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 913. Distribution of Respiratory Viral Pathogens in Infants Across Different Clinical Settings from December 2019 to April 2020

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S491-S492
Author(s):  
Zaid Haddadin ◽  
Danielle A Rankin ◽  
loren lipworth ◽  
Jon Fryzek ◽  
Mina Suh ◽  
...  
Keyword(s):  
Clinical Setting ◽  
Respiratory Viruses ◽  
Clinical Settings ◽  
Research Support ◽  
Viral Pathogens ◽  
Abrupt Decrease ◽  
Nasal Swabs ◽  
Viral Testing ◽  
Support Research ◽  
Research Grant

Abstract Background Acute respiratory infections (ARI) are a major cause of morbidity and mortality in young children, with viral pathogens being the most common etiologies. However, due to limited and inconsistent clinical diagnostic viral testing in the outpatient (OP) setting compared to the inpatient (IP) setting, the actual burden and distribution of viral pathogens across these clinical settings remain largely underreported. We aimed to evaluate the frequency of common respiratory viruses in medically attended ARI in infants. Methods We conducted a prospective viral surveillance study in Davidson County, TN. Eligible infants under one year presenting with fever and/or respiratory symptoms were enrolled from OP, emergency department (ED), or IP settings. Nasal swabs were collected and tested for common viral pathogens using Luminex® NxTAG Respiratory Pathogen Panel and for SARS-CoV-2 using Luminex® NxTAG CoV extended panel. Results From 12/16/2019 to 4/30/2020, 364 infants were enrolled, and 361 (99%) had nasal swabs collected and tested. Of those, 295 (82%) had at least one virus detected; rhinovirus/enterovirus (RV/EV) [124 (42%)], respiratory syncytial virus (RSV) [101 (32%)], and influenza (flu) [44 (15%)] were the three most common pathogens detected. No samples tested positive for SARS-CoV-2. Overall, the mean age was 6.1 months, 50% were male, 45% White and 27% Hispanic. Figure 1 shows the total number of PCR viral testing results by month. RSV was the most frequent virus detected in the IP (63%) and ED (37%) settings, while RV/EV was the most common in the OP setting (Figure 2). Figure 3 displays viral seasonality by clinical setting, showing an abrupt decrease in virus-positive cases following the implementation of a stay-at-home order on March 23, 2020 in Nashville, TN. Distribution of Respiratory Viruses in Different Settings Distribution of Respiratory Viruses in Different Settings by Season Conclusion Most medical encounters in infants are due to viral pathogens, with RSV, RV/EV, and flu being the most common. However, distributions differed by clinical setting, with RSV being the most frequently detected in the IP and ED settings, and second to RV/EV in the OP setting. Continued active viral ARI surveillance in various clinical settings is warranted. Preventative measures such as vaccines and infection control measures deserve study to reduce viral ARI burden. Disclosures Zaid Haddadin, MD, CDC (Grant/Research Support, Research Grant or Support)Quidel Corporation (Grant/Research Support, Research Grant or Support)sanofi pasteur (Grant/Research Support, Research Grant or Support) Danielle A. Rankin, MPH, CIC, Sanofi Pasteur (Grant/Research Support, Research Grant or Support) Jon Fryzek, PhD, MPH, EpidStrategies (Employee) Mina Suh, MPH, International Health, EpidStrategies (Employee) Donald S. Shepard, PhD, Sanofi Pasteur (Grant/Research Support) Natasha B. Halasa, MD, MPH, Genentech (Other Financial or Material Support, I receive an honorarium for lectures - it’s a education grant, supported by genetech)Karius (Consultant)Moderna (Consultant)Quidel (Grant/Research Support, Research Grant or Support)Sanofi (Grant/Research Support, Research Grant or Support)

scholarly journals Timing of respiratory virus molecular testing in emergency departments and its association with patient care outcomes: a retrospective observational study across six Australian hospitals

BMJ Open ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. e030104 ◽  
Author(s):  
Nasir Wabe ◽  
Ling Li ◽  
Maria R Dahm ◽  
Robert Lindeman ◽  
Ruth Yimsung ◽  
...  
Keyword(s):  
Observational Study ◽  
Patient Care ◽  
Respiratory Virus ◽  
Laboratory Data ◽  
Respiratory Viruses ◽  
Retrospective Observational Study ◽  
Molecular Diagnostic ◽  
Molecular Testing ◽  
Care Outcomes ◽  
Virus Testing

ObjectiveA rapid molecular diagnostic test (RMDT) offers a fast and accurate detection of respiratory viruses, but its impact on the timeliness of care in the emergency department (ED) may depend on the timing of the test. The aim of the study was to determine if the timing of respiratory virus testing using a RMDT in the ED had an association with patient care outcomes.DesignRetrospective observational study.SettingLinked ED and laboratory data from six EDs in New South Wales, Australia.ParticipantsAdult patients presenting to EDs during the 2017 influenza season and tested for respiratory viruses using a RMDT. The timing of respiratory virus testing was defined as the time from a patient’s ED arrival to time of sample receipt at the hospital laboratory.Outcome measuresED length of stay (LOS), >4 hour ED LOS and having a pending RMDT result at ED disposition.ResultsA total of 2168 patients were included. The median timing of respiratory virus testing was 224 min (IQR, 133–349). Every 30 min increase in the timing of respiratory virus testing was associated with a 24.0 min increase in the median ED LOS (95% CI, 21.8–26.1; p<0.001), a 51% increase in the likelihood of staying >4 hours in ED (OR, 1.51; 95% CI, 1.41 to 1.63; p<0.001) and a 4% increase in the likelihood of having a pending RMDT result at ED disposition (OR, 1.04; 95% CI, 1.02 to 1.05; p<0.001) after adjustment for confounders.ConclusionThe timing of respiratory virus molecular testing in EDs was significantly associated with a range of outcome indicators. Results suggest the potential to maximise the benefits of RMDT by introducing an early diagnostic protocol such as triage-initiated testing.

scholarly journals 1776. Step-Wise Algorithm for the Detection of Respiratory Viruses: Integrating a Rapid Influenza A/B and RSV PCR with a Multiplex Respiratory Virus Panel to Target High-Risk Patient Populations

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S654-S654 ◽  
Author(s):  
Nancy Matic ◽  
Tanya Lawson ◽  
Loretta Karakas ◽  
Willson Jang ◽  
Gordon Ritchie ◽  
...  
Keyword(s):  
Influenza A ◽  
Respiratory Virus ◽  
High Risk Patient ◽  
Multiplex Assay ◽  
Influenza B ◽  
Medical Team ◽  
Viral Pathogens ◽  
Viral Pathogen ◽  
Additional Testing ◽  
Virus Testing

Abstract Background In clinical settings, multiplex molecular panels are becoming increasingly common for the detection of respiratory pathogens. Little evidence is available to guide appropriate use of respiratory multiplex panels, particularly with respect to the patient populations most likely to benefit from such testing. Methods During the 2018–2019 influenza season, all patients with a nasopharyngeal swab submitted for respiratory virus detection were initially tested on a commercial rapid PCR platform for influenza A/B and respiratory syncytial virus (RSV) (Cepheid GeneXpert, Sunnyvale, CA). Patients with negative swabs were reviewed by a laboratory physician based on pre-defined criteria (Table 1) for additional testing by a laboratory-developed multiplex assay for parainfluenza 1/2/3, adenovirus, and human metapneumovirus (hMPV). Results In total, 1144 nasopharyngeal swabs were tested. 287 (25.1%) were positive on the GeneXpert: influenza A (234, 81.5%), influenza B (13, 4.5%), and RSV (40, 13.9%). Of the patients who tested negative, 234 (27.3%) met criteria for further respiratory virus testing. The most commonly detected viral pathogens on the multiplex assay were hMPV (20/30, 66.7%), parainfluenza 3 (7/30, 23.3%) and adenovirus (3/30, 10%). The yield of the multiplex assay was highest for patients selected for antimicrobial stewardship (AS) criteria (13/56, 23.2%), followed by transplant (2/16, 12.5%), HIV (7/64, 10.9%), cystic fibrosis (2/19, 10.5%), critical care (6/68, 8.8%), and other/upon physician request (0/11, 0%). Of the patients who received multiplex testing for AS criteria and tested positive for a viral pathogen, only 3/13 (23.1%) had antibiotics discontinued by the medical team within 48 hours of the report. Conclusion Additional testing for respiratory viral pathogens had low overall diagnostic yield, and further refinement of the algorithm is needed to better target utilization of respiratory virus testing. The patient population with the highest yield (those who met AS criteria) failed to demonstrate consistent timely discontinuation of unnecessary antibiotics by the medical team. Implementation of respiratory multiplex panels would be strengthened by collaboration with AS teams. Disclosures All authors: No reported disclosures.

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

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243762
Author(s):  
Frédéric Sangla ◽  
David Legouis ◽  
Pierre-Emmanuel Marti ◽  
Sebastian D. Sgardello ◽  
Amélie Brebion ◽  
...  
Keyword(s):  
Home Care ◽  
Functional Status ◽  
Respiratory Virus ◽  
Ventilatory Support ◽  
Community Acquired Pneumonia ◽  
Icu Patients ◽  
Icu Admission ◽  
One Year ◽  
Virus Testing

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.

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.

Community-Acquired Pneumonia Due to Virus and Mycoplasma pneumoniae Infection in Children Younger than 5 Years

2019 ◽  
Vol 14 (04) ◽  
pp. 155-160
Author(s):  
Huiming Sun ◽  
Wenqing Zhu ◽  
Zhengrong Chen ◽  
Wei Ji ◽  
Chuangli Hao ◽  
...  
Keyword(s):  
Clinical Features ◽  
Mycoplasma Pneumoniae ◽  
Viral Infections ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Direct Immunofluorescence ◽  
Symptom Duration ◽  
Viral Pathogens ◽  
Duration Of Symptoms ◽  
Viral Coinfection

AbstractThe purpose of this study was to determine the clinical features of viral pathogens and Mycoplasma pneumoniae in children hospitalized with community-acquired pneumonia (CAP). M. pneumoniae infection was diagnosed by both serology and polymerase chain reaction (PCR). Respiratory viruses were detected by direct immunofluorescence or PCR. Medical records of children younger than 5 years diagnosed with 5-day-old CAP were reviewed. Viral pathogens and/or M. pneumoniae were detected in 388 (15.59%) children in the following three groups: viral monoinfection (n = 321), M. pneumoniae with viral coinfection (n = 17), and M. pneumoniae monoinfection (n = 50). M. pneumoniae monoinfection was characterized by older age, fever, higher neutrophil count, and chest X-ray showing lobar consolidation. Wheezing was more common in children with viral infections. Elevated alanine aminotransferase and aspartate aminotransferase were commonly seen in children with Mycoplasma infections. The median symptom duration in children with viral coinfection was shorter than in the other two groups (both p < 0.05). M. pneumoniae and respiratory viruses are important etiologic agents for CAP in children younger than 5 years, with characteristic clinical features. M. pneumoniae and viral coinfection are associated with shorter duration of symptoms before admission.

scholarly journals Respiratory virus monitoring in patients with community-acquired pneumonia during COVID-19 pandemic in Khabarovsk in 2020

2021 ◽  
pp. 21-27
Author(s):  
L. V. Butakova ◽  
E. Yu. Sapega ◽  
O. E. Trotsenko ◽  
L. A. Balakhontseva ◽  
E. N. Prisyazhnyuk ◽  
...  
Keyword(s):  
Virus Type ◽  
Respiratory Virus ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Parainfluenza Virus ◽  
Sample Collection ◽  
Chain Reaction ◽  
Khabarovsk Krai ◽  
Polymerase Chain ◽  
Type 3

Introduction. Emergence and spread of new coronavirus SARS-CoV-2 among population of the Khabarovsk krai influenced the growth of reported cases of community-acquired pneumonia in year 2020. Aim. To determine proportion of other respiratory viruses in development of viral pneumonia epidemic process in the Khabarovsk city in year 2020 during COVID-19 pandemic. Materials and methods. Sputum of 346 patients with community-acquired pneumonia that were hospitalized with suspected diagnosis of COVID-19 was analyzed during year 2020 in Khabarovsk city. Identification of viral agents was performed via real-time reverse-transcriptase polymerase chain reaction. Results. SARSCOV-2 RNA was identified in 183 (52.9%) out of 346 patients. Among other respiratory viruses parainfluenza virus type 3 and rhinoviruses were dominant mostly in SARS-CoV-2 negative examined people. It should be noted that etiology of pneumonia was identified only in 12.9% of all cases in this group (163 people). Co-infection with SARS-CoV-2 and other respiratory viruses such as parainfluenza virus type 3 virus, other coronaviruses and adenovirus was detected only in 2.2% of the cases. Conclusion. Low level of respiratory viruses detection in sputum can be caused by poor technique of sample collection in the hospital, disruption of storage and transportation conditions as well as development of secondary bacterial infection in certain patients. In order to evaluate influence of other respiratory viruses on the course of COVID-19 with underlying coinfection further investigation including analysis of patients’ clinical data is needed.

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