scholarly journals Routine Broad-Range Fungal Polymerase Chain Reaction With DNA Sequencing in Patients With Suspected Mycoses Does Not Add Value and Is Not Cost-Effective

2018 ◽  
Vol 143 (5) ◽  
pp. 634-638 ◽  
Author(s):  
Lisa M. Stempak ◽  
Sherilynn A. Vogel ◽  
Sandra S. Richter ◽  
Robert Wyllie ◽  
Gary W. Procop
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequencing ◽  
Fungal Infections ◽  
Diagnostic Value ◽  
Molecular Diagnostic ◽  
Fungal Culture ◽  
Chain Reaction ◽  
Predictive Values ◽  
Polymerase Chain ◽  
The Cost

Context.— New molecular diagnostic tests regularly become available, and they may be assumed to be superior to traditional diagnostic studies. The added cost of these studies should be considered in conjunction with the value provided for patient care. Objective.— To assess the cost and diagnostic value of broad-range polymerase chain reaction (PCR) and DNA sequencing for the diagnosis of fungal infections compared with traditional studies. Design.— We reviewed the cost and clinical impact of broad-range fungal PCR/DNA sequencing for 65 specimens for which this test, a direct fungal examination, fungal culture, and a histopathologic assessment were performed. Results.— The sensitivity, specificity, and positive and negative predictive values for each of the assays studied were, respectively: histopathology (83.3%, 100%, 100%, and 98.3%); direct examination (66.7%, 100%, 100%, and 96.7%); fungal culture (83.3%, 100%, 100%, and 98.3%); and broad-range fungal PCR/DNA sequencing (83.3%, 95.0%, 62.5%, and 98.3%). The cost for broad-range fungal PCR/DNA sequencing was $32,500, compared with $8,591.70 for all traditional tests combined, for the 65 specimens included in this review. Conclusions.— Broad-range fungal PCR/DNA sequencing did not detect any infecting fungal pathogen that was not detected by at least 1 of the traditional methods, but 3 false-positives occurred. Broad-range fungal PCR/DNA sequencing is not a substitute for traditional laboratory studies and should be used judiciously to promote care affordability.

scholarly journals DNA Sequencing to Evaluate Nail Pathogens: An Investigation into Bacteria and Fungi

2021 ◽  
Vol 111 (2) ◽  
Author(s):  
Ebony Love ◽  
Jonathan D. Furmanek ◽  
Courtney M. Foote ◽  
James McGuire ◽  
Ziad Labbad
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequencing ◽  
Culture Media ◽  
Nail Plate ◽  
Polymerase Chain Reaction Analysis ◽  
Clinical Samples ◽  
Fungal Culture ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Bacteria And Fungi

Background It is well established and accepted that fungi are a major contributing factor in nail dystrophy. It has also been recognized that bacteria play a crucial role in onycholysis. However, the bacteria and fungi that can be grown on culture media in the laboratory are only a small fraction of the total diversity that exists in nature. Contemporary studies have revealed that fungi and bacteria often form physically and metabolically interdependent consortia that harbor properties and pathogenicity distinct from those of their individual components. Metagenomic DNA “shotgun” sequencing has proved useful in determining microbial etiology in clinical samples, effective for not only bacteria but also fungi, archaea, and viruses. Methods Thirty-nine consecutive nail and subungual debris samples with suspected onychomycosis were sent for laboratory analysis using three examination techniques: DNA sequencing, polymerase chain reaction analysis, and standard fungal culture. The nail plate and surrounding areas were disinfected with an ethyl alcohol swab before nail sampling. Samples from 16 patients were analyzed for suspected onychomycosis with DNA sequencing, searching a database of 25,000 known pathogens. These results were compared with 15 real-time polymerase chain reaction screening assays and eight fungal cultures sampled with the same methods. Results The DNA sequencing detected 32 species of bacteria and 28 species of fungi: 50% were solely bacterial, 6.3% were solely fungal, and 43.7% were mixed communities of bacteria and fungi. Conclusions Toenails tested with DNA sequencing demonstrated the presence of both bacteria and fungi in many samples. Further work is required to fully investigate its relevance to nail pathology and treatment.

Diagnostic Accuracy of a Direct Panfungal Polymerase Chain Reaction Assay Performed on Stained Cytology Slides

2021 ◽  
pp. 030098582199156
Author(s):  
Alexandra N. Myers ◽  
Unity Jeffery ◽  
Zachary G. Seyler ◽  
Sara D. Lawhon ◽  
Aline Rodrigues Hoffmann
Keyword(s):  
Polymerase Chain Reaction ◽  
Diagnostic Accuracy ◽  
Molecular Techniques ◽  
Fungal Culture ◽  
Chain Reaction ◽  
Identification Of Fungi ◽  
Fungal Dna ◽  
Polymerase Chain ◽  
Panfungal Pcr ◽  
Pcr Targeting

Molecular techniques are increasingly being applied to stained cytology slides for the diagnosis of neoplastic and infectious diseases. Such techniques for the identification of fungi from stained cytology slides have not yet been evaluated. This study aimed to assess the diagnostic accuracy of direct (without nucleic acid isolation) panfungal polymerase chain reaction (PCR) followed by sequencing for identification of fungi and oomycetes on stained cytology slides from dogs, cats, horses, and other species. Thirty-six cases were identified with cytologically identifiable fungi/oomycetes and concurrent identification via fungal culture or immunoassay. Twenty-nine controls were identified with no cytologically or histologically visible organisms and a concurrent negative fungal culture. Direct PCR targeting the internal transcribed spacer region followed by sequencing was performed on one cytology slide from each case and control, and the sensitivity and specificity of the assay were calculated. The sensitivity of the panfungal PCR assay performed on stained cytology slides was 67% overall, 73% excluding cases with oomycetes, and 86% when considering only slides with abundant fungi. The specificity was 62%, which was attributed to amplification of fungal DNA from control slides with no visible fungus and negative culture results. Direct panfungal PCR is capable of providing genus- or species-level identification of fungi from stained cytology slides. Given the potential of panfungal PCR to amplify contaminant fungal DNA, this assay should be performed on slides with visible fungi and interpreted in conjunction with morphologic assessment by a clinical pathologist.

Diagnostic Value of Multiplex Polymerase Chain Reaction in Detection of Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia from Sepsis in Pediatrics

2021 ◽  
Vol 15 ◽  
Author(s):  
Sara Galeb ◽  
Maysaa El Sayed Zaki ◽  
Raghdaa Shrief ◽  
Rasha Hassan ◽  
Mohamed Anies
Keyword(s):  
Polymerase Chain Reaction ◽  
Pseudomonas Aeruginosa ◽  
Acinetobacter Baumannii ◽  
Multiplex Pcr ◽  
Stenotrophomonas Maltophilia ◽  
Multiplex Polymerase Chain Reaction ◽  
Diagnostic Value ◽  
Blood Cultures ◽  
Chain Reaction ◽  
Polymerase Chain

Background: Proper identification of the causative organism in pediatric sepsis is crucial for early diagnosis and prevention of septic shock and organ failure. Objectives: The present study aimed to evaluate the multiplex Polymerase Chain Reaction (PCR) to detect Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia from positive blood cultures for these pathogens isolated from children, with hospital-acquired sepsis compared to the conventional biochemical reactions for identification of these organisms. Methods: This study was a cross-sectional study performed on 100 isolates from pediatric blood cultures, including Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia. The study also included 100 isolates of Escherichia coli as a negative control. All isolates were identified by API 20NE and the multiplex PCR, with primers specific to the 3 tested bacteria. Results: Multiplex PCR was positive in 96% of isolates, and 4 isolates had negative results. False positive results were reported with three E. coli strains. Multiplex PCR identified all the isolates of Acinetobacter baumannii, 29 isolates of Pseudomonas aeruginosa, and 27 isolates of Stenotrophomonas maltophilia. Compared to the biochemical identification, the diagnostic value of the multiplex PCR revealed 96.04% sensitivity, 96.9% specificity, 97.00%, positive predictive value, 96.00% negative predictive value, and 96.50% accuracy. Conclusion: The present study highlights the diagnostic value of multiplex PCR to identify Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia from positive blood cultures. Multiplex PCR was sensitive, specific, and accurate. The accuracy differs according to the organisms, with 100% accuracy for Acinetobacter baumannii.

scholarly journals Polymerase Chain Reaction and blood culture for diagnosis of canine sepsis

2018 ◽  
Vol 48 (6) ◽  
Author(s):  
Marcelo Marques da Silveira ◽  
Stéfhano Luis Cândido ◽  
Karin Rinaldi dos Santos ◽  
Maerle Oliveira Maia ◽  
Roberto Lopes de Souza ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Blood Culture ◽  
Diagnostic Value ◽  
Turnaround Time ◽  
Diagnostic Techniques ◽  
Pcr Analysis ◽  
Chain Reaction ◽  
Suspected Sepsis ◽  
Fungal Dna ◽  
Polymerase Chain

ABSTRACT: Sepsis is characterized by the presence of organ dysfunction secondary to the dysregulated systemic inflammatory response associated with an infection, and has high mortality rates. Traditional diagnostic techniques based on non-microbiological isolation are time-consuming and may delay treatment. Thus, this study aimed to compare bacterial and fungal broad-range polymerase chain reaction (PCR) and blood culture for diagnosis of sepsis in dogs. Blood samples from 88 dogs with suspected sepsis were analyzed by blood culture, and PCR to detect bacterial and fungal DNA. On blood culture, 20 (22.7%) samples tested positive for bacterial isolates; however, none tested positive for fungi. Through PCR analysis, bacterial DNA was detected in 46 (52.3%) animals, whereas fungal DNA was present in one (1.1%) sample. Our results showed that PCR-based testing has important diagnostic value for canine blood infections because it has a shorter turnaround time and higher sensitivity than traditional blood culture.

Sign in / Sign up

Export Citation Format

Share Document