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      Viral etiologies of lower respiratory tract infections among Egyptian children under five years of age

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          Abstract

          Background

          Lower respiratory tract infections (LRTI) are responsible for a considerable number of deaths among children, particularly in developing countries. In Egypt and the Middle East region, there is a lack of data regarding the viral causes of LRTI. In this study, we aimed to identify the relative prevalence of various respiratory viruses that contribute to LRTIs in young children. Although, nucleic acid-based methods have gained importance as a sensitive tool to determine the viral infections, their use is limited because of their prohibitive cost in low-income countries. Therefore, we applied three different laboratory methods, and presented the different virus prevalence patterns detected by each method.

          Methods

          We collected nasopharyngeal aspirate samples, demographic data and, clinical data from 450 children under five years of age who presented with LRTI at Abou El Reesh hospital in Cairo during a one-year period. To identify the viral causes of the LRTI we used direct fluorescence assay, real-time reverse-transcriptase polymerase chain reaction (rt-RT-PCR), and shell vial culture. We tested for eight major respiratory viruses.

          Results

          Two hundred sixty-nine patients (59.9%) had a viral infection, among which 10.8% had a co-infection with two or more viruses. By all three methods, respiratory syncytial virus (RSV) was the most predominant, and parainfluenza virus type 2 (HPIV-2), influenza B virus (FLUBV) were the least predominant. Other viral prevalence patterns differed according to the detection method used. The distribution of various viruses among different age groups and seasonal distribution of the viruses were also determined.

          Conclusions

          RSV and human adenovirus were the most common respiratory viruses detected by rt-RT-PCR. Co-infections were found to be frequent among children and the vast majority of co-infections were detected by nucleic acid-based detection assays.

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          Most cited references38

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          Detection of respiratory viruses by molecular methods.

          Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease.
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            Estimates of world-wide distribution of child deaths from acute respiratory infections.

            Acute respiratory infections (ARI) are among the leading causes of childhood mortality. Estimates of the number of children worldwide who die from ARI are needed in setting priorities for health care. To establish a relation between deaths due to ARI and all-cause deaths in children under 5 years we show that the proportion of deaths directly attributable to ARI declines from 23% to 18% and then 15% (95% confidence limits range from +/- 2% to +/- 3%) as under-5 mortality declines from 50 to 20 and then to 10/1000 per year. Much of the variability in estimates of ARI in children is shown to be inherent in the use of verbal autopsies. This analysis suggests that throughout the world 1.9 million (95% CI 1.6-2.2 million) children died from ARI in 2000, 70% of them in Africa and southeast Asia.
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              Etiology of community-acquired pneumonia in 254 hospitalized children.

              Childhood community-acquired pneumonia is a common illness, but there have been relatively few comprehensive studies of the viral and bacterial etiology in developed countries. The aim of the present investigation was to determine the etiology of community-acquired pneumonia in hospitalized children by several laboratory methods. In a 3-year prospective study a nasopharyngeal aspirate for viral studies and acute and convalescent serum samples for viral and bacterial serology were taken from 254 children with symptoms of acute infection and infiltrates compatible with pneumonia in the chest radiograph. The role of 17 microbes was investigated. A potential causative agent was detected in 215 (85%) of the 254 patients. Sixty-two percent of the patients had viral infection, 53% had bacterial infection and 30% had evidence of concomitant viral-bacterial infection. Streptococcus pneumoniae (37%), respiratory syncytial virus (29%) and rhinovirus (24%) were the most common agents associated with community-acquired pneumonia. Only one patient had a positive blood culture (S. pneumoniae) of 125 cultured. A dual viral infection was detected in 35 patients, and a dual bacterial infection was detected in 19 patients. The possible causative agent of childhood community-acquired pneumonia can be detected in most cases. Further studies are warranted to determine what etiologic investigations would aid in the management of pneumonia. With effective immunization for S. pneumoniae and respiratory syncytial virus infections, more than one-half of the pneumonia cases in this study could have been prevented.
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                Author and article information

                Journal
                BMC Infect Dis
                BMC Infect. Dis
                BMC Infectious Diseases
                BioMed Central
                1471-2334
                2012
                13 December 2012
                : 12
                : 350
                Affiliations
                [1 ]US Naval Medical Research Unit No.3, Cairo 11517, Egypt
                [2 ]Faculty of Pharmacy, Department of Microbiology and Immunology, Cairo University, Cairo, Egypt
                [3 ]Faculty of Medicine, Department of Clinical Pathology, Cairo University, Giza, Egypt
                [4 ]Faculty of Medicine, Department of Pediatrics, Cairo University, Giza, Egypt
                Article
                1471-2334-12-350
                10.1186/1471-2334-12-350
                3538156
                23237512
                b626c9ed-b35e-4441-9412-635f692fa7a8
                Copyright ©2012 Shafik et al.; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 23 January 2012
                : 14 November 2012
                Categories
                Research Article

                Infectious disease & Microbiology
                egypt,direct fluorescence assay,lower respiratory tract infections,pediatric,polymerase chain reaction,respiratory viruses,shell vial culture

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