Incidence of respiratory viruses in patients with community-acquired pneumonia admitted to the intensive care unit: results from the Severe Influenza Pneumonia Surveillance (SIPS) project

Antibiotic Strategies for Severe Community-Acquired Pneumonia

Despite advancements in health systems and intensive care unit (ICU) care, along with the introduction of novel antibiotics and microbiologic techniques, mortality rates in severe community-acquired pneumonia (sCAP) patients have not shown significant improvement. Delayed admission to the ICU is a major risk factor for higher mortality. Apart from choosing the appropriate site of care, prompt and appropriate antibiotic therapy significantly affects the prognosis of sCAP. Treatment regimens involving ceftaroline or ceftobiprole are currently considered the best options for managing patients with sCAP. Additionally, several other molecules, such as delafloxacin, lefamulin, and omadacycline, hold promise as therapeutic strategies for sCAP. This review aims to provide a comprehensive summary of the key challenges in managing adults with severe CAP, focusing on essential aspects related to antibiotic treatment and investigating potential strategies to enhance clinical outcomes in sCAP patients.

Imaging in pulmonary infections of immunocompetent adult patients

Pneumonia is a clinical syndrome characterised by fever, cough and alveolar infiltration of purulent fluid, caused by infection with a microbial pathogen. It can be caused by infections with bacteria, viruses or fungi, but a causative organism is identified in less than half of cases. The most common type of pneumonia is community-acquired pneumonia, which is caused by infections acquired outside the hospital. Current guidelines for pneumonia diagnosis require imaging to confirm the clinical suspicion of pneumonia. Thus, imaging plays an important role in both the diagnosis and management of pneumonia, with each modality having specific advantages and limitations. Chest radiographs are commonly used but have limitations in terms of sensitivity and specificity. Lung ultrasound shows high sensitivity and specificity. Computed tomography scans offer higher diagnostic accuracy but involve higher radiation doses. Radiological patterns, including lobar, lobular and interstitial pneumonia, provide valuable insights into causative pathogens and treatment decisions. Understanding these radiological patterns is crucial for accurate diagnosis. In this review, we will summarise the most important aspects pertaining to the role of imaging in pneumonia and will highlight the imaging characteristics of the most common causative organisms.

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.

Leveraging Influenza Virus Surveillance From 2012 to 2015 to Characterize the Burden of Respiratory Syncytial Virus Disease in Canadian Adults ≥50 Years of Age Hospitalized With Acute Respiratory Illness

Background

Respiratory syncytial virus (RSV) disease in older adults is undercharacterized. To help inform future immunization policies, this study aimed to describe the disease burden in Canadian adults aged ≥50 years hospitalized with RSV.

Methods

Using administrative data and nasopharyngeal swabs collected from active surveillance among adults aged ≥50 years hospitalized with an acute respiratory illness (ARI) during the 2012-2013, 2013-2014, and 2014-2015 influenza seasons, RSV was identified using a respiratory virus multiplex polymerase chain reaction test to describe the associated disease burden, incidence, and healthcare costs.

Results

Of 7797 patients tested, 371 (4.8%) were RSV positive (2.2% RSV-A and 2.6% RSV-B). RSV prevalence varied by season from 4.2% to 6.2%. Respiratory virus coinfection was observed in 11.6% (43/371) of RSV cases, with influenza A being the most common. RSV hospitalization rates varied between seasons and increased with age, from 8-12 per 100 000 population in adults aged 50-59 years to 174-487 per 100 000 in adults aged ≥80 years. The median age of RSV cases was 74.9 years, 63.7% were female, and 98.1% of cases had ≥1 comorbidity. Among RSV cases, the mean length of hospital stay was 10.6 days, 13.7% were admitted to the intensive care unit, 6.4% required mechanical ventilation, and 6.1% died. The mean cost per RSV case was $13 602 (Canadian dollars) but varied by age and Canadian province.

Conclusions

This study adds to the growing literature on adult RSV burden by showing considerable morbidity, mortality, and healthcare costs in hospitalized adults aged ≥50 years with ARIs such as influenza.

Clinical outcomes and economic burden of seasonal influenza and other respiratory virus infections in hospitalized adults

The cost of influenza and other respiratory virus infections should be determined to analyze the real burden of these diseases. We aimed to investigate the clinical outcomes and cost of illness due to respiratory virus infections in hospitalized adult patients. Hospitalized patients who had nasal swab sampling for a suspected viral infection between August 1, 2018 to March 31, 2019 were included. Outcome variables were oxygen requirement, mechanical ventilation need, intensive care unit admission, and cost. At least one viral pathogen was detected in 125 (47.7%) of 262 patients who were included in the study. Fifty-five (20.9%) of the patients were infected with influenza. Influenza-positive patients had higher rates for respiratory support, intensive care unit admission, and mortality compared to all other patients. The average cost of hospitalization per person was 2879.76 USD in the influenza-negative group, while the same cost was 3274.03 USD in the influenza-positive group. Although all of the vaccinated influenza-positive patients needed oxygen support, neither of them required invasive mechanical ventilation or intensive care unit admission. The average hospitalization cost per person was 779.70 USD in the vaccinated group compared to 3762.01 USD in the unvaccinated group. Disease-related direct cost of influenza in the community was estimated as 22 776 075.61 USD in the 18-65 years of age group and 15 756 120.02 USD in the 65 years of age and over group per year. Influenza, compared to other respiratory virus infections, can lead to untoward clinical outcomes and mortality as well as higher direct medical costs in adults.

Epidemiologic Characteristics and Clinical Significance of Respiratory Viral Infections Among Adult Patients Admitted to the Intensive Care Unit

Background

The diagnosis of respiratory viral infections (RVIs) in critically ill patients is important for determining treatment options and adhering to infection-control protocols. However, data on the incidence and occurrence patterns of RVIs are scarce. We investigated the epidemiology and clinical impact of RVIs in critically ill patients.

Methods

This retrospective observational study was conducted in a tertiary hospital in South Korea between November 2014 and September 2020. Adult patients (≥ 18 years of age) who tested positive for an RVI by multiplex polymerase chain reaction (mPCR) and were admitted to the intensive care unit (ICU) were included in the study. Clinical characteristics and outcomes were obtained by reviewing electronic medical records. Pearson's χ2 test and Fisher's exact test, Mann-Whitney U test was used to compare between groups of patients. Trend analysis and the χ2-based Q test was used to analyze test behavior of physicians performing mPCR test.

Results

Among 22,517 patients admitted to the ICU during the study period, 2,222 (9.9%) underwent mPCR testing for an RVI. The median timing of mPCR testing after ICU admission was 1 day (IQR, 0-2). A total of 335 (15.1%) non-duplicative RVI-positive cases were included in the analysis. The incidence rate of RVIs in ICU patients was 30.45 per 10,000 patient-days. The most frequently detected RVI was influenza A (27.8%), followed by rhinovirus (25.4%). Thirty-two (9.6%) RVI-positive patients were diagnosed with upper respiratory infections, 193 (64.1%) with community-acquired, and 108 (35.9%) with hospital-acquired pneumonia. All-cause mortality and mortality related to respiratory tract infection (RTI) were 30.7% and 22.1%, respectively. The initial presentation of septic shock, requirement for mechanical ventilation, and lymphocytopenia were significant predictors of RTI-related mortality. Of the RVI-positive patients, 151 (45.1%) had nonviral coinfections and presented with higher clinical severity and longer hospital stays than patients infected solely with viral pathogens.

Conclusion

The incidence of RVIs in ICU patients is common. ICU patients with RVIs had high mortality and frequently presented with coinfections with nonviral pathogens, which were associated with a higher clinical severity than sole RVI. Increased testing for RVIs will enhance infection-control efforts and improve patient care.

Molecular Epidemiology of Rhinovirus/Enterovirus and Their Role on Cause Severe and Prolonged Infection in Hospitalized Patients

Rhinovirus is one of the most common respiratory viruses, causing both upper and lower respiratory tract infections. It affects mainly children and could cause prolonged infections, especially in immunocompromised patients. Here we report our data on a 15-month surveillance of Rhinovirus seasonality and circulation in Lombardy Region, Italy. All rhinovirus/enterovirus-positive samples were amplified with RT-PCR for the VP4-VP2 region to assign the correct genotype. The median age of RV/EV-positive patients is 9 years, with a range of 0–96. RV-A and RV-C were detected in the majority of cases, while RV-B accounted for less than 10% of cases. An enterovirus species was detected in 6.45% of the cases. A total of 7% of the patients included in this study had a prolonged infection with a median duration of 62 days. All these patients were immunocompromised and most of them were pediatric with an RV-A infection. Two outbreaks were identified, mainly in the neonatal intensive care unit (NICU) and Oncohematology Department, caused by RV A89 and C43, respectively. Nearly 4.5% of the patients were admitted to the ICU requiring mechanical ventilation; all of which had preexisting comorbidities.

Combined use of a broad-panel respiratory multiplex PCR and procalcitonin to reduce duration of antibiotics exposure in patients with severe community-acquired pneumonia (MULTI-CAP): a multicentre, parallel-group, open-label, individual randomised trial conducted in French intensive care units

INTRODUCTION

At the time of the worrying emergence and spread of bacterial resistance, reducing the selection pressure by reducing the exposure to antibiotics in patients with community-acquired pneumonia (CAP) is a public health issue. In this context, the combined use of molecular tests and biomarkers for guiding antibiotics discontinuation is attractive. Therefore, we have designed a trial comparing an integrated approach of diagnosis and treatment of severe CAP to usual care.

METHODS AND ANALYSIS

The multiplex PCR and procalcitonin to reduce duration of antibiotics exposure in patients with severe-CAP (MULTI-CAP) trial is a multicentre (n=20), parallel-group, superiority, open-label, randomised trial. Patients are included if adult admitted to intensive care unit for a CAP. Diagnosis of pneumonia is based on clinical criteria and a newly appeared parenchymal infiltrate. Immunocompromised patients are excluded. Subjects are randomised (1:1 ratio) to either the intervention arm (experimental strategy) or the control arm (usual strategy). In the intervention arm, the microbiological diagnosis combines a respiratory multiplex PCR (mPCR) and conventional microbiological investigations. An algorithm of early antibiotic de-escalation or discontinuation is recommended, based on mPCR results and the procalcitonin value. In the control arm, only conventional microbiological investigations are performed and antibiotics de-escalation remains at the clinician's discretion. The primary endpoint is the number of days alive without any antibiotic from the randomisation to day 28. Based on our hypothesis of 2 days gain in the intervention arm, we aim to enrol a total of 450 patients over a 30-month period.

ETHICS AND DISSEMINATION

The MULTI-CAP trial is conducted according to the principles of the Declaration of Helsinki, is registered in Clinical Trials and has been approved by the Committee for Protection of Persons and the National French Drug Safety Agency. Written informed consents are obtained from all the patients (or representatives). The results will be disseminated through educational institutions, submitted to peer-reviewed journals for publication and presented at medical congresses.

TRIAL REGISTRATION NUMBER

NCT03452826; Pre-results.

Hospital utilization rates for influenza and RSV: a novel approach and critical assessment

BACKGROUND

Influenza and respiratory syncytial virus (RSV) contribute significantly to the burden of acute lower respiratory infection (ALRI) inpatient care, but heterogeneous coding practices and availability of inpatient data make it difficult to estimate global hospital utilization for either disease based on coded diagnoses alone.

METHODS

This study estimates rates of influenza and RSV hospitalization by calculating the proportion of ALRI due to influenza and RSV and applying this proportion to inpatient admissions with ALRI coded as primary diagnosis. Proportions of ALRI attributed to influenza and RSV were extracted from a meta-analysis of 360 total sources describing inpatient hospital admissions which were input to a Bayesian mixed effects model over age with random effects over location. Results of this model were applied to inpatient admission datasets for 44 countries to produce rates of hospital utilization for influenza and RSV respectively, and rates were compared to raw coded admissions for each disease.

RESULTS

For most age groups, these methods estimated a higher national admission rate than the rate of directly coded influenza or RSV admissions in the same inpatient sources. In many inpatient sources, International Classification of Disease (ICD) coding detail was insufficient to estimate RSV burden directly. The influenza inpatient burden estimates in older adults appear to be substantially underestimated using this method on primary diagnoses alone. Application of the mixed effects model reduced heterogeneity between countries in influenza and RSV which was biased by coding practices and between-country variation.

CONCLUSIONS

This new method presents the opportunity of estimating hospital utilization rates for influenza and RSV using a wide range of clinical databases. Estimates generally seem promising for influenza and RSV associated hospitalization, but influenza estimates from primary diagnosis seem highly underestimated among older adults. Considerable heterogeneity remains between countries in ALRI coding (i.e., primary vs non-primary cause), and in the age profile of proportion positive for influenza and RSV across studies. While this analysis is interesting because of its wide data utilization and applicability in locations without laboratory-confirmed admission data, understanding the sources of variability and data quality will be essential in future applications of these methods.

One year after ICU admission for severe community-acquired pneumonia of bacterial, viral or unidentified etiology. What are the outcomes?

INTRODUCTION

Multiplex polymerase chain reaction (mPCR) for respiratory virus testing is increasingly used in community-acquired pneumonia (CAP), however data on one-year outcome in intensive care unit (ICU) patients with reference to the causative pathogen are scarce.

MATERIALS AND METHODS

We performed a single-center retrospective study in 123 ICU patients who had undergone respiratory virus testing for CAP by mPCR and with known one-year survival status. Functional status including dyspnea (mMRC score), autonomy (ADL Katz score) and need for new home-care ventilatory support was assessed at a one-year post-ICU follow-up. Mortality rates and functional status were compared in patients with CAP of a bacterial, viral or unidentified etiology one year after ICU admission.

RESULTS

The bacterial, viral and unidentified groups included 19 (15.4%), 37 (30.1%), and 67 (54.5%) patients, respectively. In multivariate analysis, one-year mortality in the bacterial group was higher compared to the viral group (HR 2.92, 95% CI 1.71-7.28, p = 0.02) and tended to be higher compared to the unidentified etiology group (p = 0.06); but no difference was found between the viral and the unidentified etiology group (p = 0.43). In 64/83 one-year survivors with a post-ICU follow-up consultation, there were no differences in mMRC score, ADL Katz score and new home-care ventilatory support between the groups (p = 0.52, p = 0.37, p = 0.24, respectively). Severe dyspnea (mMRC score = 4 or death), severe autonomy deficiencies (ADL Katz score ≤ 2 or death), and major adverse respiratory events (new home-care ventilatory support or death) were observed in 52/104 (50.0%), 47/104 (45.2%), and 65/104 (62.5%) patients, respectively; with no difference between the bacterial, viral and unidentified group: p = 0.58, p = 0.06, p = 0.61, respectively.

CONCLUSIONS

CAP of bacterial origin had a poorer outcome than CAP of viral or unidentified origin. At one-year, impairment of functional status was frequently observed, with no difference according to the etiology.

The Differences in Viral Etiologies between Children with and without Severe Disability Admitted to the Pediatric Intensive Care Unit with Acute Respiratory Illness

Objectives The objectives of this study were to evaluate the differences in the viral etiologies and variability in the clinical course between children with and without severe disability (SD) admitted to the pediatric intensive care unit (PICU) with acute respiratory illness (ARI).

Methods The medical records of patients admitted to our PICU between June 2017 and July 2019 were retrospectively reviewed for viral etiology and clinical course.

Results Forty-eight of 136 patients included in the study had SD. The rates of requiring positive pressure ventilation (43.5% vs. 20.5%) or inotropic support (39.9% vs. 15.9%), and the median length of stay (11 [10] vs. 5 [8]) were significantly higher in children with SD (p < 0.01, each). Influenza infection was significantly higher in children with SD (20.8% vs. 2.3%; p < 0.01) whereas respiratory syncytial virus (RSV) infection was more common in children without SD (47.7% vs. 4.2%; p < 0.01). There was no statistically significant difference in terms of other viruses between study groups.

Conclusion In this present study, influenza was an important pathogen for children with SD, while RSV was the main cause of ARI-associated PICU admission in children without SD. By focusing on increasing the rate of immunization against influenza in children with SD and their caregivers the burden of influenza-associated PICU admissions could be decreased.

Respiratory virus-associated infections in HIV-infected adults admitted to the intensive care unit for acute respiratory failure: a 6-year bicenter retrospective study (HIV-VIR study)

Introduction

Acute respiratory failure is the main reason for admission to the intensive care unit (ICU) in HIV-infected adults. There is little data about the epidemiology of respiratory viruses in this population.

Methods

HIV-infected adults admitted to two intensive care units over a 6-year period for an acute respiratory failure and explored for respiratory viruses with multiplex polymerase chain reaction (mPCR) were retrospectively selected. Objectives were to describe the prevalence of respiratory viruses, coinfections with non-viral pathogens, and hospital outcome.

Results

A total of 123 episodes were included. An HIV infection was newly diagnosed in 9% of cases and 72% of the population were on antiretroviral therapy. Real-time mPCR tests identified at least one respiratory virus in the respiratory tract of 33 (27%) patients, but with a non-viral copathogen in two-thirds of cases. Rhinovirus was predominant, documented in 15 patients, followed by Influenza and Respiratory Syncytial Viruses (both n = 6). The prevalence of respiratory virus-associated infection did not vary along with the level of the CD4 T-cell deficiency, except for Rhinovirus which was more prevalent in patients with a CD4 lymphocyte count below 200 cells/µL (n = 13 (20%) vs. n = 2 (4%), p < 0.01). In multivariate analysis, respiratory virus-associated infection was not associated with a worse prognosis.

Conclusions

Viruses are frequently identified in the respiratory tract of HIV-infected patients with acute respiratory failure that requires ICU admission, but with a non-viral copathogen in two-thirds of cases. Rhinovirus is the predominant viral specie; its prevalence is highest in patients with a CD4 lymphocyte count below 200 cells/µL.

Updates on community acquired pneumonia management in the ICU

While the world is grappling with the consequences of a global pandemic related to SARS-CoV-2 causing severe pneumonia, available evidence points to bacterial infection with Streptococcus pneumoniae as the most common cause of severe community acquired pneumonia (SCAP). Rapid diagnostics and molecular testing have improved the identification of co-existent pathogens. However, mortality in patients admitted to ICU remains staggeringly high.

The American Thoracic Society and Infectious Diseases Society of America have updated CAP guidelines to help streamline disease management. The common theme is use of timely, appropriate and adequate antibiotic coverage to decrease mortality and avoid drug resistance. Novel antibiotics have been studied for CAP and extend the choice of therapy, particularly for those who are intolerant of, or not responding to standard treatment, including those who harbor drug resistant pathogens. In this review, we focus on the risk factors, microbiology, site of care decisions and treatment of patients with SCAP.

Spectrum of respiratory viral infections in liver disease patients with cirrhosis admitted in critical care unit

BACKGROUND:

Clinical significance of respiratory viruses (RVs) as an etiology of pneumonia in liver disease patients with cirrhosis is usually underestimated. Therefore, the aim of this study was to evaluate the spectrum of RVs in cirrhotic patients with pneumonia admitted in critical care units (CCUs) and its impact on the clinical outcome of cirrhotic patients.

MATERIAL AND METHOD:

A prospective study was conducted in a tertiary care CCU, and consecutive cirrhotic patients with pneumonia were included. Bronchoalveolar lavage or throat swab/nasal swab was collected in viral transport medium for analysis of RVs by multiplex real-time polymerase chain reaction. A total of 135 cirrhotic patients were included, viral and bacterial etiology of pneumonia was identified, and analysis was done with the clinical outcome.

RESULTS:

Overall, RVs were detected in 30 (22.2%) cirrhotic patients and viral–bacterial coinfection in 16 (11.8%) cirrhotic patients. The most common virus detected was rhinovirus in 9 (30%) patients. Mortality in cirrhotic patients with RV infection was significantly higher in comparison to cirrhotic patients with no RV infection (25 [83.3%] and 11 [12.3%], respectively, P < 0.001).

CONCLUSION:

Respiratory viruses in cirrhotic patients with pneumonia are associated with poor clinical outcome.

How can we improve clinical research in pneumonia?

PURPOSE OF REVIEW

The primary challenges in the field of clinical research include a lack of support within existing infrastructure, insufficient number of clinical research training programs and a paucity of qualified mentors. Most medical centers offer infrastructure support for investigators working with industry sponsors or government-funded clinical trials, yet there are a significant amount of clinical studies performed in the field of pneumonia which are observational studies. For this type of research, which is frequently unfunded, support is usually lacking.

RECENT FINDINGS

In an attempt to optimize clinical research in pneumonia, at the University of Louisville, we developed a clinical research coordinating center (CRCC). The center manages clinical studies in the field of respiratory infections, with the primary focus being pneumonia. Other activities of the CRCC include the organization of an annual clinical research training course for physicians and other healthcare workers, and the facilitation of international research mentoring by a process of connecting new pneumonia investigators with established clinical investigators.

SUMMARY

To improve clinical research in pneumonia, institutions need to have the appropriate infrastructure in place to support investigators in all aspects of the clinical research process.

Impact of bacterial and viral coinfection in community-acquired pneumonia in adults

Bacterial and viral coinfected community-acquired pneumonia (CAP) is poorly characterized in adults. The aim of this study was to investigate the influence of bacterial and viral coinfection in patients with CAP. A total of 235 adults who requested molecular tests of pneumonia and were diagnosed with CAP were enrolled in this study. Microbiological tests included blood and sputum cultures, PCR for bacterial and viral pathogens, antigen test for Streptococcus pneumoniae and the influenza virus, and antibody detection of Mycoplasma pneumonia. Of the 235 patients, 32 (13.6%) patients were coinfected with bacteria and virus. Among 64 severe CAP patients, the concurrent infections were confirmed in 14 patients (21.9%). The proportion of severe pneumonia was significantly higher in patients with coinfection, and they showed a significantly higher mortality rate. In conclusion, bacterial and viral coinfection in CAP is not a rare occurrence in adults. Viral and bacterial coinfections have an adverse impact on the severity of the pneumonia, and increase morbidity and mortality in patients with CAP.

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13.6% CAP patients and 21.9% severe CAP patients were coinfected with bacteria and virus in adults.

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Bacterial and viral coinfection may adversely impact the severity of pneumonia.

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Concurrent infection also increases the morbidity in adult patients with CAP.

Respiratory virus of severe pneumonia in South Korea: Prevalence and clinical implications

Background

Severe viral pneumonia is associated with a high mortality rate. However, due to the vulnerability of critically ill patients, invasive diagnostic methods should be performed with caution in the intensive care unit (ICU). It would be helpful if the prevalence, risk factors, and clinical impact of virus detection are elucidated.

Methods

We evaluated patients with severe pneumonia between January 1^st 2008 and December 31^st 2015. Reverse transcription-polymerase chain reaction (RT-PCR) analysis was performed for 8 respiratory viruses when viral pathogen could not be excluded as the origin of severe pneumonia. The baseline characteristics, laboratory results, microbiological findings, and clinical outcomes of the patients were analyzed.

Results

Of the 2,347 patients admitted to the medical ICU, 515 underwent RT-PCR for respiratory viruses, 69 of whom had positive results. The detection rate was higher during the winter, with a community onset, in patients with history of recent chemotherapy, and low platelet count. Additional bronchoscopic sampling along with upper respiratory specimen increased the yield of viral detection. Respiratory syncytial virus was the most common pathogen detected, while influenza A was the most common virus with bacterial coinfection. Respiratory virus detection led to changes in clinical management in one-third of the patients.

Conclusions

The detection of viral pathogens in patients with severe pneumonia is not rare, and can be more common in certain group of patients. Invasive sampling for RT-PCR can be helpful, and such detection can lead to positive changes in clinical management.

Pneumonia with bacterial and viral coinfection

PURPOSE OF REVIEW

We aim to review the epidemiology of pneumonia with bacterial and viral coinfection, the pathogenesis and clinical impact of coinfection along with the current state of treatment and outcomes.

RECENT FINDINGS

Emphasis is given to the pathogenesis of bacterial and viral co-infection including specific highlighting on influenza, rhinovirus, respiratory syncytial virus and cytomegalovirus. Updates on the current state of diagnosis and management are included, as well as on areas where future research can be directed to improve patient clinical outcomes regarding viral and bacterial coinfection.

SUMMARY

Bacterial and viral coinfection is increasingly recognized as an underlying etiology for community- and hospital-acquired infections. Coinfections may be a risk factor for ICU admission, severity of disease, and mortality. Clinicians must be aware of these coinfections for appropriate management and prognostication, as well as for the prevention of nosocomial spread of viral illness.

Comparison of viral infection in healthcare-associated pneumonia (HCAP) and community-acquired pneumonia (CAP)

Background

Although viruses are known to be the second most common etiological factor in community-acquired pneumonia (CAP), the respiratory viral profile of the patients with healthcare-associated pneumonia (HCAP) has not yet been elucidated. We investigated the prevalence and the clinical impact of respiratory virus infection in adult patients with HCAP.

Methods

Patients admitted with HCAP or CAP, between January and December 2016, to a tertiary referral hospital in Korea, were prospectively enrolled, and virus identification was performed using reverse-transcription polymerase chain reaction (RT-PCR).

Results

Among 452 enrolled patients (224 with HCAP, 228 with CAP), samples for respiratory viruses were collected from sputum or endotracheal aspirate in 430 (95.1%) patients and from nasopharyngeal specimens in 22 (4.9%) patients. Eighty-seven (19.2%) patients had a viral infection, and the proportion of those with viral infection was significantly lower in the HCAP than in the CAP group (13.8% vs 24.6%, p = 0.004). In both the HCAP and CAP groups, influenza A was the most common respiratory virus, followed by entero-rhinovirus. The seasonal distributions of respiratory viruses were also similar in both groups. In the HCAP group, the viral infection resulted in a similar length of hospital stay and in-hospital mortality as viral–bacterial coinfection and bacterial infection, and the CAP group showed similar results.

Conclusions

The prevalence of viral infection in patients with HCAP was lower than that in patients with CAP, and resulted in a similar prognosis as viral–bacterial coinfection or bacterial infection.

Respiratory pathogen panels in the hospital: good or unnecessary?

PURPOSE OF REVIEW

We aim to review the epidemiology of respiratory viral infections and the strengths and limitations of multiplex respiratory pathogen panels that are currently available along with their respective features and differences.

RECENT FINDINGS

We give particular emphasis to the pathogens included on each test and evaluate their performance in the hospital setting.

SUMMARY

We conclude with a discussion on the evidence for the clinical utility of respiratory pathogen multiplex panels in hospitalized patients, including the potential for coinfection with viral and bacterial pathogens.

Respiratory Viruses in Invasively Ventilated Critically Ill Patients-A Prospective Multicenter Observational Study

OBJECTIVES

The presence of respiratory viruses and the association with outcomes were assessed in invasively ventilated ICU patients, stratified by admission diagnosis.

DESIGN

Prospective observational study.

SETTING

Five ICUs in the Netherlands.

PATIENTS

Between September 1, 2013, and April 30, 2014, 1,407 acutely admitted and invasively ventilated patients were included.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Nasopharyngeal swabs and tracheobronchial aspirates were collected upon intubation and tested for 14 respiratory viruses. Out of 1,407 patients, 156 were admitted because of a severe acute respiratory infection and 1,251 for other reasons (non-severe acute respiratory infection). Respiratory viruses were detected in 28.8% of severe acute respiratory infection patients and 17.0% in non-severe acute respiratory infection (p < 0.001). In one third, viruses were exclusively detected in tracheobronchial aspirates. Rhinovirus and human metapneumovirus were more prevalent in severe acute respiratory infection patients (9.6% and 2.6% vs 4.5 and 0.2%; p = 0.006 and p < 0.001). In both groups, there were no associations between the presence of viruses and the number of ICU-free days at day 28, crude mortality, and mortality in multivariate regression analyses.

CONCLUSIONS

Respiratory viruses are frequently detected in acutely admitted and invasively ventilated patients. Rhinovirus and human metapneumovirus are more frequently found in severe acute respiratory infection patients. Detection of respiratory viruses is not associated with worse clinically relevant outcomes in the studied cohort of patients.

The epidemiology of medically attended respiratory syncytial virus in older adults in the United States: A systematic review

Objective

This review was undertaken to assess the historical evidence of the disease incidence and burden of laboratory-confirmed respiratory syncytial virus (RSV) in medically attended older adults.

Design

A qualitative systematic literature review was performed; no statistical synthesis of the data was planned, in anticipation of expected heterogeneity across studies in this population.

Methods

A literature search of PubMed, Embase, and the Cochrane Library was conducted for studies of medically attended RSV in older adults (≥ 50 years) published in the last 15 years. Two independent reviewers screened titles and abstracts based on predefined inclusion and exclusion criteria.

Results

From 10 studies reporting incidence proportions, RSV may be the causative agent in up to 12% of medically attended acute respiratory illness in older adults unselected for comorbidities, with variations in clinical setting and by year. In multiple studies, medically attended–RSV incidence among older adults not selected for having underlying health conditions increased with increasing age. Of prospectively followed lung transplant recipients, 16% tested positive for RSV. In hospitalized adults with chronic cardiopulmonary diseases, 8% to 13% were infected with RSV during winter seasons (8%-13%) or metapneumovirus season (8%). Hospitalizations for RSV in older adults typically lasted 3 to 6 days, with substantial proportions requiring intensive care unit admission and mechanical ventilation. Among older adults hospitalized with RSV, the mortality rate was 6% to 8%.

Conclusions

Protection of older adults against RSV could reduce respiratory-related burden, especially as age increases and the prevalence of comorbidities (especially cardiopulmonary comorbidities) grows.

Severe Respiratory Viral Infections: New Evidence and Changing Paradigms

Lower respiratory tract infection is a leading cause of death in the United States. Advances in diagnostic testing have improved our ability to detect pathogens. Viral pathogens are important causal pathogens in immunocompetent patients. As the number of elderly adults and those with chronic medical conditions increases, the burden of viral respiratory infections will increase. Clinicians must be familiar with the characteristics of rhinovirus, human adenoviruses, respiratory syncytial virus, and human metapneumovirus. Major challenges include distinguishing true infection from asymptomatic carriage and characterizing patients admitted with severe lower respiratory tract infection who do not have a causative pathogen identified.

Severe varicella-zoster virus pneumonia: a multicenter cohort study

BACKGROUND

Pneumonia is a dreaded complication of varicella-zoster virus (VZV) infection in adults; however, the data are limited. Our objective was to investigate the clinical features, management, and outcomes of critically ill patients with VZV-related community-acquired pneumonia (VZV-CAP).

METHODS

This was an observational study of patients with VZV-CAP admitted to 29 intensive care units (ICUs) from January 1996 to January 2015.

RESULTS

One hundred and two patients with VZV-CAP were included. Patients were young (age 39 years (interquartile range 32-51)) and 53 (52%) were immunocompromised. Time since respiratory symptom onset was 2 (1-3) days. There was a seasonal distribution of the disease, with more cases during spring and winter time. All but four patients presented with typical skin rash on ICU admission. Half the patients received mechanical ventilation within 1 (1-2) day following ICU admission (the ratio of arterial oxygen partial pressure to fractional inspired oxygen (PaO₂/FiO₂) = 150 (80-284), 80% with acute respiratory distress syndrome (ARDS)). Sequential Organ Failure Assessment (SOFA) score on day 1 (odds ratio (OR) 1.90 (1.33-2.70); p < 0.001), oxygen flow at ICU admission (OR 1.25 (1.08-1.45); p = 0.004), and early bacterial co-infection (OR 14.94 (2.00-111.8); p = 0.009) were independently associated with the need for mechanical ventilation. Duration of mechanical ventilation was 14 (7-21) days. ICU and hospital mortality rates were 17% and 24%, respectively. All patients were treated with aciclovir and 10 received adjunctive therapy with steroids. Compared to 60 matched steroid-free controls, patients treated with steroids had a longer mechanical ventilation duration, ICU length of stay, and a similar hospital mortality, but experienced more ICU-acquired infections.

CONCLUSIONS

Severe VZV-CAP is responsible for an acute pulmonary involvement associated with a significant morbidity and mortality. Steroid therapy did not influence mortality, but increased the risk of superinfection.

Frequency of respiratory virus infections and next-generation analysis of influenza A/H1N1pdm09 dynamics in the lower respiratory tract of patients admitted to the ICU

Recent molecular diagnostic methods have significantly improved the diagnosis of viral pneumonia in intensive care units (ICUs). It has been observed that 222G/N changes in the HA gene of H1N1pdm09 are associated with increased lower respiratory tract (LRT) replication and worse clinical outcome. In the present study, the frequency of respiratory viruses was assessed in respiratory samples from 88 patients admitted to 16 ICUs during the 2014–2015 winter-spring season in Lombardy. Sixty-nine out of 88 (78.4%) patients were positive for a respiratory viral infection at admission. Of these, 57/69 (82.6%) were positive for influenza A (41 A/H1N1pdm09 and 15 A/H3N2), 8/69 (11.6%) for HRV, 2/69 (2.9%) for RSV and 2/69 (2.9%) for influenza B. Phylogenetic analysis of influenza A/H1N1pdm09 strains from 28/41 ICU-patients and 21 patients with mild respiratory syndrome not requiring hospitalization, showed the clear predominance of subgroup 6B strains. The median influenza A load in LRT samples of ICU patients was higher than that observed in the upper respiratory tract (URT) (p<0.05). Overall, a greater number of H1N1pdm09 virus variants were observed using next generation sequencing on partial HA sequences (codons 180–286) in clinical samples from the LRT as compared to URT. In addition, 222G/N/A mutations were observed in 30% of LRT samples from ICU patients. Finally, intra-host evolution analysis showed the presence of different dynamics of viral population in LRT of patients hospitalized in ICU with a severe influenza infection.

Respiratory viral infections are underdiagnosed in patients with suspected sepsis

The study aim was to investigate the prevalence and clinical relevance of viral findings by multiplex PCR from the nasopharynx of clinically septic patients during a winter season. During 11 weeks of the influenza epidemic period in January–March 2012, consecutive adult patients suspected to be septic (n = 432) were analyzed with cultures from blood and nasopharynx plus multiplex PCR for respiratory viruses on the nasopharyngeal specimen. The results were compared with those from microbiology analyses ordered as part of standard care. During the winter season, viral respiratory pathogens, mainly influenza A virus, human metapneumovirus, coronavirus, and respiratory syncytial virus were clinically underdiagnosed in 70% of patients positive by the multiplex PCR assay. During the first four weeks of the influenza epidemic, few tests for influenza were ordered by clinicians, indicating low awareness that the epidemic had started. Nasopharyngeal findings of Streptococcus pneumoniae and Haemophilus influenzae by culture correlated to pneumonia diagnosis, and in those patients laboratory signs of viral co-infections were common but rarely suspected by clinicians. The role of respiratory viral infections in patients presenting with a clinical picture of sepsis is underestimated. Specific antiviral treatment might be beneficial in some cases and may reduce spread in a hospital setting. Diagnosing viral infections may promote reduction of unnecessary antibiotic use. It can also be a tool for decisions concerning patient logistics, in order to minimize exposure of susceptible patients and personnel.

Frequency of respiratory viruses among patients admitted to 26 Intensive Care Units in seven consecutive winter-spring seasons (2009-2016) in Northern Italy

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Viral infections are present in large proportion of ICU-admitted patients with CAP.

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Influenza and rhinovirus accounted for a significant number of viral CAP episodes.

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The use of LRT instead of URT samples might be useful in the diagnosis of viral CAP

Background

The role of respiratory viruses in the etiology of community-acquired pneumonia (CAP) is still debated. The advent of molecular assays has improved the identification of viruses in patients with CAP and according to published studies, viruses account for 11-55% of adult CAP cases.

Objectives and study design

In the present study, the frequency of respiratory viruses was evaluated in respiratory samples collected from 414 patients with CAP admitted to 26 ICUs in the Lombardy Region (10 million inhabitants) during seven winter-spring seasons (2009–2016).

Results

In 226 (54.6%) patients one or more respiratory viruses were identified, while 188 (45.4%) patients were negative. A single virus infection was observed in 214/226 (94.7%) patients; while, in 12/226 (5.3%) at least two respiratory viruses were detected. Influenza A was the most common virus in 140/226 patients (61.9%) followed by rhinoviruses (33/226, 14.6%), respiratory syncytial virus (13/226, 5.8%), influenza B virus (9/226, 4.0%), human coronaviruses (9/226, 4.0%), cytomegalovirus (9/226, 4.0%) and human metapneumovirus (1/226, 0.4%).

Conclusions

Viral infections are present in a consistent proportion of patients admitted to the ICU for CAP. Influenza A and rhinovirus accounted for three-quarters of all CAP in ICU patients. The use of lower respiratory instead of upper respiratory samples might be useful in the diagnosis of viral CAP.

Viral infection in community-acquired pneumonia: a systematic review and meta-analysis

The advent of PCR has improved the identification of viruses in patients with community-acquired pneumonia (CAP). Several studies have used PCR to establish the importance of viruses in the aetiology of CAP.We performed a systematic review and meta-analysis of the studies that reported the proportion of viral infection detected via PCR in patients with CAP. We excluded studies with paediatric populations. The primary outcome was the proportion of patients with viral infection. The secondary outcome was short-term mortality.Our review included 31 studies. Most obtained PCR via nasopharyngeal or oropharyngeal swab. The pooled proportion of patients with viral infection was 24.5% (95% CI 21.5-27.5%). In studies that obtained lower respiratory samples in >50% of patients, the proportion was 44.2% (95% CI 35.1-53.3%). The odds of death were higher in patients with dual bacterial and viral infection (OR 2.1, 95% CI 1.32-3.31).Viral infection is present in a high proportion of patients with CAP. The true proportion of viral infection is probably underestimated because of negative test results from nasopharyngeal or oropharyngeal swab PCR. There is increased mortality in patients with dual bacterial and viral infection.

The potential influence of human parainfluenza viruses detected during hospitalization among critically ill patients in Kuwait, 2013-2015

BACKGROUND

The four types of human parainfluenza viruses (PIV) are important causes of community-acquired pneumonia, particularly in children; however, limited information exists about the incidence of PIV in critically ill patients. The aim of this study is to describe the spectrum, incidence and clinical features of PIV-associated infections diagnosed during the hospital stay of patients admitted to pediatric intensive care unit (PICU) and intensive care unit (ICU) of 5 medical centers across Kuwait.

METHODS

This was a population-based, retrospective study from 2013 to 2015. Specimens were analyzed by molecular methods. This analysis was performed using the database of Virology Unit, Mubarak Al-Kabeer Hospital. Data from 1510 admitted patients with suspected respiratory viral infections was extracted.

RESULTS

The database contained a total of 39 (2.6%) patients infected with PIV (53.8% male and 46.2% females) and 20 (51.3%) were under 1 year of age. The most frequently isolated type was type 3 (28, 71.8%) followed by type 1 (9, 23.1%). At admission the most common clinical diagnosis was pneumonia in 12 patients (30.8%, p < 0.05) followed by bronchiolitis in 10 patients (25.6%).

CONCLUSION

PIV plays an important yet unrecognized role in the outcomes of PIUC and ICU patients. Our results contribute to the limited epidemiologic data of PIV in PIUC and ICU in this region.

Improved Detection of Respiratory Pathogens by Use of High-Quality Sputum with TaqMan Array Card Technology

New diagnostic platforms often use nasopharyngeal or oropharyngeal (NP/OP) swabs for pathogen detection for patients hospitalized with community-acquired pneumonia (CAP). We applied multipathogen testing to high-quality sputum specimens to determine if more pathogens can be identified relative to NP/OP swabs. Children (<18 years old) and adults hospitalized with CAP were enrolled over 2.5 years through the Etiology of Pneumonia in the Community (EPIC) study. NP/OP specimens with matching high-quality sputum (defined as ≤10 epithelial cells/low-power field [lpf] and ≥25 white blood cells/lpf or a quality score [q-score] definition of 2+) were tested by TaqMan array card (TAC), a multipathogen real-time PCR detection platform. Among 236 patients with matched specimens, a higher proportion of sputum specimens had ≥1 pathogen detected compared with NP/OP specimens in children (93% versus 68%; P < 0.0001) and adults (88% versus 61%; P < 0.0001); for each pathogen targeted, crossing threshold (CT) values were earlier in sputum. Both bacterial (361 versus 294) and viral detections (245 versus 140) were more common in sputum versus NP/OP specimens, respectively, in both children and adults. When available, high-quality sputum may be useful for testing in hospitalized CAP patients.

Viral-bacterial coinfection affects the presentation and alters the prognosis of severe community-acquired pneumonia

BACKGROUND

Multiplex polymerase chain reaction (mPCR) enables recovery of viruses from airways of patients with community-acquired pneumonia (CAP), although their clinical impact remains uncertain.

METHODS

Among consecutive adult patients who had undergone a mPCR within 72 hours following their admission to one intensive care unit (ICU), we retrospectively included those with a final diagnosis of CAP. Four etiology groups were clustered: bacterial, viral, mixed (viral-bacterial) and no etiology. A composite criterion of complicated course (hospital death or mechanical ventilation > 7 days) was used. A subgroup analysis compared patients with bacterial and viral-bacterial CAP matched on the bacterial pathogens.

RESULTS

Among 174 patients (132 men [76 %], age 63 [53-75] years, SAPSII 38 [27;55], median PSI score 106 [78;130]), bacterial, viral, mixed and no etiology groups gathered 46 (26 %), 53 (31 %), 45 (26 %) and 30 (17 %) patients, respectively. Virus-infected patients displayed a high creatine kinase serum level, a low platelet count, and a trend toward more frequent alveolar-interstitial infiltrates. A complicated course was more frequent in the mixed group (31/45, 69 %), as compared to bacterial (18/46, 39 %), viral (15/53, 28 %) and no etiology (12/30, 40 %) groups (p < 0.01). In multivariate analysis, the mixed (viral-bacterial) infection was independently associated with complicated course (reference: bacterial pneumonia; OR, 3.58; CI 95 %, 1.16-11; p = 0.03). The subgroup analysis of bacteria-matched patients confirmed these findings.

CONCLUSIONS

Viral-bacterial coinfection during severe CAP in adults is associated with an impaired presentation and a complicated course.

Clinical practice of respiratory virus diagnostics in critically ill patients with a suspected pneumonia: A prospective observational study

BACKGROUND

Clinical guidelines suggest testing for respiratory viruses during the influenza season, but are unclear which categories of patients on the intensive care unit (ICU) should be tested.

OBJECTIVE

We described the clinical practice of diagnostic testing for respiratory virus infections in patients presenting to ICU with suspected community-acquired pneumonia (CAP) or hospital-acquired pneumonia (HAP).

STUDY DESIGN

Prospective observational study in consecutive CAP and HAP patients with an ICU stay of more than 24h in two tertiary care hospitals in The Netherlands, from 2011 to December 2013. The proportion of patients receiving diagnostic testing with PCR for the presence of respiratory viruses in respiratory tract specimens was determined.

RESULTS

In total, 1452 patients were included, of which 712 patients presented with CAP and 740 with HAP. In CAP, 282 of 712 (40%) were tested for respiratory viruses (190 of 417 (46%) during the influenza season). In HAP, 95 of 740 (13%) were tested (50 of 372 (13%) during the influenza season). Regardless of the season, virus diagnostic tests were ordered significantly more often in patients with comorbidities, and in those presenting with elevated CRP and leucopenia. In patients who were tested during the influenza season, the prevalence of influenza was 14% in patients with CAP and 10% in those with HAP. Influenza was absent during the summer in both groups.

CONCLUSIONS

Less than half of patients admitted to the ICU with suspected pneumonia were tested for the presence of viral pathogens, either in or outside the influenza season.

Severe rhinovirus pneumonia in a young woman taking performance-enhancing drugs

A 22-year-old woman presented to the emergency room of a local hospital with pleuritic chest pain. She regularly worked out and admitted to taking performance-enhancing drugs (PEDs). Clinical findings and further diagnostic work up revealed a diagnosis of perimyocarditis, and adequate therapy was initiated. During the course of the first day, the patient had to be intubated and mechanically ventilated. A diagnosis of bilateral pneumonia and acute respiratory distress syndrome (ARDS) due to an infection by rhinovirus spp was made. A smoking habit, the intense physical training and the use of PED's may have exacerbated the course of the viral pneumonia. After 12 days the patient could be extubated. The length of stay in the intensive care unit was 16 days. After hospital discharge, the patient went to a pulmonary rehabilitation facility for 2 weeks. The outcome was favourable and the patient resumed her strength and endurance training.

Evolution over a 15-year period of the clinical characteristics and outcomes of critically ill patients with severe community-acquired pneumonia

OBJECTIVES

To study the characteristics and outcomes of patients in the ICU with severe community-acquired pneumonia (SCAP) over a 15-year surveillance period.

METHODS

We conducted a retrospective cohort study of episodes of SCAP, and assessed the epidemiology, etiology, treatment and outcomes of patients admitted to the ICU, comparing three periods (1999-2003, 2004-2008 and 2009-2013).

RESULTS

A total of 458 patients were diagnosed with SCAP. The overall cumulative incidence was 37.4 episodes/1000 admissions, with a progressive increase over the three periods (P<0.001). Patients fulfilling the two major IDSA/ATS criteria at admission increased from 64.2% in the first period to 82.5% in the last period (P=0.005). Streptococcus pneumoniae was the prevalent pathogen. The incidence of bacteremia was 23.1%, and a progressive significant reduction in overall incidence was observed over the three periods (P=0.02). Globally, 91% of the patients received appropriate empiric antibiotic treatment, increasing from 78.3% in the first period to 97.7% in the last period (P<0.001). Combination antibiotic therapy (betalactam+macrolide or fluoroquinolone) increased significantly from the first period (61%) to the last period (81.3%) (P<0.001). Global ICU mortality was 25.1%, and decreased over the three periods (P=0.001).

CONCLUSIONS

Despite a progressively higher incidence and severity of SCAP in our ICU, crude ICU mortality decreased by 18%. The increased use of combined antibiotic therapy and the decreasing rates of bacteremia were associated to improved patient prognosis.

Viral Respiratory Infections of Adults in the Intensive Care Unit

Viral lower respiratory tract infections (LRTIs) are an underappreciated cause of critical illness in adults. Recent advances in viral detection techniques over the past decade have demonstrated viral LRTIs are associated with rates of morbidity, mortality, and health care utilization comparable to those of seen with bacterial community acquired and nosocomial pneumonias. In this review, we describe the relationship between viral LRTIs and critical illness, as well as discuss relevant clinical features and management strategies for the more prevalent respiratory viral pathogens.

Incidence of respiratory viral infections detected by PCR and real-time PCR in adult patients with community-acquired pneumonia: a meta-analysis

Background

With the development of more rapid and sensitive detection methods based on PCR techniques, the contributions of respiratory viral infections to community-acquired pneumonia (CAP) in adult patients are being more and more recognized. Yet, up to now, there has been a lack of synthetic data that clearly demonstrates the incidence of respiratory viral infections in adult patients with CAP.

Objectives

We intended to demonstrate the incidence of respiratory viral infections detected by PCR and real-time PCR in adult patients with CAP.

Methods

We searched PubMed and Embase for studies providing the incidence of respiratory viral infections in adult patients with CAP. We investigated potential sources of heterogeneity by a univariant metaregression analysis and calculated the combined incidence of viral infections, viral infections mixed with other pathogens and individual respiratory virus species.

Results

We eventually identified 23 eligible reports with a total number of 6,404 patients. Incidences ranged from 8.6 to 56.2% for overall respiratory viral infections. We noted significant heterogeneity in incidence estimates for the incidence of viral infections (Cochran's χ² = 269.9, p < 0.0001, I² = 91.8%). The combined incidence of viral infections was 22.4% (95% CI = 19.0-25.7). Incidences of viral coinfections with other pathogens ranged from 3 to 28%. A high level of heterogeneity was identified as well during the estimates for incidences of coinfections (χ² = 200.9, p < 0.0001, I² = 91.5%). The combined incidence of viral coinfections with other pathogens was 12.4% (95% CI = 9.7-15.0). Our heterogeneity analyses suggested that a lower respiratory tract sample was associated with higher overall viral incidence. Moreover, the influenza virus, rhinovirus and coronavirus were the 3 most frequently detected viral pathogens in adult patients with CAP according to our study.

Conclusions

Respiratory viruses are probably crucial pathogens of adult patients with CAP, with the influenza virus being the most frequent viral pathogen identified. More than half of the viral infections are characterized as mixed infections with other pathogens.

Incidence of viral infection detected by PCR and real-time PCR in childhood community-acquired pneumonia: a meta-analysis

Several studies examining the incidence of viral infection in childhood community‐acquired pneumonia (CAP) utilizing polymerase chain reaction (PCR) or real‐time PCR methods have been reported. We systematically searched Pubmed and Embase for studies reporting the incidence of respiratory viral infection in childhood CAP. The pooled incidences of viral infection were calculated with a random‐effects model. Sources of heterogeneity were explored by subgroup analysis and a univariant metaregression analysis. We included 21 eligible reports in our study. We found significant heterogeneity on the incidence of viral infection in childhood CAP. The random effects pooled incidence was 57.4% (95% confidence interval (CI): 50.8–64.1). The pooled incidence of mixed infection was 29.3% (95%CI: 23.0–35.6) with considerable heterogeneity. The pooled incidence of mixed infection was 29.3% (95%CI: 23.0–35.6). Rhinovirus, respiratory syncytial virus (RSV) and bocavirus were found to be the three most common viruses in childhood CAP. We also demonstrated that respiratory viruses were detected in 76.1% of patients aged ≤1 year, 63.1% of patients aged 2–5 years and 27.9% of patients aged ≥ 6 years. We conclude that respiratory viruses are widely detected in paediatric patients with CAP by PCR or real‐time PCR methods. More than half of viral infections are probably concurrent with bacterial infections. Rhinovirus, RSV and bocavirus are the three most frequent viruses identified in childhood CAP; the incidence of viral infection decreased with age.

Utilization of the respiratory virus multiplex reverse transcription-polymerase chain reaction test for adult patients at a Korean tertiary care center

BACKGROUND/AIMS

Respiratory viruses (RVs) are considered to be important respiratory pathogens in adult patients, and the multiplex reverse transcription-polymerase chain reaction (RT-PCR) test is used frequently in adult patients with respiratory infections. However, clinical data regarding utilization of the multiplex RT-PCR test for RVs are lacking.

METHODS

We investigated the utilization of the multiplex RT-PCR test for RVs at Chung-Ang University Hospital in Seoul, Korea, between January 2012 and April 2013.

RESULTS

During the study period, the multiplex RT-PCR test was performed for 291 adult patients. The test frequency was 4.9% of rapid influenza antigen detection tests and 0.8% of respiratory bacterial culture studies. A turnaround time of < 48 hours was observed in 25.9% of positive tests. Most of the tests were performed for admitted patients (97.9%) with a community-acquired infection (84.2%) during the flu season (82.5%). RVs were detected in 81 of 291 cases (27.8%). The RV positivity rates for community- and hospital-acquired infections did not differ (28.6% vs. 23.9%, p = 0.52). Of 166 patients with pneumonia, 44 (26.5%) had a viral infection. Among the patients with RV-associated pneumonia, an RV other than influenza was detected in 20 patients (45.4%).

CONCLUSIONS

The multiplex RT-PCR test for RVs was infrequently performed at a tertiary care center, and the test results were often reported late. The test was most often performed for admitted adult patients with community-acquired infections during the flu season. The utilization of multiplex RT-PCR testing for RVs in current clinical practice should be improved.

Quels prélèvements aux urgences pour le diagnostic microbiologique d’une infection pulmonaire communautaire grave du sujet immunocompétent ?

Grâce aux méthodes de diagnostic actuelles, l’identification microbiologique des pneumonies communautaires graves (PCG) peut être établie dans la moitié des cas. Si les études épidémiologiques ont permis d’établir des recommandations préconisant l’antibiothérapie empirique à débuter, l’identification microbiologique du ou des pathogène(s) responsable(s) est nécessaire pour la conduite ultérieure du traitement. Les principaux examens à effectuer pour l’identification bactérienne sont la réalisation d’hémocultures, d’un examen cytobactériologique des sécrétions respiratoires et la recherche d’une antigénurie pneumococcique ou légionnelle. Les hémocultures sont positives dans 15 à 25 % des cas de PCG. L’examen cytobactériologique des crachats ou l’aspiration endotrachéale, chez le patient intubé, aide au diagnostic sous réserve que le prélèvement ne soit pas contaminé par la flore oropharyngée. La positivité d’une antigénurie est également fonction de la sévérité de la pneumonie. Cet examen permet un diagnostic rapide et n’est pas influencé par une antibiothérapie préalable. Les virus à tropisme respiratoire seraient responsables de 10 à 40 % des PCG. En période épidémique, des prélèvements par écouvillonnage nasal à la recherche du virus influenza sont recommandés, en raison du bénéfice attendu avec l’instauration d’un traitement par oseltamivir. Les sérologies permettant de faire le diagnostic de pneumonie à germes intracellulaires ont peu d’intérêt aux urgences de même que la réalisation de prélèvements sous fibroscopie bronchique. Enfin, la recherche qualitative par reverse transcriptase (PCR) sérique présente peu d’intérêt pour le diagnostic de pneumonie bactérienne par rapport aux méthodes usuelles.

Influenza and other respiratory viruses involved in severe acute respiratory disease in northern Italy during the pandemic and postpandemic period (2009-2011)

Since 2009 pandemic, international health authorities recommended monitoring severe and complicated cases of respiratory disease, that is, severe acute respiratory infection (SARI) and acute respiratory distress syndrome (ARDS). We evaluated the proportion of SARI/ARDS cases and deaths due to influenza A(H1N1)pdm09 infection and the impact of other respiratory viruses during pandemic and postpandemic period (2009-2011) in northern Italy; additionally we searched for unknown viruses in those cases for which diagnosis remained negative. 206 respiratory samples were collected from SARI/ARDS cases and analyzed by real-time RT-PCR/PCR to investigate influenza viruses and other common respiratory pathogens; also, a virus discovery technique (VIDISCA-454) was applied on those samples tested negative to all pathogens. Influenza A(H1N1)pdm09 virus was detected in 58.3% of specimens, with a case fatality rate of 11.3%. The impact of other respiratory viruses was 19.4%, and the most commonly detected viruses were human rhinovirus/enterovirus and influenza A(H3N2). VIDISCA-454 enabled the identification of one previously undiagnosed measles infection. Nearly 22% of SARI/ARDS cases did not obtain a definite diagnosis. In clinical practice, great efforts should be dedicated to improving the diagnosis of severe respiratory disease; the introduction of innovative molecular technologies, as VIDISCA-454, will certainly help in reducing such "diagnostic gap."

Lower respiratory tract virus findings in mechanically ventilated patients with severe community-acquired pneumonia

BACKGROUND

The role of viral infections in the etiology of severe community-acquired pneumonia (SCAP) was prospectively evaluated from 2008 to 2012 at a university-level intensive care unit.

METHODS

Clinical data and microbiological tests were assessed: blood cultures, urine pneumococcal and legionella antigens, Mycoplasma pneumoniae and Chlamydia pneumoniae antibodies from paired serums, and respiratory virus detection by multiplex, real-time polymerase chain reaction (PCR) from nasopharyngeal swabs and lower tracheal specimens via intubation tube.

RESULTS

Of 49 mechanically ventilated SCAP patients (21 men and 28 women; median age, 54 years), the etiology was identified in 45 cases (92%). There were 21 pure bacterial infections (43%), 5 probably pure viral infections (10%), and 19 mixed bacterial-viral infections (39%), resulting in viral etiology in 24 patients (49%). Of 26 viruses, 21 (81%) were detected from bronchial specimens and 5 (19%) from nasopharyngeal swabs. Rhinovirus (15 cases, 58%) and adenovirus (4 cases, 15%) were the most common viral findings. The bacterial-viral etiology group had the highest peak C-reactive protein levels (median, 356 [25th-75th percentiles, 294-416], P = .05), whereas patients with probably viral etiology had the lowest peak procalcitonin levels (1.7 [25th-75th percentiles, 1.6-1.7]). The clinical characteristics of pure bacterial and mixed bacterial-viral etiologies were comparable. Hospital stay was longest among the bacterial group (17 vs 14 days; P = .02).

CONCLUSIONS

Viral findings were demonstrated in almost half of the SCAP patients. Clinical characteristics were similar between the pure bacterial and mixed bacterial-viral infections groups. The frequency of viral detection depends on the availability of PCR techniques and lower respiratory specimens.