Diagnosis of Lower Respiratory Tract Infections Using Biofire Filmarray

Comparison of pathogens causing lower respiratory tract infections in ventilated versus non ventilated pediatric patients in intensive care unit using biofire filmarray and vitek2

* Antibiotic sensitivity using vitek2
* Comparison of the type of antibiotic resistance using biofire filmarray and vitek2
* To provide information about prevalence of these organisms.

Acute respiratory infections (ARI) are a leading cause of morbidity and mortality worldwide. Although usually more severe in children, the elderly and immunocompromised patients, all populations and age groups are susceptible.

Lower respiratory infections are the third leading cause of death worldwide and nearly two million childhood deaths worldwide are attributable to ARI, with the vast majority occurring in developing countries.The World Health Organization estimates that in 2013, over 8% of all deaths in the Eastern Mediterranean Region were attributable to ARIs. However, regional data on morbidity and etiology of these infections are lacking.

These infections have a significant impact on antimicrobial prescriptions, hospitalizations and lost time from work and school. The most frequent agents responsible for ARI are respiratory viruses followed by bacteria .Empiric treatment with antibiotics is frequently initiated even when viral infection is a strong possibility,leading to unnecessary antibiotic use . The early diagnosis of the pathogen is beneficial for the precise selection of medication,which can largely avoid the overuse or even abuse of the antibiotics and improve the clinical care of patients. More importantly, the early diagnosis of contagious pathogens, such as Bordetella pertussis (B. pertussis) and influenza viruses, can enable early isolation of patients, thus reducing the spread of pathogens.

At present, the routine detection methods for respiratory pathogens are mostly based on immunological methods.

Direct diagnosis of respiratory viruses by antigen detection using immunofluorescence assays (IFA), is still used but is typically limited to eight viruses (adenovirus \[AdV\], influenza A \[FluA\], influenza B \[FluB\], parainfluenza \[PIV\], human metapneumovirus \[HMPV\] and respiratory syncytial virus \[RSV\]) and may lack sensitivity depending on the viral titer, patient´s age and time of testing in relation to the onset of symptoms .

Molecular methods such as Polymerase chain reaction (PCR) increase viral detection due to a greater analytic sensitivity compared to conventional methods such as antigen detection and/or viral culture.

Microbiological analysis and identification of organisms may take 48-72 h,false negative results may occur as a result of concomitant or previous antibiotic treatment , whereas false positive may represent colonization or sampling errors.

The VITEK 2 is a fully automated system for microbial identification and antimicrobial susceptibility testing (AST ), after a primary inoculums has been prepared and standardized . With its colorimetric reagent cards, the VITEK 2 offers a state of the art technology platform for phenotypic identification methods.(6) The application of FilmArray respiratory panel in the diagnosis of lower respiratory tract infections is designed to reduce the time for identification of the microorganisms FilmArray is a small, desktop, fully automated multiplex PCR device. The molecular system includes automated nucleic acid extraction, an initial reverse transcription step and multiplex nested PCR, followed by a melting curve analysis .

The BIOFIRE® FILMARRAY® Pneumonia Panel plus tests for 18 bacteria (11 Gram negative, 4 Gram positive and 3 atypical), 7 antibiotic resistance markers, and 9 viruses that cause pneumonia and other lower respiratory tract infections. It offers an overall sensitivity and specificity for bronchoalveolar (BAL)-like samples of 96,2% and 98.3%, respectively, and for sputum samples a sensitivity and specificity of 96.3% and 97.2%, respectively.The test is performed in a closed system that requires 5 min of hands-on time and 65 min of instrumentation time. Several comparison studies between FilmArray and other tests for respiratory organisms showed comparable results .

Eligibility Criteria:
Inclusion Criteria:

- Pediatric patients with acute lower respiratory tract infections.

Exclusion Criteria:

* Age above 18 years old