title: Evaluation of chest radiography, lytA real-time PCR, and other routine tests for diagnosis of community-acquired pneumonia and estimation of possible attributable fraction of pneumococcus in northern Togo.
abstract: Streptococcus pneumoniae (Spn) is a leading cause of community-acquired pneumonia (CAP), yet existing diagnostic tools remain inadequate. We aimed to evaluate laboratory and radiological methods for detecting pneumococcal aetiology in CAP patients and to estimate Spn prevalence in this group. All-aged patients hospitalized with clinically defined CAP in northern Togo were enrolled during 2010-2013. Latent class analysis pooled results of semi-automated blood culture (SABC), whole blood lytA real-time polymerase chain reaction (rt-PCR), serum C-reactive protein (CRP), and chest radiography (CXR) and categorized patients as likely pneumococcal or non-pneumococcal CAP. We enrolled 1684 patients; 1501 had results for all tests. CXR, SABC, lytA rt-PCR and CRP >71·2 mg/l had sensitivities of 94% [95% confidence interval (CI) 87-100], 13% (95% CI 10-16), 17% (95% CI 14-21) and 78% (95% CI 75-80), and specificities of 88% (95% CI 84-93), 100% (95% CI 99-100), 97% (95% CI 96-99) and 77% (95% CI 75-79), respectively. Pneumococcal attributable proportion was 34% (95% CI 32-37), increasing with age and in men. We estimated that Spn caused one third of CAP. Whole blood lytA rt-PCR was more sensitive than SABC; both had low sensitivity and high specificity. Conversely CXR was highly sensitive and reasonably specific; it could be a useful tool for epidemiological studies aiming to define Spn pneumonia incidence across all ages.
authors.affiliation: Agence de Médecine Préventive,Paris,France.
authors.forename: A
authors.identifier: 0000-0002-1627-4992
authors.initials: A
authors.lastname: Blake
authors.affiliation: Agence de Médecine Préventive,Paris,France.
authors.forename: B M
authors.initials: BM
authors.lastname: Njanpop-Lafourcade
authors.affiliation: Fondation Mérieux - Laboratoire des Pathogènes Emergents,Lyon,France.
authors.forename: J N
authors.initials: JN
authors.lastname: Telles
authors.affiliation: Fondation Mérieux - Laboratoire des Pathogènes Emergents,Lyon,France.
authors.forename: A
authors.initials: A
authors.lastname: Rajoharison
authors.affiliation: Ministère de la Santé,Lomé,Togo.
authors.forename: M S
authors.initials: MS
authors.lastname: Makawa
authors.affiliation: Ministère de la Santé,Lomé,Togo.
authors.forename: K
authors.initials: K
authors.lastname: Agbenoko
authors.affiliation: Ministère de la Santé,Lomé,Togo.
authors.forename: S
authors.initials: S
authors.lastname: Tamekloe
authors.affiliation: EHESP French School of Public Health,Sorbonne Paris Cité,Rennes France.
authors.forename: J E
authors.initials: JE
authors.lastname: Mueller
authors.affiliation: Ministère de la Santé,Lomé,Togo.
authors.forename: H
authors.initials: H
authors.lastname: Tall
authors.affiliation: Agence de Médecine Préventive,Paris,France.
authors.forename: B D
authors.initials: BD
authors.lastname: Gessner
authors.affiliation: Fondation Mérieux - Laboratoire des Pathogènes Emergents,Lyon,France.
authors.forename: G
authors.initials: G
authors.lastname: Paranhos-Baccalà
authors.affiliation: Agence de Médecine Préventive,Paris,France.
authors.forename: J C
authors.initials: JC
authors.lastname: Moïsi
mesh_terms: D001431:Bacteriological Techniques / Q000379:methods; D002097:C-Reactive Protein / Q000032:analysis; D017714:Community-Acquired Infections / Q000175:diagnosis* / Q000000981:diagnostic imaging / Q000453:epidemiology*; D003955:Diagnostic Tests, Routine / Q000379:methods*; D006801:Humans; D011018:Pneumonia, Pneumococcal / Q000175:diagnosis* / Q000000981:diagnostic imaging / Q000453:epidemiology*; D015995:Prevalence; D013902:Radiography, Thoracic / Q000379:methods*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D014037:Togo / Q000453:epidemiology
chemical_list: D002097:C-Reactive Protein
keywords: 
                 Streptococcus pneumoniae
              ; Aetiology; chest radiography; latent class analysis; pneumonia