Community-acquired Acute Respiratory Infections Research Articles

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

Infectious agents associated with community-acquired acute respiratory infections (ARIs) remain understudied in Lebanon. We aim to assess the microbiological profiles of ARIs by employing polymerase chain reaction (PCR) and identifying predictors of positive PCR results among patients admitted for ARI. We conducted a retrospective single-center study at the American University of Beirut Medical Center, including all respiratory PCR panels performed on pediatric (< 18) and adult (≥ 18) patients presenting with an ARI from January 2015 to March 2018, prior to the onset of the COVID-19 pandemic. We aimed to identify the epidemiological patterns of ARIs and the factors associated with positive PCRs in both adult and pediatric patients. Among 281 respiratory PCRs, 168 (59.7%) were positive for at least one pathogen, with 54.1% positive PCR for viruses, 7.8% for bacteria species, and 3.9% with virus-bacteria codetection. Almost 60% of the patients received antibiotics prior to PCR testing. PCR panels yielded more positive results in pediatric patients than in adults (P = 0.005). Bacterial detection was more common in adults compared to pediatrics (P < 0.001). The most common organism recovered in the entire population was Human Rhinovirus (RhV) (18.5%). Patients with pleural effusion on chest CT were less likely to have a positive PCR (95% Cl: 0.22-0.99). On multivariate analysis, pediatric age group (P < 0.001), stem cell transplant (P = 0.006), fever (P = 0.03) and UTRI symptoms (P = 0.004) were all predictive of a positive viral PCR. Understanding the local epidemiology of ARI is crucial for proper antimicrobial stewardship. The identification of factors associated with positive respiratory PCR enhances our understanding of clinical characteristics and potential predictors of viral detection in our population.

Comparison of common acute respiratory infection case definitions for identification of hospitalized influenza cases at a population-based surveillance site in Egypt.

BackgroundMultiple case definitions are used to identify hospitalized patients with community-acquired acute respiratory infections (ARI). We evaluated several commonly used hospitalized ARI case definitions to identify influenza cases.MethodsThe study included all patients from a population-based surveillance site in Damanhour, Egypt hospitalized for a broad set of criteria consistent with community acquired ARIs. Naso- and oropharyngeal (NP/OP) swabs were tested for influenza using RT-PCR. Sensitivity, specificity and PPV for influenza identification was compared between the 2014 WHO Severe Acute Respiratory Infection (SARI) definition (fever ≥38°C and cough with onset within 10 days), the 2011 WHO SARI definition (fever ≥38°C and cough with onset within 7 days), the 2006 PAHO SARI definition, the International Emerging Infections Program (IEIP) pneumonia case definition, and the International Management of Childhood Illness (IMCI) case definitions for moderate and severe pneumonia.ResultsFrom June 2009-December 2012, 5768 NP/OP swabs were obtained from 6113 hospitalized ARI patients; 799 (13.9%) were influenza positive. The 2014 WHO SARI case definition captured the greatest number of ARI patients, influenza positive patients and ARI deaths compared to the other case definitions examined. Sensitivity for influenza detection was highest for the 2014 WHO SARI definition with 88.6%, compared to the 2011 WHO SARI (78.2%) the 2006 PAHO SARI (15.8%) the IEIP pneumonia (61.0%) and the IMCI moderate and severe pneumonia (33.8% and 38.9%) case definitions (IMCI applies to <5 only).ConclusionsOur results support use of the 2014 WHO SARI definition for identifying influenza positive hospitalized SARI cases as it captures the highest proportion of ARI deaths and influenza positive cases. Routine use of this case definition for hospital-based surveillance will provide a solid, globally comparable foundation on which to build needed response efforts for novel pandemic viruses.

Respiratory pathogens in infants less than two months old hospitalized with acute respiratory infection

Lower acute respiratory infections (ARI) are a frequent cause of morbidity and mortality in infants, respiratory viruses being the major causative agents. The aim of this work was to determine the respiratory pathogen frequency, the clinical characteristics and the outcome in infants <2 months old hospitalized with ARI. A retrospective study was performed during a five-year period (2008–2011, 2014–2016). Respiratory viruses and atypical bacteria were studied using the FilmArray-Respiratory Panel. Demographic and clinical characteristics, hospitalization course and outcomes were evaluated. Of the 137 infants <2 months old hospitalized with ARI studied, a 94.9% positivity rate as determined in 117 infants with community-acquired infection and 20.0% in 20 infants who acquired the infection during their birth hospitalization in the neonatal intensive care units (NICU) (nosocomial ARI) (p<0.001). In infants with community-acquired infection, Respiratory syncytial virus (RSV) (52.1%) and Rhinovirus/Enterovirus (RV/EV) (41.0%) were the most frequent detected pathogens. Coinfections were determined in one quarter of the infants, RSV-RV/EV being the most frequent combination. In infants with nosocomial infection, RV/EV, RSV or Parainfluenza-3 were detected as single pathogens. Most infants with community-acquired infection presented lower ARI (81.2%) while most infants in the NICU had upper ARI (55.0%). The median length of stay (LOS) in infants with community-acquired ARI was 4 days (IQR: 2–6). Positive infants with nosocomial infection had longer median LOS (71 days [IQR:42–99]) compared to negative infants (58 days [IQR: 49–71]) (p=0.507). Respiratory viruses were detected as the major causative agents of community-acquired infection in hospitalized infants <2-months old, RSV and RV/EV being the most frequently detected. Although a low pathogen positivity rate was observed in infants with nosocomial infection, they may prolong the LOS.

FebriDx®: A Rapid Diagnostic Test for Differentiating Bacterial and Viral Aetiologies in Acute Respiratory Infections.

FebriDx® is a rapid, point-of-care diagnostic test that is designed to aid in the differentiation of bacterial and viral acute respiratory infections (ARIs), thus helping to guide decisions regarding the prescription of antibiotics in the outpatient setting. FebriDx carries a CE mark for use in the EU and is also approved in several other countries, including Canada, Saudi Arabia and Singapore. It is indicated for use in patients > 2 years old with symptoms consistent with a community-acquired ARI. The test involves the use of an immunoassay on a fingerstick blood sample to provide simultaneous, qualitative measurement of elevated levels of C-reactive protein (CRP) and myxovirus resistance protein A (MxA). In two prospective, multicentre studies in patients with acute upper respiratory tract infections, FebriDx was shown to be both sensitive and specific in identifying patients with a clinically significant infection and in differentiating between infections of bacterial and viral aetiology. The test is simple, requires no additional equipment and produces actionable results in ~ 10 min. As was demonstrated in a small, retrospective analysis, FebriDx results can help guide (improve) antibiotic prescribing decisions. Reducing the unnecessary or inappropriate prescription of antibiotics for ARIs of probable viral aetiology is important for antibiotic stewardship and can also reduce the unnecessary exposure of patients to the risk of antibiotic-related adverse events. FebriDx thus represents a useful diagnostic tool in the outpatient setting.

A Diagnostic Platform Predicts Presymptomatic Exposure to Respiratory Viral Infection.

INTRODUCTION Communicable diseases can be a significant burden during military operations in which missions rely on each and every team member for optimal performance. Community-acquired acute respiratory infections are particularly difficult to contain, given their rapid transmissibility and the lack of early diagnostic tests. Disease prevention using vaccination has shown low effectiveness, notably the overall flu vaccine effectiveness estimate for 2014–2015 flu season was 19%. Contemporary approaches to diagnose respiratory infection rely on time-consuming pathogen-specific assessment during the symptomatic window of the infection. In the last decade, however, the genomics revolution—and specifically, systems genomics approaches combined with mathematical modeling, has led to better understanding of disease at the individual level and the emergence of new diagnostic and therapeutic paradigms. The diagnostic limitations to control infections nonetheless remain a medical challenge as evidenced by the most recent H1N1 influenza pandemic outbreak of 2009. As emphasized by a U.S. Department of Health and Human Services retrospective analysis: “The absence of readily available, rapid, simple, and highly sensitive diagnostic tests which could detect the 2009 H1N1 virus made infection control more difficult.” In 2006, the Defense Advanced Research Projects Agency (DARPA) launched an ambitious program to devise models and methods that predict incipient infection after exposure. The program known as Predicting Health and Disease (PHD) aimed to enable the capability to diagnose individuals with a respiratory infection before they become symptomatic. DEVELOPMENT AND VALIDATION OF MODELS THAT DISTINGUISH INFLUENZA INFECTED SYMPTOMATIC PATIENTS To develop novel predictive models of incipient respiratory infectious disease, a group at Duke University led by Dr. Geoff Ginsburg, in collaboration with Dr. Alfred Hero at University of Michigan, performed studies with healthy volunteers experimentally infected with live unattenuated Influenza (H1N1 or H3N2), respiratory syncytial virus, or human rhinovirus, and who underwent serial blood sampling at regular time intervals preand postinoculation. Using factor analysis of mRNA expression arrays with ~22,000 genes, the team identified patterns of “host-derived gene expression signatures” in blood that were highly specific for infection in symptomatic individuals, and distinct from asymptomatic subjects. The discriminatory factors (designated viral factors) encompassed a collection of highly correlated host genes involved in antiviral responses (i.e. Toll-like receptor signaling genes, Interferon response genes, etc.), and were closely associated with disease dynamics and symptom scores.

Contribution of Viruses, Chlamydia spp. and Mycoplasma pneumoniae to Acute Respiratory Infections in Iranian Children

The study reports the frequency and clinical presentation of respiratory syncytial virus (RSV), human metapneumovirus, influenza (Inf V), parainfluenza, adenovirus (Adv), Chlamydia spp. and Mycoplasma pneumoniae in children with acute respiratory infections (ARI) in Rasht, Iran. Nasopharyngeal aspirates and swabs were collected from 261 children in 2003 and 2004. Pathogens were detected using polymerase chain reaction (PCR) and reverse transcription-PCR (RT-PCR), confirmed with sequence analysis. Ninety-three pathogens were detected in 83 children. RSV was present in 39 (15%), Adv in 37 (14%), Inf A in 11 (4%), C. trachomatis in 4 (2%) and M. pneumoniae, in 2 (1%) children. Neither parainfluenza nor metapneumovirus were detected. RSV, Inf A and C. trachomatis were more frequent in children with lower respiratory infections. Adv presented more frequently as upper respiratory infection. All pathogens, except M. pneumoniae, were detected in children with severe pneumonia. Viruses play a significant role in Iranian children with community-acquired ARI.

Appropriateness of antibiotic prescriptions in community-acquired acute pediatric respiratory infections in Spanish emergency rooms.

To describe the variability and appropriateness of antibiotic prescriptions in community-acquired acute respiratory infections (ARI) during childhood in Spain. A descriptive, multicenter study of variability in clinical practice was conducted by evaluating a prospective series of pediatric patients attending the emergency rooms of 11 Spanish hospitals and diagnosed with community-acquired ARI. The appropriateness of the antibiotic prescriptions was assessed by comparing our clinical practice with consensus guidelines developed for this study. We collected data from 6,249 ARI emergencies studied on 30 separate days. Antibiotics were prescribed in 58.7% of the ARI (bronchiolitis, 11.5%; bronchitis, 40.2%; pharyngotonsillitis, 80.9%; nonspecified ARI, 34.8%; pneumonia, 92.4%; otitis, 93.4%; sinusitis, 92.6%). The most commonly used antibiotics were amoxicillin/clavulanate (33.2%), amoxicillin (30.2%), cefuroxime axetil (8.5%) and azithromycin (6%). According to the consensus guidelines developed for this study, therapy was considered to be appropriate in 63.1% of the ARI (first choice, 52.1%; alternative choice, 11.0%) and inappropriate in 36.9%. The percentages of inappropriate prescription according to ARI groups were: bronchiolitis, 11.5%; bronchitis, 31.5%; pharyngotonsillitis, 54.8%; nonspecified ARI, 34.7%; pneumonia, 13.9%; otitis, 25.6%; and sinusitis, 22.2%. There is excessive use of antibiotics in acute respiratory infections that are presumably viral in origin. An important number of ARI of potentially bacterial origin are treated with antibiotics that are not sufficiently efficacious or that have a broader spectrum than necessary.

The differentiation of Chlamydia species by antigen detection in sputum specimens from patients with community-acquired acute respiratory infections

An amplified enzyme immunoassay (IDEIA III: Dako Diagnostics Ltd) for detecting genus-specific chlamydia antigen was evaluated prospectively on 286 respiratory specimens from 275 patients presenting with community-acquired pneumonia or persistent chest infection. Nineteen patients had evidence of recent chlamydial infection, having two or more positive sputum or serological markers. Sputa from two other patients were ELISA-positive in the absence of other positive criteria and were regarded as false-positive results. When compared with a direct immunofluorescence test for chlamydial elementary bodies (EBs) using a genus-specific monoclonal antibody, the ELISA gave a positive predictive value of 91% and a negative predictive value of 99%. Non-specific problems with a wide variety of other micro-organisms isolated from the sputa were not encountered. Attempts to differentiate between Chlamydia psittaci, Chlamydia pneumoniae and Chlamydia trachomatis using genus-specific lipopolysaccharide reactive--and species-specific major outer membrane protein--monoclonal antibodies were encouraging and results were substantiated, in most patients, by the species-specific serological assays of the whole-cell-inclusion immunofluorescence or micro-immunofluorescence assays. The study demonstrated that antigen detection techniques offer scope for routine laboratories to diagnose chlamydial respiratory infections rapidly and reliably and may enable differentiation to species level. Although immunofluorescence offers marginally greater sensitivity and specificity when compared with ELISA, the latter is less subjective and less demanding. Sixty-eight per cent of these infections would have remained undiagnosed despite the general availability of ELISA tests.