scholarly journals Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

2016 ◽  
Vol 62 (7) ◽  
pp. 817-823 ◽  
Author(s):  
Naomi J. Gadsby ◽  
Clark D. Russell ◽  
Martin P. McHugh ◽  
Harriet Mark ◽  
Andrew Conway Morris ◽  
...  
Keyword(s):  
Community Acquired Pneumonia ◽  
Molecular Testing ◽  
Respiratory Pathogens

scholarly journals Comprehensive Description of Pathogens and Antibiotic Treatment Guidance in Children With Community-Acquired Pneumonia Using Combined Mass Spectrometry Methods

2021 ◽  
Vol 11 ◽  
Author(s):  
Liying Sun ◽  
Chi Zhang ◽  
Shuhua An ◽  
Xiangpeng Chen ◽  
Yamei Li ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Antibiotic Therapy ◽  
Antibiotic Treatment ◽  
Community Acquired Pneumonia ◽  
Molecular Testing ◽  
Respiratory Pathogens ◽  
National Guidelines ◽  
Culture Methods ◽  
Identification Rate ◽  
Infection Pattern

The objective of this study was to evaluate the value of molecular methods in the management of community-acquired pneumonia (CAP) in children. Previously developed mass spectrometry (MS)-based methods combined with quantitative real-time PCR (combined-MS methods) were used to describe the aetiology and evaluate antibiotic therapy in the enrolled children. Sputum collected from 302 children hospitalized with CAP were analyzed using the combined-MS methods, which can detect 19 viruses and 12 bacteria related to CAP. Based on the results, appropriate antibiotics were determined using national guidelines and compared with the initial empirical therapies. Respiratory pathogens were identified in 84.4% of the patients (255/302). Co-infection was the predominant infection pattern (51.7%, 156/302) and was primarily a bacterial-viral mixed infection (36.8%, 111/302). Compared with that using culture-based methods, the identification rate for bacteria using the combined-MS methods (61.8%, 126/204) increased by 28.5% (p <0.001). Based on the results of the combined-MS methods, the initial antibiotic treatment of 235 patients was not optimal, which mostly required switching to β-lactam/β-lactamase inhibitor combinations or reducing unnecessary macrolide treatments. Moreover, using the combined-MS methods to guide antibiotic therapy showed potential to decrease the length of stay in children with severe CAP. For children with CAP, quantitative molecular testing on sputum can serve as an important complement to traditional culture methods. Early aetiology elucidated using molecular testing can help guide the antibiotic therapy.

scholarly journals Cerebrospinal fluid neopterin as a biomarker of neuroinflammatory diseases

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marta Molero-Luis ◽  
Didac Casas-Alba ◽  
Gabriela Orellana ◽  
Aida Ormazabal ◽  
Cristina Sierra ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Discriminant Analysis ◽  
Bacterial Infections ◽  
Pediatric Patients ◽  
Canonical Discriminant Analysis ◽  
Control Group ◽  
Csf Biomarkers ◽  
Molecular Testing ◽  
Respiratory Pathogens

Abstract The elevation of neopterin in cerebrospinal fluid (CSF) has been reported in several neuroinflammatory disorders. However, it is not expected that neopterin alone can discriminate among different neuroinflammatory etiologies. We conducted an observational retrospective and case–control study to analyze the CSF biomarkers neopterin, total proteins, and leukocytes in a large cohort of pediatric patients with neuroinflammatory disorders. CSF samples from 277 subjects were included and classified into four groups: Viral meningoencephalitis, bacterial meningitis, acquired immune-mediated disorders, and patients with no-immune diseases (control group). CSF neopterin was analyzed with high-performance liquid chromatography. Microbiological diagnosis included bacterial CSF cultures and several specific real-time polymerase chain reactions. Molecular testing for multiple respiratory pathogens was also included. Antibodies against neuronal and glial proteins were tested. Canonical discriminant analysis of the three biomarkers was conducted to establish the best discriminant functions for the classification of the different clinical groups. Model validation was done by biomarker analyses in a new cohort of 95 pediatric patients. CSF neopterin displayed the highest values in the viral and bacterial infection groups. By applying canonical discriminant analysis, it was possible to classify the patients into the different groups. Validation analyses displayed good results for neuropediatric patients with no-immune diseases and for viral meningitis patients, followed by the other groups. This study provides initial evidence of a more efficient approach to promote the timely classification of patients with viral and bacterial infections and acquired autoimmune disorders. Through canonical equations, we have validated a new tool that aids in the early and differential diagnosis of these neuroinflammatory conditions.

scholarly journals The prevalence of respiratory pathogens in adults with community-acquired pneumonia in an outpatient cohort

2019 ◽  
Vol Volume 12 ◽  
pp. 2335-2341 ◽  
Author(s):  
Jing Chen ◽  
Xiaoguang Li ◽  
Wei Wang ◽  
Ying Jia ◽  
Fei Lin ◽  
...  
Keyword(s):  
Community Acquired Pneumonia ◽  
Respiratory Pathogens

scholarly journals Comparison of Once-Daily versus Twice-Daily Administration of Cefdinir against Typical Bacterial Respiratory Tract Pathogens

2001 ◽  
Vol 45 (10) ◽  
pp. 2936-2938 ◽  
Author(s):  
Gigi H. Ross ◽  
Laurie Baeker Hovde ◽  
Khalid H. Ibrahim ◽  
Yasir H. Ibrahim ◽  
John C. Rotschafer
Keyword(s):  
Respiratory Tract ◽  
Community Acquired Pneumonia ◽  
Pharmacodynamic Model ◽  
Daily Administration ◽  
Respiratory Pathogens ◽  
Daily Regimen ◽  
Dosing Regimen ◽  
Once Daily ◽  
Dosing Strategy

ABSTRACT In an in vitro pharmacodynamic model, a twice-daily cefdinir dosing regimen was more effective than a once-daily regimen against common bacterial respiratory pathogens in producing 3-log10killing and preventing the occurrence of regrowth at 24 h. Twice-daily administration is likely the more appropriate cefdinir dosing strategy for the treatment of community-acquired pneumonia.

scholarly journals A Droplet Digital PCR Assay to Detect SARS-CoV-2 RNA

2020 ◽  
Author(s):  
Martin J. Romeo ◽  
Christian P. DiPaola ◽  
Cassidy Mentus ◽  
Cynthia D. Timmers
Keyword(s):  
Limit Of Detection ◽  
Digital Pcr ◽  
The United States ◽  
Cross Reactivity ◽  
Droplet Digital Pcr ◽  
Molecular Testing ◽  
Guidance Document ◽  
Respiratory Pathogens ◽  
Limit Of Quantification ◽  
United States Food

AbstractWe describe a quantitative droplet digital PCR (ddPCR) assay for detection of SARS-CoV-2 viral ribonucleic acid (RNA) in total RNA extracted from human sputum. This method was validated using the guidance of the United States Food and Drug Administration’s Accelerated Emergency Use Authorization (EUA) Template for SARS-CoV-2 that Causes Coronavirus Disease (COVID-19) Molecular Testing of Respiratory Speciment in CLIA Certified High-Complexity Laboratories. Though our laboratory is not CLIA certified, this method met all criteria specified by the guidance document with a Limit of Detection (LOD) of 0.25 copies/μL in the final ddPCR (at least 19/20 replicates reactive), which we consider to be a Lower Limit of Quantification (LLOQ); inclusivity of all known annotated SARS-CoV-2 genomes; no cross-reactivity with other respiratory pathogens; and reactivity of all contrived positives at or above the LOD.

Tigecycline in the Treatment of Community-Acquired Pneumonia

2009 ◽  
Vol 1 ◽  
pp. CMT.S2351
Author(s):  
Daniel Curcio
Keyword(s):  
Tetracycline Resistance ◽  
Multidrug Resistant ◽  
Community Acquired Pneumonia ◽  
Phase Iii ◽  
Resistant Bacteria ◽  
Respiratory Pathogens ◽  
Evaluable Population ◽  
Intent To Treat ◽  
Cure Rates

Tigecycline is a first-in-class glycylcycline, broad-spectrum, intravenous antibacterial developed to overcome the two major mechanisms of tetracycline resistance (ribosomal protection and efflux). The drug has been approved in US for community-acquired bacterial pneumonia in adults. In vitro, tigecycline had good activity against a range of Gram-positive, Gram-negative and atypical community-acquired respiratory tract pathogens implicated in community-acquired pneumonia (CAP), including community-acquired Staphylococcus aureus, penicillin-resistant Streptococus pneumoniae and multidrug-resistant Enterobacteriaceae. Nonetheless, tigecycline shows in vitro low activity against against P. aeruginosa. Tigecycline provides high intrapulmonary concentrations that exceed the MIC90 of most of these respiratory pathogens. The combined results of two well designed, phase III studies demonstrated that tigecycline 100 mg initially, followed by 50 mg every 12 hours for 7-14 days was not inferior to recommended dosages of levofloxacin in the treatment of hospitalized patients with CAP. Clinical cure rates were 89.7% versus 86.3% in the clinically evaluable population and 81.0% versus 79.7% in the clinical modified intent-to-treat population. Tigecycline represents an appropriate choice for empirical monotherapy in the treatment of CAP, mainly in patients with risk factors for infections due to resistant bacteria.

scholarly journals 281. Hypersensitivity Pneumonitis Diagnosed with Broad-Range PCR Testing after Exposure to Battarrea Mushroom Spores

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S153-S154
Author(s):  
Laura Selby ◽  
Justin D Jacobs ◽  
Adam C Brady
Keyword(s):  
Emergency Department ◽  
Hypersensitivity Pneumonitis ◽  
Supplemental Oxygen ◽  
Community Acquired Pneumonia ◽  
Molecular Testing ◽  
Methamphetamine Use ◽  
Routine Work ◽  
Oral Corticosteroids ◽  
History Of ◽  
Primer Sets

Abstract Background Battarrea puffball mushrooms are found extensively worldwide and contain spore-containing sacs. Inhalation of the spores of similar mushrooms, such as Lycoperdon, have been implicated in cases of lycoperdonosis—a syndrome of hypersensitivity pneumonitis. We report a case of hypersensitivity pneumonitis confirmed to be secondary to Battarrea spore exposure diagnosed by broad-range PCR. Methods A 23-year-old homeless man with a history of methamphetamine use presented to the emergency department with a 2-week history of fevers, chills, productive cough, and malaise. He reported his symptoms began soon after eating a long-stemmed mushroom he found growing next to a building. He reported inhaling particles from the mushroom when he picked it up prior to eating it. He vomited within 1 hour of ingestion, and then had a worsening progression of cough and malaise over the following 2 weeks. In the emergency department, he was noted to have leukocytosis and mild elevation of transaminases. He required supplemental oxygen due to hypoxemia. CT scan of his chest demonstrated extensive bilateral nodular pulmonary infiltrates. He was admitted and started on treatment for community-acquired pneumonia. Over the next several days, he had worsening respiratory failure, and routine work up for infectious etiologies was unrevealing. To further investigate, bronchoscopy and bronchoalveolar lavage (BAL) was performed and routine bacterial, fungal and mycobacterial cultures and cytology with Gomori Methanamine-silver and acid-fast stains were negative. BAL fluid was sent for broad range DNA testing by PCR. Antibiotic therapy was stopped, and he was started on steroids to treat presumed hypersensitivity pneumonitis. He recovered rapidly and was discharged on a course of oral corticosteroids. Results After the patient was discharged, molecular testing of BAL fluid resulted with detection of Battarrea species DNA using 28s and ITS primer sets. DNA from no other pathogens was detected. Conclusion Identified through broad range DNA PCR testing, exposure to Battarrea mushroom spores may be a previously unreported cause of hypersensitivity pneumonitis. PCR testing should be considered in the workup of hypersensitivity pneumonitis with known or suspected exposure to mushroom spores. Disclosures All authors: No reported disclosures.

scholarly journals Identification of P1 types and variants of Mycoplasma pneumoniae during an epidemic in Chile

2010 ◽  
Vol 59 (8) ◽  
pp. 925-929 ◽  
Author(s):  
María A. Martínez ◽  
Mauricio Ruiz ◽  
Enna Zunino ◽  
Vivian Luchsinger ◽  
Raúl Aguirre ◽  
...  
Keyword(s):  
Variable Region ◽  
Community Acquired Pneumonia ◽  
Respiratory Pathogens ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Epidemic Period ◽  
Transition Mutation ◽  
Type Sequence

This study was conducted to determine the types of M. pneumoniae prevalent in adults presenting with community-acquired pneumonia during an epidemic period, and to scrutinize a variable region of the RepMP4 element for the detection of P1 variants. All 23 clinical specimens PCR-positive for M. pneumoniae obtained in two hospitals in Santiago, Chile, from 2005 to 2006 were typed by a multiplex PCR directly and then the RepMP4 fragment of 18 specimens was sequenced. A predominance of M. pneumoniae type 2 was found, 18 (78.3 %) specimens being grouped as type 2 and 5 (21.7 %) as type 1. Co-infection of M. pneumoniae with other respiratory pathogens was found in 10/23 (43.4 %) patients, but their frequency was not related to the M. pneumoniae type. Sequence analysis revealed a single nucleotide polymorphism, a transition mutation, in 50 % of amplicons belonging to type 1 and in 71.4 % of amplicons of type 2. The nucleotide changes were synonymous in each P1 variant. In conclusion, during the 2005–2006 epidemic in Santiago, both types of M. pneumoniae circulated. Although the analysed area in the RepMP4 was small, we detected the existence of P1 variants in the two types of this organism.

scholarly journals 2213. Etiology of Community-Acquired Pneumonia (CAP) in Hospitalized Native American Adults

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S754-S755
Author(s):  
Laura Hammitt ◽  
Amanda Driscoll ◽  
Robert Weatherholtz ◽  
Raymond Reid ◽  
Janene Colelay ◽  
...  
Keyword(s):  
Native American ◽  
Native Americans ◽  
Blood Culture ◽  
Influenza A ◽  
Virus Detection ◽  
Community Acquired Pneumonia ◽  
Respiratory Pathogens ◽  
Common Etiology ◽  
Case Status ◽  
Type 3

Abstract Background Native Americans experience a high burden of community-acquired pneumonia (CAP). Thirteen-valent pneumococcal conjugate vaccine (PCV13) was introduced for adults ≥65yrs in 2014. Data on CAP etiology can guide prevention and treatment. Methods We enrolled adults hospitalized with CAP and age-group-matched non-hospitalized controls on Navajo and White Mountain Apache tribal lands. Nasopharyngeal/oropharyngeal (NP/OP) swabs from cases and controls were tested by multiplex PCR for respiratory pathogens. Urine from cases and controls was tested for pneumococcus (Sp) by conventional (BinaxNOW) and serotype-specific urine antigen detection (UAD) for 24 serotypes (PCV13 types plus 2, 8, 9N, 10A, 11A, 12F, 15B, 17F, 20, 22F, 33F). Blood culture and chest radiographs (CXRs) were obtained from cases at the provider’s discretion. Radiographic pneumonia was determined by clinical interpretation of CXRs. Results From March 2016 to March 2018, we enrolled 580 CAP cases with CXR confirmation and 411 controls. Positive blood culture was identified in 42/483 (9%), of which 29 (69%) were Sp. Sp was detected in 164/572 (29%) cases (table). Of 125 cases with serotype information available, serotypes 3 (n = 35; 28%) 8 (n = 19; 15%) and 20 (n = 15; 12%) were the most common. Among 53 Sp cases aged ≥65 years, 26 (49%) were PCV13-type. Compared with blood culture, UAD was 100% sensitive and 100% concordant (n = 24). Viruses were detected by NP/OP PCR in 43% of CAP cases and 18% of controls. Influenza A, parainfluenza type 3, rhinovirus, and RSV were statistically significantly associated with case status. Among 263 cases in whom all diagnostic tests were collected, 63% had a pathogen detected: bacteria alone in 19%, viruses alone in 23%, and both bacterial and viral infection in 22%. Bacterial causes outnumbered viral causes when adjusting for virus detection in the control population. Conclusion Pneumococci were the most common etiology identified among Native American adults with CAP. UAD improved detection of pneumococcal CAP. Respiratory viruses also contributed substantially to CAP burden. Broader prevention strategies, including new vaccines, are required to prevent viral pneumonia and pneumococcal pneumonia caused by serotypes not contained in currently-available vaccines. Disclosures All authors: No reported disclosures.

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