Microorganisms in Respiratory Tract of Patients Diagnosed with Atypical Pneumonia: Results of a Research Based on the Use of Reverse Transcription Polymerase Chain Reaction (RT-PCR) DNA

Tokman, Hrisi Bahar; Aslan, Mustafa; Ortakoylu, Gonenc; Algingil, Reyhan Çalişkan; Yüksel, Pelin; Karakullukçu, Asiye; Kalaycı, Fatma; Sarıbaş, Suat; Çakan, Hüseyin; Demir, Türkay; Kocazeybek, Bekir

doi:10.7754/clin.lab.2013.130731

Cited by 7 publications

(8 citation statements)

References 2 publications

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“…Nevertheless, given the high overall sensitivity of CLART® PneumoVir, we cannot rule out the possibility of these being true positives that remained undetected by the nested PCR assay employed for resolution of discrepancies. This is in contrast to previously published data (Pillet et al, 2013;Tokman et al, 2014). The use of different criteria for resolving discordant results among the studies may account for these discrepancies.…”

Section: Discussioncontrasting

confidence: 92%

“…On the contrary, the CLART® PneumoVir was poorly sensitive for detection of picornaviruses. This has also been reported in other studies (Pillet et al, 2013;Tokman et al, 2014) and may likely be due to the fact that the assay only detects enterovirus type B (Pillet et al, 2013). False-positive results were scarce, and most frequently obtained with the CLART® PneumoVir assay, especially for hBoV and some PIVs, and notably in the context of mixed infections.…”

Section: Discussionsupporting

confidence: 73%

“…The CLART® PneumoVir assay (Genomica, Coslada, Spain) is a reverse transcription-polymerase chain reaction (RT-PCR) DNA microarray method that makes it possible to detect simultaneously 17 RVs. The reliability of this procedure for the detection of RVs in children and adults has been previously shown (Culebras et al, 2013;Frobert et al, 2011;Pillet et al, 2013;Renois et al, 2010;Tokman et al, 2014). Nevertheless, little is known as to how this system compares with other multiplex platforms.…”

Section: Introductionmentioning

confidence: 90%

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Comparison of the performance of 2 commercial multiplex PCR platforms for detection of respiratory viruses in upper and lower tract respiratory specimens

Costa¹,

Rodríguez-Domínguez

Clari³

et al. 2015

Diagnostic Microbiology and Infectious Disease

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The performance of the CLART® PneumoVir system with that of the Luminex xTAG RVP Fast v1 assay for detection of most common respiratory viruses in upper and lower tract respiratory specimens (n=183) from unique patients with influenza-like syndrome or lower tract respiratory infection. Nested PCR coupled to automated sequencing was used for resolution of discrepancies. Fully concordant results were obtained for a total of 122 specimens, whereas 56 specimens gave partially (n=21) or fully discordant (n=35) results (Kappa coefficient, 0.62). The overall specificity of the Luminex xTAG RVP Fast v1 assay was slightly higher than that of the CLART® PneumoVir assay for human bocavirus, influenza A virus/H3N2, influenza B virus, human metapneumovirus, and parainfluenza virus, whereas the sensitivity of the latter was higher for most targeted viruses except, notably, for picornaviruses. This was irrespective of either the origin of the respiratory specimen or the age group to which the patients belonged.

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Section: Discussioncontrasting

confidence: 92%

Section: Discussionsupporting

confidence: 73%

Section: Introductionmentioning

confidence: 90%

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Comparison of the performance of 2 commercial multiplex PCR platforms for detection of respiratory viruses in upper and lower tract respiratory specimens

Costa¹,

Rodríguez-Domínguez

Clari³

et al. 2015

Diagnostic Microbiology and Infectious Disease

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“…Microarray technology showed a higher sensitivity (99.5%) and similar specificity (98.5%) to real-time PCR. However, another study with the same microarray kit used in this study showed a high specificity (100%) and low sensitivity (52%) in the clinical scenario of atypical pneumonia [ 24 ]. A study in Japan using near patient automated microarray technology showed not only a higher sensitivity and specificity compared to immunochromatographic antigen detection (the gold standard used was virus isolation) but also quicker results for children infected with Influenza and RSV [ 25 ].…”

Section: Discussionmentioning

confidence: 93%

Viral Infection in Adults with Severe Acute Respiratory Infection in Colombia

Remolina

Ulloa

Vargas³

et al. 2015

PLoS ONE

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ObjectivesTo identify the viral aetiology in adult patients with severe acute respiratory infection (SARI) admitted to sentinel surveillance institutions in Bogotá in 2012.DesignA cross-sectional study was conducted in which microarray molecular techniques for viral identification were used on nasopharyngeal samples of adult patients submitted to the surveillance system, and further descriptions of clinical features and relevant clinical outcomes, such as mortality, need for critical care, use of mechanical ventilation and hospital stay, were obtained.SettingRespiratory infections requiring hospital admission in surveillance centres in Bogotá, Colombia.ParticipantsNinety-one adult patients with acute respiratory infection (55% were female).MeasurementsViral identification, intensive care unit admission, hospital stay, and mortality.ResultsViral identification was achieved for 63 patients (69.2%). Comorbidity was frequently identified and mainly involved chronic pulmonary disease or pregnancy. Influenza, Bocavirus and Adenovirus were identified in 30.8%, 28.6% and 18.7% of the cases, respectively. Admission to the intensive care unit occurred in 42.9% of the cases, while mechanical ventilation was required for 36.3%. The average hospital stay was 9.9 days, and mortality was 15.4%. Antibiotics were empirically used in 90.1% of patients.ConclusionsThe prevalence of viral aetiology of SARI in this study was high, with adverse clinical outcomes, intensive care requirements and high mortality.

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“…While microarrays have been used extensively in the fields of cancer research and clinical genetics [8–13], more recently they have drawn growing attention for their potential application to infectious diseases [14–19]. While several studies have explored the comparative sensitivity and specificity of diagnostic microarrays in identifying a broad range of pathogens [20–32], the value and implications of their introduction to clinical practice remain undetermined. This study sought to evaluate the use of a 22-pathogen TaqMan Array Card (TAC) for diagnosing bacterial, viral and fungal pathogens in deep respiratory samples from adult ICU patients, in terms of comparative diagnostic yield, turnaround time (TAT) and influence on clinical decision-making.…”

Section: Introductionmentioning

confidence: 99%

Evaluating the use of a 22-pathogen TaqMan array card for rapid diagnosis of respiratory pathogens in intensive care

Jones

Morris

Curran

et al. 2020

Journal of Medical Microbiology

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Introduction. Pneumonia is highly prevalent in intensive care units (ICUs), with high associated mortality. Empirical treatment prioritizes breadth of coverage while awaiting laboratory diagnosis, often at the expense of antimicrobial stewardship. Microarrays use multiple parallel polymerase chain reactions to enable a rapid syndromic approach to laboratory diagnosis. Aim. To evaluate the clinical and laboratory implications of introducing a bespoke 22-pathogen TaqMan Array Card (TAC) for rapid pathogen detection in deep respiratory samples from adult ICUs. Methodology. TAC results from all ICU patients prospectively tested over a 9-month period at Cambridge’s Clinical Microbiology and Public Health Laboratory were compared to those of corresponding conventional microbiological assays (culture-, PCR- or serology-based) in terms of result agreement and time-to-result availability. Clinical impact was assessed by retrospective review of medical records. Results. Seventy-one patients were included [45 (63 %) male, median age 59). Overall result agreement was 94 %, with TAC detecting more pathogens than conventional methods. TAC detected Streptococcus pneumoniae more readily than culture (7 vs 0 cases; P=0.02). TAC did not detect Aspergillus spp. in eight culture- or galactomannan-positive cases. The median turnaround time (1 day) was significantly shorter than that of bacterial/fungal culture, Pneumocystis jirovecii PCR and galactomannan testing (each 3 days; P<0.001), atypical bacteria serology (13 days; P<0.001) and Mycobacterium tuberculosis culture (46 days; P<0.001). Earlier result availability prompted discontinuation of unnecessary antimicrobials in 15/71 (21 %) cases, but had no bearing on patient isolation/deisolation. Conclusion. TAC provided greater overall yield of pathogen detection and faster turnaround times, permitting earlier discontinuation of unnecessary antimicrobials.

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Microorganisms in Respiratory Tract of Patients Diagnosed with Atypical Pneumonia: Results of a Research Based on the Use of Reverse Transcription Polymerase Chain Reaction (RT-PCR) DNA

Cited by 7 publications

References 2 publications

Comparison of the performance of 2 commercial multiplex PCR platforms for detection of respiratory viruses in upper and lower tract respiratory specimens

Comparison of the performance of 2 commercial multiplex PCR platforms for detection of respiratory viruses in upper and lower tract respiratory specimens

Viral Infection in Adults with Severe Acute Respiratory Infection in Colombia

Evaluating the use of a 22-pathogen TaqMan array card for rapid diagnosis of respiratory pathogens in intensive care

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