Improved detection of Pneumocystis jirovecii in upper and lower respiratory tract specimens from children with suspected pneumocystis pneumonia using real-time PCR: a prospective study

BMC Infectious Diseases, Nov 2011

Background Pneumocystis pneumonia (PCP) is a major cause of hospitalization and mortality in HIV-infected African children. Microbiologic diagnosis relies predominantly on silver or immunofluorescent staining of a lower respiratory tract (LRT) specimens which are difficult to obtain in children. Diagnosis on upper respiratory tract (URT) specimens using PCR has been reported useful in adults, but data in children are limited. The main objectives of the study was (1) to compare the diagnostic yield of PCR with immunofluorescence (IF) and (2) to investigate the usefulness of upper compared to lower respiratory tract samples for diagnosing PCP in children. Methods Children hospitalised at an academic hospital with suspected PCP were prospectively enrolled. An upper respiratory sample (nasopharyngeal aspirate, NPA) and a lower respiratory sample (induced sputum, IS or bronchoalveolar lavage, BAL) were submitted for real-time PCR and direct IF for the detection of Pneumocystis jirovecii. A control group of children with viral lower respiratory tract infections were investigated with PCR for PCP. Results 202 children (median age 3.3 [inter-quartile range, IQR 2.2 - 4.6] months) were enrolled. The overall detection rate by PCR was higher than by IF [180/349 (52%) vs. 26/349 (7%) respectively; p < 0.0001]. PCR detected more infections compared to IF in lower respiratory tract samples [93/166 (56%) vs. 22/166 (13%); p < 0.0001] and in NPAs [87/183 (48%) vs. 4/183 (2%); p < 0.0001]. Detection rates by PCR on upper (87/183; 48%) compared with lower respiratory tract samples (93/166; 56%) were similar (OR, 0.71; 95% CI, 0.46 - 1.11). Only 2/30 (6.6%) controls were PCR positive. Conclusion Real-time PCR is more sensitive than IF for the detection of P. jirovecii in children with PCP. NPA samples may be used for diagnostic purposes when PCR is utilised. Wider implementation of PCR on NPA samples is warranted for diagnosing PCP in children.

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Improved detection of Pneumocystis jirovecii in upper and lower respiratory tract specimens from children with suspected pneumocystis pneumonia using real-time PCR: a prospective study

Catherine M Samuel 0 Andrew Whitelaw 0 Craig Corcoran 2 Brenda Morrow 1 Nei-Yuan Hsiao 2 Marco Zampoli 1 Heather J Zar 1 0 Division of Medical Microbiology, University of Cape Town and National Health Laboratory Service , Cape Town , South Africa 1 Department of Paediatrics and Child Health, University of Cape Town, Red Cross War Memorial Children's Hospital , Cape Town , South Africa 2 Division of Clinical Virology, University of Cape Town and National Health Laboratory Service , Cape Town , South Africa Background: Pneumocystis pneumonia (PCP) is a major cause of hospitalization and mortality in HIV-infected African children. Microbiologic diagnosis relies predominantly on silver or immunofluorescent staining of a lower respiratory tract (LRT) specimens which are difficult to obtain in children. Diagnosis on upper respiratory tract (URT) specimens using PCR has been reported useful in adults, but data in children are limited. The main objectives of the study was (1) to compare the diagnostic yield of PCR with immunofluorescence (IF) and (2) to investigate the usefulness of upper compared to lower respiratory tract samples for diagnosing PCP in children. Methods: Children hospitalised at an academic hospital with suspected PCP were prospectively enrolled. An upper respiratory sample (nasopharyngeal aspirate, NPA) and a lower respiratory sample (induced sputum, IS or bronchoalveolar lavage, BAL) were submitted for real-time PCR and direct IF for the detection of Pneumocystis jirovecii. A control group of children with viral lower respiratory tract infections were investigated with PCR for PCP. Results: 202 children (median age 3.3 [inter-quartile range, IQR 2.2 - 4.6] months) were enrolled. The overall detection rate by PCR was higher than by IF [180/349 (52%) vs. 26/349 (7%) respectively; p < 0.0001]. PCR detected more infections compared to IF in lower respiratory tract samples [93/166 (56%) vs. 22/166 (13%); p < 0.0001] and in NPAs [87/183 (48%) vs. 4/183 (2%); p < 0.0001]. Detection rates by PCR on upper (87/183; 48%) compared with lower respiratory tract samples (93/166; 56%) were similar (OR, 0.71; 95% CI, 0.46 - 1.11). Only 2/30 (6.6%) controls were PCR positive. Conclusion: Real-time PCR is more sensitive than IF for the detection of P. jirovecii in children with PCP. NPA samples may be used for diagnostic purposes when PCR is utilised. Wider implementation of PCR on NPA samples is warranted for diagnosing PCP in children. - Background Pneumocystis pneumonia (PCP), caused by Pneumocystis jirovecii, is an important opportunistic infection in HIVinfected children [1,2]. The incidence of PCP in developed countries has declined since the introduction of highly active anti-retroviral therapy and use of chemoprophylaxis. However, PCP remains a major cause of hospitalization and mortality in HIV-infected children in low or middle income countries, [1,3-5] with reported incidence rates of 10 - 49%, [1,3,6] and in-hospital casefatality rates of 20 - 63% [1,3,4,6]. Apart from HIV infection, there are other factors that predispose children to developing PCP including malnutrition, other immune deficiencies or HIV exposure. Untreated, the case fatality rate in children with PCP approximates 100% [1,3,4,6]. However, diagnosis can be difficult as clinical and radiological findings are non-specific. Therefore, a rapid, accurate laboratory diagnosis is important for timely use of appropriate medication. Detection of P. jirovecii is hampered by the lack of a sustainable in-vitro culture method [7]. Standard laboratory diagnostic methods are microscopic examination of a lower respiratory tract sample with Gomori Grocotts methenamine silver nitrate stain or the more sensitive immunofluorescence assay (IF) [8] on bronchoalveolar lavage (BAL) or induced sputum (IS) specimens. Using microscopy, the yield from IS has been reported to be similar compared to that from BAL [9]. However, sputum induction in children is not widely performed, requires staff trained to do the procedure and may result in clinical deterioration or nosocomial transmission of respiratory pathogens. Diagnosis using a noninvasive sample such as a nasopharyngeal aspirate (NPA) is, therefore, desirable. The clinical sensitivity from a NPA has been reported to be low and variable when microscopy is utilised [4,5,10]. The development of polymerase chain reaction (PCR) techniques has provided a more reliable diagnostic method. In adult studies, PCR is as specific as and more sensitive than microscopy for diagnosis when performed on respiratory specimens, including oral washes [7,11-21]. In a study of oropharyngeal washes from HIV-infected adult patients, P. jirovecii DNA-amplification had a sensitivity of 44% using a nested PCR protocol compared to trans-bronchial biopsy, [16] increasing to 90% when touch-down real-time PCR was utilised [7,11]. Real-time PCR also allows for quantification of the organism load and with application of cutoff values, co (...truncated)


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Catherine M Samuel, Andrew Whitelaw, Craig Corcoran, Brenda Morrow, Nei-Yuan Hsiao, Marco Zampoli, Heather J Zar. Improved detection of Pneumocystis jirovecii in upper and lower respiratory tract specimens from children with suspected pneumocystis pneumonia using real-time PCR: a prospective study, BMC Infectious Diseases, 2011, pp. 329, 11, DOI: 10.1186/1471-2334-11-329