Postviral Complications: Bacterial Pneumonia

Exploring the role of respiratory virus infections in aspiration pneumonia: a comprehensive analysis of cases with lower respiratory tract infections

BACKGROUND

While respiratory virus infection has been implicated in the onset of bacterial pneumonia, no research has investigated the association of respiratory viruses with the onset of aspiration pneumonia (AP). This study aimed to investigate the role of respiratory virus infections in AP.

METHODS

Patients presenting with acute respiratory symptoms and undergoing influenza antigen testing at the emergency department of Okinawa Chubu Hospital from February 2020 to January 2021, and diagnosed with lower respiratory tract infections, were included. Cases were categorized into AP, pneumonia other than AP (non-AP), and acute bronchitis (AB) based on physician diagnoses recorded in medical records. The residual nasal swab specimens were further tested with multiplex PCR tests for respiratory viruses.

RESULTS

A total of 209 subjects were included in the study: 59 in the AP group, 118 in the non-AP group, and 32 in the AB group. The AP group was characterized by older age, higher rates of nursing home residency, a greater prevalence of comorbidities such as cerebrovascular disease and dementia, a lower sputum culture positivity rate, and a different spectrum of causative pathogens compared to the other groups. The virus positivity rate in the AP group was 47%, compared to 50% in the non-AP group and 53% in the AB group, with no significant difference observed. The AP group exhibited the highest rate of only respiratory viruses detected and the lowest rate of both respiratory viruses and bacteria detected among the groups. There was no significant difference in the types of viruses detected between the AP group and the other groups, with rhinovirus being the most frequently detected virus across all groups. In the AP group, virus-negative cases were significantly older on average. No other significant differences in background, symptoms, or clinical data were observed between virus-positive and virus-negative cases within the AP group.

CONCLUSION

In the AP group, the rate of respiratory virus detections was comparable to that of the non-AP and AB groups. This suggests a potential link between respiratory virus infections and the development of AP, emphasizing the need for novel preventive strategies. While distinguishing between AP patients with and without respiratory virus detections based on clinical findings was challenging, recognizing the frequent involvement of respiratory virus infections in AP highlights the importance of enhanced infection control and awareness in its management.

Influenza B virus infection alters the regenerative potential of murine alveolar type 2 pneumocytes

Respiratory epithelial cells can survive direct infection by influenza viruses, and the long-term consequences of that infection have been characterized in a subset of proximal airway cell types. The impact on the cells that survive viral infection in the distal lung epithelia, however, is much less well-characterized. Utilizing a Cre-expressing influenza B virus (IBV) and a lox-stop-lox tdTomato reporter mouse model, we identified that alveolar type 2 (AT2) pneumocytes, a progenitor cell type in the distal lung, can survive viral infection. We show that survival of infection is associated with transcriptional dysregulation compared to bystander AT2 pneumocytes from the same lung. Furthermore, ex vivo experiments revealed a significant reduction in proliferation rates in survivor AT2 pneumocytes compared to matched, non-directly infected bystander cells. Our findings not only enhance our understanding of the AT2 pneumocyte response to IBV infection but could also have broader implications for the mechanisms of respiratory epithelial repair post-viral infection.

IMPORTANCE

Alveolar type 2 (AT2) pneumocytes are a cell type critical for repair of the distal lung after an injury, such as a viral infection. After epithelial damage, AT2 pneumocytes proliferate for both self-renewal and differentiation into type I pneumocytes to repopulate the epithelium. Theoretically, some of the long-term lung sequelae associated with viral infections could be the result of inappropriate AT2 behavior. Here, the authors report that during an influenza B virus infection, some of the actively infected AT2 pneumocytes can ultimately eliminate all traces of the viral RNA and persist in the host long term. As a consequence of having been infected, however, the cells display an altered transcriptional profile and decreased proliferative capacity. These data together suggest a mechanism for how an acute viral infection can have long-term impacts on the pulmonary system.

Common viral respiratory infections in children with cancer during the COVID-19 pandemic: a multicenter study from Türkiye

BACKGROUND

Microbiologic confirmation of respiratory tract infections gained importance during the coronavirus disease 2019 (COVID-19) pandemic. This study retrospectively evaluated seasonal distribution, clinical presentation, and complications of respiratory viral infections (RVIs) other than COVID-19 in children with cancer during and after the pandemic lockdown.

METHODS

Two hundred and sixty-five inpatient and outpatient RVI episodes in 219 pediatric cancer patients confirmed by multiplex reverse transcriptase polymerase chain reaction (RT-PCR) panels from 13 centers were enrolled.

RESULTS

Eighty-six (32.5%) of the total 265 episodes occurred in 16 months corresponding to the lockdowns in Türkiye, and the remaining 67.5% in 10 months thereafter. Human rhinovirus/enterovirus (hRE) (48.3%) was the most common agent detected during and after lockdown. Parainfluenza virus (PIV) (23.0%), influenza virus (9.8%), and respiratory syncytial virus (RSV) (9.1%) were the other common agents. The 28.7% of episodes were lower respiratory tract infections (LRTIs), and complications and mortality were higher than upper respiratory tract infections (URTIs) (25.0% vs 5.3%). Bacteremia was identified in 11.5% of culture-drawn episodes. Treatment delay in one-third and death within four weeks after RVI in 4.9% of episodes were observed.

CONCLUSION

During the pandemic, fewer episodes of RVIs occurred during the lockdown period. Respiratory viruses may cause complications, delays in treatment, and even death in children with cancer. Therefore, increased awareness of RVIs and rapid detection of respiratory viruses will benefit the prevention and, in some cases, abrupt supportive and some antiviral treatment of RVI in children with cancer.

Supporting vaccine (co)-administration decisions: Development and validation of a tool for assessing the risk of severe outcomes due to lower respiratory tract infections

OBJECTIVE

To develop and validate a score to predict the 90-day risk of hospitalization/death in patients with low respiratory tract infections (LRTIs) with the aim to support clinical decision making on vaccine (co)-administration.

METHODS

We formed a cohort of patients aged 18 years or older being diagnosed with LRTIs in the period between January 1, 2012 and December 31, 2022. Each patient was followed until occurrence of respiratory-related hospitalization/death up to the end of the study period (December 31, 2022). Along with age and sex, forty determinants were adopted to assemble the respiratory tract infection (RTI)-Health Search (HS) core using the development sub-cohort. The prediction accuracy of the score was therefore assessed in the validation sub-cohort.

RESULTS

We identified 252,319 patients being diagnosed with LRTIs (females: 54.7 %; mean age: 60 (SD:18.1)). When the risk of LRTIs-related hospitalizations/deaths was estimated via RTI-HScore, its predicted value was equal to 1.4 % over a 90-day event horizon. The score showed explained variation and discrimination accuracy were equal to 45 % (95 % CI: 44-47 %) and 81 % (95 % CI: 79-84 %), respectively. The calibration slope did not significantly differ from the unit (p = 0.8314).

CONCLUSIONS

The RTI-HScore was featured by good accuracy for prediction of LRTIs-related complications over a 90-day follow-up. Such a tool might therefore support general practitioners to enhance patients' care by facilitating approaches for (co)-administration of vaccines for respiratory infections through a score-based decision support system.

At Early Rheumatoid Arthritis Stage, the Infectious Spectrum Is Driven by Non-Familial Factors and Anti-CCP Immunization

Background/Objectives: Patients with rheumatoid arthritis (RA) are prone to develop infections. Methods: Accordingly, 195 untreated early (e)RA patients and 398 healthy controls were selected from women in Tatarstan's cohort to study infectious history in the anamnesis (four criteria) and in the previous year (16 criteria). Information about annual infections was collected face-to-face from year to year by a qualified rheumatologist/general practitioner and included the active use of information from medical records. Results: In the anamnesis, tuberculosis, and pneumonia, and in the previous year, respiratory tract infections, skin infections, and herpes simplex virus reactivation incidence were reported to be increased in eRA patients, as well as the event number and duration of acute and chronic tonsillitis. Moreover, more bacterial-suspected upper respiratory infections and urinary tract infections were retrieved in sporadic eRA patients as compared to familial eRA patients. An elevated immunization against CCP prevented respiratory tract infection in those with HSV exacerbation. Finally, associations were retrieved between infection (event number/delay) and RA indices: (i) chronic tonsillitis exacerbations with disease activity and health assessment (HAQ) in familial eRA; (ii) bacterial-suspected upper respiratory infections with the number of swollen and tender joints in sporadic eRA; and (iii) HSV exacerbation with inflammation in eRA patients with negative/low response against CCP. Here, we demonstrate the complex nature of the interplay of RA with specific infections. Conclusions: For the first time, differences in the patterns of annual trivial infections and their links with RA indices were found in cohorts of familial and sporadic cases of the disease. Additionally, for the first time, we identified a remarkable relationship between early RA and exacerbations of chronic tonsillitis, as well as tuberculosis in the patient's history. Altogether, this study supports the existence of a complex interplay between infections and RA at onset driven by familial status and the presence of anti-CCP Ab at elevated levels.

The burden of recurrent respiratory tract infections in adult population: a population-based study in primary care

BACKGROUND

Viral infections are the main original cause of recurrent respiratory tract infections (RRTIs), but their complications and recurrences are due to bacteria as well. While some operational definitions and epidemiology of RRTIs are reported in paediatrics, no similar definitions have been proposed for adults.

AIM

To assess the epidemiology and characteristics of RRTIs in the adult population.

DESIGN AND SETTING

Cohort study in the primary care setting.

METHODS

Using the Health Search Database, we selected a cohort of patients aged 18 years or older between 2002 and 2022. Yearly, we counted upper and lower respiratory tract infections (RTIs) per patient. We investigated 2 cut-offs defining RRTIs, nominally 3+ RRTIs/patient/year or greater than the mean value of RTIs/patient/year. The associations between these two event definitions and the correlates defining the patients' vulnerability were assessed by estimating a logistic regression model.

RESULTS

Over the study years, the mean number of RTIs/patient/year ranged from 0.07-0.16 or 1.10-1.13 events, when the denominator was formed by the overall population or those diagnosed with RTIs, respectively. When the analysis was focussed on 2022, we obtained 0.2% (1.3% among those with RTIs) or 13% (11.3% among those with RTIs) cases of RRTIs, using a cut-off of 3+ or >=0.16 events (mean value/patient), respectively. Consistent associations were found for these two operational definitions and the investigated clinical correlates.

CONCLUSION

We provided evidence on the epidemiology and concurrent/predisposing factors of RRTIs in adults. These data should support health authorities and general practitioners for the application of the most appropriate preventive and/or treatment strategies.

Impact of bronchoalveolar lavage from influenza A virus diseased pigs on neutrophil functions and growth of co-infecting pathogenic bacteria

Introduction

Influenza A viruses (IAVs) infect the respiratory tract of mainly humans, poultry, and pigs. Co-infections with pathogenic lung bacteria are a common event and contribute to the severity of disease progression. Neutrophils are a major cell type of the innate immune system and are rapidly recruited to the site of infection. They have several effector functions to fight invading pathogens such as the secretion of reactive oxygen species (ROS) or the release of neutrophil extracellular traps (NETs). NETs are known to promote the growth of Pasteurellaceae bacteria, especially if degraded by nucleases.

Methods

In this study, bronchoalveolar lavage fluid (BALF) from 45 field-infected pigs was analyzed for 1) NET markers, 2) influence on growth of lung bacteria, and 3) impact on neutrophil functions. BALF samples from 21 IAV-positive pigs and 24 lung diseased but IAV-negative pigs were compared.

Results

Here, we show that neutrophils in the lungs of IAV-positive pigs release vesicular NETs. Several NET markers were increased in the BALF of IAV-positive pigs compared with the BALF from IAV-negative pigs. The amount of NET markers positively correlated with the viral load of the IAV infection. Interestingly, the BALF of IAV-positive pigs enhanced the growth of bacteria belonging to the family of Pasteurellaceae as potential coinfecting bacteria. These effects were weaker with the BALF derived from IAV-negative pigs with other lung infections. The intensity of oxidative burst in neutrophils was significantly decreased by BALF from IAVpositive pigs, indicating impaired antimicrobial activity of neutrophils. Finally, the lung milieu reflected by IAV-positive BALF does not enable neutrophils to kill Actinobacillus pleuropneumoniae but rather enhances its growth.

Discussion

In summary, our data show that an IAV infection is affecting neutrophil functions, in particular the release of NETs and ROS. Furthermore, IAV infection seems to provide growth-enhancing factors for especially coinfecting Pasteurellaceae and reduces the killing efficiency of neutrophils.

Acute COVID-19, the Lived Experience, and Lessons to Learn for Future Pandemics

OBJECTIVES

The study aimed to increase the understanding of the lived experience of patients during the acute phase of a coronavirus disease 2019 (COVID-19) infection.

METHOD

A Web-based survey was distributed through established patient and public engagement and involvement groups and networks, social media, and by means of word of mouth. The survey covered questions relating to patient demographics, COVID-19 diagnosis, symptom profile, and patient experience during acute COVID-19.

RESULTS

The findings demonstrate the varying symptom profiles experienced by people in the acute stage of COVID-19 infection, with participants sharing how they managed care at home, and/or accessed medical advice. Findings also highlight themes that people were concerned with being unable to receive care and believed they needed to rely heavily on family, with extreme thoughts of death.

CONCLUSIONS

Although the urgent threat to public health has been negated by efficacious vaccines and enhanced treatment strategies, there are key lessons from the lived experience of COVID-19 that should be used to prepare for future pandemics and public health emergencies.

Tracking severe acute respiratory syndrome coronavirus 2 transmission and co-infection with other acute respiratory pathogens using a sentinel surveillance system in Rift Valley, Kenya

BACKGROUND

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the most significant public health challenge in over a century. SARS-CoV-2 has infected over 765 million people worldwide, resulting in over 6.9 million deaths. This study aimed to detect community transmission of SARS-CoV-2 and monitor the co-circulation of SARS-CoV-2 with other acute respiratory pathogens in Rift Valley, Kenya.

METHODS

We conducted a cross-sectional active sentinel surveillance for the SARS-CoV-2 virus among patients with acute respiratory infections at four sites in Rift Valley from January 2022 to December 2022. One thousand two hundred seventy-one patients aged between 3 years and 98 years presenting with influenza-like illness (ILI) were recruited into the study. Nasopharyngeal swab specimens from all study participants were screened using a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for SARS-CoV-2, influenza A, influenza B and respiratory syncytial virus (RSV).

RESULTS

The samples that tested positive for influenza A (n = 73) and RSV (n = 12) were subtyped, while SARS-CoV-2 (n = 177) positive samples were further screened for 12 viral and seven bacterial respiratory pathogens. We had a prevalence of 13.9% for SARS-CoV-2, 5.7% for influenza A, 2% for influenza B and 1% for RSV. Influenza A-H1pdm09 and RSV B were the most dominant circulating subtypes of influenza A and RSV, respectively. The most common co-infecting pathogens were Streptococcus pneumoniae (n = 29) and Haemophilus influenzae (n = 19), accounting for 16.4% and 10.7% of all the SARS-CoV-2 positive samples.

CONCLUSIONS

Augmenting syndromic testing in acute respiratory infections (ARIs) surveillance is crucial to inform evidence-based clinical and public health interventions.

Clinical significance of human metapneumovirus detection in critically ill adults with lower respiratory tract infections

BACKGROUND

Unlike other viruses, the pathogenicity of human metapneumovirus (hMPV) in adults remains uncertain. To address this question, a retrospective monocentric cohort including all patients admitted to ICU with hMPV infection between January 1, 2010, and June 30, 2018 was performed. The characteristics of hMPV infected patients were studied and compared to matched influenza infected patients. Consecutively, a systematic review and meta-analyses investigating PUBMED, EMBASE and COCHRANE databases was conducted to explore the hMPV infections in adult patients (PROSPERO number: CRD42018106617). Trials, case series, and cohorts published between January 1, 2008 and August 31, 2019 compiling adults presenting hMPV infections were included. Pediatric studies were excluded. Data were extracted from published reports. Primary endpoint was the rate of low respiratory tract infections (LRTIs) among all hMPV infected patients.

RESULTS

During the study period, 402 patients were tested positive for hMPV. Among them 26 (6.5%) patients were admitted to the ICU, 19 (4.7%) for acute respiratory failure. Twenty-four (92%) were immunocompromised. Bacterial coinfections were frequent 53.8%. Hospital mortality rate was 30.8%. In the case-control analysis, the clinical and imaging characteristics were not different between hMPV and influenza infected patients. The systematic review identified 156 studies and 69 of them (1849 patients) were eligible for analysis. Although there was heterogeneity between the studies, the rate of hMPV LRTIs was 45% (95% CI 31-60%; I² = 98%). Intensive care unit (ICU) admission was required for 33% (95% CI 21-45%; I² = 99%). Hospital mortality rate was 10% (95% CI 7-13%; I² = 83%) and ICU mortality rate was 23% (95% CI 12-34%; I² = 65%). Underlying malignancy was independently associated with increased mortality rate.

CONCLUSIONS

This preliminary work suggested that hMPV may be associated with severe infection and high mortality in patients with underlying malignancies. However, regarding the small size of the cohort and the heterogeneity of the review, more cohort studies are warranted.

Applying symptom dynamics to accurately predict influenza virus infection: An international multicenter influenza-like illness surveillance study

BACKGROUND

Public health organizations have recommended various definitions of influenza-like illnesses under the assumption that the symptoms do not change during influenza virus infection. To explore the relationship between symptoms and influenza over time, we analyzed a dataset from an international multicenter prospective emergency department (ED)-based influenza-like illness cohort study.

METHODS

We recruited patients in the US and Taiwan between 2015 and 2020 with: (1) flu-like symptoms (fever and cough, headache, or sore throat), (2) absence of any of the respiratory infection symptoms, or (3) positive laboratory test results for influenza from the current ED visit. We evaluated the association between the symptoms and influenza virus infection on different days of illness. The association was evaluated among different subgroups, including different study countries, influenza subtypes, and only patients with influenza.

RESULTS

Among the 2471 recruited patients, 45.7% tested positive for influenza virus. Cough was the most predictive symptom throughout the week (odds ratios [OR]: 7.08-11.15). In general, all symptoms were more predictive during the first 2 days (OR: 1.55-10.28). Upper respiratory symptoms, such as sore throat and productive cough, and general symptoms, such as body ache and fatigue, were more predictive in the first half of the week (OR: 1.51-3.25). Lower respiratory symptoms, such as shortness of breath and wheezing, were more predictive in the second half of the week (OR: 1.52-2.52). Similar trends were observed for most symptoms in the different subgroups.

CONCLUSIONS

The time course is an important factor to be considered when evaluating the symptoms of influenza virus infection.

Epidemiological characteristics of community-acquired pneumonia and effects from the COVID-19 pandemic in Shenzhen of China

OBJECTIVE

This study aimed to observe the impact of the coronavirus disease 2019 (COVID-19) pandemic on the incidence of non-COVID-19 community-acquired pneumonia (CAP) in Shenzhen of China, offering new ideas for evaluating the effects of non-pharmaceutical interventions.

METHODS

A retrospective analysis was conducted of inpatients with pneumonia from 2017 to 2021. Epidemiological characteristics of CAP and effects from the COVID-19 pandemic were analyzed by the basic characteristics, time distribution, etiology and disease burden.

RESULTS

There were a total of 5746 CAP inpatient cases included from 2017 to 2021. The number of CAP hospitalizations decreased during the pandemic from 2020 to 2021, with seasonal variations of being higher in spring and winter and lower in summer and autumn, whereas it was prevalent throughout the year prior to the pandemic. The children group decreased significantly during the pandemic, with a 15% decrease in the share of CAP inpatients. The detection rates of bacteria and mycoplasma decreased in CAP patients, while the detection rate of the virus increased, and the number of moderate and severe cases reduced more than that of the mild.

CONCLUSION

Non-pharmaceutical interventions from COVID-19 have led to a decrease in the number of CAP inpatients, especially for children, with a specific seasonal prevalence in spring and winter, when the prevention interventions should be strengthened further for adults during the pandemic.

Incidence and Impact of Ventilator Associated Multidrug Resistant Pneumonia in Patients with SARS-COV2

Introduction

Ventilator Associated Pneumonia (VAP) is associated with significant cost, morbidity, and mortality. There is limited data on the incidence of VAP, appropriate antibiotic timing, and the impact of multidrug resistant VAP in intubated Coronavirus disease-19 (COVID-19) patients.

Methods

A retrospective study was conducted at 2 tertiary urban academic centers involving 132 COVID-19 patients requiring invasive mechanical ventilation (IMV). The epidemiology of VAP, the impact of prior empiric antibiotic administration on the development of Multidrug Resistant Organism (MDRO) infections, and the impact of VAP on patient outcomes were studied.

Results

The average age of the patients was 60.58% were males, 70% were African-Americans and two-thirds of patients had diabetes, hypertension, or heart disease. The average Body Mass Index (BMI) was 32.9. Forty-one patients (27%) developed VAP. Patients with VAP had a significantly higher Sequential Organ Failure Assessment (SOFA) score prior to Intensive Care Unit (ICU) admission. Sixty percent received empiric antibiotics before initiation of IMV, mostly on hospital admission, and 81% received empiric antibiotics at the time of intubation. The administration of empiric antibiotics was not associated with a higher prevalence of VAP. The prevalence of VAP was 22 per 1000 days on ventilation. No difference in mortality was seen between VAP and non-VAP groups at 49% and 57% respectively (p = 0.4). VAP was associated with increased ICU length of stay (LOS), 30 vs. 16 days (p < 0.001), and longer hospital LOS 35 vs. 17 days (p < 0.001). 40% of VAPs were caused by MDROs. The most common organism was Staphylococcus aureus (28%), with almost half (48%) being methicillin resistant Staphylococcus aureus (MRSA).

Conclusion

VAP was a common complication of patients intubated for COVID-19 pneumonia. Most patients received empiric antibiotics upon the hospital and/or ICU admission. There was a 40% incidence of multidrug resistant pneumonia. Patients who developed VAP had almost twice as long hospital and ICU LOS.

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.

School Closures in the United States and Severe Respiratory Illnesses in Children: A Normalized Nationwide Sample

OBJECTIVES

To determine the association between nationwide school closures and prevalence of common admission diagnoses in the pediatric critical care unit.

DESIGN

Retrospective cohort study.

SETTING

National database evaluation using the Virtual Pediatric Systems LLC database.

PATIENTS

All patients admitted to the PICU in 81 contributing hospitals in the United States.

MEASUREMENTS AND MAIN RESULTS

Diagnosis categories were determined for all 110,418 patients admitted during the 20-week study period in each year (2018, 2019, and 2020). Admission data were normalized relative to statewide school closure dates for each patient using geographic data. The "before school closure" epoch was defined as 8 weeks prior to school closure, and the "after school closure" epoch was defined as 12 weeks following school closure. For each diagnosis, admission ratios for each study day were calculated by dividing 2020 admissions by 2018-2019 admissions. The 10 most common diagnosis categories were examined. Significant changes in admission ratios were identified for bronchiolitis, pneumonia, and asthma. These changes occurred at 2, 8, and 35 days following school closure, respectively. PICU admissions decreased by 82% for bronchiolitis, 76% for pneumonia, and 76% for asthma. Nonrespiratory diseases such as diabetic ketoacidosis, status epilepticus, traumatic injury, and poisoning/ingestion did not show significant changes following school closure.

CONCLUSIONS

School closures are associated with a dramatic reduction in the prevalence of severe respiratory disease requiring PICU admission. School closure may be an effective tool to mitigate future pandemics but should be balanced with potential academic, economic, mental health, and social consequences.

Post-COVID-19 Infection With Meticillin-Sensitive Staphylococcus aureus (MSSA) Bacteremia, Discitis/Osteomyelitis, and Diffuse Abscesses: A Case Report

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), has been associated with a plethora of symptoms weeks after the acute infection. While many reports have investigated the novel syndrome of post-acute sequelae of COVID-19, fewer studies have examined post-COVID-19 secondary infections, which may be distinct from typical post-viral bacterial infections due to the multiorgan involvement of COVID-19. This case report aims to highlight a presentation in which a 65-year-old man had COVID-19 and subsequently developed methicillin-sensitive Staphylococcus aureus (MSSA) bacteremia with widespread seeding of secondary infections, including abscesses in the hand and paravertebral regions as well as discitis/osteomyelitis of the cervical spine. Further studies are needed to investigate whether an increased susceptibility to unusual secondary bacterial infections is present in post-COVID-19 patients.

Bacterial and Fungal Coinfection in Critically Ill COVID-19 Cases and Predictive Role of Procalcitonin During the First Wave at an Academic Health Center

BACKGROUND

Coinfection at various sites can complicate the clinical course of coronavirus disease of 2019 (COVID-19) patients leading to worse prognosis and increased mortality. We aimed to investigate the occurrence of coinfection in critically ill COVID-19 cases, and the predictive role of routinely tested biomarkers on admission for mortality.

METHODS

This is a retrospective study of all SARS-CoV-2-infected cases, who were admitted to King Fahad Hospital of the University between March 2020 and December 2020. We reviewed the data in the electronic charts in the healthcare information management system including initial presentation, clinical course, radiological and laboratory findings and reported all significant microbiological cultures that indicated antimicrobial therapy. The mortality data were reviewed for severely ill patients who were admitted to critical care units.

RESULTS

Of 1091 admitted patients, there were 70 fatalities (6.4%). 182 COVID-19 persons were admitted to the critical care service, of whom 114 patients (62.6%) survived. The in-hospital mortality was 13.4%. Coinfection was noted in 67/68 non-survivors, and Gram-negative pathogens (Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumanni) represented more than 50% of the etiological agents. We noted that the serum procalcitonin on admission was higher for non-survivors (Median = 1.6 ng/mL ± 4.7) than in survivors (Median = 0.2 ng/mL ± 4.2) (p ≤ 0.05).

CONCLUSION

Coinfection is a serious complication for COVID-19 especially in the presence of co-morbidities. High levels of procalcitonin on admission may predict non-survival in critically ill cases in whom bacterial or fungal co-infection is likely.

Distinct Immunological Profiles Help in the Maintenance of Salivary Secretory IgA Production in Mild Symptoms COVID-19 Patients

BACKGROUND

Relevant aspects regarding the SARS-CoV-2 pathogenesis and the systemic immune response to this infection have been reported. However, the mucosal immune response of the upper airways two months after SARS-CoV-2 infection in patients with mild/moderate symptoms is still not completely described. Therefore, we investigated the immune/inflammatory responses of the mucosa of the upper airways of mild/moderate symptom COVID-19 patients two months after the SARS-CoV-2 infection in comparison to a control group composed of non-COVID-19 healthy individuals.

METHODS

A cohort of 80 volunteers (age 37.2 ± 8.2), including non-COVID-19 healthy individuals (n=24) and COVID-19 patients (n=56) who presented mild/moderate symptoms during a COVID-19 outbreak in Brazil in November and December of 2020. Saliva samples were obtained two months after the COVID-19 diagnosis to assess the levels of SIgA by ELISA and the cytokines by multiplex analysis.

RESULTS

Salivary levels of SIgA were detected in 39 volunteers into the COVID-19 group and, unexpectedly, in 14 volunteers in the control group. Based on this observation, we distributed the volunteers of the control group into without SIgA or with SIgA sub-groups, and COVID-19 group into without SIgA or with SIgA sub-groups. Individuals with SIgA showed higher levels of IL-10, IL-17A, IFN-γ, IL-12p70, IL-13, and IFN-α than those without SIgA. In intergroup analysis, the COVID-19 groups showed higher salivary levels of IL-10, IL-13, IL-17A, and IFN-α than the control group. No statistical differences were verified in the salivary levels of IL-6 and IFN-β. Lower IL-12p70/IL-10 and IFN-γ/IL-10 ratios were found in the control group without SIgA than the control group with SIgA and the COVID-19 group with SIgA.

CONCLUSION

We were able to present, for the first time, that associations between distinct immunological profiles can help the mucosal immunity to maintain the salivary levels of SIgA in COVID-19 patients two months after the SARS-CoV-2 infection.

Secondary Infection Risk in Patients With Severe COVID-19 Pneumonia Treated With Tocilizumab

BACKGROUND

Severe SARS-CoV-2 (COVID) pneumonia is characterized by marked inflammation. Current guidelines recommend the addition of the tocilizumab to dexamethasone in critically ill patients. In randomized trials, the use of tocilizumab was not associated with a statistically significant increased risk of secondary infections but concerns remain.

STUDY QUESTION

Do patients with severe COVID pneumonia treated with tocilizumab experienced high rates of secondary infection.

STUDY DESIGN

We performed a retrospective electronic chart review of patients with COVID pneumonia who received tocilizumab and dexamethasone (n = 62) from January 2021 to October 2021 and compared them with a cohort of patients (n = 49) who received only dexamethasone and admitted from July 2020 to December 2020 (before institutional use of tocilizumab). Patients received tocilizumab only if they had acute hypoxic respiratory failure and were felt to be clinically worsening. Patients were deemed to have a secondary infection only if a diagnosis of infection was confirmed via positive cultures.

RESULTS

Sixty-six patients received tocilizumab; of which, 30 (45.5%) subsequently had culture-positive secondary infections compared with 24.5% of controls. Thirty-one patients (47.0%) who received tocilizumab died by the time of analysis, 14 (45.2%) of whom had a secondary infection. Gram-negative bacterial infections predominated, followed by fungal infections. Patients who received tocilizumab had over twice as many gram-negative pneumonias (30.3% vs. 14.3%).

CONCLUSIONS

Patients with severe COVID pneumonia treated with tocilizumab experienced high rates of secondary infection. Although the benefit of tocilizumab in reducing mortality is well-established and almost certainly outweighs secondary infection risks, we question if the "real-world" infection rates are much higher than those reported in trials or if the infection risk could be mitigated with dose reductions in tocilizumab without losing the mortality benefit. Further study into the infection risk, and risk-benefit analysis of dose adjustments, of tocilizumab in the critical care setting is warranted.

Emergence of synergistic and competitive pathogens in a coevolutionary spreading model

Cooperation and competition between pathogens can alter the amount of individuals affected by a coinfection. Nonetheless, the evolution of the pathogens' behavior has been overlooked. Here, we consider a coevolutionary model where the simultaneous spreading is described by a two-pathogen susceptible-infected-recovered model in an either synergistic or competitive manner. At the end of each epidemic season, the pathogens species reproduce according to their fitness that, in turn, depends on the payoff accumulated during the spreading season in a hawk-and-dove game. This coevolutionary model displays a rich set of features. Specifically, the evolution of the pathogens' strategy induces abrupt transitions in the epidemic prevalence. Furthermore, we observe that the long-term dynamics results in a single, surviving pathogen species, and that the cooperative behavior of pathogens can emerge even under unfavorable conditions.

Bacterial and fungal co-infections among ICU COVID-19 hospitalized patients in a Palestinian hospital: a retrospective cross-sectional study

Background: Diagnosis of co-infections with multiple pathogens among hospitalized coronavirus disease 2019 (COVID-19) patients can be jointly challenging and essential for appropriate treatment, shortening hospital stays and preventing antimicrobial resistance. This study proposes to investigate the burden of bacterial and fungal co-infections outcomes on COVID-19 patients. It is a single center cross-sectional study of hospitalized COVID-19 patients at Beit-Jala hospital in Palestine. Methods: The study included 321 hospitalized patients admitted to the ICU between June 2020 and March 2021 aged ≥20 years, with a confirmed diagnosis of COVID-19 via reverse transcriptase-polymerase chain reaction assay conducted on a nasopharyngeal swab. The patient's information was gathered using graded data forms from electronic medical reports. Results: The diagnosis of bacterial and fungal infection was proved through the patient's clinical presentation and positive blood or sputum culture results. All cases had received empirical antimicrobial therapy before the intensive care unit (ICU) admission, and different regimens during the ICU stay. The rate of bacterial co-infection was 51.1%, mainly from gram-negative isolates ( Enterobacter species and K.pneumoniae). The rate of fungal co-infection caused by A.fumigatus was 48.9%, and the mortality rate was 8.1%. However, it is unclear if it had been attributed to SARS-CoV-2 or coincidental. Conclusions: Bacterial and fungal co-infection is common among COVID-19 patients at the ICU in Palestine, but it is not obvious if these cases are attributed to SARS-CoV-2 or coincidental, because little data is available to compare it with the rates of secondary infection in local ICU departments before the pandemic. Comprehensively, those conclusions present data supporting a conservative antibiotic administration for severely unwell COVID-19 infected patients. Our examination regarding the impacts of employing antifungals to manage COVID-19 patients can work as a successful reference for future COVID-19 therapy.

Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens

A prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, which significantly reduces the background signal and increases the sensitivity of the analysis. The use of a specialized detector makes it possible to read the signals of elongated primers directly through the transparent cover film of the reaction chamber. This solution is designed to prevent cross-contamination and is suitable for simultaneous testing of a large number of test samples. The proposed platform is able to detect the presence of several pathogens of pneumonia in a sample and has an open architecture that allows expansion of the range of pathogenic bacteria and viruses that can be detected.

Etiology of viral respiratory tract infections in hospitalized adults, and evidence of the high frequency of prehospitalization antibiotic treatment in Norway

BACKGROUND AND AIMS

Respiratory tract infections (RTIs) cause considerable morbidity and mortality in all age groups, but the epidemiology and role of several of the viral RTIs in the adult and elderly patients are still unclear, as is the extent of prehospitalization antibacterial drug use in this population.

METHODS

We conducted a three-year (2015-2018) observational study of viral RTIs in hospitalized patients in a 500-bed hospital in Southeastern Norway, including all patients ≥18 years with RTI symptoms where one of the following viral agents was detected in a respiratory specimen (Seegene Allplex): Influenza A/B, RSV A/B, human metapneumovirus (hMPV), adenovirus and parainfluenza virus 1-4. Viral findings, demographical data, and information on prehospital antibiotic prescriptions were recorded.

RESULTS

In 1182 patients 1222 viral infection events occurred. The mean patient age was 69.6 years, and 53% were females. Influenza virus A/B (63%), RSV A/B (15%) and hMPV (13%) were the most common agents detected. The proportional burden of influenza A H1 was found to be relatively high (65%) in the age groups <69 years, compared to older patients (P = .001, chi-square).As many as 20% of the patients had been treated with antibiotics prior to admission, with the lowest rate for influenza A H3 group at 17% (P = .036, chi-square), and highest for the RSV group at 28% (P = .004, chi-square).Oseltamivir was prescribed prior to hospitalization in only 3 cases (0.2%).

CONCLUSIONS

We found a high rate of prehospital antibiotic prescription in adults hospitalized with viral RTIs, warranting better stewardship programs to tackle the increasing antibiotic resistance problem.

Efficacy and Safety of Ergoferon in Children from 6 Months to 6 Years Old with Acute Respiratory Viral Infections in Contemporary Outpatient Practice: A Multicenter, Double-Blind, Placebo-Controlled Randomized Trial

To evaluate the efficacy and safety of Ergoferon in combination with symptomatic therapy in children from 6 months to 6 years old with acute respiratory infections (ARI) in contemporary outpatient practice, an international, multicenter, double-blind, placebo-controlled, randomized, parallel-group clinical trial was performed. Derived by technological treatment of antibodies to interferon gamma, histamine, and CD4, Ergoferon was previously proved to modulate its molecular targets promoting effective antiviral protection. The data of 282 patients with oral temperature ≥38.0°C plus mild to moderate severity of flu-like nonspecific and nasal/throat/chest symptoms were included in intention-to-treat analysis (n = 140, Ergoferon group; n = 142, placebo group). Time to alleviation of all ARI symptoms was the primary endpoint, and 8 outcome measures were estimated as the secondary endpoints. Respiratory viruses were confirmed in 57.1% (Ergoferon) and 54.9% (Placebo) of patients. Compared to placebo, Ergoferon reduced time to alleviation of all ARI symptoms (4.5 ± 1.7 versus 5.2 ± 2.2 days in placebo; p=0.026) including fever (2.8 ± 1.5 vs 3.4 ± 2.0; p=0.031), flu-like nonspecific (4.0 ± 1.8 vs 4.7 ± 2.2, p=0.022), and nasal/throat/chest (4.3 ± 2.0 versus 5.0 ± 2.3; p=0.024) symptoms. Ergoferon add-on therapy decreased the mean total symptom severity score (according to 4-point scale for each symptom), ARI severity, frequency of antipyretic use, and percentage of complication requiring antibiotics and increased the percentage of recovered patients. The incidence of adverse events (AEs) in the Ergoferon group was significantly lower compared to the placebo group (7.0% versus 18.8%; p=0.004) including infectious diseases (3.5% vs 12.5%; p=0.008). In the Ergoferon group, AEs were mild or moderate. In 8 (57.1%) cases, AEs were unrelated to Ergoferon, in 5 (35.7%), the relationship was uncertain, and in 1 (7.1%), it was possible (mild rash on the face). Ergoferon treatment is beneficial for infants and young children with ARI in contemporary outpatient practice. Being well-tolerated, Ergoferon increases the symptomatic therapy effectiveness and improves the patient condition and disease outcomes.

The impact of human vaccines on bacterial antimicrobial resistance. A review

At present, the dramatic rise in antimicrobial resistance (AMR) among important human bacterial pathogens is reaching a state of global crisis threatening a return to the pre-antibiotic era. AMR, already a significant burden on public health and economies, is anticipated to grow even more severe in the coming decades. Several licensed vaccines, targeting both bacterial (Haemophilus influenzae type b, Streptococcus pneumoniae, Salmonella enterica serovar Typhi) and viral (influenza virus, rotavirus) human pathogens, have already proven their anti-AMR benefits by reducing unwarranted antibiotic consumption and antibiotic-resistant bacterial strains and by promoting herd immunity. A number of new investigational vaccines, with a potential to reduce the spread of multidrug-resistant bacterial pathogens, are also in various stages of clinical development. Nevertheless, vaccines as a tool to combat AMR remain underappreciated and unfortunately underutilized. Global mobilization of public health and industry resources is key to maximizing the use of licensed vaccines, and the development of new prophylactic vaccines could have a profound impact on reducing AMR.

Leonurine protects against influenza A virus infection-induced pneumonia in mice

Influenza A virus (H1N1), a swine-origin influenza A virus, causes seasonal epidemics that result in severe illnesses and deaths. Leonurine has been reported to function as an anti-inflammatory agent with protective effects on nervous, urinary and cardiovascular systems. However, the therapeutic effects of leonurine on the pneumonia caused by H1N1 infection remain unclear. Hematoxylin and eosin staining was performed to evaluate the lung injuries of mice infected by H1N1. The amount of immune cells was analyzed by flow cytometry. Enzyme-linked immunosorbent assay was used to evaluate the alteration of multiple cytokines in lung tissues. Real-time quantitative polymerase chain reaction assay was performed to investigate the ribonucleic acid (RNA) levels of certain genes. The protein levels in toll-like receptor 4/nuclear factor kappa-light-chain-enhancer of activated B cells (TLR4/NF-κB) signaling were estimated by western blot assay. Leonurine treatment significantly inhibited the mortality caused by H1N1 infection. Leonurine treatment (60 mg/kg) alleviated the lung injuries caused by virus infection. The inflammatory cell accumulation and cytokine expression were inhibited by the leonurine administration. Leonurine inhibited the mRNA expression of pro-inflammatory cytokines in the lung homogenates at day 5 postinfection. Leonurine regulated the TLR4/NF-κB signaling in the lung homogenates of H1N1-infected mice at day 5 postinfection. Leonurine protects against H1N1 infection-induced pneumonia in mice.

Inhaled Corticosteroids Use and Risk of Invasive Pneumococcal Disease in a Population-based Study

Rationale: The use of inhaled corticosteroids (ICS) is associated with increased pneumonia risk, but the risk of invasive pneumococcal disease (IPD) associated with ICS is not characterized.

Objectives: The aim was to test the hypothesis that the use of ICS increases the risk of IPD.

Methods: Cases were persons 20–65 years of age included in a Swedish national registry of invasive infection caused by Streptococcus pneumoniae classified as any IPD as well as the subset of IPD with pneumonia. The case index date was the day the infection was diagnosed. Six control subjects for each case (matched for sex, age, and region) were selected from the Swedish National Population Registry and were assigned the index date of their corresponding case. Current and past users of ICS were defined by the last prescriptions dispensed within 60 or 61–365 days of the index date. Nonusers were defined as those with no dispensed prescription the last 365 days. Current users were characterized by use of fluticasone or budesonide. We used conditional logistic analysis, including matching and covariates, to estimate the odds ratios (ORs) and 95% confidence intervals (CIs) of IPD, IPD with pneumonia, and IPD without pneumonia associated with current or past use of ICS.

Results: Current use of ICS increased the risk for IPD and IPD with pneumonia (OR, 1.71; 95% CI, 1.39–2.10 and OR, 1.94; 95% CI, 1.53–2.47, respectively), but there was no statistical association between current use of ICS and IPD without pneumonia (OR, 1.18; 95% CI 0.78–1.80). Past use of ICS increased the risk for IPD and IPD with pneumonia but not for IPD without pneumonia. Among current ICS users, the odds for IPD were similar for budesonide (OR, 1.34; 95% CI, 1.14–1.57) and fluticasone (OR, 1.41; 95% CI, 1.04–1.90). Among current ICS users, the odds for IPD with pneumonia were slightly higher but of similar magnitude for both budesonide and for fluticasone.

Conclusions: ICS use is associated with an increased risk of IPD and IPD with pneumonia. The risk is driven by IPD with pneumonia. We found similar risks for budesonide and fluticasone.

Impacts of Pharmacy Intervention on Appropriateness of Antibiotics Use in Pneumonia Patients

AIM: This study analyzed the impact of pharmacy intervention on appropriateness of antibiotics use in the treatment of inpatients with pneumonia admitted to Universitas Sumatera Utara (USU) Hospital, Medan, Indonesia. METHODS: This cohort study analyzed appropriateness of antibiotic use in the treatment of in-patients with pneumonia without interventions or baseline group (n = 33) admitted to USU Hospital year 2018 and 3-month period admission with pharmacy intervention (n = 42) year 2019. Characteristics of the patients and antibiotics provided to both groups were descriptively analyzed. The appropriateness of antibiotics use in both groups was analyzed based on their medical conditions, culture and sensitivity tests, and trustable literatures, and then categorized applying Gyssens method regarding dose, intervals, routes, length of provision, effectivity, and costs. The significant difference in inappropriate use of antibiotics between groups with and without interventions was analyzed applying unpaired t-test (p < 0.05 was considered statistically significant). RESULTS: Most of the pneumonia patients in both groups were male. Mean age of the patients (years) in group: without intervention, 60.20 ± 15.48; with intervention, 60.48 ± 14.76. The three most widely provided antibiotics were ceftriaxone, meropenem, and ciprofloxacin. Incidence of inappropriate use of antibiotics per patient in group: without intervention, 0.66; with intervention, 0.33. The inappropriate use of antibiotics reduced significantly in group with intervention, p = 0.049. CONCLUSIONS: Pharmacy intervention is crucial to reduce the inappropriate use of antibiotics in the treatment of pneumonia.

Evodiamine Enhanced the Anti-Inflammation Effect of Clindamycin in the BEAS-2B Cells Infected with H5N1 and Pneumoniae D39 Through CREB-C/EBPβ Signaling Pathway

Pneumonia is a pulmonary disease among children. Evodiamine, a traditional Chinese medicine, is known for anti-inflammatory effect. This study aimed to investigate the impact of evodiamine on severe pneumonia-like cells and the underlying mechanism involved. H5N1 and pneumoniae D39 was used to induce severe pneumonia-like conditions in BEAS-2B cells. The cell viability in BEAS-2B cells after treatments with 0, 20, 40, 60, 80, and 100 μM evodiamine was examined using MTT assays. The protein concentrations of inflammatory cytokines tumor necrosis factor (TNF)-α, interleukin (IL)-6 and IL-1β, and Toll-like receptors (TLRs) were measured by enzyme-linked immunosorbent assay methods and the protein and mRNA changes in C/EBPβ/CREB were measured using Real Time-quantitative polymerase chain reaction and Western blot methods. Our results revealed that Evodiamine significantly decreased TNF-α, IL-6, and IL-1β in BEAS-2B cells. Moreover, evodiamine markedly reduced TLR2,3,4 protein expression and the phosphorylated protein of C/EBPβ and CREB. Besides, evodiamine combined with clindamycin exerted more significant effects than clindamycin alone. Taken together, our results demonstrated that evodiamine enhanced the anti-inflammation effect of clindamycin in the BEAS-2B cells infected with H5N1 and pneumoniae D39 through CREB-C/EBPβ signaling pathway.

Regulation and Function of ILC3s in Pulmonary Infections

Lower respiratory infections are among the leading causes of morbidity and mortality worldwide. These potentially deadly infections are further exacerbated due to the growing incidence of antimicrobial resistance. To combat these infections there is a need to better understand immune mechanisms that promote microbial clearance. This need in the context of lung infections has been further heightened with the emergence of SARS-CoV-2. Group 3 innate lymphoid cells (ILC3s) are a recently discovered tissue resident innate immune cell found at mucosal sites that respond rapidly in the event of an infection. ILC3s have clear roles in regulating mucosal immunity and tissue homeostasis in the intestine, though the immunological functions in lungs remain unclear. It has been demonstrated in both viral and bacterial pneumonia that stimulated ILC3s secrete the cytokines IL-17 and IL-22 to promote both microbial clearance as well as tissue repair. In this review, we will evaluate regulation of ILC3s during inflammation and discuss recent studies that examine ILC3 function in the context of both bacterial and viral pulmonary infections.

A brief review of influenza virus infection

Influenza is an acute viral respiratory infection that affects all age groups and is associated with high mortality during pandemics, epidemics, and sporadic outbreaks. Nearly 10% of the world's population is affected by influenza annually, with about half a million deaths each year. Influenza vaccination is the most effective method for preventing influenza infection and its complications. The influenza vaccine's efficacy varies each season based on the circulating influenza strains and vaccine uptake rates. Currently, three antiviral drugs targeting the influenza virus surface glycoprotein neuraminidase are available for treatment and prophylaxis of disease. Given the significant burden of influenza infection globally, this review is focused on the latest findings in the etiology, epidemiology, transmission, clinical manifestation, diagnosis, prevention, and treatment of influenza.

Hospitalization of mild cases of community-acquired pneumonia decreased more than severe cases during the COVID-19 pandemic

OBJECTIVE

The coronavirus disease 2019 (COVID-19) pandemic has affected all healthcare systems. This study aimed to assess the impact of the COVID-19 pandemic on the number and severity of cases of community-acquired pneumonia (CAP) in Japan.

METHODS

Using claims data from the Quality Indicator/Improvement Project (QIP) database, urgent cases of inpatients for CAP from 01 August 2018 to 30 July 2020 were included. The monthly ratios of inpatient cases were compared from August 2018 to July 2019 and August 2019 to July 2020 as a year-over-year comparison. These ratios were also compared according to the "A-DROP" severity score, and an interrupted time series (ITS) analysis was performed to evaluate the impact of the COVID-19 pandemic on the monthly number of inpatient cases.

RESULTS

This study included a total of 67,900 inpatient cases for CAP in 262 hospitals. During the COVID-19 pandemic (defined as the period between March and July 2020) the number of inpatient cases for CAP drastically decreased compared with the same period in the previous year (-48.1%), despite a temporary reduction in the number of other urgent admissions. The number of inpatient cases decreased according to the severity of pneumonia. Milder cases showed a greater decrease in the year-over-year ratio than severe ones: mild -55.2%, moderate -45.8%, severe -39.4%, and extremely severe -33.2%. The ITS analysis showed that the COVID-19 pandemic significantly reduced the monthly number of inpatient cases for CAP (estimated decrease: -1233 cases; 95% CI -521 to -1955).

CONCLUSIONS

This study showed a significant reduction in the number of inpatient cases for CAP during the COVID-19 pandemic in Japan. The milder cases showed a greater decrease in the year-over-year ratio of the number of inpatient cases.

Bacterial infections and patterns of antibiotic use in patients with COVID-19

Bacterial coinfection is associated with poor outcomes in patients with viral pneumonia, but data on its role in the mortality of patients with coronavirus disease 2019 (COVID-19) is limited. This is a single-center retrospective analysis of 242 patients with confirmed COVID-19 admitted to both intensive care and non-intensive care settings. Bacterial coinfection was determined by the presence of characteristic clinical features and positive culture results. Multivariable logistic regression was used to analyze the association of concomitant bacterial infection with inpatient death after adjusting for demographic factors and comorbidities. Antibiotic use pattern was also determined. Bacterial coinfection was detected in 46 (19%) patients. Genitourinary source was the most frequent, representing 57% of all coinfections. The overall mortality rate was 21%. Concomitant bacterial infections were independently associated with increased inpatient mortality (OR, 5.838; 95% CI, 2.647-12.876). Patients with bacterial coinfection were relatively older (71.35 ± 11.20 vs 64.78 ± 15.23; P = .006). A total of 67% of patients received antibiotic therapy, yet 72% did not have an obvious source of bacterial infection. There was a significantly higher rate of inpatient mortality in patients who received antibiotics compared to those who did not (30% vs 5%; P < .0001). Bacterial coinfection in COVID-19 is associated with increased mortality.

COVID-19 pandemic and the incidence of community-acquired pneumonia in elderly people

The impact of the COVID-19 pandemic on the incidence of community-acquired pneumonia in elderly people remains uncertain. We compared the number of elderly patients admitted to our hospital for community-acquired pneumonia from January to June 2020 to the numbers from the same period in each of the last three years. The number of patients began decreasing in February 2020, and by April 2020 the number was significantly lower than those from the same period in the three years prior. There is no evidence regarding the impact of general infection control measures, such as wearing a face mask or washing one's hands, on the development of community-acquired pneumonia, because causative bacteria are not believed to be transmitted from human to human. However, these measures might have indirectly contributed to a decreased number of cases through the prevention of common viral infections which could be a trigger of community-acquired pneumonia.

Respiratory Microbial Co-infection With SARS-CoV-2

Co-infection with additional pathogens is a well-known feature of pandemics. We determined the prevalence and type of a wide variety of respiratory pathogens in 12,075 United States subjects tested for SARS-CoV-2 infection in March and April 2020. Infections with other respiratory pathogens, which on their own produce at least some SARS-CoV-2 symptoms including mortality, were present in both SARS-CoV-2 + and SARS-CoV-2- subjects. Non-SARS-CoV-2 infection rates were significantly higher in SARS-CoV-2 + (86%) patients than SARS-CoV-2– patients (76%) (p < 0.0001). Among the co-pathogens present in both subject groups were K. pneumoniae and M. catarrhalis which can produce serious respiratory illness on their own, Advanced age and nursing home status were associated with higher SARS-CoV-2 + and co-infection rates. Testing for the presence of co-pathogens going forward will assist in the diagnosis and optimal treatment of suspected SARS-CoV-2 respiratory infections in the current pandemic.

Alcohol Use Disorders Are Associated With a Unique Impact on Airway Epithelial Cell Gene Expression

BACKGROUND

Alcohol use disorders (AUDs) and cigarette smoking both increase risk for the development of community-acquired pneumonia (CAP), likely through adverse effects on proximal airway mucociliary clearance and pathogen recognition. Smoking-related alterations on airway gene expression are well described, but little is known about the impact of AUDs. We measured gene expression in human airway epithelial cells (AECs), hypothesizing that AUDs would be associated with novel differences in gene expression that could alter risk for CAP.

METHODS

Bronchoscopy with airway brushings was performed in participants with AUDs and controls to obtain AECs. An AUD Identification Test was used to define AUD. RNA was extracted from AECs, and mRNA expression data were collected on an Agilent micro-array. Differential expression analyses were performed on the filtered and normalized data with correction for multiple testing. Enrichment analyses were performed using clusterProfiler.

RESULTS

Expression data from 19 control and 18 AUD participants were evaluated. After adjustment for smoking, AUDs were associated with significant differential expression of 520 AEC genes, including genes for ribosomal proteins and genes involved in protein folding. Enrichment analyses indicated significant differential expression of 24 pathways in AUDs, including those implicated in protein targeting to membrane and viral gene expression. Smoking-associated AEC gene expression differences mirrored previous reports, but differed from those associated with AUDs.

CONCLUSIONS

AUDs have a distinct impact on AEC gene expression that may influence proximal airway function independent of smoking. Alcohol-associated alterations may influence risk for CAP through modifying key mechanisms important in protecting proximal airway integrity.

Impact of the 10-valent pneumococcal conjugate vaccine on hospital admissions in children under three years of age in Iceland

INTRODUCTION

Pneumococcus is an important respiratory pathogen. The 10-valent pneumococcal vaccine (PHiD-CV) was introduced into the Icelandic vaccination programme in 2011. The aim was to estimate the impact of PHiD-CV on paediatric hospitalisations for respiratory tract infections and invasive disease.

METHODS

The 2005-2015 birth-cohorts were followed until three years of age and hospitalisations were recorded for invasive pneumococcal disease (IPD), meningitis, sepsis, pneumonia and otitis media. Hospitalisations for upper- and lower respiratory tract infections (URTI, LRTI) were used as comparators. The 2005-2010 birth-cohorts were defined as vaccine non-eligible cohorts (VNEC) and 2011-2015 birth-cohorts as vaccine eligible cohorts (VEC). Incidence rates (IR) were estimated for diagnoses, birth-cohorts and age groups, and incidence rate ratios (IRR) between VNEC and VEC were calculated assuming Poisson variance. Cox regression was used to estimate the hazard ratio (HR) of hospitalisation between VNEC and VEC.

RESULTS

51,264 children were followed for 142,315 person-years, accumulating 1,703 hospitalisations for the respective study diagnoses. Hospitalisations for pneumonia decreased by 20% (HR 0.80, 95%CI:0.67-0.95) despite a 32% increase in admissions for LRTI (HR 1.32, 95%CI:1.14-1.53). Hospital admissions for culture-confirmed IPD decreased by 93% (HR 0.07, 95%CI:0.01-0.50) and no hospitalisations for IPD with vaccine-type pneumococci were observed in the VEC. Hospitalisations for meningitis and sepsis did not change. A decrease in hospital admissions for otitis media was observed, but did not coincide with PHiD-CV introduction.

CONCLUSION

Following the introduction of PHiD-CV in Iceland, hospitalisations for pneumonia and culture confirmed IPD decreased. Admissions for other LRTIs and URTIs increased during this period.

Alcohol potentiates RSV-mediated injury to ciliated airway epithelium

Alcohol impairs resolution of respiratory viral infections. Numerous immune response pathways are altered in response to alcohol misuse, including alcohol-induced ciliary dysfunction in the lung. We hypothesized that mucociliary clearance-mediated innate immunity to respiratory syncytial virus (RSV) would be compromised by alcohol exposure. Cilia were assayed using Sisson-Ammons Video Analysis by quantitating the average number of motile points in multiple whole field measurements of mouse tracheal epithelial cells grown on an air-liquid interface. Pretreatment with ethanol alone (100 mM for 24 hours) had no effect on the number of motile cilia. A single dose (TCID50 1 × 105) of RSV resulted in a significant (p < 0.05) decrease in motile cilia after 2 days. Ethanol pretreatment significantly (p < 0.05) potentiated RSV-induced cilia loss by 2 days. Combined RSV and ethanol treatment led to a sustained activation-induced auto-downregulation of PKC epsilon (PKCε). Ethanol-induced enhancement of ciliated cell detachment was confirmed by dynein ELISA and LDH activity from the supernates. RSV-induced cilia loss was evident until 7 days, when RSV-only infected cells demonstrated no significant cilia loss vs. control cells. However, cells pretreated with ethanol showed significant cilia loss until 10 days post-RSV infection. To address the functional significance of ethanol-enhanced cilia detachment, mice fed alcohol ad libitum (20% for 12 weeks) were infected once with RSV, and clearance was measured by plaque-forming assay from lung homogenates for up to 7 days. After 3 days, RSV plaque formation was no longer detected from the lungs of control mice, while significant (p < 0.01) RSV plaque-forming units were detected at 7 days in alcohol-fed mice. Alcohol-fed mice demonstrated enhanced cilia loss and delayed cilia recovery from tracheal measurements in wild-type C57BL/6 mice, but not PKCε KO mice. These data suggest that alcohol worsens RSV-mediated injury to ciliated epithelium in a PKCε-dependent manner.

Human metapneumovirus as cause of severe community-acquired pneumonia in adults: insights from a ten-year molecular and epidemiological analysis

Background

Information on the clinical, epidemiological and molecular characterization of human metapneumovirus in critically ill adult patients with severe community-acquired pneumonia (CAP) and the role of biomarkers identifying bacterial coinfection is scarce.

Methods

This is a retrospective epidemiological study of adult patients with hMPV severe CAP admitted to ICU during a ten-year period with admission PSI score ≥ 3.

Results

The 92.8% of the 28 patients with severe CAP due to human metapneumovirus were detected during the first half of the year. Median age was 62 years and 60.7% were male. The genotyping of isolated human metapneumovirus showed group B predominance (60.7%). All patients had acute respiratory failure. Median APACHE II and SOFA score were 13 and 6.55, respectively. The 25% were coinfected with Streptococcus pneumoniae. 60.7% of the patients had shock at admission and 50% underwent mechanical ventilation. Seven patients developed ARDS, three of them younger than 60 years and without comorbidities. Mortality in ICU was 14.3%. Among survivors, ICU and hospital stay were 6.5 and 14 days, respectively. Plasma levels of procalcitonin were higher in patients with bacterial coinfection (18.2 vs 0.54; p < 0.05). The levels of C-reactive protein, however, were similar.

Conclusion

Human metapneumovirus was associated with severe CAP requiring ICU admission among elderly patients or patients with comorbidities, but also in healthy young subjects. These patients often underwent mechanical ventilation with elevated health resource consumption. While one out of four patients showed pneumococcal coinfection, plasma procalcitonin helped to implement antimicrobial stewardship.

Electronic supplementary material

The online version of this article (10.1186/s13613-019-0559-y) contains supplementary material, which is available to authorized users.

Personalizing the Management of Pneumonia

Pneumonia is a highly prevalent disease with considerable morbidity and mortality. However, diagnosis and therapy still rely on antiquated methods, leading to the vast overuse of antimicrobials, which carries risks for both society and the individual. Furthermore, outcomes in severe pneumonia remain poor. Genomic techniques have the potential to transform the management of pneumonia through deep characterization of pathogens as well as the host response to infection. This characterization will enable the delivery of selective antimicrobials and immunomodulatory therapy that will help to offset the disorder associated with overexuberant immune responses.

Epidemiology and molecular characterization of influenza viruses in Burkina Faso, sub-Saharan Africa

Background

The importance of influenza viruses in respiratory infections in sub‐Saharan Africa has been historically overlooked, including in Burkina Faso.

Objectives

This study therefore aimed at evaluating the prevalence and seasonal occurrence of influenza viruses in children under 5 years old, at risk of influenza‐related complications, presenting with influenza‐like illness (ILI) or severe acute respiratory infection (SARI). The study also aimed at identifying the periods with increased influenza transmission for vaccination recommendations in Burkina Faso.

Methods

From January 2014 to December 2015, ILI and SARI (2015 only) patients were recruited in six healthcare centers in Burkina Faso. Influenza A and B molecular detection and subtyping were performed. Clade clustering of a subset of A(H1N1)pdm09 and A(H3N2) strains was deduced by performing phylogenetic analyses on hemagglutinin gene sequences. Weekly surveillance data from FluNet (2011‐2013; 2016) and this study (2014‐2015) were used to identify periods of increased influenza activity.

Results

Influenza A and B viruses were detected in 15.1% (112 of 743) of ILI and 6.6% (12 of 181) of SARI patients. Overall, influenza A viruses were largely predominant (81 of 124, 65.3%), with 69.1% of A(H3N2) and 30.9% of A(H1N1)pdm09 strains. Four waves of increased transmission were identified in 2014‐2015, each dominated by different influenza subtypes and clades. Between 2011 and 2016, periods of increased influenza activity varied in their frequency, duration, and timing.

Conclusion

Influenza A and B viruses were detected in a substantial number of ILI and SARI cases in Burkina Faso. Vaccination in September‐October would likely protect the highest number of patients.