Respiratory Publications

2017 Article - "Does azithromycin given to women in labour decrease ocular bacterial infection in neonates? A double-blind, randomized trial" (pdf, 365KB)

Background: Vertical transmission can result in neonatal infection and disease. Reducing the transmission of bacterial pathogens from mother to infant may be an effective means of preventing neonatal infection, including bacterial conjunctivitis.

Methods: In a double-blind, randomized trial, we assessed the effect of administering a single dose of oral azithromycin to women in labour on bacterial colonization of the neonate. A reduction in purulent neonatal conjunctivitis was a secondary objective of the trial. Ocular samples were collected from the lower fornix of infants presenting with clinical signs of purulent conjunctivitis during the first eight weeks of life. Incidence of purulent conjunctivitis was compared between trial arms. Bacterial infection was assessed using PCR and incidence of purulent conjunctivitis due to bacteria was also compared between arms.

Results: Forty of 843 infants (4.7%) presented clinical signs of purulent conjunctivitis. No significant difference in incidence of purulent conjunctivitis was seen between azithromycin and placebo arms [4.3% (18/419) versus 5.2% (22/424), OR = 0.82,95% CI (0.44,1.54), p=0.628]. S. aureus was the most commonly identified pathogen, detected in 38% of cases. Incidence of purulent-conjunctivitis due to bacterial infection was lower in the azithromycin arm [1.2% (5/419) versus 3.8% (16/424), OR = 0.31, 95% CI (0.12–0.82), p = 0.025)]. The incidence of gram-positive bacteria was also lower in the azithromycin arm [1.0% (4/419) versus 3.3% (14/424), OR = 0.28, 95%CI (0.10–0.82), p = 0.029].

Conclusions: Oral azithromycin given to women during labour may have the potential to reduce the incidence of bacterial neonatal conjunctivitis.

Kit used: FTD SPn/Staph/MC/Hi
FTD Vaginal Swab

2017 Article - "Performance of the Alere i RSV assay for point of care detection of respiratory syncytial virus in children" (pdf, 510KB)

Summary: Respiratory syncytial virus (RSV) is the most important cause of severe acute respiratory tract infection in young children. Alere i RSV is a novel molecular rapid test which identifies respiratory syncytial virus. The group evaluated the clinical performance of the Alere i RSV assay in a pediatric point-of-care setting during winter season 2016 / 2017. Test results from 518 nasopharyngeal swab samples were compared to FTD Respiratory pathogens 21 seen as reference standard. The overall sensitivity and specificity of the Alere i RSV test assay was 93% (CI95 89% – 96%) and 96% (CI95 93% – 98%), respectively. An optimal sensitivity of 98% (CI95 94% - 100%) and specificity of 96% (CI95 90% - 99%) was obtained in children < 6 months. In children ≥ 2 years, sensitivity and specificity remained at 87% (CI95 73% – 96%) and 98% (CI95 92% – 100%), respectively. False negative Alere i RSV test results mostly occurred in samples with low viral load (mean CT value 31.1; CI95 29.6 – 32.6).


Kit used: FTD Respiratory pathogens 21

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 - "Evaluation of quantitative FTD Pneumocystis jirovecii kit for Pneumocystis infection diagnosis" (limited access)

Summary: In this study the Fast track Diagnostics (FTD) Pneumocystis PCR kit was evaluated, targeting the mitochondrial large subunit ribosomal RNA gene (mtLSU rRNA) of Pneumocystis jirovecii (P. jirovecii). A hundred and thirty-three patients were prospectively enrolled. Respiratory specimens were examined using both microscopy and the PCR assay. Twenty-six patients led to P. jirovecii detection. Fourteen patients presented with Pneumocystis pneumonia (PCP)whereas 12 patients were considered to be colonized. The median copy numbers in bronchoalveolar lavage fluid were significantly different in the PCP and colonization groups (1.35×10^8/ml vs. 1.45×10^5/ml, P <0.0001). Lower and upper cut-off values of 3.9×10^5 copies/ml and 3.2×10^6 copies/ml allowed differentiating PCP and colonization. The FTD P. jirovecii assay was secondarily compared to an in-house reference PCR assay targeting the mtLSU rRNA gene. A concordance rate of 97.5% was observed (Cohen's kappa coefficient κ=0.935). The FTD Pneumocystis PCR kit showed good performance and represents an alternative method to diagnose P. jirovecii infections.

Kit used: FTD Pneumocystis jirovecii
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2017 Article - "Density of Upper Respiratory Colonization With Streptococcus pneumoniae and Its Role in the Diagnosis of Pneumococcal Pneumonia Among Children Aged <5 Years in the PERCH Study" (pdf, 692KB)

Summary: Previous studies suggested an association between upper airway pneumococcal colonization density and pneumococcal pneumonia, but data in children are limited. Using data from the Pneumonia Etiology Research for Child Health (PERCH) study, we assessed this potential association.
PERCH is a case-control study in 7 countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. Cases were children aged 1–59 months hospitalized with World Health Organization–defined severe or very severe pneumonia. Controls were randomly selected from the community. Microbiologically confirmed pneumococcal pneumonia (MCPP) was confirmed by detection of pneumococcus in a relevant normally sterile body fluid. Colonization density was calculated with quantitative polymerase chain reaction analysis of nasopharyngeal/oropharyngeal specimens.
Median colonization density among 56 cases with MCPP (MCPP cases; 17.28 ×106copies/mL) exceeded that of cases without MCPP (non-MCPP cases; 0.75 ×106) and controls (0.60 ×106) (each P < .001). The optimal density for discriminating MCPP cases from controls using the Youden index was >6.9 log10 copies/mL; overall, the sensitivity was 64% and the specificity 92%, with variable performance by site. Pneumococcal colonization density >6.9 log10 copies/mL was strongly associated with MCPP and could be used to improve estimates of pneumococcal pneumonia prevalence in childhood pneumonia studies. Our findings do not support its use for individual diagnosis in a clinical setting.

Kit used: FTD Respiratory pathogens 33

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