Systematic review of respiratory viral pathogens identified in adults with community-acquired pneumonia in Europe

Decoding viral and host microRNA signatures in airway-derived biosamples: Insights for biomarker discovery in viral respiratory infections

The global public health crisis caused by the COVID-19 pandemic has intensified the global concern regarding viral respiratory tract infections. Despite their considerable impact on health, society and the economy, effective management of these conditions remains a significant challenge. Integrating high-throughput analyses is pivotal for early detection, prognostication of adverse outcomes, elucidating pathogenetic pathways and developing therapeutic approaches. In recent years, microRNAs (miRNAs), a subset of small noncoding RNAs (ncRNAs), have emerged as promising tools for molecular phenotyping. Current evidence suggests that miRNAs could serve as innovative biological markers, aiding in informed medical decision-making. The cost-effective quantification of miRNAs in standardized samples using techniques routinely employed in clinical laboratories has become feasible. In this context, samples obtained from the airways represent a valuable source of information due to their direct exposure to the infectious agent and host response within the respiratory tract. This review explores viral and host miRNA profiling in airway-derived biosamples as a source of molecular information to guide patient management, with a specific emphasis on SARS-CoV-2 infection.

Microbiota and Immunity during Respiratory Infections: Lung and Gut Affair

Bacterial and viral respiratory tract infections are the most common infectious diseases, leading to worldwide morbidity and mortality. In the past 10 years, the importance of lung microbiota emerged in the context of pulmonary diseases, although the mechanisms by which it impacts the intestinal environment have not yet been fully identified. On the contrary, gut microbial dysbiosis is associated with disease etiology or/and development in the lung. In this review, we present an overview of the lung microbiome modifications occurring during respiratory infections, namely, reduced community diversity and increased microbial burden, and of the downstream consequences on host-pathogen interaction, inflammatory signals, and cytokines production, in turn affecting the disease progression and outcome. Particularly, we focus on the role of the gut-lung bidirectional communication in shaping inflammation and immunity in this context, resuming both animal and human studies. Moreover, we discuss the challenges and possibilities related to novel microbial-based (probiotics and dietary supplementation) and microbial-targeted therapies (antibacterial monoclonal antibodies and bacteriophages), aimed to remodel the composition of resident microbial communities and restore health. Finally, we propose an outlook of some relevant questions in the field to be answered with future research, which may have translational relevance for the prevention and control of respiratory infections.

Burden of Respiratory Syncytial Virus-Associated Acute Respiratory Infections During Pregnancy

BACKGROUND

With the licensure of maternal respiratory syncytial virus (RSV) vaccines in Europe and the United States, data are needed to better characterize the burden of RSV-associated acute respiratory infections (ARI) in pregnancy. The current study aimed to determine among pregnant individuals the proportion of ARI testing positive for RSV and the RSV incidence rate, RSV-associated hospitalizations, deaths, and perinatal outcomes.

METHODS

We conducted a systematic review, following PRISMA 2020 guidelines, using 5 databases (Medline, Embase, Global Health, Web of Science, and Global Index Medicus), and including additional unpublished data. Pregnant individuals with ARI who had respiratory samples tested for RSV were included. We used a random-effects meta-analysis to generate overall proportions and rate estimates across studies.

RESULTS

Eleven studies with pregnant individuals recruited between 2010 and 2022 were identified, most of which recruited pregnant individuals in community, inpatient and outpatient settings. Among 8126 pregnant individuals, the proportion with ARI that tested positive for RSV ranged from 0.9% to 10.7%, with a meta-estimate of 3.4% (95% confidence interval [CI], 1.9%-54%). The pooled incidence rate of RSV among pregnant individuals was 26.0 (95% CI, 15.8-36.2) per 1000 person-years. RSV hospitalization rates reported in 2 studies were 2.4 and 3.0 per 1000 person-years. In 5 studies that ascertained RSV-associated deaths among 4708 pregnant individuals, no deaths were reported. Three studies comparing RSV-positive and RSV-negative pregnant individuals found no difference in the odds of miscarriage, stillbirth, low birth weight, and small size for gestational age. RSV-positive pregnant individuals had higher odds of preterm delivery (odds ratio, 3.6 [95% CI, 1.3-10.3]).

CONCLUSIONS

Data on RSV-associated hospitalization rates are limited, but available estimates are lower than those reported in older adults and young children. As countries debate whether to include RSV vaccines in maternal vaccination programs, which are primarily intended to protect infants, this information could be useful in shaping vaccine policy decisions.

Patterns and predictors of positive multiplex polymerase chain reaction respiratory panel among patients with acute respiratory infections in a single center in Lebanon

BACKGROUND

Infectious agents associated with community-acquired acute respiratory infections (ARIs) remain understudied in Lebanon. We aim to assess the microbiological profiles of ARIs by employing polymerase chain reaction (PCR) and identifying predictors of positive PCR results among patients admitted for ARI.

METHODS AND RESULTS

We conducted a retrospective single-center study at the American University of Beirut Medical Center, including all respiratory PCR panels performed on pediatric (< 18) and adult (≥ 18) patients presenting with an ARI from January 2015 to March 2018, prior to the onset of the COVID-19 pandemic. We aimed to identify the epidemiological patterns of ARIs and the factors associated with positive PCRs in both adult and pediatric patients. Among 281 respiratory PCRs, 168 (59.7%) were positive for at least one pathogen, with 54.1% positive PCR for viruses, 7.8% for bacteria species, and 3.9% with virus-bacteria codetection. Almost 60% of the patients received antibiotics prior to PCR testing. PCR panels yielded more positive results in pediatric patients than in adults (P = 0.005). Bacterial detection was more common in adults compared to pediatrics (P < 0.001). The most common organism recovered in the entire population was Human Rhinovirus (RhV) (18.5%). Patients with pleural effusion on chest CT were less likely to have a positive PCR (95% Cl: 0.22-0.99). On multivariate analysis, pediatric age group (P < 0.001), stem cell transplant (P = 0.006), fever (P = 0.03) and UTRI symptoms (P = 0.004) were all predictive of a positive viral PCR.

CONCLUSION

Understanding the local epidemiology of ARI is crucial for proper antimicrobial stewardship. The identification of factors associated with positive respiratory PCR enhances our understanding of clinical characteristics and potential predictors of viral detection in our population.

Effectiveness of Influenza Vaccination and Early Antiviral Treatment in Reducing Pneumonia Risk in Severe Influenza Cases

INTRODUCTION

Influenza vaccination may be effective in preventing influenza infection and may reduce the risk of influenza-associated pneumonia. The study aim was to evaluate the effect of influenza vaccination in preventing pneumonia when it failed to prevent influenza hospitalization.

METHODS

This was a case-control study comparing hospitalized cases of influenza with and without pneumonia in patients aged ≥18 years in 16 hospitals in Catalonia over 10 influenza seasons (2010-11 to 2019-20). Data on sociodemographic, virological characteristics, comorbidities, vaccination history, and antiviral treatment were collected and analysed. The crude odds ratio (OR) and adjusted OR (aOR) with the corresponding 95% confidence interval (CI) values were calculated.

RESULTS

In total, 5080 patients hospitalized for severe influenza were included, 63.5% (3224/5080) of whom had pneumonia-mostly men (56.8%; 1830/3224) and mostly in the ≥75 age group (39.3%; 1267/3224)-and of whom 14.0% died (451/3224). Virus A and virus B accounted for 78.1% (2518/3224) and 21.9% (705/3224) of influenza types, respectively. Starting antiviral treatment ≤48 h after symptom onset (aOR = 0.69; 95%CI: 0.53-0.90) and a history of seasonal influenza vaccination (aOR = 0.85; 95%CI: 0.72-0.98) were protective factors in developing pneumonia.

CONCLUSIONS

Adherence to seasonal influenza vaccination and starting antiviral treatment within 48 h of symptom onset can reduce pneumonia risk in severe influenza cases.

Adult vaccination against respiratory infections in Egypt: a review of expert opinions

INTRODUCTION

Lower respiratory tract infection is one of the leading causes of morbidity and mortality all over the world, with a substantial impact on healthcare costs. In Egypt, local consensus on its burden, diagnosis, and vaccination is scarce. This expert opinion is the first to address the local recommendations for vaccinating adults against respiratory infection. It sheds light on the growing need to understand the barriers and underpublicized concept of adult vaccination in Egypt.

AREAS COVERED

A collaborative multidisciplinary panel from Egypt developed an expert opinion-based suggestions/points, including epidemiology, microbiology, and highlights on vaccination in Egypt, as well as challenges and recommendations regarding adult vaccination.

EXPERT OPINION

Adult vaccinations against respiratory infections are now recommended for high-risk people by all healthcare regulatory bodies. However, it was acknowledged that there may be hesitancy and concerns among patients; in addition, healthcare professionals' awareness about vaccination guidelines and benefits needs improvement. There are several strategies that could be implemented to enhance vaccine adherence in Egypt. These approaches encompass conducting community education programs, addressing the concerns of patients, and enhancing awareness among healthcare professionals through education, policy changes, and periodical reminders in each healthcare setting.

Severe Parainfluenza Viral Infection-A Retrospective Study of Adult Intensive Care Patients

There is little known about parainfluenza virus (PIV) infection in adult intensive care unit (ICU) patients. Here, we aim to describe the characteristics, clinical course and outcomes of PIV infection in adults requiring intensive care. In this retrospective study of consecutive patients admitted to our ICU with confirmed PIV infection over a 7-year period, we report the patient characteristics, laboratory tests and prognostic scores on ICU admission. The main outcomes reported are 30-day mortality and organ support required. We included 50 patients (52% male, mean age 67.6 years). The mean PaO2/FiO2 and neutrophil/lymphocyte ratios on ICU admission were 198 ± 82 mmHg and 15.7 ± 12.5. Overall, 98% of patients required respiratory support and 24% required cardiovascular support. The median length of ICU stay was 5.9 days (IQR 3.7-9.1) with a 30-day mortality of 40%. In conclusion, PIV infection in adult ICU patients is associated with significant mortality and morbidity. There were significant differences between patients who presented with primary hypoxemic respiratory failure and hypercapnic respiratory failure.

A high α1-antitrypsin/interleukin-10 ratio predicts bacterial pneumonia in adults with community-acquired pneumonia: a prospective cohort study

BACKGROUND

Current microbiological tests fail to identify the causative microorganism in more than half of all pneumonia cases. We explored biomarkers that could be used for differentiating between bacterial and viral pneumonia in patients with community-acquired pneumonia (CAP).

METHODS

In this prospective cohort study conducted in Japan, data obtained from adult patients with bacterial pneumonia, including bacterial and viral coinfections (bacterial pneumonia [BP] group), and purely viral pneumonia (VP group) at diagnosis were analyzed using multivariate logistic regression analysis to identify predictors of bacterial pneumonia. Furthermore, a decision tree was developed using the predictors.

RESULTS

A total of 210 patients were analyzed. The BP and VP groups comprised 108 and 18 patients, respectively. The other 84 patients had no identified causative microorganism. The two groups shared similar characteristics, including disease severity; however, a significant difference (p < 0.05) was observed between the two groups regarding sputum type; sputum volume score; neutrophil counts; and serum levels of interleukin (IL)-8, IL-10, and α1-antitrypsin (AAT). Sputum volume score (p < 0.001), IL-10 (p < 0.001), and AAT (p = 0.008) were ultimately identified as predictors of BP. The area under the curve for these three variables on the receiver operating characteristic (ROC) curve was 0.927 (95% confidence interval [CI]: 0.881-0.974). The ROC curve for sputum volume score and an AAT/IL-10 ratio showed a diagnostic cutoff of 1 + and 65, respectively. Logistic regression analysis using dichotomized variables at the cutoff values showed that the odds ratios for the diagnosis of BP were 10.4 (95% CI: 2.2-50.2) for sputum volume score (absence vs. presence) and 19.8 (95% CI: 4.7-83.2) for AAT/IL-10 ratio (< 65 vs. ≥ 65).

CONCLUSIONS

Considering that obtaining a definitive etiologic diagnosis with the current testing methods is difficult and time consuming, a decision tree with two predictors, namely sputum volume and the AAT/IL-10 ratio, can be useful in predicting BP among patients diagnosed with CAP and facilitating the appropriate use of antibiotics.

TRIAL REGISTRATION

UMIN000034673 registered on November 29, 2018.

Prognosis of critically ill immunocompromised patients with virus-detected acute respiratory failure

BACKGROUND

Acute respiratory failure (ARF) is the leading cause of ICU admission. Viruses are increasingly recognized as a cause of pneumonia in immunocompromised patients, but epidemiologic data are scarce. We used the Groupe de Recherche en Réanimation Respiratoire en Onco-Hématologie's database (2003-2017, 72 intensive care units) to describe the spectrum of critically ill immunocompromised patients with virus-detected ARF and to report their outcomes. Then, patients with virus-detected ARF were matched based on clinical characteristics and severity (1:3 ratio) with patients with ARF from other origins.

RESULTS

Of the 4038 immunocompromised patients in the whole cohort, 370 (9.2%) had a diagnosis of virus-detected ARF and were included in the study. Influenza was the most common virus (59%), followed by respiratory syncytial virus (14%), with significant seasonal variation. An associated bacterial infection was identified in 79 patients (21%) and an invasive pulmonary aspergillosis in 23 patients (6%). The crude in-hospital mortality rate was 37.8%. Factors associated with mortality were: neutropenia (OR = 1.74, 95% confidence interval, CI [1.05-2.89]), poor performance status (OR = 1.84, CI [1.12-3.03]), and the need for invasive mechanical ventilation on the day of admission (OR = 1.97, CI [1.14-3.40]). The type of virus was not associated with mortality. After matching, patients with virus-detected ARF had lower mortality (OR = 0.77, CI [0.60-0.98]) than patients with ARF from other causes. This result was mostly driven by influenza-like viruses, namely, respiratory syncytial virus, parainfluenza virus, and human metapneumovirus (OR = 0.54, CI [0.33-0.88]).

CONCLUSIONS

In immunocompromised patients with virus-detected ARF, mortality is high, whatever the species, mainly influenced by clinical severity and poor general status. However, compared to non-viral ARF, in-hospital mortality was lower, especially for patients with detected viruses other than influenza.

Real-life impact of respiratory panel PCR assay on antibiotic prescription in geriatric acute care in the pre-COVID-19 era

OBJECTIVES

In this era of bacterial resistance, avoiding inappropriate use of antibiotic treatments is of major importance. Respiratory tract infections are frequent among older patients, and differentiating viral from bacterial infections is a challenge. The aim of our study was to evaluate the impact of recently available respiratory PCR testing on antimicrobial prescription in geriatric acute care.

METHODS

We performed a retrospective study, including all hospitalized geriatric patients who had had multiplex respiratory PCR testing prescribed from 1st October 2018 to 30th September 2019. The PCR test comprised a respiratory viral panel (RVP) and a respiratory bacterial panel (RBP). PCR testing could be prescribed at any time during hospitalization by geriatricians. Our primary endpoint was antibiotic prescription after viral multiplex PCR testing results.

RESULTS

All in all, 193 patients were included, 88 (45.6%) of whom had positive RVP, while none had positive RBP. Patients with positive RVP had significantly fewer antibiotic prescriptions following test results than patients with negative RVP (odds ratio (OR) 0.41, 95% confidence interval (CI) 0.22-0.77; p = 0.004). Among positive-RVP patients, factors associated with antibiotic continuation were presence of radiological infiltrate (OR 12.02, 95%CI 3.07-30.29), and detected Respiratory Syncytial Virus (OR 7.54, 95%CI 1.74-32.65). That said, discontinuation of antibiotic treatment seems safe.

CONCLUSION

In this population, the impact of viral detection by respiratory multiplex PCR on antibiotic therapy was low. It could be optimized by means of clearly formulated local guidelines, qualified staff and specific training by infectious disease specialists. Cost-effectiveness studies are necessary.

ERS/ESICM/ESCMID/ALAT guidelines for the management of severe community-acquired pneumonia

PURPOSE

Severe community-acquired pneumonia (sCAP) is associated with high morbidity and mortality, and whilst European and non-European guidelines are available for community-acquired pneumonia, there are no specific guidelines for sCAP.

METHODS

The European Respiratory Society (ERS), European Society of Intensive Care Medicine (ESICM), European Society of Clinical Microbiology and Infectious Diseases (ESCMID), and Latin American Thoracic Association (ALAT) launched a task force to develop the first international guidelines for sCAP. The panel comprised a total of 18 European and four non-European experts, as well as two methodologists. Eight clinical questions for sCAP diagnosis and treatment were chosen to be addressed. Systematic literature searches were performed in several databases. Meta-analyses were performed for evidence synthesis, whenever possible. The quality of evidence was assessed with GRADE (Grading of Recommendations, Assessment, Development and Evaluation). Evidence to Decision frameworks were used to decide on the direction and strength of recommendations.

RESULTS

Recommendations issued were related to diagnosis, antibiotics, organ support, biomarkers and co-adjuvant therapy. After considering the confidence in effect estimates, the importance of outcomes studied, desirable and undesirable consequences of treatment, cost, feasibility, acceptability of the intervention and implications to health equity, recommendations were made for or against specific treatment interventions.

CONCLUSIONS

In these international guidelines, ERS, ESICM, ESCMID, and ALAT provide evidence-based clinical practice recommendations for diagnosis, empirical treatment, and antibiotic therapy for sCAP, following the GRADE approach. Furthermore, current knowledge gaps have been highlighted and recommendations for future research have been made.

ERS/ESICM/ESCMID/ALAT guidelines for the management of severe community-acquired pneumonia

BACKGROUND

Severe community-acquired pneumonia (sCAP) is associated with high morbidity and mortality, and while European and non-European guidelines are available for community-acquired pneumonia, there are no specific guidelines for sCAP.

MATERIALS AND METHODOLOGY

The European Respiratory Society (ERS), European Society of Intensive Care Medicine (ESICM), European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and Latin American Thoracic Association (ALAT) launched a task force to develop the first international guidelines for sCAP. The panel comprised a total of 18 European and four non-European experts, as well as two methodologists. Eight clinical questions for sCAP diagnosis and treatment were chosen to be addressed. Systematic literature searches were performed in several databases. Meta-analyses were performed for evidence synthesis, whenever possible. The quality of evidence was assessed with GRADE (Grading of Recommendations, Assessment, Development and Evaluation). Evidence to Decision frameworks were used to decide on the direction and strength of recommendations.

RESULTS

Recommendations issued were related to diagnosis, antibiotics, organ support, biomarkers and co-adjuvant therapy. After considering the confidence in effect estimates, the importance of outcomes studied, desirable and undesirable consequences of treatment, cost, feasibility, acceptability of the intervention and implications to health equity, recommendations were made for or against specific treatment interventions.

CONCLUSIONS

In these international guidelines, ERS, ESICM, ESCMID and ALAT provide evidence-based clinical practice recommendations for diagnosis, empirical treatment and antibiotic therapy for sCAP, following the GRADE approach. Furthermore, current knowledge gaps have been highlighted and recommendations for future research have been made.

Can Some Viral Respiratory Infections Observed Before the Pandemic Announcement Be Related to SARS-CoV-2?

OBJECTIVE

There have been doubts that SARS-CoV-2 has been circulating before the first case was announced. The aim of this study was to evaluate the possibility of COVID-19 in some cases diagnosed to be viral respiratory tract infection in the pre-pandemic period in our center.

MATERIAL AND METHODS

Patients who were admitted to our hospital's pulmonary diseases, infectious diseases, and intensive care clinics with the diagnosis of viral respiratory system infection within a 6-month period between October 2019 and March 12, 2020, were screened. Around 248 archived respiratory samples from these patients were analyzed for SARS-CoV-2 ribonucleic acid by real-timequantitative polymerase chain reaction. The clinical, laboratory, and radiological data of the patients were evaluated.

RESULTS

The mean age of the study group was 47.5 (18-89 years); 103 (41.5%) were female and 145 (58.4%) were male. The most common presenting symptoms were cough in 51.6% (n = 128), fever in 42.7% (n = 106), and sputum in 27.0% (n = 67). Sixty-nine percent (n = 172) of the patients were pre-diagnosed to have upper respiratory tract infection and 22.0% (n = 55) had pneumonia, one-third of the patients (n = 84, 33.8%) were followed in the service. Respiratory viruses other than SARS-CoV-2 were detected in 123 (49.6%) patients. Influenza virus (31.9%), rhinovirus (10.5%), and human metapneumovirus (6.5%) were the most common pathogens, while none of the samples were positive for SARS-CoV-2 RNA. Findings that could be significant for COVID-19 pneumonia were detected in the thorax computed tomography of 7 cases.

CONCLUSION

The negative SARS-CoV-2 real-time-quantitative polymerase chain reaction results in the respiratory samples of the cases followed up in our hospital for viral pneumonia during the pre-pandemic period support that there was no COVID-19 among our cases during the period in question. However, if clinical suspicion arises, both SARS and non-SARS respiratory viral pathogens should be considered for differential diagnosis.

Characteristics, Management, and Outcomes of Community-Acquired Pneumonia due to Respiratory Syncytial Virus: A Retrospective Study

Background

Respiratory syncytial virus (RSV), a well-known cause of bronchiolitis in children, can cause community-acquired pneumonia (CAP) in adults, but this condition is not well studied. Hence, we described the characteristics and outcomes of patients hospitalized for CAP due to RSV.

Methods

This was a retrospective study of patients admitted to a tertiary-care hospital between 2016 and 2019 with CAP due to RSV diagnosed by a respiratory multiplex PCR within 48 hours of admission. We compared patients who required ICU admission to those who did not.

Results

Eighty adult patients were hospitalized with CAP due to RSV (median age 69.0 years, hypertension 65.0%, diabetes 58.8%, chronic respiratory disease 52.5%, and immunosuppression 17.5%); 19 (23.8%) patients required ICU admission. The median pneumonia severity index score was 120.5 (140.0 for ICU and 102.0 for non-ICU patients; p = 0.09). Bacterial coinfection was rare (10.0%). Patients who required ICU admission had more hypotension (systolic blood pressure < 90 mmHg) and a higher prevalence of bilateral infiltrates on chest X-ray (CXR) (89.5% versus 32.7%; p < 0.001). Systemic corticosteroids were used in 57.3% of patients (median initial dose was 40 mg of prednisone equivalent) with ICU patients receiving a higher dose compared to non-ICU patients (p = 0.02). Most (68.4%) ICU patients received mechanical ventilation (median duration of 4 days). The overall hospital mortality was 8.8% (higher for ICU patients: 31.6% versus 1.6%, p < 0.001).

Conclusions

Most patients with CAP due to RSV were elderly and had significant comorbidities. ICU admission was required in almost one in four patients and was associated with higher mortality.

Clinical, economic, and humanistic burden of community acquired pneumonia in Europe: a systematic literature review

BACKGROUND

Community-acquired pneumonia (CAP) is an infectious lung inflammation contracted outside the hospital. CAP is a leading cause of death among young children, elderly, and immunocompromised persons. Incidence can reach 14 cases/1,000 adults. Up to 50% of cases require inpatient hospitalization. Mortality is 0.7/1,000 cases or 4 million deaths per year. We sought to summarize multi-dimensional burden of CAP for selected European countries.

METHODS

We conducted a systematic literature review of literature published from 2011 to 2021 whereby we sought information pertaining to the epidemiologic, clinical, economic, and humanistic burden of CAP. Findings were summarized descriptively.

RESULTS

CAP incidence in Europe is variable, with the highest burden among those of advanced age and with chronic comorbidities. Etiology is primarily bacterial infection with Streptococcus pneumoniae being the most frequently implicated. Direct medical costs are primarily attributable to inpatient stay, which is exacerbated among high-risk populations. Higher mortality rates are associated with increasing age, the need for inpatient hospitalization, and antibiotic resistance.

CONCLUSIONS

A better understanding of CAP is needed, specifically the economic and quality of life burden on patients and caregivers. We recommend further assessments using population-level and real-world data employing consistent disease definitions.

Respiratory viruses: their importance and lessons learned from COVID-19

Respiratory virus infection can cause severe illnesses capable of inducing acute respiratory failure that can progress rapidly to acute respiratory distress syndrome (ARDS). ARDS is related to poor outcomes, especially in individuals with a higher risk of infection, such as the elderly and those with comorbidities, i.e. obesity, asthma, diabetes mellitus and chronic respiratory or cardiovascular disease. Despite this, effective antiviral treatments available for severe viral lung infections are scarce. The coronavirus disease 2019 (COVID-19) pandemic demonstrated that there is also a need to understand the role of airborne transmission of respiratory viruses. Robust evidence supporting this exists, but better comprehension could help implement adequate measures to mitigate respiratory viral infections. In severe viral lung infections, early diagnosis, risk stratification and prognosis are essential in managing patients. Biomarkers can provide reliable, timely and accessible information possibly helpful for clinicians in managing severe lung viral infections. Although respiratory viruses highly impact global health, more research is needed to improve care and prognosis of severe lung viral infections. In this review, we discuss the epidemiology, diagnosis, clinical characteristics, management and prognosis of patients with severe infections due to respiratory viruses.

Characteristics, Management, and Outcomes of Community-Acquired Pneumonia Due to Human Rhinovirus-A Retrospective Study

INTRODUCTION

Human rhinovirus (HRV) can lead to a variety of respiratory illnesses; it is also an uncommon cause of community-acquired pneumonia (CAP). We described the characteristics and outcomes of patients hospitalized for CAP due to HRV.

METHODS

We retrospectively studied consecutive adult patients admitted to King Abdulaziz Medical City-Riyadh with CAP due to HRV between 2016 and 2019. The diagnosis was made by respiratory multiplex PCR within 48 hours of hospitalization. We compared patients requiring ICU admission to those who did not.

RESULTS

One-hundred-and-six patients were studied (peak hospitalization between November and January, median age 71.5 years, hypertension 59%, diabetes 50%, and chronic respiratory disease 44.3%); 16 (15.1%) patients required ICU admission. The median pneumonia severity index score (PSI) was 107, with no significant difference between ICU and nonICU patients. ICU patients had a higher prevalence of tachypnea (62.5% vs. 26.7%, p=0.005), hemoptysis (12.5% vs 0%, p=0.001), and lymphopenia (71.4% vs 26.3%, p=0.01). Chest X-ray on presentation showed bilateral infiltrates in 47/101 (46.5%) patients and unilateral infiltrates in 26/101 (25.7%) patients. Systemic corticosteroids were used in 54.7% of patients (the median initial dose was 120 mg of prednisone equivalent and was higher in nonICU patients). Most (69.2%) ICU patients received mechanical ventilation (median duration of 8 days). Bacterial coinfection (6.6%) and superinfection (3.8%) were rare. The overall hospital mortality was 9.4% (higher for ICU patients: 37.5% vs. 4.4%, p < 0.001).

CONCLUSIONS

Most patients with CAP due to HRV were elderly and had significant comorbidities. ICU admission was required in almost one in six patients and was associated with higher mortality.

Comparison of Length of Hospital Stay for Community-Acquired Infections Due to Enteric Pathogens, Influenza Viruses and Multidrug-Resistant Bacteria: A Cross-Sectional Study in Hungary

Community-acquired infections (CAI) can affect the duration of care and mortality of patients. Therefore, we aimed to investigate these as well as factors influencing the length of hospital stay in patients with CAI due to enteric pathogens, influenza viruses and multidrug-resistant (MDR) bacteria. We obtained data on 531 patients with CAI from the medical databases of a Hungarian university hospital and analyzed their characteristics using a regression model. Patients with MDR bacterial infection had the highest mortality (26.24%) and they stayed significantly longer in the hospital than cases with other CAIs. Our results showed that infection by Clostridioides difficile (odds ratio (OR): 6.98, 95% confidence interval (CI): 1.03-47.48; p = 0.047), MDR Escherichia coli (OR: 7.64, 95% CI: 1.24-47.17; p = 0.029), MDR Klebsiella spp. (OR: 7.35, 95% CI: 1.15-47.07; p = 0.035) and hospitalization in the department of pulmonology (OR: 5.48, 95% CI: 1.38-21.76; p = 0.016) and surgery (OR: 4.19, 95% CI: 1.18-14.81; p = 0.026) significantly increased, whereas female sex (OR: 0.62, 95% CI: 0.40-0.97; p = 0.037) and hospitalization in the department of pediatrics (OR: 0.17, 95% CI: 0.04-0.64; p = 0.009) decreased the odds of staying in the hospital for more than 6 days. Our findings provide new information on the epidemiology of CAI and can contribute to the development of public health programs that decrease the burden of infections acquired in the community.

Diagnostic des pneumonies aiguës communautaires aux urgences et distinction entre étiologie virale ou bactérienne

La pandémie actuelle liée à l’émergence du SARSCoV-2 en 2019 a considérablement modifié la perception des médecins de l’impact des virus respiratoires et de leur rôle dans les pneumonies aiguës communautaires (PAC). Alors que plus de 25 % des tableaux de PAC chez l’adulte étaient d’origine virale, les virus respiratoires étaient souvent perçus comme des agents pathogènes peu graves. Devant le défi que représente encore à nos jours la documentation microbiologique d’une PAC, l’instauration d’un traitement empirique par antibiotiques est souvent réalisée aux urgences. La pandémie de COVID-19 a surtout mis en exergue le rôle déterminant de la biologie moléculaire et du scanner thoracique dans l’algorithme diagnostique de la PAC. En effet, un diagnostic rapide et fiable est la clé pour améliorer les mesures de précaution et réduire la prescription inutile d’antibiotiques. Du fait de prises en charges très différentes, il est nécessaire de distinguer l’étiologie virale de la bactérienne d’une PAC.

Characteristics of patients with viral infections of the lower respiratory tract: A retrospective study

While the impact of respiratory virus infections has been well researched in some respiratory diseases, no clinical studies have discussed the subject of who would be more likely to develop respiratory virus infections among patients with various respiratory illnesses who come from different backgrounds. This study aimed to identify respiratory diseases that are frequently associated with respiratory virus infections along with the characteristics of patients who develop such infections in clinical settings. Tested specimens were obtained from the lower respiratory tract by bronchoscopy to provide more accurate data. Data of bronchoscopies at Ryukyu University Hospital between August 2012 and September 2016 were reviewed, and patients who underwent multiplex polymerase chain reaction (PCR) tests for detecting respiratory viruses in bronchoscopy specimens were retrospectively recruited for descriptive statistics. Differences among patients' primary pulmonary diseases and backgrounds were compared between the PCR-positive and -negative patients, and multivariate statistical analysis was performed to analyze factors associated with a positive PCR test result. Overall, 756 bronchoscopies were performed during the study period and PCR tests were performed for 177 patients. Of them, 27 tested positive for respiratory viruses, mainly parainfluenza virus and rhinovirus, and out of those, 7 were hospitalized for >1 month. Overall, all patients did not experience typical upper respiratory infection symptoms. In positive patients, 13 and 7 had diagnoses of interstitial lung disease and bacterial pneumonia, respectively. The diagnoses of 3 bacterial pneumonia cases were changed to viral pneumonia after receiving their PCR-positive tests. Respiratory virus infections were confirmed in 14 patients on immunosuppressant therapy and 4 on maintenance dialysis. Multivariate analysis revealed that immunosuppressant therapy and maintenance dialysis were independently associated with respiratory virus infections. Viruses were commonly detected in patients with interstitial lung diseases and bacterial pneumonia, while few patients were diagnosed with pure viral pneumonia. These illnesses were considered to be induced by respiratory infections. Immunosuppressant therapy and maintenance dialysis were associated with respiratory virus infections. Multiplex PCR testing is an essential diagnostic tool for respiratory virus infections in immunocompromised patients.

Epidemiology of Community-Acquired Respiratory Tract Infections in Patients Admitted at the Emergency Departments

Objectives: Community-acquired respiratory infections (CARTIs) are responsible for serious morbidities worldwide. Identifying the aetiology can decrease the use of unnecessary antimicrobial therapy. In this study, we intend to determine the pathogenic agents responsible for respiratory infections in patients presenting to the emergency department of several Lebanese hospitals. Methods: A total of 100 patients presenting to the emergency departments of four Lebanese hospitals and identified as having CARTIs between September 2017 and September 2018 were recruited. Specimens of upper and lower respiratory tract samples were collected. Pathogens were detected by a multiplex polymerase chain reaction respiratory panel. Results: Of 100 specimens, 84 contained at least one pathogen. Many patients were detected with ≥2 pathogens. The total number of pathogens from these 84 patients was 163. Of these pathogens, 36 (22%) were human rhinovirus, 28 (17%) were Streptococcus pneumoniae, 16 (10%) were metapneumovirus, 16 (10%) were influenza A virus, and other pathogens were detected with lower percentages. As expected, the highest occurrence of pathogens was observed between December and March. Respiratory syncytial virus accounted for 2% of the cases and only correlated to paediatric patients. Conclusion: CARTI epidemiology is important and understudied in Lebanon. This study offers the first Lebanese data about CARTI pathogens. Viruses were the most common aetiologies of CARTIs. Thus, a different approach must be used for the empirical management of CARTI. Rapid testing might be useful in identifying patients who need antibiotic therapy.

Rhinoviruses: molecular diversity and clinical characteristics

BACKGROUND

Rhinoviruses are commonly considered simple "common cold" agents. The link between their molecular epidemiology and patient clinical presentation and outcomes remains unclear in adult populations.

MATERIALS/METHODS

All nasopharyngeal or bronchoalveolar lavages were screened using multiplex PCR in three Parisian hospitals from January to September 2018. For all detected rhinoviruses, the VP2/VP4 region was subtyped by sequencing.

RESULTS

The study included 178 human rhinovirus (HRV) positive unique patients. They were primarily male (56%), with a median age of 62.2 [IQR: 46.8-71.4], frequently presenting chronic respiratory diseases (56%) and/or immunosuppression (46%). Of these, 63% were admitted for respiratory distress, including pneumonia for 25%; 95 (53%), 27 (15%), and 56 (32%) were positive for HRV-A, -B, and -C, respectively. HRV-B appeared more associated with immunosuppressive treatments (58% vs. 30% and 36% of patients for HRV-A and -C, respectively, p = 0.038), higher coinfection rates (54% vs. 34% and 23%, p = 0.03), and higher ICU admission rates (35% vs. 17% and 13%, p = 0.048). Conversely, HRV-A was more frequently associated with pneumonia (54% vs. 31% and 11% for HRV-B and -C, respectively, p = 0.01).

CONCLUSIONS

This study highlights the high proportion of chronic respiratory diseases or immunosuppression among hospitalized patients infected with a rhinovirus.

Severe Infections Due to Respiratory Viruses

Severe viral infections may result in severe illnesses capable of causing acute respiratory failure that could progress rapidly to acute respiratory distress syndrome (ARDS), related to worse outcomes, especially in individuals with a higher risk of infection, including the elderly and those with comorbidities such as asthma, diabetes mellitus and chronic respiratory or cardiovascular disease. In addition, in cases of severe viral pneumonia, co-infection with bacteria such as Streptococcus pneumoniae and Staphylococcus aureus is related to worse outcomes. Respiratory viruses like influenza, rhinovirus, parainfluenza, adenovirus, metapneumovirus, respiratory syncytial virus, and coronavirus have increasingly been detected. This trend has become more prevalent, especially in critically ill patients, due to the availability and implementation of molecular assays in clinical practice. Respiratory viruses have been diagnosed as a frequent cause of severe pneumonia, including cases of community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia. In this review, we will discuss the epidemiology, diagnosis, clinical characteristics, management, and prognosis of patients with severe infections due to respiratory viruses, with a focus on influenza viruses, non-influenza viruses, and coronaviruses.

Community-acquired Respiratory Virus Cases Mimic COVID-19 on Lung Computed Tomography

We herein report four patients with community-acquired respiratory virus (CRV) infection. Although they had no history of contact with any individual with coronavirus disease 2019 (COVID-19), they were suspected of having COVID-19 based on findings of high-resolution computed tomography (CT) of the lungs. Among the four patients, two were infected with rhinovirus, one with metapneumovirus, and one with influenza A. Their chest CT findings were similar to those of COVID-19 patients reported in previous studies. Both CRV infection and COVID-19 can show various patterns on chest CT. CRV infection is thus indistinguishable from COVID-19 based on CT findings alone.

Place des virus respiratoires dans les pneumonies aiguës communautaires de l'adulte : quels changements depuis la Covid-19 ?

L’émergence du SARS-CoV-2 a renforcé l'intérêt pour la place des virus respiratoires, dans les pneumonies aiguës communautaires, en mettant en exergue de nombreux points encore mal connus tels que la part des infections asymptomatiques, les interactions entre virus respiratoires et pathogènes non viraux, leurs périodes d'incubation, leur pathogénicité ou encore la durée d'excrétion variable.

La présentation clinique et radiologique des pneumonies aiguës communautaires ne permet pas toujours de distinguer l'origine virale de l'origine bactérienne.

L'absence de réelle conséquence thérapeutique semble un frein à l'utilisation des PCR multiplex dans la pratique quotidienne. Toutefois, l'amélioration en termes de délai de rendu des résultats et du nombre de pathogènes inclus dans les panels, ainsi que l'accumulation récente de données épidémiologiques et cliniques, devraient aider à rationaliser l'utilisation de ces tests, faciliter l'interprétation de leurs résultats et guider l'utilisation des molécules antivirales en développement.

Outcomes of early oseltamivir treatment for hospitalized adult patients with community-acquired influenza pneumonia

Early initiation of oseltamivir within 48 h to 5 days from illness onset has been associated with improved survival among patients with community-acquired influenza pneumonia. Delay of hospitalization limits early treatment and the survival of patients. To date, the effects of early oseltamivir initiation within 24 hours from admission on patient mortality has remained unknown. This retrospective study reviewed and analyzed the clinical and non-clinical outcomes of 143 patients, with community-acquired influenza pneumonia, who received oseltamivir within 24 h (group A) and after 24 h (group B) from admission. Among the patients, 82 (57.3%) received oseltamivir within 24 h while 61 (42.7%) received oseltamivir after 24 h. The median time from symptom onset to admission for group A and group B was not statistically significant (P < 0.001). The 14-day mortality rate was 9% and 23% for group A and B, respectively (P = 0.03), while the 30-day mortality were 15% and 30% for group A and B, respectively (P = 0.05). Administration of oseltamivir within 24 h significantly affected 30-day mortality rates (adjust OR: 0.14, 95% CI: 0.47–0.04, P < 0.01), particularly among patients with respiratory failure at admission (adjust OR: 0.08, 95% CI: 0+.30–0.06, P < 0.01). Survival analysis of patient with influenza pneumonia and respiratory failure at admission demonstrated significant difference between those who received oseltamivir within and after 24 h (P = 0.002). The results indicated that early oseltamivir initiation within 24 h improved the survival outcome mainly among those with respiratory failure at admission.

Management of pneumonia in critically ill patients

Severe pneumonia is associated with high mortality (short and long term), as well as pulmonary and extrapulmonary complications. Appropriate diagnosis and early initiation of adequate antimicrobial treatment for severe pneumonia are crucial in improving survival among critically ill patients. Identifying the underlying causative pathogen is also critical for antimicrobial stewardship. However, establishing an etiological diagnosis is challenging in most patients, especially in those with chronic underlying disease; those who received previous antibiotic treatment; and those treated with mechanical ventilation. Furthermore, as antimicrobial therapy must be empiric, national and international guidelines recommend initial antimicrobial treatment according to the location's epidemiology; for patients admitted to the intensive care unit, specific recommendations on disease management are available. Adherence to pneumonia guidelines is associated with better outcomes in severe pneumonia. Yet, the continuing and necessary research on severe pneumonia is expansive, inviting different perspectives on host immunological responses, assessment of illness severity, microbial causes, risk factors for multidrug resistant pathogens, diagnostic tests, and therapeutic options.

Parainfluenza Virus Types 1-3 Infections Among Children and Adults Hospitalized With Community-acquired Pneumonia

BACKGROUND

Parainfluenza virus (PIV) is a leading cause of lower respiratory tract infections. Although there are several distinct PIV serotypes, few studies have compared the clinical characteristics and severity of infection among the individual PIV serotypes and between PIV and other pathogens in patients with community-acquired pneumonia.

METHODS

We conducted active population-based surveillance for radiographically confirmed community-acquired pneumonia hospitalizations among children and adults in 8 US hospitals with systematic collection of clinical data and respiratory, blood, and serological specimens for pathogen detection. We compared clinical features of PIV-associated pneumonia among individual serotypes 1, 2, and 3 and among all PIV infections with other viral, atypical, and bacterial pneumonias. We also compared in-hospital disease severity among groups employing an ordinal scale (mild, moderate, severe) using multivariable proportional odds regression.

RESULTS

PIV was more commonly detected in children (155/2354; 6.6%) than in adults (66/2297; 2.9%) (P < .001). Other pathogens were commonly co-detected among PIV cases (110/221; 50%). Clinical features of PIV-1, PIV-2, and PIV-3 infections were similar to one another in both children and adults with pneumonia. In multivariable analysis, children with PIV-associated pneumonia exhibited similar severity to children with other nonbacterial pneumonia, whereas children with bacterial pneumonia exhibited increased severity (odds ratio, 8.42; 95% confidence interval, 1.88-37.80). In adults, PIV-associated pneumonia exhibited similar severity to other pneumonia pathogens.

CONCLUSIONS

Clinical features did not distinguish among infection with individual PIV serotypes in patients hospitalized with community-acquired pneumonia. However, in children, PIV pneumonia was less severe than bacterial pneumonia.

A prospective observational study of community acquired pneumonia in Kenya: the role of viral pathogens

BACKGROUND

Lower respiratory tract infections continue to contribute significantly to morbidity and mortality across all age groups globally. In sub-Saharan Africa, many studies of community acquired pneumonia in adults have focused on HIV-infected patients and little attention has been given to risk factors and etiologic agents in an urban area with a more moderate HIV prevalence.

METHODS

We prospectively enrolled 77 patients admitted to a 280 bed teaching hospital in Kenya with radiographically confirmed community acquired pneumonia from May 2019 to March 2020. The patients were followed for etiology and clinical outcomes. Viral PCR testing was performed using the FTD respiratory pathogen-21 multiplex kit on nasopharyngeal or lower respiratory samples. Additional microbiologic workup was performed as determined by the treating physicians.

RESULTS

A potential etiologic agent(s) was identified in 57% including 43% viral, 5% combined viral and bacterial, 5% bacterial and 4% Pneumocystis. The most common etiologic agent was Influenza A which was associated with severe clinical disease. The most common underlying conditions were cardiovascular disease, diabetes and lung disease, while HIV infection was identified in only 13% of patients. Critical care admission was required for 24, and 31% had acute kidney injury, sometimes in combination with acute respiratory distress or sepsis.

CONCLUSION

Viruses, especially influenza, were commonly found in patients with CAP. In contrast to other studies from sub-Saharan Africa, the underlying conditions were similar to those reported in high resource areas and point to the growing concern of the double burden of infectious and noncommunicable diseases.

Comorbidities and in-hospital death of viral pneumonia adults admitted to SUS (2002-2015)

OBJECTIVE

To identify demographic and clinical characteristics of adult patients hospitalized in the Brazilian Unified Health System (SUS) due to viral pneumonia and investigate the association between some comorbidities and death during hospitalization.

METHODS

This retrospective cohort study was conducted with secondary data of adults admitted to SUS due to viral pneumonia between 2002 and 2015. Patient profile was characterized based on demographic and clinical variables. The association between the ten Elixhauser comorbidities and in-hospital death was investigated using Poisson regression models with robust standard errors. Results were quantified as incidence rate ratio (IRR) with 95% confidence intervals (CI), and we built five models using successive inclusion of variables blocks.

RESULTS

Hospital admissions for viral pneumonias decreased throughout the study period, and it was observed that 5.8% of hospitalized patients had an in-hospital death. We observed significant differences in demographic and clinical characteristics by comparing individuals who died during hospitalization with those who did not, with the occurrence of one or more comorbidities being more expressive among patients who died. Although not considered risk factors for in-hospital death, chronic pulmonary disease and congestive heart failure were the most common comorbidities. Conversely, IRR for in-hospital death increased with other neurological disorders, diabetes, cancer, obesity, and especially with HIV/AIDS.

CONCLUSIONS

Individuals presenting with pulmonary and cardiovascular diseases require proper attention during hospitalization, as well as those with other neurological diseases, diabetes, cancer, obesity, and especially HIV/AIDS. Understanding the influence of chronic diseases on viral infections may support the healthcare system in achieving better outcomes.

COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity

Coronavirus disease 2019 (COVID-19) is an acute infection of the respiratory tract that emerged in December 2019 in Wuhan, China. It was quickly established that both the symptoms and the disease severity may vary from one case to another and several strains of SARS-CoV-2 have been identified. To gain a better understanding of the wide variety of SARS-CoV-2 strains and their associated symptoms, thousands of SARS-CoV-2 genomes have been sequenced in dozens of countries. In this article, we introduce COVIDomic, a multi-omics online platform designed to facilitate the analysis and interpretation of the large amount of health data collected from patients with COVID-19. The COVIDomic platform provides a comprehensive set of bioinformatic tools for the multi-modal metatranscriptomic data analysis of COVID-19 patients to determine the origin of the coronavirus strain and the expected severity of the disease. An integrative analytical workflow, which includes microbial pathogens community analysis, COVID-19 genetic epidemiology and patient stratification, allows to analyze the presence of the most common microbial organisms, their antibiotic resistance, the severity of the infection and the set of the most probable geographical locations from which the studied strain could have originated. The online platform integrates a user friendly interface which allows easy visualization of the results. We envision this tool will not only have immediate implications for management of the ongoing COVID-19 pandemic, but will also improve our readiness to respond to other infectious outbreaks.

Pneumonia Caused by Severe Acute Respiratory Syndrome Coronavirus 2 and Influenza Virus: A Multicenter Comparative Study

Background

Detailed differences in clinical information between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia (CP), which is the main phenotype of SARS-CoV-2 disease, and influenza pneumonia (IP) are still unclear.

Methods

A prospective, multicenter cohort study was conducted by including patients with CP who were hospitalized between January and June 2020 and a retrospective cohort of patients with IP hospitalized from 2009 to 2020. We compared the clinical presentations and studied the prognostic factors of CP and IP.

Results

Compared with the IP group (n = 66), in the multivariate analysis, the CP group (n = 362) had a lower percentage of patients with underlying asthma or chronic obstructive pulmonary disease (P < .01), lower neutrophil-to-lymphocyte ratio (P < .01), lower systolic blood pressure (P < .01), higher diastolic blood pressure (P < .01), lower aspartate aminotransferase level (P < .05), higher serum sodium level (P < .05), and more frequent multilobar infiltrates (P < .05). The diagnostic scoring system based on these findings showed excellent differentiation between CP and IP (area under the receiver operating characteristic curve, 0.889). Moreover, the prognostic predictors were different between CP and IP.

Conclusions

Comprehensive differences between CP and IP were revealed, highlighting the need for early differentiation between these 2 pneumonias in clinical settings.

Characteristics of viral pneumonia in the COVID-19 era: an update

Influenza virus, rhinovirus, and adenovirus frequently cause viral pneumonia, an important cause of morbidity and mortality especially in the extreme ages of life. During the last two decades, three outbreaks of coronavirus-associated pneumonia, namely Severe Acute Respiratory Syndrome, Middle-East Respiratory Syndrome, and the ongoing Coronavirus Infectious Disease—2019 (COVID-19) were reported. The rate of diagnosis of viral pneumonia is increasingly approaching 60% among children identified as having community-acquired pneumonia (CAP). Clinical presentation ranges from mild to severe pneumonitis complicated by respiratory failure in severe cases. The most vulnerable patients, the elderly and those living with cancer, report a relevant mortality rate. No clinical characteristics can be useful to conclusively distinguish the different etiology of viral pneumonia. However, accessory symptoms, such as anosmia or ageusia together with respiratory symptoms suggest COVID-19. An etiologic-based treatment of viral pneumonia is possible in a small percentage of cases only. Neuraminidase inhibitors have been proven to reduce the need for ventilatory support and mortality rate while only a few data support the large-scale use of other antivirals. A low-middle dose of dexamethasone and heparin seems to be effective in COVID-19 patients, but data regarding their possible efficacy in viral pneumonia caused by other viruses are conflicting. In conclusion, viral pneumonia is a relevant cause of CAP, whose interest is increasing due to the current COVID-19 outbreak. To set up a therapeutic approach is difficult because of the low number of active molecules and the conflicting data bearing supportive treatments such as steroids.

The Clinical Characteristics and Outcomes of Adult Patients With Pneumonia Related to Three Paramyxoviruses

Background: Respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and human parainfluenza virus (hPIV) are paramyxoviruses (PMVs) that are important etiologies of community-acquired pneumonia. However, current knowledge about the clinical features and outcomes of PMV-related pneumonia (PMV-p) is limited. We aimed to investigate the clinical characteristics and disease severity in immunocompetent adults hospitalized with hMPV-related pneumonia (hMPV-p), hPIV-related pneumonia (hPIV-p), or RSV-related pneumonia (RSV-p).

Methods: We retrospectively recruited 488 patients with PMV-p (153 with RSV-p, 137 with hMPV-p, and 198 with hPIV-p) from five teaching hospitals in China during 2011–2019. Univariate and multivariate analyses were performed to identify predictors to distinguish hMPV-p/hPIV-p from RSV-p and evaluate the effects of virus types on the clinical outcomes.

Results: Compared with RSV-p, sputum production [odds ratio (OR) 5.029, 95% confidence interval (CI) 2.452–10.312, P < 0.001] was positively associated with hMPV-p, while solid malignant tumor (OR 0.346, 95% CI 0.126–0.945, P = 0.038), nasal congestion (OR 0.102, 95% CI 0.041–0.251, P < 0.001), and respiratory rate ≥ 30 breaths/min (OR 0.296, 95% CI 0.136–0.640, P = 0.002) were negatively related to hMPV-p. Sputum production (OR 13.418, 95% CI 6.769–26.598, P < 0.001) was positively associated with hPIV-p, while nasal congestion (OR 0.194, 95% CI 0.098–0.387, P < 0.001), dyspnea (OR 0.469, 95% CI 0.272–0.809, P < 0.001), and respiratory rate ≥30 breaths/min (OR 0.090, 95% CI 0.032–0.257, P < 0.001) on admission were negatively related to hPIV-p. After adjustment for confounders, multivariate logistic regression analysis suggested that hMPV-p (OR 0.355, 95% CI 0.135–0.932, P = 0.035) and hPIV-p (OR 0.311, 95% CI 0.121–0.784, P = 0.013) were associated with decreased 30-day mortality compared with RSV-p. RSV infection (OR 4.183, 95% CI 1.709–10.236, P = 0.002) was identified as an independent predictor of 30-day mortality in patients with PMV-p.

Conclusion: RSV-p caused more severe disease than hMPV-p and hPIV-p. Although some clinical features are helpful for distinguishing the diseases, etiologic diagnosis is critical in the management of the PMV-p.

[Virological diagnosis of lower respiratory tract infections]

INTRODUCTION

The etiological diagnosis of bronchopulmonary infections cannot be assessed with clinical, radiological and epidemiological data alone. Viruses have been demonstrated to cause a large proportion of these infections, both in children and adults.

BACKGROUND

The diagnosis of viral bronchopulmonary infections is based on the analysis of secretions, collected from the lower respiratory tract when possible, by techniques that detect either influenza and respiratory syncytial viruses, or a large panel of viruses that can be responsible for respiratory disease. The latter, called multiplex PCR assays, allow a syndromic approach to respiratory infection. Their high cost for the laboratory raises the question of their place in the management of patients in terms of antibiotic economy and isolation. In the absence of clear recommendations, the strategy and equipment are very unevenly distributed in France.

OUTLOOK

Medico-economic analyses need to be performed in France to evaluate the place of these tests in the management of patients. The evaluation of the role of the different viruses often detected in co-infection, especially in children, also deserves the attention of virologists and clinicians.

CONCLUSIONS

The availability of new diagnostic technologies, the recent emergence of SARS-CoV-2, together with the availability of new antiviral drugs are likely to impact future recommendations for the management of viral bronchopulmonary infections.

Respiratory viral infections in the elderly

With the global over 60-year-old population predicted to more than double over the next 35 years, caring for this aging population has become a major global healthcare challenge. In 2016 there were over 1 million deaths in >70 year olds due to lower respiratory tract infections; 13-31% of these have been reported to be caused by viruses. Since then, there has been a global COVID-19 pandemic, which has caused over 2.3 million deaths so far; increased age has been shown to be the biggest risk factor for morbidity and mortality. Thus, the burden of respiratory viral infections in the elderly is becoming an increasing unmet clinical need. Particular challenges are faced due to the interplay of a variety of factors including complex multimorbidities, decreased physiological reserve and an aging immune system. Moreover, their atypical presentation of symptoms may lead to delayed necessary care, prescription of additional drugs and prolonged hospital stay. This leads to morbidity and mortality and further nosocomial spread. Clinicians currently have limited access to sensitive detection methods. Furthermore, a lack of effective antiviral treatments means there is little incentive to diagnose and record specific non-COVID-19 viral infections. To meet this unmet clinical need, it is first essential to fully understand the burden of respiratory viruses in the elderly. Doing this through prospective screening research studies for all respiratory viruses will help guide preventative policies and clinical trials for emerging therapeutics. The implementation of multiplex point-of-care diagnostics as a mainstay in all healthcare settings will be essential to understand the burden of respiratory viruses, diagnose patients and monitor outbreaks. The further development of novel targeted vaccinations as well as anti-viral therapeutics and new ways to augment the aging immune system is now also essential.The reviews of this paper are available via the supplemental material section.

The increasing importance of Haemophilus influenzae in community-acquired pneumonia: results from a Danish cohort study

BACKGROUND

Numerous studies have shown that the aetiology of community-acquired pneumonia (CAP) varies considerably among different healthcare settings. Because empiric therapies for CAP should cover the major pathogens, reports examining CAP aetiology are considered crucial, particularly in Nordic countries that still rely on penicillin G or V treatments for most patients with CAP. The primary objective of our study was to report CAP aetiology. Secondary objectives included the estimation of positivity rates for different tests and the odds of a positive test for various subgroups.

METHODS

In this cohort study, microbiological data were analysed for an overall cohort (variable degree of microbiological testing) and for a subgroup that was tested for both, bacteria, viruses and fungi, using routine methods (defined as extensive testing).

RESULTS

The overall cohort comprised 2,264 patients, including 315 who were extensively tested. Bacterial and viral monoinfections were the most commonly identified infections. The dominant pathogen identified among extensively tested patients was Haemophilus influenzae (23.7%), followed by Streptococcus pneumoniae (20.6%). The tests with the highest positivity rates were sputum cultures (34.7%) and viral polymerase chain reaction (PCR, 24.4%). The odds of achieving a microbiological diagnosis increased significantly when extensive testing was performed compared with selective testing (OR 2.86, 95% CI 2.24-3.64).

CONCLUSION

Our study indicated that H. influenzae is the dominant responsible pathogen for bacterial CAP in Denmark. Thus, we believe that the current treatment recommendations that encourage the use of penicillin G or V for the majority of patients with CAP need to be revised.

Comparison of the Clinical Characteristics and Severity of Influenza and Non-influenza Respiratory Virus-Related Pneumonia in China: A Multicenter, Real-World Study

Purpose

Respiratory viruses are important etiologies of community-acquired pneumonia (CAP). However, the impact of different RVs on the outcomes of CAP is not well elucidated. This study aims to compare the clinical features and severity of influenza (Flu-p) and non-influenza respiratory viruses-related pneumonia (NIRVs-p) onset in the community among immunocompetent adults.

Methods

The data of the patients hospitalized with laboratory-confirmed RVs-p were retrospectively reviewed from five teaching hospitals in China from January 2013 to May 2019. Univariate and multivariate logistic regressions were performed to compare the clinical characteristics and outcomes between Flu-p and NIRVs-p.

Results

A total of 1079 patients with Flu-p and 341 patients with NIRVs-p were included in this study. A multivariate logistic regression model revealed chronic pulmonary disease [odd ratio (OR) 0.341, 95% confidence interval (CI) 0.225–0.515, p < 0.001], solid malignant tumor (OR 0.330, 95% CI 0.163–0.668, p = 0.002), myalgia (OR 1.697, 95% CI 1.236–2.330, p < 0.001), lymphocytes <0.8×10⁹/L (OR 10.811, 95% CI 6.949–16.818, p < 0.001) and blood albumin <35 g/L (OR 0.327, 95% CI 0.242–0.442, p < 0.001) were predictors for Flu-p. After adjusting for confounders, the multivariate logistic regression analysis confirmed that influenza B-related pneumonia (FluB-p) (OR 0.419, 95% CI 0.272–0.646, p < 0.001) and NIRVs-p (OR 0.260, 95% CI 0.158–0.467, p < 0.001) were associated with a decreased risk of 30-day mortality compared with the influenza A-related pneumonia (FluA-p).

Conclusion

Our results showed that patients with FluA-p experience a more severe disease than those with FluB-p and NIRVs-p. Some clinical features are helpful to distinguish between NIRVs-p and Flu-p.

Derivation and validation of a prediction rule for mortality of patients with respiratory virus-related pneumonia (RV-p score)

Background:

Respiratory viruses are important etiologies of community-acquired pneumonia. However, current knowledge on the prognosis of respiratory virus-related pneumonia (RV-p) is limited. Thus, here we aimed to establish a clinical predictive model for mortality of patients with RV-p.

Methods:

A total of 1431 laboratory-confirmed patients with RV-p, including 1169 and 262 patients from respective derivation and validation cohorts from five teaching hospitals in China were assessed between January 2010 and December 2019. A prediction rule was established on the basis of risk factors for 30-day mortality of patients with RV-p from the derivation cohort using a multivariate logistic regression model.

Results:

The 30-day mortality of patients with RV-p was 16.8% (241/1431). The RV-p score was composed of nine predictors (including respective points of mortality risk): (a) age ⩾65 years (1 point); (b) chronic obstructive pulmonary disease (1 point); (c) mental confusion (1 point); (d) blood urea nitrogen (1 point); (e) cardiovascular disease (2 points); (f) smoking history (2 points); (g) arterial pressure of oxygen/fraction of inspiration oxygen (P_aO₂/FiO₂) < 250 mmHg (2 points); (h) lymphocyte counts <0.8 × 10⁹/L (2 points); (i) arterial PH < 7.35 (3 points). A total of six points was used as the cut-off value for mortality risk stratification. Our model showed a sensitivity of 0.831 and a specificity of 0.783. The area under the receiver operating characteristic curve was more prominent for RV-p scoring [0.867, 95% confidence interval (CI)0.846–0.886] when compared with both pneumonia severity index risk (0.595, 95% CI 0.566–0.624, p < 0.001) and CURB-65 scoring (0.739, 95% CI 0.713–0.765, p < 0.001).

Conclusion:

RV-p scoring was able to provide a good predictive accuracy for 30-day mortality, which accounted for a more effective stratification of patients with RV-p into relevant risk categories and, consequently, help physicians to make more rational clinical decisions.

The reviews of this paper are available via the supplemental material section.

Predicting COVID-19 Using Retrospective Data: Impact of Obesity on Outcomes of Adult Patients With Viral Pneumonia

Background

Community-acquired pneumonia due to viral pathogens is an under-recognized cause of healthcare-associated mortality and morbidity worldwide. We aimed to compare mortality rates and outcome measures of disease severity in obese vs non-obese patients admitted with viral pneumonia.

Methods

Adult patients admitted with viral pneumonia were selected from the Nationwide Inpatient Sample of 2016 and 2017. The arms were stratified based on the presence of a secondary discharge diagnosis of obesity. The primary outcome was inpatient mortality. Secondary outcomes included sepsis, acute respiratory failure, acute respiratory distress syndrome, acute kidney injury, and pulmonary embolism.

Results and interpretation

In total, 89,650 patients admitted with viral pneumonia were analyzed, and 17% had obesity. There was no significant difference in mortality between obese and non-obese patients (aOR: 0.98, 95% CI: 0.705 - 1.362, p < 0.001). Compared to non-obese patients, obese patients had higher adjusted odds of developing acute hypoxic respiratory failure (aOR: 1.37, 95% CI: 1.255 - 1.513, p < 0.001), acute respiratory distress syndrome (aOR: 2.29, 95% CI: 1.554 - 3.381, p < 0.001), need for mechanical ventilation (aOR: 1.50, 95% CI: 1.236 - 1.819, p < 0.001), and pulmonary embolism (aOR: 1.69, 95% CI: 1.024 - 2.788, p = 0.040).

Conclusions

Obesity was not found to be an independent predictor of inpatient mortality in patients admitted with viral pneumonia. However, obesity is associated with worse clinical outcomes and disease severity as defined by the presence of complications, greater incidence of acute respiratory failure (ARF), acute respiratory distress syndrome (ARDS), need for mechanical ventilation, acute kidney injury (AKI), pulmonary embolism (PE), stroke, and sepsis.

Detection of community-acquired respiratory viruses in allogeneic stem-cell transplant recipients and controls-A prospective cohort study

Background

Community‐acquired respiratory viruses (CARV) cause upper and lower respiratory tract infections (URTI/LRTI) and may be life‐threatening for recipients of an allogeneic stem cell transplantation (allo‐SCT).

Methods

In a prospective study encompassing 4 winter‐seasons, we collected throat gargles (TG) at random time points from allo‐SCT recipients (patients) and controls and followed them up for at least 3 weeks including repetitive sampling and documentation of symptoms. A Multiplex‐PCR system to identify 20 CARV and Mycoplasma pneumoniae was used to detect CARV.

Results

One hundred ninety‐four patients with 426 TG and 273 controls with 549 TG were included. There were more patients with a positive test result (25% vs 11% in the controls), and the patients had a higher number of positive TG (70 = 16%) compared to controls (32 = 6%) (P < .001). Altogether, 115 viruses were detected. Multiple viruses in one TG (11/48, 34%) and prolonged shedding were only observed in patients (13/48, 27%). Patients had more RSV (18/83, 26%) and adenovirus (15/83, 21%) than controls (both viruses 2/32, 6%). Independent risk factors for the detection of CARV included age >40 years (OR 3.38, 95% CI 1.8‐6.4, P < .001) and presence of URTI‐symptoms (OR 3.22, 95% CI 1.9‐5.5, P < .001). No controls developed a LRTI or died whereas 4/48 (8%) patients developed a LRTI (coronavirus in 2, RSV in 1 and influenza A H1N1 in 1 patient). One patient died of CARV (influenza A H1N1).

Conclusion

Allo‐SCT‐recipients have more CARV‐infections, exhibit a different epidemiology, have more cases of co‐infection or prolonged shedding and have a higher rate of LRTI and mortality.

Therapeutic potential of resveratrol against emerging respiratory viral infections

Resveratrol has been widely studied for its therapeutic potential due to its antioxidant, anti-inflammatory and anti-microbial properties. In particular, resveratrol has shown promising antiviral activity against numerous viruses responsible for severe respiratory infections. Amongst these, influenza virus, respiratory syncytial virus and the emerging SARS-cov-2 are known to cause pneumonia, acute respiratory distress syndrome or multi-organ failure, especially, in vulnerable individuals like immunocompromised patients or the elderly, leading to a considerable economic burden worldwide. In this context, resveratrol may have potential value for its anti-inflammatory activity, since most of the severe virus-associated complications are related to the overactivation of the host-immune response, leading to lung damage. Herein, we present an overview of the antiviral activity and potential mechanisms of resveratrol against the respiratory tract viruses considered as a public threat for their rapid transmission and high morbidity and mortality in the general population.

Prevalence and clinical impact of VIral Respiratory tract infections in patients hospitalized for Community-Acquired Pneumonia: the VIRCAP study

Prevalence and clinical impact of viral respiratory tract infections (VRTIs) on community-acquired pneumonia (CAP) has not been well defined so far. The aims of this study were to investigate the prevalence and the clinical impact of VRTIs in patients with CAP. Prospective study involving adult patients consecutively admitted at medical wards for CAP and tested for VRTIs by real-time PCR on pharyngeal swab. Patients' features were evaluated with regard to the presence of VRTI and aetiology of CAP. Clinical failure was a composite endpoint defined by worsening of signs and symptoms requiring escalation of antibiotic treatment or ICU admission or death within 30 days. 91 patients were enrolled, mean age 65.7 ± 10.6 years, 50.5% female. 62 patients (68.2%) had no viral co-infection while in 29 patients (31.8%) a VRTI was detected; influenza virus was the most frequently identified (41.9%). The two groups were similar in terms of baseline features. In presence of a VRTI, pneumonia severity index (PSI) was more frequently higher than 91 and patients had received less frequently pre-admission antibiotic therapy (adjusted OR 2.689, 95% CI 1.017-7.111, p = 0.046; adjusted OR 0.143, 95% CI 0.030-0.670, p = 0.014). Clinical failure and antibiotic therapy duration were similar with regards to the presence of VRTI and the aetiology of CAP. VRTIs can be detected in almost a third of adults with CAP; influenza virus is the most relevant one. VRTI was associated with higher PSI at admission, but it does not affect patients' outcome.

The Clinical Presentation and Immunology of Viral Pneumonia and Implications for Management of Coronavirus Disease 2019

This review will briefly examine the clinical presentation and important immunology of viral pneumonia with a focus on severe acute respiratory syndrome coronavirus 2 (coronavirus disease 2019).

Community-acquired respiratory viruses

PURPOSE OF REVIEW

Community-acquired respiratory viruses (CARV) have been historically linked to upper respiratory tract infections; however, new data has emerged in recent years that has provided new insight into their role as causative pathogens for lower respiratory tract infections. We aim to discuss the importance of recognition of viruses both epidemiologically and clinically as causes of lower respiratory tract infection.

RECENT FINDINGS

With advances of molecular testing it is now possible to identify viruses from clinical specimens which have many implications that range from therapeutics to antibiotic stewardship. Recent studies suggest that most of the cases of community-acquired pneumonia are caused by viruses, which corresponds to a paradigm shift for most clinicians.

SUMMARY

As community-acquired lower respiratory infections are the most common cause of ICU admission in the USA, it is important for medical providers to be aware of the association with viruses, especially in patients with immunosuppression because of solid organ transplant and hematologic malignancies when sometimes diagnosis can be challenging and patients can be exposed to unnecessary antibiotics.

Burden of Community-Acquired Pneumonia and Unmet Clinical Needs

Community-acquired pneumonia (CAP) is the leading cause of death among infectious diseases and an important health problem, having considerable implications for healthcare systems worldwide. Despite important advances in prevention through vaccines, new rapid diagnostic tests and antibiotics, CAP management still has significant drawbacks. Mortality remains very high in severely ill patients presenting with respiratory failure or shock but is also high in the elderly. Even after a CAP episode, higher risk of death remains during a long period, a risk mainly driven by inflammation and patient-related co-morbidities. CAP microbiology has been altered by new molecular diagnostic tests that have turned viruses into the most identified pathogens, notwithstanding uncertainties about the specific role of each virus in CAP pathogenesis. Pneumococcal vaccines also impacted CAP etiology and thus had changed Streptococcus pneumoniae circulating serotypes. Pathogens from specific regions should also be kept in mind when treating CAP. New antibiotics for CAP treatment were not tested in severely ill patients and focused on multidrug-resistant pathogens that are unrelated to CAP, limiting their general use and indications for intensive care unit (ICU) patients. Similarly, CAP management could be personalized through the use of adjunctive therapies that showed outcome improvements in particular patient groups. Although pneumococcal vaccination was only convincingly shown to reduce invasive pneumococcal disease, with a less significant effect in pneumococcal CAP, it remains the best therapeutic intervention to prevent bacterial CAP. Further research in CAP is needed to reduce its population impact and improve individual outcomes.

Respiratory syncytial virus in the Western Pacific Region: a systematic review and meta-analysis

Background

Respiratory syncytial virus (RSV) is the leading cause of viral pneumonia and bronchiolitis, especially in younger children. The burden of RSV infection in adults, particularly in the older age group, is increasingly recognised. However, RSV disease burden and molecular epidemiology in the World Health Organization (WHO) Western Pacific Region (WPR) has not been reviewed systematically. The aim of this systematic review is to investigate the epidemiological aspects of RSV (incidence, prevalence, seasonality and hospitalisation status) and the associated molecular data in the WPRO countries.

Methods

A systematic search was conducted in international literature databases (MEDLINE, EMBASE, Scopus and Web of Science) to identify RSV-related publications from January 2000 to October 2017 in the WPR countries.

Results

A total of 196 studies from 15 WPR countries were included. The positivity rate for RSV among respiratory tract infection patients was 16.73% (95% confidence interval (CI) = 15.12%-18.4%). The RSV-positive cases were mostly found in hospitalised compared with outpatients (18.28% vs 11.54%, P < 0.001), and children compared with adults (20.72% vs 1.87%, P < 0.001). The seasonality of RSV in the WPR countries follows the latitude, with the peak of RSV season occurring in the winter in temperate countries, and during the rainy season in tropical countries. The molecular epidemiology pattern of RSV in WPR countries was similar to the global pattern, with NA1 (RSV A) and BA (RSV B) being the predominant genotypes.

Conclusions

The available data on RSV are limited in several countries within the WPR, with most data focusing on children and hospitalised patients. Further studies and surveillance, incorporating laboratory testing, are needed to determine the burden of RSV infection in the WPR countries.

Pneumococcal vaccination in lung transplant patients

Introduction: This review analyzes the efficacy of pneumococcal vaccinations in lung transplant patients before and after transplantation.Areas covered: This review addresses the risk for respiratory infections, in particular pneumococcal infections, in lung transplantation patients in the context of immunodeficiency and immunosuppressive medication. Vaccination is recommended to counteract the increased risk of pneumococcal infection, and the relevant guidelines are discussed in this review. The design of specific vaccination schedules is required because of the impaired antibody response in specific patient categories.Expert opinion: Lung transplantation candidates should be vaccinated with pneumococcal vaccines prior to transplantation. Currently, the 23-valent pneumococcal polysaccharide vaccine offers the broadest coverage, but the antibody response should be monitored. New generation pneumococcal conjugate vaccines with equally broad serotype coverage could be used in the future. During the post-transplantation period, the immune status of the patients should be monitored regularly, and vaccination should be repeated when indicated.

Predicting the microbial cause of community-acquired pneumonia: can physicians or a data-driven method differentiate viral from bacterial pneumonia at patient presentation?

BACKGROUND

Community-acquired pneumonia (CAP) requires urgent and specific antimicrobial therapy. However, the causal pathogen is typically unknown at the point when anti-infective therapeutics must be initiated. Physicians synthesize information from diverse data streams to make appropriate decisions. Artificial intelligence (AI) excels at finding complex relationships in large volumes of data. We aimed to evaluate the abilities of experienced physicians and AI to answer this question at patient admission: is it a viral or a bacterial pneumonia?

METHODS

We included patients hospitalized for CAP and recorded all data available in the first 3-h period of care (clinical, biological and radiological information). For this proof-of-concept investigation, we decided to study only CAP caused by a singular and identified pathogen. We built a machine learning model prediction using all collected data. Finally, an independent validation set of samples was used to test the pathogen prediction performance of: (i) a panel of three experts and (ii) the AI algorithm. Both were blinded regarding the final microbial diagnosis. Positive likelihood ratio (LR) values > 10 and negative LR values < 0.1 were considered clinically relevant.

RESULTS

We included 153 patients with CAP (70.6% men; 62 [51-73] years old; mean SAPSII, 37 [27-47]), 37% had viral pneumonia, 24% had bacterial pneumonia, 20% had a co-infection and 19% had no identified respiratory pathogen. We performed the analysis on 93 patients as co-pathogen and no-pathogen cases were excluded. The discriminant abilities of the AI approach were low to moderate (LR+ = 2.12 for viral and 6.29 for bacterial pneumonia), and the discriminant abilities of the experts were very low to low (LR+ = 3.81 for viral and 1.89 for bacterial pneumonia).

CONCLUSION

Neither experts nor an AI algorithm can predict the microbial etiology of CAP within the first hours of hospitalization when there is an urgent need to define the anti-infective therapeutic strategy.