Respiratory Publications

2017 Article - "The 2015–2016 influenza epidemic: Late onset, clinical severity and emergence of the B Victoria virus" (pdf, 144KB)

Summary:Flu is a viral infection caused by influenza viruses. There are three types (A, B and C) and only A (A1H1N1 and AH3N2) and B (Victoria line and Yamagata line) are responsible for major seasonal epidemics with a circulation predominance for virus A. However, the 2015-2016 epidemic was different with an unusually high circulation of virus B (Victoria), leading to carry out a descriptive retrospective study at the university hospital (CHU) in Bordeaux.
A total of 110 patients with a positive PCR with a mean age of 53.3 years (16-90 years) were involved in the study. The positive diagnosis was made using a multiplex PCR with the kits available at the CHU de Bordeaux (Anyplex® II RV16, Allplex®Respiratory Panel and Fast Track®Flu Differentiation). Virus B positive sample subtyping was performed by the CNR de Lyon. Type A virus was mostly isolated in 57 patients (52%) with a predominance of subtype A (H1N1) in 50 patients (45% of the total). Type B viruses were isolated from 53 patients (48%) with the Victoria line virus in 47 patients (43% of the workforce). It was late onset epidemic (March-May), 23% of the patient were vaccinated. Same severity for type A (25%) and type B Victoria strain (23%).
Conclusion: The flu epidemic of 2015-2016 was different from the other years of an unusual overrepresentation of B / Victoria in hospital. There was a mismatch between vaccine lineage B / Yamagata and the circulating major strain Victoria with unprotected patients at risk. This study probably provides additional arguments to encourage seasonal influenza vaccination by a quadrivalent vaccine containing both subtypes A and the two B-line viruses (Victoria and Yamagata).

Kit used: FTD Flu differentiation

2017 Article - "Pertussis and Pertussis like Illness: Pediatric Experience in Oman" (pdf, 844KB)

Summary: A resurgence of pertussis or whooping cough has been observed worldwide despite broad vaccination coverage. Pertussis like illness (PLI) refers to a clinical syndrome compatible with pertussis infection but lacking laboratory confirmation or an epidemiological link to a confirmed case. Our study aimed to estimate the contribution of Bordetella pertussis infection and identifying predictors of its diagnosis in a cohort of children with PLI. Demographic and clinical information were retrospectively collected from the medical records of children < 13 years old and hospitalized for PLI in two pediatric units in Oman from 1 January 2012 to 31 December 2013. The laboratory data of all cases were reviewed and confirmed cases of pertussis were identified, analyzed, and compared with non-confirmed cases.A total of 131 patients were enrolled in this study. The majority (95.4% [125/131]) were infants. Only 54.1% (71/131) of admitted children with PLI were tested for pertussis. The incidence of pertussis infection among the tested group was 16.9% (12/71) with a 95% confidence interval 8.2−25.6. Severe illness occurred in 56.4% (74/131) of patients, and six were confirmed to have pertussis. Pediatric intensive care unit admission was required for one confirmed case of pertussis and eight cases from the PLI group (three were negative for pertussis, and five were not tested). Receiver operator characteristic curve analysis revealed that a white blood cell count 3 23.5 × 109/L had 96.6% specificity and lymphocytes 3 17 × 109/L had 98.3% specificity. Taking into consideration that the number tested for pertussis was limited, the incidence of pertussis was 16.9% (12 out of 71 patients). Lymphocytosis can be used as a reliable predictor for the diagnosis of pertussis especially in the absence of specific confirmatory tests or until their results are available.

Kit used: FTD Respiratory pathogens 21

2017 Article - "Standardization of Laboratory Methods for the PERCH study" (pdf, 395KB)

Summary: The Pneumonia Etiology Research for Child Health study was conducted across 7 diverse research sites and relied on standardized clinical and laboratory methods for the accurate and meaningful interpretation of pneumonia etiology data. Blood, respiratory specimens, and urine were collected from children aged 1–59 months hospitalized with severe or very severe pneumonia and community controls of the same age without severe pneumonia and were tested with an extensive array of laboratory diagnostic tests. As molecular diagnostic tool FTD Respiratory pathogens 33 was used. A standardized testing algorithm and standard operating procedures were applied across all study sites. Site laboratories received uniform training, equipment, and reagents for core testing methods. Standardization was further assured by routine teleconferences, in-person meetings, site monitoring visits, and internal and external quality assurance testing. Targeted confirmatory testing and testing by specialized assays were done at a central reference laboratory.

Kit used: FTD respiratory pathogens 33

2017 Article - "Association of C-Reactive Protein With Bacterial and Respiratory Syncytial Virus–Associated Pneumonia Among Children Aged <5 Years in the PERCH Study" (pdf, 430KB)

Summary: Lack of a gold standard for identifying bacterial and viral etiologies of pneumonia has limited evaluation of C-reactive protein (CRP) for identifying bacterial pneumonia. We evaluated the sensitivity and specificity of CRP for identifying bacterial vs respiratory syncytial virus (RSV) pneumonia in the Pneumonia Etiology Research for Child Health (PERCH) multicenter case-control study. We measured serum CRP levels in cases with World Health Organization–defined severe or very severe pneumonia and a subset of community controls. We evaluated the sensitivity and specificity of elevated CRP for “confirmed” bacterial pneumonia (positive blood culture or positive lung aspirate or pleural fluid culture or polymerase chain reaction [PCR]/FTD Respiratory pathogens 33) compared to “RSV pneumonia” (nasopharyngeal/oropharyngeal or induced sputum PCR-positive without confirmed/suspected bacterial pneumonia). Receiver operating characteristic (ROC) curves were constructed to assess the performance of elevated CRP in distinguishing these cases. Among 601 human immunodeficiency virus (HIV)–negative tested controls, 3% had CRP ≥40 mg/L. Among 119 HIV-negative cases with confirmed bacterial pneumonia, 77% had CRP ≥40 mg/L compared with 17% of 556 RSV pneumonia cases. The ROC analysis produced an area under the curve of 0.87, indicating very good discrimination; a cut-point of 37.1 mg/L best discriminated confirmed bacterial pneumonia (sensitivity 77%) from RSV pneumonia (specificity 82%). CRP ≥100 mg/L substantially improved specificity over CRP ≥40 mg/L, though at a loss to sensitivity. Elevated CRP was positively associated with confirmed bacterial pneumonia and negatively associated with RSV pneumonia in PERCH. CRP may be useful for distinguishing bacterial from RSV-associated pneumonia, although its role in discriminating against other respiratory viral-associated pneumonia needs further study.

Kit used: FTD respiratory pathogens 33

2017 Article - "The potential influence of human parainfluenza viruses detected during hospitalization among critically ill patients in Kuwait, 2013–2015" (pdf, 485KB)

Summary: The aim of this study is to describe the spectrum, incidence and clinical features of of human parainfluenza viruses (PIV)-associated infections diagnosed during the hospital stay of patients admitted to pediatric intensive care unit (PICU) and intensive care unit (ICU) of 5 medical centers across Kuwait.This was a population-based, retrospective study from 2013 to 2015. Specimens were analyzed by FTD Respiratory pathogens 21. This analysis was performed using the database of Virology Unit, Mubarak Al-Kabeer Hospital. Data from 1510 admitted patients with suspected respiratory viral infections was extracted.The database contained a total of 39 (2.6%) patients infected with PIV (53.8% male and 46.2% females) and 20 (51.3%) were under 1 year of age. The most frequently isolated type was type 3 (28, 71.8%) followed by type 1 (9, 23.1%). At admission the most common clinical diagnosis was pneumonia in 12 patients (30.8%, p < 0.05) followed by bronchiolitis in 10 patients (25.6%).PIV plays an important yet unrecognized role in the outcomes of PIUC and ICU patients. These results contribute to the limited epidemiologic data of PIV in PIUC and ICU in this region.

Kit used: FTD Respiratory pathogens 21

2017 Article - "Viral aetiology of bronchiolitis in hospitalised children in Qatar" (pdf, 836KB)

Summary: Bronchiolitis is considered one of the earliest and most common causes of hospitalisation in young children. Development of molecular technologies allowed a better understanding of bronchiolitis aetiology. Results from cohort studies evaluating the association between single, multiple viral infections and clinical outcomes are conflicting. Data on viral bronchiolitis in children were found to be limited in Qatar. This study aimed to determine frequency and seasonal trends of viral pathogens causing acute bronchiolitis, and to explore association between viral pathogens, disease severity and length of stay (LOS). Multiplex, real-time, polymerase chain reaction (RT-PCR) using FTDResp21 kit (Fast Track Diagnostics, Silema, Malta) was used for the detection of respiratory pathogens.

Kit used: FTD Respiratory pathogens 21

2017 Article - "Genotyping of human rhinovirus in adult patients with acute respiratory infections identified predominant infections of genotype A21" (pdf, 1MB)

Summary: The aim of this study was the assessment of the prevalence of HRV and its specific genotypes in patients suffering from acute respiratory tract infections (ARTIs). Samples from 147 adult inpatients with community-acquired pneumonia (CAP) and 291 adult outpatients with upper ARTIs (URTIs) were collected. The presence of HRVs and other common respiratory pathogens were screened using the FTD Respiratory pathogens 21 plus kit. HRV was detected in 42 patients, with 35 species A, five B and two C. Seventeen genotypes were identified, and HRV-A21 ranked the highest (9/42, 21.4%). The HRV-A21 genome sequenced in this study contained 12 novel coding polymorphisms in viral proteins. The infections of HRV-A21 virus obtained in this study could not be neutralized by antiserum of HRVA21 prototype strain (VR-1131), indicating remarkable antigenic variation. The results highlight an unexpected infection of genotype HRV-A21 in the clinic, indicating the necessity of precise genotyping and surveillance of HRVs to improve the clinical management of ARTIs.

Kit used: FTD Respiratory pathogens 21 plus

2017 Article - "Assessment of the Usefulness of Multiplex Real-Time PCR Tests in the Diagnostic and Therapeutic Process of Pneumonia in Hospitalized Children: A Single-Center Experience" (1) (pdf, 1MB)

Summary: The aim of the study was assessment of the usefulness of multiplex real-time PCR tests in the diagnostic and therapeutic process in children hospitalized due to pneumonia and burdened with comorbidities. The study group included 97 children hospitalized due to pneumonia at the Karol Jonscher Teaching Hospital in Poznań, in whom multiplex real-time PCR tests (FTD Respiratory pathogens 33) were used. Positive test results of the test were achieved in 74 patients (76.3%). The average age in the group was 56 months. Viruses were detected in 61 samples (82% of all positive results); bacterial factors were found in 29 samples (39% of all positive results). The presence of comorbidities was established in 90 children (92.78%). The analysis demonstrated that the participation of viruses in causing severe lung infections is significant in children with comorbidities. Multiplex real-time PCR tests proved to be more useful in establishing the etiology of pneumonia in hospitalized children than the traditional microbiological examinations.

Kits used: FTD Respiratory pathogens 33

2017 Article - "Performance evaluation of Direct Fluorescent Antibody, Focus Diagnostics SimplexaTM Flu A/B and RSV and Multi-parameter Customized Respiratory Taqman® Array Card in Immunocompromised Patients" (limited access)

Summary: Molecular assays for diagnosis of Flu A, Flu B, and RSV with short turnaround time (TAT) are of considerable clinical importance. In addition, rapid and accurate diagnosis of a large panel of viral and atypical pathogens can be crucial in immunocompromised patients. The objective of the study was to evaluate the performance of the Simplexa™ Direct assay system in comparison with direct fluorescent antibody (DFA) and customized Taqman® Array Card (TAC) testing for RSV, Flu A, and Flu B in immunocompromised patients. FTD Flu/HRSV was used as golden standard reference method for verification testing. Secondly, they evaluate different algorithms for the detection of respiratory pathogens in terms of cost, turn-around-time (TAT) and diagnostic yield. They collected 125 nasopharyngeal swabs (NTS) and 25 BAL samples from symptomatic immunocompromised patients. The overall sensitivity was significantly lower for DFA testing than for the two molecular methods (p<0.05). Performance characteristics of Simplexa™ testing were not significantly different compared to TAC testing (p>0.1). For BAL samples only, the sensitivity and specificity of the Simplexa™ assay was 100%. In total, 6.7%, 16% and 18% of samples were positive for Flu A, Flu B or RSV by DFA, Simplexa™ and TAC testing respectively. When considering not only these pathogens but all results for TAC, the method identified 93 samples with one or more respiratory pathogens (62%). A co-infection rate of 15.3% was found by TAC. The estimated costs and TAT were 8.2€ and 2 hours for DFA, 31.8€ and 1.5 hours for Simplexa™ and 55€ and 3 hours for TAC testing. Taken all this together diagnostic using FTD kits, especially in lyophilized formulation, is extremely time and cost saving!

Kit used: FTD FLU/HRSV
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2017 Article - "Respiratory multiplex polymerase chain reaction: An important diagnostic tool in immunocompromised patients" (pdf, 530KB)

Summary: Viruses and atypical pathogens can cause significant respiratory illness in immunocompromised patients. Multiplex polymerase chain reaction (MPCR) has improved the diagnostic yield of pathogens, and it is easier to identify the co-infections also. The present study was done to evaluate the performance of MPCR on bronchoalveolar lavage (BAL) samples in immunocompromised patients. MPCR identified the causative pathogen in 59.3% of patients while culture could identify only in 37.8% of patients. Most frequent etiological agent was Klebsiella pneumoniae (32%), followed by cytomegalovirus (21%), and Pneumocystis jirovecii (10%). Mortality was significantly higher in patients having mixed infections. MPCR is highly sensitive and rapid tool which can be considered in the routine diagnostic algorithm of respiratory illness in immunocompromised patients.

Kit used: FTD Respiratory pathogens 33