Other Respiratory Viruses as a Cause of Community-Acquired Pneumonia

2020 ◽  
Vol 41 (04) ◽  
pp. 579-591
Author(s):  
James M. Walter
Keyword(s):  
Pneumococcal Vaccination ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Nucleic Acid Amplification ◽  
Respiratory Pathogens ◽  
Viral Pathogens ◽  
Vaccination Programs ◽  
Syncytial Virus ◽  
Human Parainfluenza Virus ◽  
Immunocompetent Patients

AbstractCommunity-acquired pneumonia (CAP) is a major cause of morbidity and mortality worldwide. There is growing appreciation of the burden of noninfluenza viral pathogens in CAP. Due to multiple factors including pneumococcal vaccination programs, declining rates of cigarette smoking, an aging population, and increasingly sensitive diagnostic tests, respiratory viruses are now the most common pathogens detected in CAP, outpacing Streptococcus pneumoniae. Noninfluenza respiratory pathogens are widely accepted as causal pathogens in CAP including in immunocompetent patients. This review provides an overview of five noninfluenza respiratory viral pathogens commonly implicated in CAP pathogenesis: rhinovirus, human metapneumovirus, respiratory syncytial virus, human parainfluenza virus, and human adenoviruses. Nucleic acid amplification testing platforms and their impact on antimicrobial stewardship efforts are also considered.

scholarly journals Acute respiratory viral infections in children in Rio de Janeiro and Teresópolis, Brazil

2012 ◽  
Vol 54 (5) ◽  
pp. 249-255 ◽  
Author(s):  
Maria Carolina M. Albuquerque ◽  
Rafael B. Varella ◽  
Norma Santos
Keyword(s):  
Rio De Janeiro ◽  
Influenza A ◽  
Viral Infections ◽  
Respiratory Infections ◽  
Respiratory Viruses ◽  
Respiratory Pathogens ◽  
Viral Pathogens ◽  
Nasal Swabs ◽  
Syncytial Virus ◽  
Viral Respiratory Infections

The frequency of viral pathogens causing respiratory infections in children in the cities of Rio de Janeiro and Teresópolis was investigated. Nasal swabs from children with acute respiratory illnesses were collected between March 2006 and October 2007. Specimens were tested for viral detection by conventional (RT)-PCR and/or real time PCR. Of the 205 nasal swabs tested, 64 (31.2%) were positive for at least one of the viral pathogens. Single infections were detected in 56 samples, 50 of those were caused by RNA viruses: 33 samples tested positive for rhinovirus, five for influenza A, five for metapneumovirus, four for coronavirus and, three for respiratory syncytial virus. For the DNA viruses, five samples were positive for bocavirus and one for adenovirus. Co-infections with these viruses were detected in eight samples. Our data demonstrate a high frequency of viral respiratory infections, emphasizing the need for a more accurate diagnosis particularly for the emerging respiratory viruses. The fact that the emerging respiratory viruses were present in 9.2% of the tested samples suggests that these viruses could be important respiratory pathogens in the country.

Respiratory viral testing and antibacterial treatment in patients hospitalized with community-acquired pneumonia

2020 ◽  
pp. 1-9
Author(s):  
Michael Klompas ◽  
Peter B. Imrey ◽  
Pei-Chun Yu ◽  
Chanu Rhee ◽  
Abhishek Deshpande ◽  
...  
Keyword(s):  
Retrospective Cohort ◽  
Respiratory Virus ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Blood Cultures ◽  
Antibacterial Treatment ◽  
Viral Pathogens ◽  
Antimicrobial Utilization ◽  
Viral Testing ◽  
Virus Testing

Abstract Objective: Viruses are more common than bacteria in patients hospitalized with community-acquired pneumonia. Little is known, however, about the frequency of respiratory viral testing and its associations with antimicrobial utilization. Design: Retrospective cohort study. Setting: The study included 179 US hospitals. Patients: Adults admitted with pneumonia between July 2010 and June 2015. Methods: We assessed the frequency of respiratory virus testing and compared antimicrobial utilization, mortality, length of stay, and costs between tested versus untested patients, and between virus-positive versus virus-negative patients. Results: Among 166,273 patients with pneumonia on admission, 40,787 patients (24.5%) were tested for respiratory viruses, 94.8% were tested for influenza, and 20.7% were tested for other viruses. Viral assays were positive in 5,133 of 40,787 tested patients (12.6%), typically for influenza and rhinovirus. Tested patients were younger and had fewer comorbidities than untested patients, but patients with positive viral assays were older and had more comorbidities than those with negative assays. Blood cultures were positive for bacterial pathogens in 2.7% of patients with positive viral assays versus 5.3% of patients with negative viral tests (P < .001). Antibacterial courses were shorter for virus-positive versus -negative patients overall (mean 5.5 vs 6.4 days; P < .001) but varied by bacterial testing: 8.1 versus 8.0 days (P = .60) if bacterial tests were positive; 5.3 versus 6.1 days (P < .001) if bacterial tests were negative; and 3.3 versus 5.2 days (P < .001) if bacterial tests were not obtained (interaction P < .001). Conclusions: A minority of patients hospitalized with pneumonia were tested for respiratory viruses; only a fraction of potential viral pathogens were assayed; and patients with positive viral tests often received long antibacterial courses.

scholarly journals Circulation of Respiratory Viruses in Hospitalized Adults before and during the COVID-19 Pandemic in Brescia, Italy: A Retrospective Study

2021 ◽  
Vol 18 (18) ◽  
pp. 9525
Author(s):  
Maria Antonia De Francesco ◽  
Caterina Pollara ◽  
Franco Gargiulo ◽  
Mauro Giacomelli ◽  
Arnaldo Caruso
Keyword(s):  
Respiratory Syncytial Virus ◽  
Influenza A ◽  
Statistical Significance ◽  
Respiratory Viruses ◽  
Influenza Viruses ◽  
Contact Tracing ◽  
Nucleic Acid Detection ◽  
Respiratory Pathogens ◽  
Syncytial Virus ◽  
Human Coronaviruses

Different preventive public health measures were adopted globally to limit the spread of SARS-CoV-2, such as hand hygiene and the use of masks, travel restrictions, social distance actions such as the closure of schools and workplaces, case and contact tracing, quarantine and lockdown. These measures, in particular physical distancing and the use of masks, might have contributed to containing the spread of other respiratory viruses that occurs principally by contact and droplet routes. The aim of this study was to evaluate the prevalence of different respiratory viruses (influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses 1, 2, 3 and 4, rhinovirus, adenovirus, metapneumovirus and human coronaviruses) after one year of the pandemic. Furthermore, another aim was to evaluate the possible impact of these non-pharmaceutical measures on the circulation of seasonal respiratory viruses. This single center study was conducted between January 2017–February 2020 (pre-pandemic period) and March 2020–May 2021 (pandemic period). All adults >18 years with respiratory symptoms and tested for respiratory pathogens were included in the study. Nucleic acid detection of all respiratory viruses was performed by multiplex real time PCR. Our results show that the test positivity for influenza A and B, metapneumovirus, parainfluenza virus, respiratory syncytial virus and human coronaviruses decreased with statistical significance during the pandemic. Contrary to this, for adenovirus the decrease was not statistically significant. Conversely, a statistically significant increase was detected for rhinovirus. Coinfections between different respiratory viruses were observed during the pre-pandemic period, while the only coinfection detected during pandemic was between SARS-CoV-2 and rhinovirus. To understand how the preventive strategies against SARS-CoV-2 might alter the transmission dynamics and epidemic patterns of respiratory viruses is fundamental to guide future preventive recommendations.

scholarly journals 1484. Microbial Etiology of Community-acquired Pneumonia in Immunocompromised Patients

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S743-S744
Author(s):  
Abhishek Deshpande ◽  
Pei-Chun Yu ◽  
Michael Rothberg
Keyword(s):  
Panel Member ◽  
Positive Culture ◽  
Empiric Therapy ◽  
Community Acquired Pneumonia ◽  
Immunocompromised Patients ◽  
Viral Pathogens ◽  
Chest X Ray ◽  
Microbial Etiology ◽  
Almost All ◽  
Immunocompetent Patients

Abstract Background Community-acquired pneumonia (CAP) is a leading cause of infection related mortality. Few studies have specifically evaluated the microbial etiology of CAP in immunocompromised patients. Using a large national inpatient database, we compared the microbial etiology of CAP in immunocompromised patients compared to immunocompetent patients. Methods We included adult patients admitted with pneumonia from 2010-2015 to 176 US hospitals participating in Premier. Patients were identified as having CAP if they had a chest X-ray and were on antimicrobials on the first day. Immunocompromised was defined by the receipt of immunosuppressive medications or ICD-9 codes for neutropenia/ hematological malignancy/ organ transplantation or comorbidities with AIDS. For microbial etiology, patients were included if they had a positive culture or test collected by hospital day 0 through 3. Patients with identical bacteria in blood and urine were excluded. Results A total of 168,159 patients had a diagnosis of CAP with a culture/test performed on first 3 days. A pathogen was detected in 18.8% of patients. Among pathogen positive patients, 4,851 patients were identified as immunocompromised and 26,752 as immunocompetent. Almost all patients (99%) had at least one culture, blood (96%) and respiratory (51%). Among patients who were immunocompromised, the most common bacterial pathogens (compared to immunocompetent patients) were, S. pneumoniae (17.7% vs 19.0%), MRSA (13.1% vs 14.4%), MSSA (12.0% vs 11.8%), P. aeruginosa (12.0% vs 9.9%), E. coli (7.4% vs 6.4%), K. pneumoniae (5.8% vs 4.9%), H. influenzae (5.5% vs 5.5%), M. pneumoniae (3.0% vs 3.0%) and L. pneumophila (0.93% vs 1.2%). Among viral pathogens, while the most common were influenza virus (12.9% vs 14.1%) followed by rhinovirus (1.5% vs 0.89%), immunocompromised patients has a higher prevalence of noninfluennza viruses (3.42% vs 2.43%). Conclusion In a large US inpatient sample, the causative organisms in immunocompromised patients did not differ much from those in immunocompetent patients. CAP pathogens in immunocompromised patients were more likely to involve gram-negative bacilli such as P.aeruginosa and E.coli, than gram-positive cocci. These findings may have implications when deciding on empiric therapy in these patients. Disclosures Abhishek Deshpande, MD, PhD, Ferring Pharmaceuticals (Advisor or Review Panel member)Merck (Consultant)

scholarly journals PO 8565 PREVALENCE AND CLINICAL SIGNIFICANCE OF RESPIRATORY VIRUSES AND BACTERIA DETECTED IN TUBERCULOSIS PATIENTS COMPARED TO HOUSEHOLD CONTACT CONTROLS IN TANZANIA

2019 ◽  
Vol 4 (Suppl 3) ◽  
pp. A54.2-A54
Author(s):  
Francis Mhimbira ◽  
Jerry Hella ◽  
Hellen Hiza ◽  
Emmanuel Mbuba ◽  
Magreth Chiryamkubi ◽  
...  
Keyword(s):  
Clinical Significance ◽  
Bacterial Pathogens ◽  
Severe Disease ◽  
Respiratory Viruses ◽  
Household Contact ◽  
Nasopharyngeal Swab ◽  
Respiratory Pathogens ◽  
Viral Pathogens ◽  
Tuberculosis Patients ◽  
Study Participants

BackgroundThe study aim is to describe the prevalence of respiratory pathogens in tuberculosis (TB) patients and in their household contact controls, and to determine the clinical significance of respiratory pathogens in TB patients.MethodsWe studied 489 smear-positive adult TB patients and 305 household contact controls without TB with nasopharyngeal swab samples within an ongoing prospective cohort study in Dar es Salaam, Tanzania, between 2013 and 2015. We used multiplex real-time PCR to detect 16 respiratory viruses and seven bacterial pathogens from nasopharyngeal swabs.ResultsThe median age of the study participants was 33 years; 61% (484/794) were men, and 21% (168/794) were HIV-positive. TB patients had a higher prevalence of HIV (28.6%; 140/489) than controls (9.2%; 28/305). Overall prevalence of respiratory viral pathogens was 20.4% (160/794; 95% CI 17.7%–23.3%) and of bacterial pathogens 38.2% (303/794; 95% CI 34.9%–41.6%). TB patients and controls did not differ in the prevalence of respiratory viruses (Odds Ratio [OR] 1.00, 95% CI 0.71–1.44), but respiratory bacteria were less frequently detected in TB patients (OR 0.70, 95% CI 0.53–0.94). TB patients with both respiratory viruses and respiratory bacteria were likely to have more severe disease (adjusted OR [aOR] 1.6, 95% CI 1.1–2.4; p 0.011). TB patients with respiratory viruses tended to have more frequent lung cavitations (aOR 1.6, 95% CI 0.93–2.7; p 0.089).ConclusionRespiratory viruses are common for both TB patients and household controls. TB patients may present with more severe TB disease, particularly when they are co-infected with both bacteria and viruses.

scholarly journals Respiratory Viral Pathogens in Children Evaluated at Military Treatment Facilities in Oahu, Hawaii From 2014 to 2018: Seasonality and Climatic Factors

2020 ◽  
Author(s):  
Agnes S Montgomery ◽  
Michael B Lustik ◽  
Milissa U Jones ◽  
Timothy S Horseman
Keyword(s):  
Respiratory Syncytial Virus ◽  
Influenza A ◽  
Climatic Factors ◽  
Medical Center ◽  
Respiratory Viruses ◽  
Preventive Strategies ◽  
Viral Pathogens ◽  
Treatment Facilities ◽  
Syncytial Virus ◽  
Military Treatment Facilities

Abstract Five-year retrospective analysis of respiratory viruses in children less than 18 years old at Tripler Army Medical Center and outlying clinics in Oahu. Respiratory syncytial virus and influenza A showed pronounced seasonality with peaks from September to December and December to March, respectively. Results provide a better understanding of the timing of viral preventive strategies in Oahu.

scholarly journals The burden of influenza and other respiratory viruses in hospitalized infants and children in a university hospital, Jordan

2021 ◽  
Vol 16 ◽  
Author(s):  
Enas Al-Zayadneh ◽  
Dina Mohammad Abu Assab ◽  
Esraa Adeeb Arabiat ◽  
Montaha Al-Iede ◽  
Hanin Ahmad Kayed ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Influenza Infection ◽  
Influenza Virus Infection ◽  
Respiratory Viruses ◽  
University Hospital ◽  
Acute Lower Respiratory Infection ◽  
Respiratory Pathogens ◽  
Syncytial Virus ◽  
Viral Surveillance ◽  
Viral Respiratory

Background: Acute lower respiratory infection (ALRI) is a major cause of morbidity and mortality worldwide in young children and is predominately caused by viral respiratory pathogens. This study aims to identify the viral etiologies of acute ALRI in hospitalized children in Jordan University Hospital and compare the clinical characteristics of influenza virus infection with other respiratory viruses. Methods: a retrospective viral surveillance study that included 152 children below 15 years of age admitted with ALRI from December 2018  through April 2019. We recorded results of real-time reverse transcriptase-polymerase chain reaction (RT- PCR ) for common respiratory viruses. Clinical and demographic information of the study population was collected from patients’ electronic medical records. Results: 152 were identified with a median age of 1 year (mean was 2.1 years). Ninety-five patients (62.5%) were males. One or more viral respiratory pathogens were detected in 145 (95.3%) children. Respiratory syncytial virus was the most commonly detected virus in 68 patients (44.8%). Influenza virus was detected in 25 (16.4%). Children with influenza infection had more fever and less leukocyte count compared to children infected with other viruses. The severity of the ALRI correlated significantly with several factors, including age less than 6 months and the presence of neuromuscular disease (p<0.05). Conclusion: Viral detection was common among children admitted with viral ALRI. Viruses, including influenza, are recognized as major contributors to the morbidity associated with ALRI. More attention is needed on strategies for the prevention and detection of viral ALRI in developing countries.

scholarly journals Risk of community-acquired pneumonia requiring hospitalization in patients with spondyloarthritis

2020 ◽  
Vol 12 ◽  
pp. 1759720X2096261
Author(s):  
Ho Yin Chung ◽  
Lai Shan Tam ◽  
Shirley Chiu Wai Chan ◽  
Jason Pui Yin Cheung ◽  
Pui Yan Wong ◽  
...  
Keyword(s):  
Risk Factors ◽  
Cox Regression ◽  
Demographic Data ◽  
Pneumococcal Vaccination ◽  
Community Acquired Pneumonia ◽  
Vaccination Programs ◽  
Increased Risk ◽  
Drinking Status ◽  
Traditional Risk Factors ◽  
Micro Organisms

Aims: To compare the risk of community-acquired pneumonia (CAP) requiring hospitalization in spondyloarthritis (SpA) and non-specific back pain (NSBP), and to identify the risk factors for CAP in SpA. Methods: A total of 2984 patients with SpA from 11 rheumatology centers and 2526 patients with NSBP from orthopedic units were reviewed from the centralized electronic database in Hong Kong. Incidence of CAP requiring hospitalization and demographic data including age, gender, smoking and drinking status, use of sulfasalazine, individual biological-disease modifying anti-rheumatic drugs (DMARDs) used, micro-organisms, other immunosuppressants or immunosuppressive states, use of steroid for more than ½ year, and co-morbidities were identified. Risks of CAP in SpA were compared with those in NSBP using propensity score regression method. Multivariate Cox regression model was used to identify the risk factors in SpA. Results: CAP requiring hospitalization was found in 183 patients with SpA and 138 patients with NSBP. Increased risk for CAP was found in the following groups with SpA: all subgroups (hazard ratio (HR) 2.14, p < 0.001), without use of DMARDs (HR 2.64, p < 0.001), without psoriasis and not taking DMARDs (HR 2.38, p < 0.001). Infliximab (HR2.55, p = 0.04), smoking (HR 1.68, p = 0.003), comorbid psoriasis (HR 1.67, p = 0.003), and use of steroid for more than ½ year (HR 1.94, p = 0.003) were found to associate with CAP after adjustments for traditional risk factors. Conclusion: Risk of CAP is increased in patients with SpA. Our data favor universal influenza and pneumococcal vaccination programs in the population. Rheumatologists should also advise smoking cessation and avoid long term steroid therapy.

scholarly journals The rapid reemergence of seasonal respiratory viruses in Houston, Texas, after relaxing COVID-19 restrictions

2021 ◽  
Author(s):  
Parsa Hodjat ◽  
Paul Christensen ◽  
Sishir Subedi ◽  
Randall James Olsen ◽  
David W Bernard ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Respiratory Infections ◽  
State Level ◽  
Complete Removal ◽  
Respiratory Viruses ◽  
Rapid Decrease ◽  
The State ◽  
Respiratory Pathogens ◽  
Containment Measures ◽  
Syncytial Virus

Implementation of measures to limit the spread of the SARS-CoV-2 virus at the start of the COVID-19 pandemic resulted in a rapid decrease in all other respiratory pathogens. As COVID-19 containment measures were relaxed, the first non-COVID respiratory viruses to return to prepandemic levels were members of the rhinovirus/enterovirus, followed by the rapid return of seasonal coronaviruses, parainfluenza, and respiratory syncytial virus after the complete removal of COVID-19 precautions at the state level, including an end to mask mandates. Inasmuch as COVID-19 has dominated the landscape of respiratory infections since early 2020, it is important for clinicians to recognize the return of non-COVID respiratory pathogens may be rapid and significant when COVID-19 containment measures are removed.

scholarly journals Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
My V. T. Phan ◽  
Charles N. Agoti ◽  
Patrick K. Munywoki ◽  
Grieven P. Otieno ◽  
Mwanajuma Ngama ◽  
...  
Keyword(s):  
Parvovirus B19 ◽  
Respiratory Pathogens ◽  
Metagenomic Sequencing ◽  
Viral Pathogens ◽  
Mortality And Morbidity ◽  
Local Standard ◽  
Virus Diagnostics ◽  
Diagnostic Panel ◽  
Syncytial Virus ◽  
Ngs Data

AbstractPneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing (viral NGS) on respiratory samples which tested negative for the common viral respiratory pathogens by a local standard diagnostic panel. Among 95 hospitalised pneumonia patients and 95 household-cohort individuals, analysis of viral NGS identified at least one respiratory-associated virus in 35 (37%) and 23 (24%) samples, respectively. The majority (66%; 42/64) belonged to the Picornaviridae family. The NGS data analysis identified a number of viruses that were missed by the diagnostic panel (rhinovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus), and these failures could be attributed to PCR primer/probe binding site mismatches. Unexpected viruses identified included parvovirus B19, enterovirus D68, coxsackievirus A16 and A24 and rubella virus. The regular application of such viral NGS could help evaluate assay performance, identify molecular causes of missed diagnoses and reveal gaps in the respiratory virus set used for local screening assays. The results can provide actionable information to improve the local pneumonia diagnostics and reveal locally important viral pathogens.

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