCLUSION

The patient had to have his allografted kidney removed owing to ATIN possibly caused by COVID-19 infection. Acute kidney injury caused by SARS-CoV-2 can be either by direct viral infection or as consequence of immunological response. The exact immunological mechanism of AIHA secondary to COVID-19 infection remains to be elucidated.

Respiratory Viral Infection Patterns in Hospitalised Children Before and After COVID-19 in Hong Kong

The study highlights the significant changes in respiratory virus epidemiology following the lifting of COVID-19 restrictions.

METHOD

In this single-centre retrospective study, the virological readouts of adenovirus (AdV), influenza virus A (IAV), influenza virus B (IBV), parainfluenza viruses (PIV) 1, 2, 3, 4, respiratory syncytial virus (RSV), and coupled enterovirus and rhinovirus (EV/RV) were extracted from the respiratory specimens of paediatric patients in Hong Kong from January 2015 to February 2024. The subjects were stratified into five age groups.

RESULTS

The study included 18,737 and 6001 respiratory specimens in the pre-COVID-19 and post-COVID-19 mask mandate period, respectively. The mean age of hospitalised patients increased from 3.49 y ± 0.03 y to 4.37 y ± 0.05 y after the COVID-19 lockdown. The rates of single-virus infection and co-infection were significantly higher in the post-COVID-19 mask mandate period. The odds ratio for AdV for all age groups (OR: 4.53, 4.03, 2.32, 2.46, 1.31) and RSV in older children from 3 years old and above (OR: 1.95, 3.38, p < 0.01) were significantly elevated after the COVID-19 outbreak.

CONCLUSIONS

Our findings suggest that public health measures to contain COVID-19 may have unintended consequences on children's natural exposure and immunity to other respiratory viruses, potentially increasing their morbidity in the post-pandemic era.

Burden and Risk Factors for Coinfections in Patients with a Viral Respiratory Tract Infection

Which patients should be monitored for coinfections or should receive empirical antibiotic treatment, in patients with an acute viral respiratory infection, is largely unknown. We evaluated the prevalence, characteristics, outcomes of coinfected patients, and risk factors associated with a coinfection among patients with an acute viral infection. A retrospective, single-center study recruited consecutive patients from October 2022 to March 2023 presenting to the emergency department with signs of a respiratory tract infection. Patients were screened for respiratory viruses and bacterial/fungal secondary infections according to local standard procedures. Outcomes included severe disease, in-hospital complications, all-cause in-hospital and ICU-related mortality, time to death, time to discharge, and time to coinfection. The analysis included 652 patients. A viral infection and a secondary bacterial/fungal infection were detected in 39.1% and 40% of cases. Compared with the rest of the cohort, coinfected patients had more frequently severe disease (88.3%, p < 0.001; 51% in patients with SARS-CoV-2) and higher in-hospital mortality (16.5%, p = 0.010). Nephropathy (OR 3.649, p = 0.007), absence of COVID-19 vaccination (OR 0.160, p < 0.001), SARS-CoV-2 infection (OR 2.390, p = 0.017), and lower blood pressure at admission (OR 0.980, p = 0.007) were independent risk factors for coinfection. Multidrug-resistant pathogens were detected in 30.8% of all coinfections. Patients with a viral infection are at high risk of bacterial coinfections, which carry a significant morbidity and mortality burden.

First Reported Case of Breast Sporotrichosis in Bahrain

Granulomatous mastitis is a chronic inflammation of the breast, mostly of unknown etiology. The treatment would be definitive if the causative organism were isolated. It is characterized histologically by granulomas, formed mostly by polymorph nuclear neutrophils and central necrosis. Herein, we report a 46-year-old woman who presented with a non-responding to treatment right breast abscess of six months duration. The abscess was associated with multiple fistula formation. Radiological investigations were inconclusive. She needed incision and drainage many times. The diagnosis of granulomatous mastitis secondary to sporotrichosis can only be made after breast tissue biopsy and culture. She was started on itraconazole. She responded slowly and later needed resection of the remaining mass.

Developing a Coccidioides posadasii and SARS-CoV-2 Co-infection Model in the K18-hACE2 Transgenic Mouse

BACKGROUND

Early reports showed that patients with COVID-19 had recrudescence of previously resolved coccidioidomycosis (Valley fever, VF), and there were indications that coinfection had more severe outcomes. We therefore investigated serial infection of Coccidioides posadasii and SARS-CoV-2 in a K18-hACE2 mouse model to assess disease outcomes.

METHODS

In our model, we challenged K18-hACE2 mice sequentially with a sub-lethal dose of SARS-CoV-2 and 24 hours later with low virulence strain of Coccidioides posadasii, and vice versa, compared to mice that only received a single infection challenge. We performed survival and pathogenesis mouse studies as well as looked at the systemic immune response differences between treatment groups.

RESULTS

Here we show that co-infected groups have a more severe disease progression as well as a decrease in survival. Importantly, results differ depending on the SARS-CoV-2 variant (WA-1, Delta, or Omicron) and infection timing (SARS-CoV-2 first, C. posadasii second or vice versa). We find that groups that are infected with the virus first had a decrease in survival, increased morbidity and weight loss, increased fungal and viral burdens, differences in immune responses, and the amount and size of fungal spherules. We also find that groups coinfected with C. posadasii first have a decrease fungal burden and inflammatory responses.

CONCLUSIONS

This is the first in vivo model investigation of a coinfection of SARS-CoV-2 and Coccidioides. Because of the potential for increased severity of disease in a coinfection, we suggest populations that live in areas of high coccidioidomycosis endemicity may experience higher incidence of complicated disease progression with COVID-19.

Bacterial and Viral Co-Infections in COVID-19 Patients: Etiology and Clinical Impact

BACKGROUND

Mixed infections can worsen disease symptoms. This study investigated the impact of mixed infections with viral and bacterial pathogens in patients positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

Using the in-house multiplex PCR method, we tested 337 SARS-CoV-2 positive samples for co-infections with three bacterial and 14 other viral pathogens.

RESULTS

Between August 2021 and May 2022, 8% of 337 SARS-CoV-2-positive patients had bacterial co-infections, 5.6% had viral co-infections, and 1.4% had triple mixed infections. The most common causes of mixed infections were Haemophilus influenzae (5.93%) and respiratory syncytial virus (RSV) (1.18%). Children < 5 years old had more frequent co-infections than adults < 65 years old (20.8% vs. 16.4%), while adults showed a more severe clinical picture with a higher C-reactive protein (CRP) level (78.1 vs.16.2 mg/L; p = 0.033), a lower oxygen saturation (SpO2) (89.5 vs. 93.2%), and a longer hospital stay (8.1 vs. 3.1 days; p = 0.025) (mean levels). The risk of a fatal outcome was 41% in unvaccinated patients (p = 0.713), which increased by 2.66% with co-infection with two pathogens (p = 0.342) and by 26% with three pathogens (p = 0.005). Additionally, 50% of intensive care unit (ICU) patients had a triple infection, compared with only 1.3% in the inpatient unit (p = 0.0029). The risk of death and/or ICU admission was 12 times higher (p = 0.042) with an additional pathogen and increased by 95% (p = 0.003) with a third concomitant pathogen.

CONCLUSIONS

Regular multiplex testing is important for prompt treatment and targeted antibiotic use.

To prescribe or not: a two-center retrospective observational study of antibiotics usage and outcomes of COVID-19 in Turkey

This retrospective cohort study conducted in Turkey between December 2020 and June 2022 aimed to assess antibiotic use, bacterial co-infections, and the associated factors on mortality in hospitalized patients with mild-to-severe COVID-19. Among the 445 patients, 80% received antibiotics, with fluoroquinolones being the most common choice, followed by beta-lactams and combinations. Various clinical and laboratory parameters, including symptoms, comorbidities, CCI, oxygen requirements, and CRP levels were observed to be elevated in the antibiotic group. Non-survivors had more ICU admissions and longer hospital stays compared to survivors. We conducted a multivariate Cox regression analysis to evaluate factors related to mortality. However, we did not find an association between antibiotic use and mortality [HR 2.7 (95% CI 0.4-20)]. The study identified significant factors associated with an antibiotic prescription, such as CCI (OR 1.6), CRP (OR 2.3), and ICU admission (OR 8.8), (p < 0.05). The findings suggest re-evaluating the necessity of antibiotics in COVID-19 cases based on clinical assessments, focusing on the presence of bacterial infections rather than empirical treatment. Further research is necessary to more accurately identify patients with bacterial co-infections who would benefit from antibiotic treatment.

Comparative Cross-Kingdom DDA- and DIA-PASEF Proteomic Profiling Reveals Novel Determinants of Fungal Virulence and a Putative Druggable Target

Accurate and reliable detection of fungal pathogens presents an important hurdle to manage infections, especially considering that fungal pathogens, including the globally important human pathogen, Cryptococcus neoformans, have adapted diverse mechanisms to survive the hostile host environment and moderate virulence determinant production during coinfections. These pathogen adaptations present an opportunity for improvements (e.g., technological and computational) to better understand the interplay between a host and a pathogen during disease to uncover new strategies to overcome infection. In this study, we performed comparative proteomic profiling of an in vitro coinfection model across a range of fungal and bacterial burden loads in macrophages. Comparing data-dependent acquisition and data-independent acquisition enabled with parallel accumulation serial fragmentation technology, we quantified changes in dual-perspective proteome remodeling. We report enhanced and novel detection of pathogen proteins with data-independent acquisition-parallel accumulation serial fragmentation (DIA-PASEF), especially for fungal proteins during single and dual infection of macrophages. Further characterization of a fungal protein detected only with DIA-PASEF uncovered a novel determinant of fungal virulence, including altered capsule and melanin production, thermotolerance, and macrophage infectivity, supporting proteomics advances for the discovery of a novel putative druggable target to suppress C. neoformans pathogenicity.

A large scale study of portable sweat test sensor for accurate, non-invasive and rapid COVID-19 screening based on volatile compound marker detection

This study established a novel infield sensing approach based on detection of the volatile compound markers in skin secretions. This was based on analysis of volatile compounds in axillary sweat samples collected from RT-PCR-proven Coronavirus disease 2019 (COVID-19) positive and negative populations using gas chromatography-mass spectrometry (GC-MS). The analysis proposed the possible markers of the monoaromatic compounds and ethyl hexyl acrylate. A portable photo ionization detector (PID) incorporated with the selective material towards the marker compounds was then developed with the pressurized injection approach. This provided the accuracy of 100% in the research phase (n = 125). The developed approach was then applied for screening of 2207 COVID-19 related cases covering the periods of the Alpha, Beta, Delta and Omicron variants of SARS-CoV-2 infection in Bangkok, Thailand. This offered the sensitivity, specificity and accuracy ranges of 92-99, 93-98 and 95-97%, respectively.

Microbial infection among SARS-COV-2-infected patients in a COVID-19-dedicated tertiary care hospital of Bangladesh: a cross-sectional study

Objectives. This study aimed to determine patterns of respiratory, blood-borne and uropathogenic microbial pathogens among SARS-CoV-2-infected patients in a COVID-19-(coronavirus disease 2019) dedicated tertiary care hospital in Dhaka, Bangladesh. Design.This was a cross-sectional study. Setting. In a COVID-19-dedicated tertiary care hospital in Dhaka, Bangladesh, conducted from March to June 2021. Participants. Hospitalized individuals with COVID-19 infection regardless of age or sex. Primary and secondary outcome measures. The percentage of co-infected COVID-19 patients and the characterization of the micro-organisms responsible for co-infection served as the primary outcome measures. Finding any associations between co-infection and age, co-infection and sex and co-infection and comorbidity was the secondary outcome variable. Interventions. Not applicable. Results.Out of 79 patients, 61 % were male, and the mean age was 49.53 years. Co-infection was seen in 7.7 % of patients, out of which 5.1 % of isolates were from urine samples, followed by 2.6 % from blood. Bacteria isolated from urine were Enterococcus (2.6 %), coagulase-negative Staphylococcus (CONS) (1.3 %) and Enterobacter spp. (1.3 %). Pseudomonas spp. was the only organism isolated from blood sample. Mixed growth was found in nasopharyngeal and throat swabs, with the predominant species being Staphylococcus aureus and Streptococcus spp. At the time of data collection, 55.7 % of patients had been given antimicrobials, and 30.4 % of patients had been given a single antimicrobial. HBsAg was positive in 1.3 % of patients and none were anti-hepatitis C or dengue NS1Ag positive. Conclusion. Microbial infection has been seen to be associated with SARS-CoV-2 infections and is of great value in prescribing antimicrobials and reducing fatal outcomes of hospitalized patients.

Prevalence, risk factors, and outcomes of secondary infections among hospitalized patients with COVID-19 or post-COVID-19 conditions in Victoria, 2020-2023

OBJECTIVES

Estimates of secondary infections are variedly reported, with few studies done in Australia. We investigated the occurrence and impact of secondary infections complicating COVID-19 and post-COVID-19 admissions in Victoria, Australia, 2020-2023.

METHODS

We used linked population-wide data sets and specific International Classification of Disease, 10th Revision codes to identify and estimate the occurrence of secondary infections. Using hospital/intensive care unit length of stay in negative binomial regression and mortality, we examined the impact of secondary infections.

RESULTS

Secondary infections were identified in 6.9% (13,467 of 194,660) of COVID-19 and post-COVID-19 admissions: 6.0% (11,651 of 194,660) bacterial, 0.9% (1691 of 194,660) viral, and 0.2% (385 of 194,660) fungal. Prevalence was highest during the pre-Delta (10.4%) and Omicron-BA2 (8.1%) periods. Sepsis and pneumonia were the most reported syndromes; the occurrence of sepsis declined gradually over time. The odds of secondary infections were higher among the ≥70-year-olds (adjusted odds ratio (aOR) 3.76, 95% confidence interval [CI] 3.43-4.14, vs 20-29-year-olds), individuals with chronic conditions (aOR 3.15, 95% CI 2.88-3.45, vs those without), the unvaccinated (aOR 1.59, 95% CI 1.45-1.75), and the lowest socioeconomic group (aOR 1.12, 95% CI 1.05-1.19). Patients with secondary infections had 2.43 times longer hospital length of stay and 9.60 times longer intensive care unit length of stay than those without secondary infections. The mortality risk was 2.17 times higher in those with secondary infections.

CONCLUSIONS

Secondary infections occurred in 69 per 1000 COVID-19-associated hospital admissions in Victoria, mostly in high-risk groups, and were associated with severe outcomes.

Influence of Mycobiota in the Nasopharyngeal Tract of COVID-19 Patients

The nasopharyngeal tract contains a complex microbial community essential to maintaining host homeostasis. Recent studies have shown that SARS-CoV-2 infection changes the microbial composition of the nasopharynx. Still, little is known about how it affects the fungal microbiome, which could provide valuable insights into disease pathogenesis. Nasopharyngeal swabs were collected from 55 patients, during three distinct COVID-19 waves that occurred in the Campania Region (southern Italy). An RNA-seq-based analysis was performed to evaluate changes in mycobiota diversity, showing variations depending on the disease's severity and the sample collection wave. The phyla Basidiomycota and Ascomycota were shown to have higher abundance in patients with severe symptoms. Furthermore, the diversity of the fungal population was greater in the second wave. Conclusion: According to our research, COVID-19 induces significant dysbiosis of the fungal microbiome, which may contribute to disease pathogenesis, and understanding its underlying mechanisms could contribute to developing effective treatments.

Laboratory data and broncho-alveolar lavage on Covid-19 patients with no intensive care unit admission: Correlation with chest CT features and clinical outcomes

Broncho-alveolar lavage (BAL) is indicated in cases of uncertain diagnosis but high suspicion of Sars-Cov-2 infection allowing to collect material for microbiological culture to define the presence of coinfection or super-infection. This prospective study investigated the correlation between chest computed tomography (CT) findings, Covid-19 Reporting and Data System score, and clinical outcomes in Coronavirus disease 2019 (Covid-19) patients who underwent BAL with the aim of predicting outcomes such as lung coinfection, respiratory failure, and hospitalization length based on chest CT abnormalities. Study population included 34 patients (range 38-90 years old; 20 males, 14 females) with a positive nucleic acid amplification test for Covid-19 infection, suitable BAL examination, and good quality chest CT scan in the absence of lung cancer history. Pulmonary coinfections were found in 20.6% of patients, predominantly caused by bacteria. Specific correlations were found between right middle lobe involvement and pulmonary co-infections. Severe lung injury (PaO2/FiO2 ratio of 100-200) was associated with substantial involvement of right middle, right upper, and left lower lobes. No significant correlation was found between chest CT findings and inflammatory markers (C-reactive protein, procalcitonin) or hospitalization length of stay. Specific chest CT patterns, especially in right middle lobe, could serve as indicators for the presence of co-infections and disease severity in noncritically ill Covid-19 patients, aiding clinicians in timely interventions and personalized treatment strategies.

Mortality Rate of COVID-19 With Comorbid Pneumonia in a Rural Area

BACKGROUND

A myriad of risk factors and comorbidities have been determined to influence COVID-19 mortality rates; among these is pneumonia. This study considers pneumonia as a risk factor for increased mortality in patients admitted with COVID-19 in a rural healthcare system. We predicted that the presence of pneumonia of any kind would increase mortality rates in patients admitted with COVID-19.

METHODS

A retrospective observational study was conducted using data collected from hospitals in the Freeman Health System (FHS) located in Joplin and Neosho, Missouri. Data were collected between April 1, 2020, and December 31, 2021. Using International Classification of Diseases, Tenth Revision (ICD-10) codes, the investigators identified five distinct patient populations: patients with COVID-19 and pneumonia due to COVID-19 (P1); patients with COVID-19 but without pneumonia due to COVID-19 (P2); patients with COVID-19 and any type of pneumonia (P3); patients with COVID-19 but without any type of pneumonia (P4); and patients without COVID-19 and with any type of pneumonia (P5). In order to understand how pneumonia influences COVID-19 outcomes, the investigators used Wald's method and a two-sample proportion summary hypothesis test to determine the confidence interval and to compare the mortality rates between these populations, respectively.

RESULTS

The population of patients with COVID-19 and any type of pneumonia (P3) and the population of patients with COVID-19 and pneumonia due to COVID-19 (P1) showed the highest mortality rates. The population of patients with COVID-19 but without any type of pneumonia (P4) had the lowest mortality rate. The data revealed that having pneumonia combined with COVID-19 in any patient population led to a higher mortality rate than COVID-19 alone.

CONCLUSION

Mortality rates were higher among COVID-19 patients with pneumonia compared to COVID-19 patients without pneumonia. Additionally, pneumonia, by itself, was found to have a higher mortality rate compared to COVID-19 alone.

Clinical features and multiomics profiles indicate coagulation and platelet dysfunction in COVID-19 viral sepsis

Increased cases of sepsis during COVID-19 in the absence of known bacterial pathogens highlighted role of viruses as causative agents of sepsis. In this study, we investigated clinical, laboratory, proteomic, and metabolomic characteristics of viral sepsis patients (n = 45) and compared them to non-sepsis patients with COVID-19 (n = 186) to identify molecular mechanisms underlying the pathology of viral sepsis in COVID-19. We identified unique metabolomic and proteomic signatures that suggest a substantial perturbation in the coagulation, complement, and platelet activation pathways in viral sepsis. Our proteomic data indicated elevated coagulation pathway protein (fibrinogen), whereas a decrease in many of the complement proteins was observed. These alterations were associated with the functional consequences such as susceptibility to secondary bacterial infections and potentially contributing to both local and systemic disease phenotypes. Our data provide novel aspect of COVID-19 pathology that is centered around presence of sepsis phenotype in COVID-19.

Epidemiological and Genetic Characteristics of Respiratory Viral Coinfections with Different Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

This study aimed to determine the incidence and etiological, seasonal, and genetic characteristics of respiratory viral coinfections involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between October 2020 and January 2024, nasopharyngeal samples were collected from 2277 SARS-CoV-2-positive patients. Two multiplex approaches were used to detect and sequence SARS-CoV-2, influenza A/B viruses, and other seasonal respiratory viruses: multiplex real-time polymerase chain reaction (PCR) and multiplex next-generation sequencing. Coinfections of SARS-CoV-2 with other respiratory viruses were detected in 164 (7.2%) patients. The most common co-infecting virus was respiratory syncytial virus (RSV) (38 cases, 1.7%), followed by bocavirus (BoV) (1.2%) and rhinovirus (RV) (1.1%). Patients ≤ 16 years of age had the highest rate (15%) of mixed infections. Whole-genome sequencing produced 19 complete genomes of seasonal respiratory viral co-pathogens, which were subjected to phylogenetic and amino acid analyses. The detected influenza viruses were classified into the genetic groups 6B.1A.5a.2a and 6B.1A.5a.2a.1 for A(H1N1)pdm09, 3C.2a1b.2a.2a.1 and 3C.2a.2b for A(H3N2), and V1A.3a.2 for the B/Victoria lineage. The RSV-B sequences belonged to the genetic group GB5.0.5a, with HAdV-C belonging to type 1, BoV to genotype VP1, and PIV3 to lineage 1a(i). Multiple amino acid substitutions were identified, including at the antibody-binding sites. This study provides insights into respiratory viral coinfections involving SARS-CoV-2 and reinforces the importance of genetic characterization of co-pathogens in the development of therapeutic and preventive strategies.

Role and significance of virus-bacteria interactions in disease progression

Understanding disease pathogenesis caused by bacteria/virus, from the perspective of individual pathogen has provided meaningful insights. However, as viral and bacterial counterparts might inhabit the same infection site, it becomes crucial to consider their interactions and contributions in disease onset and progression. The objective of the review is to highlight the importance of considering both viral and bacterial agents during the course of coinfection. The review provides a unique perspective on the general theme of virus-bacteria interactions, which either lead to colocalized infections that are restricted to one anatomical niche, or systemic infections that have a systemic effect on the human host. The sequence, nature, and underlying mechanisms of certain virus-bacteria interactions have been elaborated with relevant examples from literature. It also attempts to address the various applied aspects, including diagnostic and therapeutic strategies for individual infections as well as virus-bacteria coinfections. The review aims to aid researchers in comprehending the intricate interplay between virus and bacteria in disease progression, thereby enhancing understanding of current methodologies and empowering the development of novel health care strategies to tackle coinfections.

Concomitant tuberculosis and aspergillosis in patients with COVID-19: a case report

Coexisting pulmonary aspergillosis and tuberculosis in a post-COVID-19 patient is rare. Here, we are going to report a case of combined pulmonary aspergillosis and tuberculosis in a 51-year-old female who was previously diagnosed with COVID-19 pneumonia. The patient was treated with voriconazole and anti-tuberculosis agents.

Microbiome in the nasopharynx: Insights into the impact of COVID-19 severity

Background

The respiratory tract harbors a variety of microbiota, whose composition and abundance depend on specific site factors, interaction with external factors, and disease. The aim of this study was to investigate the relationship between COVID-19 severity and the nasopharyngeal microbiome.

Methods

We conducted a prospective cohort study in Mexico City, collecting nasopharyngeal swabs from 30 COVID-19 patients and 14 healthy volunteers. Microbiome profiling was performed using 16S rRNA gene analysis. Taxonomic assignment, classification, diversity analysis, core microbiome analysis, and statistical analysis were conducted using R packages.

Results

The microbiome data analysis revealed taxonomic shifts within the nasopharyngeal microbiome in severe COVID-19. Particularly, we observed a significant reduction in the relative abundance of Lawsonella and Cutibacterium genera in critically ill COVID-19 patients (p < 0.001). In contrast, these patients exhibited a marked enrichment of Streptococcus, Actinomyces, Peptostreptococcus, Atopobium, Granulicatella, Mogibacterium, Veillonella, Prevotella_7, Rothia, Gemella, Alloprevotella, and Solobacterium genera (p < 0.01). Analysis of the core microbiome across all samples consistently identified the presence of Staphylococcus, Corynebacterium, and Streptococcus.

Conclusions

Our study suggests that the disruption of physicochemical conditions and barriers resulting from inflammatory processes and the intubation procedure in critically ill COVID-19 patients may facilitate the colonization and invasion of the nasopharynx by oral microorganisms.

Impact of a History of COVID-19 Infection on Postoperative Outcomes for Free Flap Patients

Objectives: This study examines the impact of a history of coronavirus disease 2019 (COVID-19) infection on patients' outcomes after microvascular free flap surgery and to examine the recommendations on when to perform microvascular surgery after a COVID-19 infection. Methods: A retrospective chart review using the TriNetX database was completed on March 5, 2023. Two cohorts were created: (1) patients who had a positive COVID-19 diagnosis within 1 year before microvascular free flap surgery, and (2) patients with no history of COVID-19 who underwent free flap surgery. Current Procedural Terminology codes were used to identify procedures and International Classification of Diseases-10 codes were used to identify outcomes. Results: There was a total of 31,505 patients who underwent microvascular free flap surgery, 500 of whom had a diagnosis of COVID-19 within 1 year of free flap surgery and 31,005 without history of COVID-19. There was increased risk of sepsis, surgical site infection (SSI), generalized infection, gangrene, dehiscence, hematoma, seroma, intensive care unit admission, and death in patients who underwent free flap surgery within a year of COVID-19 infection. After propensity score matching, there were 498 patients in both groups. Increased risk remained for SSI and gangrene in patients with a history of COVID-19 after matching. When comparing surgical timing between 0 to 2 months after COVID-19 infection and 2 to 12 months after COVID-19 infection, there were no significant differences between groups. Conclusions: After propensity score matching, patients with a history of COVID-19 infection were at increased risk for SSI and gangrene. However, many flap surgeries cannot be delayed. This study may help counsel patients regarding the possible complications after surgery and provide a heightened awareness in the surgical team of a possible increase in infectious complications in this population. Additional studies should investigate optimal timing of free flap surgery after COVID-19 infection and ways to mitigate the risk of infectious complications.

The Impact of COVID-19 on the Tuberculosis Features in a Romanian Pneumology Hospital

Introduction

The COVID-19 pandemic and tuberculosis have epidemiological similarities, being transmitted airborne, favored by direct contact, crowded environments, and vulnerable biological status.

Methods

We performed a retrospective study of 45 cases of pulmonary tuberculosis associated with COVID-19 (TB+COV+) compared to 45 cases with tuberculous monoinfection (TB+COV-), hospitalized during 2021-2022.

Results

The demographic characteristics were similar in the two groups, predominating men, a median age of 51 years, living in rural areas, medium level of education and smoking. Common symptoms of the two groups were cough, weight loss, profuse sweating, loss of appetite and hemoptysis, while fever, headache, myo-arthralgias, and digestive symptoms characterized the TB+COV+ forms. The scores of radiological lesions in the TB+COV+ compared to TB+COV- group were significantly higher and persistent, revealing more frequent bilateral extensive lung lesions. There were no significant differences in the biological parameters between the two groups. Mortality was 2.2%, regardless of the association of COVID-19. The frequency of infections with Clostridioides difficile was higher in TB+COV+ cases.

Conclusion

The co-infection of COVID-19 had a mild impact on the clinical and biological expression of tuberculosis diagnosed in a pandemic context.

Physicians' irrational attitudes on the antibiotic prescribing for the treatment of COVID-19 in Turkey: A multicenter survey

BACKGROUND

The inappropriate and excessive use of antibiotics during the coronavirus pandemic has become an important issue.

OBJECTIVE

Our primary aim is to ascertain the attitudes of physicians toward the antibiotics prescribing for the treatment of COVID-19 in Turkey. Our secondary aim was to identify factors affecting to physicians' decisions regarding antibiotic therapy for the treatment of COVID-19 and risk factors associated with antibiotic overprescribing.

METHODS

It was a multicenter cross-sectional survey. Physicians from 63 different cities were invited to survey through social media (Facebook, Instagram, WhatsApp). Data were collected from respondents through an online questionnaires during November-December 2021.

RESULTS

The survey was completed by 571 participants from 63 cities. Pulmonologists comprised the majority (35.20%), followed by internal medical specialists (27.85%) and general practitioners (23.29%). The rates of participants who started empirical antibiotics in the outpatient, ward, and ICU (intensive care unit) were 70.2%, 85.5%, and 74.6%, respectively. When the practice of prescribing antibiotics by physicians for the treatment of COVID-19 in outpatients was compared according to the healthcare setting (primary, secondary, tertiary care hospitals) no significant difference was found. Sputum purulence (68.2%) was recognized as the most important factor for the decision of antibiotic therapy, followed by procalcitonin levels (64.9%) and abnormal radiological findings (50.3%). The most prescribed antibiotics were respiratory quinolones. (48%, 65.9%, 62.7% outpatient, ward, ICU respectively) CONCLUSIONS: In this study, we found that physicians frequently had irrational attitudes toward antibiotic prescription to COVID-19 patients, including those with minor diseases. Our findings underline that the necessity of particular, workable interventions to guarantee the prudent use of antibiotics in COVID-19.

Superinfections of the Spine: A Single-Institution Experience

Background/Objectives: A superinfection occurs when a new, secondary organism colonizes an existing infection. Spine infections are associated with high patient morbidity and sometimes require multiple irrigations and debridements (I&Ds). When multiple I&Ds are required, the risk of complications increases. The purpose of this study was to report our experience with spine superinfections and determine which patients are typically affected. Methods: A retrospective case series of spine superinfections and a retrospective case-control analysis were conducted. Data were collected manually from electronic medical records. Spine I&Ds were identified. Groups were created for patients who had multiple I&Ds for (1) a recurrence of the same causative organism or (2) a superinfection with a novel organism. Preoperative demographic, clinical, and microbiologic data were compared between these two outcomes. A case series of superinfections with descriptive data was constructed. Lastly, two illustrative cases were provided in a narrative format. Results: A total of 92 patients were included in this analysis. Superinfections occurred after 6 out of the 92 (7%) initial I&Ds and were responsible for 6 out of the 24 (25%) repeat I&Ds. The preoperative erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) of the patients with a superinfection were significantly lower than those in the control group (p = 0.022 and p = 0.032). Otherwise, the observed differences in the preoperative variables were not statistically different. In the six cases of superinfection, the presence of high-risk comorbidities, a history of substance abuse, or a lack of social support were commonly observed. The superinfecting organisms included Candida, Pseudomonas, Serratia, Klebsiella, Enterobacter, and Staphylococcus species. Conclusions: Superinfections are a devastating complication requiring reoperation after initial spine I&D. Awareness of the possibility of superinfection and common patient archetypes can be helpful for clinicians and care teams. Future work is needed to examine how to identify, help predict, and prevent spine superinfections.

Molecular characterization of hypermucoviscous carbapenemase-encoding Klebsiella pneumoniae isolates from an Egyptian hospital

This study aimed to screen antibiotic resistance and virulence genes in carbapenem-resistant hypermucoviscous Klebsiella pneumoniae isolates from an Egyptian hospital. Among 38 previously confirmed carbapenem-nonsusceptible K. pneumoniae isolates, a string test identified three isolates as positive for hypermucoviscosity. Phenotypic characterization and molecular detection of carbapenemase- and virulence-encoding genes were performed. PCR-based multilocus sequence typing and phylogenetics were used to determine the clonality and global epidemiology of the strains. The coexistence of virulence and resistance genes in the isolates was analyzed statistically using a chi-square test. Three isolates showed the presence of carbapenemase-encoding genes (blaNDM, blaVIM, and blaIMP), adhesion genes (fim-H-1 and mrkD), and siderophore genes (entB); the isolates belonged to sequence types (STs) 101, 1310, and 1626. The relatedness between these sequence types and the sequence types of globally detected hypermucoviscous K. pneumoniae that also harbor carbapenemases was determined. Our analysis showed that the resistance and virulence profiles were not homogenous. Phylogenetically, different clones clustered together. There was no significant association between the presence of resistance and virulence genes in the isolates. There is a need for periodic surveillance of the healthcare settings in Egypt and globally to understand the true epidemiology of carbapenem-resistant, hypermucoviscous K. pneumoniae.

Towards Understanding and Identification of Human Viral Co-Infections

Viral co-infections, in which a host is infected with multiple viruses simultaneously, are common in the human population. Human viral co-infections can lead to complex interactions between the viruses and the host immune system, affecting the clinical outcome and posing challenges for treatment. Understanding the types, mechanisms, impacts, and identification methods of human viral co-infections is crucial for the prevention and control of viral diseases. In this review, we first introduce the significance of studying human viral co-infections and summarize the current research progress and gaps in this field. We then classify human viral co-infections into four types based on the pathogenic properties and species of the viruses involved. Next, we discuss the molecular mechanisms of viral co-infections, focusing on virus-virus interactions, host immune responses, and clinical manifestations. We also summarize the experimental and computational methods for the identification of viral co-infections, emphasizing the latest advances in high-throughput sequencing and bioinformatics approaches. Finally, we highlight the challenges and future directions in human viral co-infection research, aiming to provide new insights and strategies for the prevention, control, diagnosis, and treatment of viral diseases. This review provides a comprehensive overview of the current knowledge and future perspectives on human viral co-infections and underscores the need for interdisciplinary collaboration to address this complex and important topic.

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.

Prior infection with unrelated neurotropic virus exacerbates influenza disease and impairs lung T cell responses

Immunity to infectious diseases is predominantly studied by measuring immune responses towards a single pathogen, although co-infections are common. In-depth mechanisms on how co-infections impact anti-viral immunity are lacking, but are highly relevant to treatment and prevention. We established a mouse model of co-infection with unrelated viruses, influenza A (IAV) and Semliki Forest virus (SFV), causing disease in different organ systems. SFV infection eight days before IAV infection results in prolonged IAV replication, elevated cytokine/chemokine levels and exacerbated lung pathology. This is associated with impaired lung IAV-specific CD8+ T cell responses, stemming from suboptimal CD8+ T cell activation and proliferation in draining lymph nodes, and dendritic cell paralysis. Prior SFV infection leads to increased blood brain barrier permeability and presence of IAV RNA in brain, associated with increased trafficking of IAV-specific CD8+ T cells and establishment of long-term tissue-resident memory. Relative to lung IAV-specific CD8+ T cells, brain memory IAV-specific CD8+ T cells have increased TCR repertoire diversity within immunodominant DbNP366+CD8+ and DbPA224+CD8+ responses, featuring suboptimal TCR clonotypes. Overall, our study demonstrates that infection with an unrelated neurotropic virus perturbs IAV-specific immune responses and exacerbates IAV disease. Our work provides key insights into therapy and vaccine regimens directed against unrelated pathogens.

Identification and Clinical Characteristics of Community-Acquired Acinetobacter baumannii in Patients Hospitalized for Moderate or Severe COVID-19 in Peru

Acinetobacter baumannii has been described as a cause of serious community-acquired infections in tropical countries. Currently, its implications when simultaneously identified with other pathogens are not yet adequately understood. A descriptive study was conducted on hospitalized patients with a diagnosis of moderate/severe SARS-CoV-2-induced pneumonia confirmed via real-time RT-PCR. Patients aged > 18 years who were admitted to a specialized COVID-19 treatment center in Peru were selected for enrollment. A. baumannii was detected via the PCR amplification of the blaOXA-51 gene obtained from nasopharyngeal swabs within 48 h of hospitalization. A total of 295 patients with COVID-19 who met the study inclusion criteria were enrolled. A. baumannii was simultaneously identified in 40/295 (13.5%) of COVID-19-hospitalized patients. Demographic data and comorbidities were comparable in both Acinetobacter-positive and -negative subgroups. However, patients identified as being infected with Acinetobacter were more likely to have received outpatient antibiotics prior to hospitalization, had a higher requirement for high-flow nasal cannula and a higher subjective incidence of fatigue, and were more likely to develop Acinetobacter-induced pneumonia during hospitalization. Conclusions: The group in which SARS-CoV-2 and A. baumannii were simultaneously identified had a higher proportion of fatigue, a higher frequency of requiring a high-flow cannula, and a higher proportion of superinfection with the same microorganism during hospitalization.

Changes in Spectrum of Respiratory Pathogen Infections and Disease Severity Among Children in Hohhot, China: Impact of COVID-19 Prevention Measures

BACKGROUND This retrospective study evaluated the effects of specific COVID-19 preventive measures, including the use of medical masks, nucleic acid testing, and patient isolation, on respiratory infections, disease severity, and seasonal patterns among children in Hohhot, located in northern China. Understanding these alterations is pivotal in developing effective strategies to handle pediatric respiratory infections within the context of continuous public health initiatives. MATERIAL AND METHODS At the First Hospital of Hohhot, throat swabs were collected from 605 children with community-acquired respiratory between January 2022 and March 2023 for pathogen infection spectrum detection using microarray testing. RESULTS Among the patients, 56.03% were male, and their average age was 3.45 years. SARS-CoV-2 infections were highest between October 2022 and January 2023. Influenza A peaked in March 2023, and other pathogens such as respiratory syncytial virus and influenza B virus disappeared after December 2022. The proportion of mixed infections was 41.94% among SARS-CoV-2 patients, while other pathogens had mixed infection rates exceeding 57.14%. Before December 2022, the mean WBC count for Streptococcus pneumoniae and Haemophilus influenzae was 8.83×10⁹/L, CRP was 18.36 mg/L, and PCT was 1.11 ng/ml. After December 2022, these values decreased significantly. Coughing, difficulty breathing, running nose, and lower respiratory tract infection diagnoses decreased in December 2022, except for SARS-CoV-2 infections. CONCLUSIONS SARS-CoV-2 peaked around November 2022, influenza A peaked in March 2023, and other pathogens like respiratory syncytial virus and influenza B virus were greatly reduced after December 2022. Inflammatory markers and respiratory symptoms decreased after December 2022, except for SARS-CoV-2.

Long COVID in Icelandic Children: A Matched Cohort Study of Nonspecific Symptoms Following SARS-CoV-2 Infection

PURPOSE

Pediatric severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections are usually mild and the mortality rates are low, but concerns have been raised about long-term symptoms that may resemble other postinfectious syndromes. Studies with robust control groups and high response rates have been few.

METHODS

We obtained identifiers for all 837 Icelandic children diagnosed with SARS-CoV-2 by PCR between March 2020 and June 2021 and contacted them by telephone. We asked about 10 physical and mental symptoms being present at least twice weekly for at least 2 months. Participants who reported symptoms were contacted again a year later. For each subject who completed the questionnaire, an age- and sex-matched comparator without SARS-CoV-2 infection was asked to complete the same questionnaire, and the risk difference was calculated.

RESULTS

Responses from 643 cases and 602 comparators were analyzed. Children who had been infected with SARS-CoV-2 were more likely to report one or more symptoms, except for anxiety/depression and sleep disturbances. Fatigue and loss of concentration were evidently more common in cases among teenagers (risk difference: 15%; 95% CI: 7-22% and 15%; 95% CI: 7-23%, respectively). At the second follow-up, close to a third of Long COVID cases had resolved but some participants had developed new persistent symptoms.

CONCLUSION

Symptoms of Long COVID in children are common and impact their quality of life. The importance of further unraveling the pathophysiology of acute and long-term symptoms following SARS-CoV-2 infection in children is vital as well as potential preventive measures.

Deciphering the impact of microbial interactions on COPD exacerbation: An in-depth analysis of the lung microbiome

In microbiome studies, the diversity and types of microbes have been extensively explored; however, the significance of microbial ecology is equally paramount. The comprehension of metabolic interactions among the wide array of microorganisms in the lung microbiota is indispensable for understanding chronic pulmonary disease and for the development of potent treatments. In this investigation, metabolic networks were simulated, and ecological theory was employed to assess the diagnosis of COPD, subsequently suggesting innovative treatment strategies for COPD exacerbation. Lung sputum 16S rRNA paired-end data from 112 COPD patients were utilized, and a supervised machine-learning algorithm was applied to identify taxa associated with sex and mortality. Subsequently, an OTU table with Greengenes 99 % dataset was generated. Finally, the interactions between bacterial species were analyzed using a simulated metabolic network. A total of 1781 OTUs and 1740 bacteria at the genus level were identified. We employed an additional dataset to validate our analyses. Notably, among the more abundant genera, Pseudomonas was detected in females, while Lactobacillus was detected in males. Additionally, a decrease in bacterial diversity was observed during COPD exacerbation, and mortality was associated with the high abundance of the Staphylococcus and Pseudomonas genera. Moreover, an increase in Proteobacteria abundance was observed during COPD exacerbations. In contrast, COPD patients exhibited decreased levels of Firmicutes and Bacteroidetes. Significant connections between microbial ecology and bacterial diversity in COPD patients were discovered, highlighting the critical role of microbial ecology in the understanding of COPD. Through the simulation of metabolic interactions among bacteria, the observed dysbiosis in COPD was elucidated. Furthermore, the prominence of anaerobic bacteria in COPD patients was revealed to be influenced by parasitic relationships. These findings have the potential to contribute to improved clinical management strategies for COPD patients.

Bacterial Community- and Hospital-Acquired Pneumonia in Patients with Critical COVID-19-A Prospective Monocentric Cohort Study

The impact of bacterial pneumonia on patients with COVID-19 infection remains unclear. This prospective observational monocentric cohort study aims to determine the incidence of bacterial community- and hospital-acquired pneumonia (CAP and HAP) and its effect on mortality in critically ill COVID-19 patients admitted to the intensive care unit (ICU) at University Hospital Olomouc between 1 November 2020 and 31 December 2022. The secondary objectives of this study include identifying the bacterial etiology of CAP and HAP and exploring the capabilities of diagnostic tools, with a focus on inflammatory biomarkers. Data were collected from the electronic information hospital system, encompassing biomarkers, microbiological findings, and daily visit records, and subsequently evaluated by ICU physicians and clinical microbiologists. Out of 171 patients suffering from critical COVID-19, 46 (27%) had CAP, while 78 (46%) developed HAP. Critically ill COVID-19 patients who experienced bacterial CAP and HAP exhibited higher mortality compared to COVID-19 patients without any bacterial infection, with rates of 38% and 56% versus 11%, respectively. In CAP, the most frequent causative agents were chlamydophila and mycoplasma; Enterobacterales, which were multidrug-resistant in 71% of cases; Gram-negative non-fermenting rods; and Staphylococcus aureus. Notably, no strains of Streptococcus pneumoniae were detected, and only a single strain each of Haemophilus influenzae and Moraxella catarrhalis was isolated. The most frequent etiologic agents causing HAP were Enterobacterales and Gram-negative non-fermenting rods. Based on the presented results, commonly used biochemical markers demonstrated poor predictive and diagnostic accuracy. To confirm the diagnosis of bacterial CAP in our patient cohort, it was necessary to assess the initial values of inflammatory markers (particularly procalcitonin), consider clinical signs indicative of bacterial infection, and/or rely on positive microbiological findings. For HAP diagnostics, it was appropriate to conduct regular detailed clinical examinations (with a focus on evaluating respiratory functions) and closely monitor the dynamics of inflammatory markers (preferably Interleukin-6).

Mortality and Morbidity of Human Metapneumovirus Infection in the Pre-COVID-19 Era: The Value of the Charlson Comorbidity Index on Outcome Prediction

INTRODUCTION

Human metapneumovirus (HMPV) is an important cause of seasonal respiratory tract infections, mainly in children and immunocompromised adults. The use of the Charlson Comorbidity Index (CCI) to predict outcomes in hospitalized patients has been validated in several settings.

OBJECTIVE

This study aims to describe the clinical characteristics of adult patients with HMPV infection and evaluate the value of the CCI in predicting outcomes in patients with acute HMPV infections requiring hospitalization.

METHOD

This is a single-center case-series study of hospitalized patients with HMPV infection in 2017.

RESULTS

Twenty-two adult patients with a mean age of 65 years were reviewed. The mean CCI was 4.6±2.6. The overall mortality was 22%. An abnormal chest X-ray (CXR) was reported in 15 patients. CCI was not different between survivors and non-survivors. Non-survivors were more likely to have abnormal CXR and a higher fever at the time of diagnosis, required mechanical ventilation, or had other concomitant infections.

CONCLUSION

The average CCI was 4.5, which was not significantly different between survivors and non-survivors. The mortality rate was elevated by 22% and was likely associated with admission to the ICU as well as the presence of another concomitant infection.

Is there a correlation between antibiotic use and the severity or post-infection conditions of COVID-19 and other viral infections?

Antibiotics are one of the most frequently prescribed medications in modern medicine; besides treating bacterial infections, they may often be utilized for prophylactic purposes, including during select viral infections. It has been shown that 74.9% of COVID-19 patients received antibiotics as a part of their treatment regimen during the pandemic. However, studies suggest that the actual incidence of bacterial coinfection was relatively uncommon with a mere 3.5% of overall cases reported. A recent study revealed that antibiotic administration would not improve disease progression or shorten the length of hospitalization in COVID-19 patients; additionally, some antibiotics, such as linezolid, promote the production of free radicals that might be responsible for exacerbated clinical symptoms during and post-infection. Notably, antibiotic use disturbs the normal gut microbiome, and this interference impedes antiviral immune response enhancing severity and susceptibility to a list of viral infections. Thus, resultant augmented severity of these infections may be a consequence of higher susceptibility to respiratory viral co-infection.

A cooperativity between virus and bacteria during respiratory infections

Respiratory tract infections remain the leading cause of morbidity and mortality worldwide. The burden is further increased by polymicrobial infection or viral and bacterial co-infection, often exacerbating the existing condition. Way back in 1918, high morbidity due to secondary pneumonia caused by bacterial infection was known, and a similar phenomenon was observed during the recent COVID-19 pandemic in which secondary bacterial infection worsens the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) condition. It has been observed that viruses paved the way for subsequent bacterial infection; similarly, bacteria have also been found to aid in viral infection. Viruses elevate bacterial infection by impairing the host's immune response, disrupting epithelial barrier integrity, expression of surface receptors and adhesion proteins, direct binding of virus to bacteria, altering nutritional immunity, and effecting the bacterial biofilm. Similarly, the bacteria enhance viral infection by altering the host's immune response, up-regulation of adhesion proteins, and activation of viral proteins. During co-infection, respiratory bacterial and viral pathogens were found to adapt and co-exist in the airways of their survival and to benefit from each other, i.e., there is a cooperative existence between the two. This review comprehensively reviews the mechanisms involved in the synergistic/cooperativity relationship between viruses and bacteria and their interaction in clinically relevant respiratory infections.

Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients

The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infected a substantial proportion of Chinese population, and understanding the factors underlying the severity of the disease and fatality is valuable for future prevention and clinical treatment. We recruited 64 patients with invasive ventilation for COVID-19 and performed metatranscriptomic sequencing to profile host transcriptomic profiles, plus viral, bacterial, and fungal content, as well as virulence factors and examined their relationships to 28-day mortality were examined. In addition, the bronchoalveolar lavage fluid (BALF) samples from invasive ventilated hospital/community-acquired pneumonia patients (HAP/CAP) sampled in 2019 were included for comparison. Genomic analysis revealed that all Omicron strains belong to BA.5 and BF.7 sub-lineages, with no difference in 28-day mortality between them. Compared to HAP/CAP cohort, invasive ventilated COVID-19 patients have distinct host transcriptomic and microbial signatures in the lower respiratory tract; and in the COVID-19 non-survivors, we found significantly lower gene expressions in pathways related viral processes and positive regulation of protein localization to plasma membrane, higher abundance of opportunistic pathogens including bacterial Alloprevotella, Caulobacter, Escherichia-Shigella, Ralstonia and fungal Aspergillus sydowii and Penicillium rubens. Correlational analysis further revealed significant associations between host immune responses and microbial compositions, besides synergy within viral, bacterial, and fungal pathogens. Our study presents the relationships of lower respiratory tract microbiome and transcriptome in invasive ventilated COVID-19 patients, providing the basis for future clinical treatment and reduction of fatality.

Epidemiology, Clinical Profile, and Analysis of Risk Factors in COVID Associated Rhino-orbito-cerebral Mucormycosis Patients - An Observational Study

Aim of Study

To study the clinico-epidemiological profile and identify risk factors for the development of COVID-19-associated mucormycosis (CAM) among the patients treated at our regional mucormycosis center.

Materials and Methods

This was a cross-sectional single-centre observational study. All CAM patients admitted to Government Rajaji Hospital, Madurai from April 2021- August 2021 were included in the study. Information regarding clinical features, potential risk factors, diagnostic workup, and comorbid illness was collected.

Results

A total of 164 patients of CAM were admitted to our hospital with a mean age of 51.7 years. Out of 164 patients, 12 patients were not covid positive, based on imaging and RT-PCR, however subclinical infection could not be ruled out. Out of the 164 patients studied, 160 patients had diabetes, out of which 66% (n = 105) patients had a previous history of diabetes, and 34% (n = 55) had newly detected diabetes. Most of the patients admitted with mucormycosis had uncontrolled diabetes (94%) and were not on insulin therapy, but were on oral antidiabetic drugs alone. The majority of the patients (68%) have received steroids (IV/oral) during the COVID-19 illness. 74% of these patients were under hospitalization for COVID-19 disease. Only 30% (n = 50) of CAM patients had a history of oxygen therapy and 7% of these patients were treated in ICU during active COVID-19 illness. 59% of patients used cloth masks without adequate hygiene, rest 41% (n = 67) patients reused disposable masks. We also found that 87% of the patients developing mucormycosis had exposure to organic material in the convalescence period of COVID-19 illness.

Conclusions

From our study, we found steroid use, poorly controlled diabetes mellitus, reuse of masks, daily steam inhalation, and exposure to organic matter to be more associated with CAM, but oxygen therapy was less associated with CAM. Hence, we could suggest screening for hyperglycemia and daily use of disposable surgical masks to be continued for at least 4 weeks post-COVID-19. It is preferable to continue insulin in titrated doses along with OHA for at least 4 weeks following steroid cessation in the post-COVID-19 period as there is are considerably increased inflammatory cytokine levels in the convalescence phase. Clean environmental hygiene would also help prevent CAM.

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.

The Influence of the COVID-19 Pandemic on Seasonal Influenza Vaccine Uptake Among Patients Visiting a University Hospital in Saudi Arabia

INTRODUCTION

Influenza vaccination is a subject of importance in Saudi Arabia. The study measured the uptake of annual influenza vaccination from 2019 to 2021 among patients attending outpatient clinic of a University Hospital.  Materials and methods: A cross-sectional study design was used, and the questionnaire was administered by trained interviewers. Descriptive and inferential statistics were done using the Statistical Package for the Social Sciences (SPSS) version 21 (IBM, Armonk, New York).  Results: The three-year annual influenza vaccine uptake for 2019-2021 was 19.7%, 11.4%, and 14.2%, respectively. In the year 2022, only 28.2% of the patients were offered influenza vaccines by their physicians, and among those offered, 49.6% showed vaccine acceptance. Higher vaccine acceptance was significantly associated with past episodes of influenza infection (p<0.001) and vaccination history before the COVID-19 pandemic (p<0.001). Lower acceptance of the influenza vaccine was observed during the pandemic (p<0.001) and lower uptake among those who were not offered influenza vaccines (p=0.02). No association was found between influenza vaccine acceptance and smoking status, chronic illness, history of COVID-19 infection, or living with those susceptible to influenza. Reasons for vaccine denial include an assumption of not being at risk, a lack of information about the vaccine, and a fear of side effects.

CONCLUSION

The COVID-19 pandemic has had a detrimental effect on annual influenza vaccination. Efforts must be taken to increase influenza vaccination among vulnerable groups.

COVID-19, Obesity, and GRP78: Unraveling the Pathological Link

The coronavirus disease 2019 (COVID-19) pandemic, driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an unprecedented global surge in infections and fatalities. Notably, obesity has emerged as an important susceptibility factor for COVID-19; however, the pathological mechanisms for this remain poorly understood. Recent studies proposed a role for glucose-regulated protein 78 (GRP78), a protein implicated in both obesity and metabolic syndrome, which may function as a binding partner and/or co-receptor for SARS-CoV-2. Given its crucial involvement in diverse biological processes, GRP78 likely plays a major role in multiple facets of the viral life cycle and the pathology of COVID-19. This perspective review discusses the potential contributions of GRP78 to the dynamics of SARS-CoV-2 infection and pathology, particularly in the context of obesity. The primary objective is to facilitate a deeper understanding of the pathogenesis of COVID-19. Through this exploration, we aim to illuminate the complex interactions underpinning the nexus of COVID-19, obesity, and GRP78, ultimately paving the way for informed therapeutic strategies and preventive measures.

Impact of the COVID-19 Pandemic on the Epidemiology of Bloodstream Infections in Hospitalized Patients-Experience from a 4th Military Clinical Hospital in Poland

Bloodstream infections (BSIs) are associated with high mortality and inappropriate or delayed antimicrobial therapy. The purpose of this study was to investigate the impact of the COVID-19 pandemic on the epidemiology of BSIs in hospitalized patients. The research aimed to compare the incidence of BSIs and blood culture results in patients hospitalized before and during the COVID-19 pandemic.

METHODS

Retrospective and prospective data were collected from blood cultures obtained from 4289 patients hospitalized between June 2018 and July 2022. Two groups of patients were distinguished: those with BSIs admitted during the pre-COVID-19 period and those admitted during the COVID-19 surge. Demographic and clinical data, blood cytology, and biochemistry results were analyzed, and the usefulness of PCT was assessed in patients with COVID-19.

RESULTS

The study showed a significant increase in the incidence of BSIs during the pandemic compared to the pre-COVID-19 period. Positive blood cultures were obtained in 20% of patients hospitalized during the pandemic (vs. 16% in the pre-COVID-19 period). The incidence of BSIs increased from 1.13 to 2.05 cases per 1000 patient days during COVID-19, and blood culture contamination was more frequently observed. The mortality rate was higher for patients hospitalized during the COVID-19 pandemic. An increased frequency of MDRO isolation was observed in the COVID-19 period.

CONCLUSIONS

The incidence of BSIs increased and the mortality rate was higher in the COVID-19 period compared to the pre-COVID-19 period. The study showed limited usefulness of procalcitonin in patients with COVID-19, likely due to the administered immunosuppressive therapy.

Characteristics and risk factors of secondary bacterial infections in COVID-19 patients

Objective

To describe the characteristics and find out risk factors of COVID-19 patients infected with different categories of bacteria.

Design

Case-control.

Methods

We conducted a retrospective study including 129 COVID-19 patients admitted to a tertiary hospital between October 13, 2022 and December 31, 2022. Patients' data were collected from the hospital information system. Patients were classified as having or not having confirmed secondary bacterial infections, or gram-positive and gram-negative bacterial infections for analysis. Categories and sources of isolated bacteria, characteristics of the patients, and the risk factors for developing secondary bacterial infections were analyzed.

Results

Gram-negative bacteria accounted for the majority of secondary bacterial infections of the included patients. Critical type of COVID-19 (OR = 12.98, 95%CI 3.43∼49.18, p < 0.001), invasive therapy (OR = 9.96, 95%CI 3.01∼32.95, p < 0.001), and previous antibiotics use (OR = 17.23, 95%CI 1.38∼215.69, p = 0.027) were independent risk factors of secondary bacterial infections in COVID-19 patients. Ceftriaxone/cefotaxime use (OR = 15.45, 95%CI 2.72∼87.79, p = 0.002) was associated with gram-positive bacterial infections while age over 70 (OR = 3.30, 95%CI 1.06∼10.26, p = 0.039), invasive therapy (OR = 4.68, 95%CI 1.22∼17.93, p = 0.024), and carbapenems use (OR = 8.48, 95%CI 2.17∼33.15, p = 0.002) were associated with gram-negative bacterial infections.

Conclusions

Critical patients with invasive therapy and previous antibiotics use should be cautious with secondary bacterial infections. Third-generation cephalosporins and carbapenems should be used carefully because both are risk factors for gram-positive or gram-negative bacterial infections.

Respiratory co-infections in COVID-19-positive patients

BACKGROUND

Opportunistic respiratory infections may complicate critically ill patients with COVID-19. Early detection of co-infections helps to administrate the appropriate antimicrobial agent, to guard against patient deterioration. This study aimed at estimating co-infections in COVID-19-positive patients.

METHODS

Eighty-nine COVID-19-positive patients confirmed by SARS-COV-2 PCR were tested for post-COVID-19 lower respiratory tract co-infections through bacterial culture, fungal culture and galactomannan (GM) testing.

RESULTS

Fourteen patients showed positive coinfection with Klebsiella, nine with Acinetobacter, six with Pseudomonas and three with E. coli. As for fungal infections, nine showed coinfection with Aspergillus, two with Zygomycetes and four with Candida. Galactomannan was positive among one patient with Aspergillus coinfection, one with Zygomycetes coinfection and three with Candida, 13 samples with negative fungal culture were positive for GM. Ten samples showed positive fungal growth, however, GM test was negative.

CONCLUSION

In our study, SARS-COV-2 respiratory coinfections were mainly implicated by bacterial pathogens; most commonly Klebsiella species (spp.), Aspergillus spp. were the most common cause of fungal coinfections, GM test showed low positive predictive value for fungal infection. Respiratory coinfections may complicate SARS-COV-2 probably due to the prolonged intensive care units (ICU) hospitalization, extensive empiric antimicrobial therapy, steroid therapy, mechanical ventilation during the COVID-19 outbreak. Antimicrobial stewardship programs are required so that antibiotics are prescribed judiciously according to the culture results.

Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients

During the COVID-19 pandemic, impaired immunity and medical interventions resulted in cases of secondary infections. The clinical difficulties and dangers associated with secondary infections in patients necessitate the exploration of their microbiome. Metaproteomics is a powerful approach to study the taxonomic composition and functional status of the microbiome under study. In this study, the mass spectrometry (MS)-based data of nasopharyngeal swab samples from COVID-19 patients was used to investigate the metaproteome. We have established a robust bioinformatics workflow within the Galaxy platform, which includes (a) generation of a tailored database of the common respiratory tract pathogens, (b) database search using multiple search algorithms, and (c) verification of the detected microbial peptides. The microbial peptides detected in this study, belong to several opportunistic pathogens such as Streptococcus pneumoniae, Klebsiella pneumoniae, Rhizopus microsporus, and Syncephalastrum racemosum. Microbial proteins with a role in stress response, gene expression, and DNA repair were found to be upregulated in severe patients compared to negative patients. Using parallel reaction monitoring (PRM), we confirmed some of the microbial peptides in fresh clinical samples. MS-based clinical metaproteomics can serve as a powerful tool for detection and characterization of potential pathogens, which can significantly impact the diagnosis and treatment of patients.

Prediction of tsunami of resistance to some antibiotics is not far-fetched which used during COVID-19 pandemic

One of the most tragic events in recent history was the COVID-19 outbreak, which has caused thousands of deaths. A variety of drugs were prescribed to improve the condition of patients, including antiparasitic, antiviral, antibiotics, and anti-inflammatory medicines. It must be understood, however, that COVID-19 is like a tip of an iceberg on the ocean, and the consequences of overuse of antibiotics are like the body of a mountain under water whose greatness has not yet been determined for humanity, and additional study is needed to understand them. History of the war between microbes and antimicrobial agents has shown that microbes are intelligent organisms that win over antimicrobial agents over time through many acquired or inherent mechanisms. The key terms containing "COVID-19," "Severe acute respiratory syndrome coronavirus-2," "SARS-CoV2," "Antibiotic Resistance," "Coronavirus," "Pandemic," "Antibiotics," and "Antimicrobial Resistance" were used for searching in PubMed, Scopus, and Google Scholar databases. The COVID-19 pandemic has resulted in an increased prescription of antibiotics. Infections caused by secondary or co-bacterial infections or beneficial bacteria in the body can be increased as a result of this amount of antibiotic prescription and exposure to antibiotics. Antibiotic resistance will likely pose a major problem in the future, especially for last resort antibiotics. In order to address the antibiotic resistance crisis, it is imperative that researchers, farmers, veterinarians, physicians, public and policymakers, pharmacists, other health and environmental professionals, and others collaborate during and beyond this pandemic.