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Background: We investigated the pathogenesis of pneumococcal pneumonia using clinical specimens collected for pneumonia surveillance in The Gambia., Methods: Lung aspirates and nasopharyngeal swabs from 31 patients were examined by culture, quantitative polymerase chain reaction (qPCR), whole genome sequencing, serotyping, and reverse-transcription qPCR., Results: Five lung aspirates cultured pneumococci, with a matching strain identified in the nasopharynx. Three virulence genes including ply (pneumolysin) were upregulated >20-fold in the lung compared with the nasopharynx. Nasopharyngeal pneumococcal density was higher in pediatric pneumonia patients compared with controls (P < .0001)., Conclusions: Findings suggest that changes in pneumococcal gene expression occurring in the lung environment may be important in pathogenesis., (© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America.)

Background: Distinguishing between bacterial and viral lower respiratory tract infection (LRTI) remains challenging. Transcriptional profiling is a promising tool for improving diagnosis in LRTI., Methods: We performed whole blood transcriptional analysis in 118 patients (median age [interquartile range], 61 [50-76] years) hospitalized with LRTI and 40 age-matched healthy controls (median age, 60 [46-70] years). We applied class comparisons, modular analysis, and class prediction algorithms to identify and validate diagnostic biosignatures for bacterial and viral LRTI., Results: Patients were classified as having bacterial (n = 22), viral (n = 71), or bacterial-viral LRTI (n = 25) based on comprehensive microbiologic testing. Compared with healthy controls, statistical group comparisons (P < .01; multiple-test corrections) identified 3376 differentially expressed genes in patients with bacterial LRTI, 2391 in viral LRTI, and 2628 in bacterial-viral LRTI. Patients with bacterial LRTI showed significant overexpression of inflammation and neutrophil genes (bacterial > bacterial-viral > viral), and those with viral LRTI displayed significantly greater overexpression of interferon genes (viral > bacterial-viral > bacterial). The K-nearest neighbors algorithm identified 10 classifier genes that discriminated between bacterial and viral LRTI with a 95% sensitivity (95% confidence interval, 77%-100%) and 92% specificity (77%-98%), compared with a sensitivity of 38% (18%-62%) and a specificity of 91% (76%-98%) for procalcitonin., Conclusions: Transcriptional profiling is a helpful tool for diagnosis of LRTI., (© The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Diagnosis of pneumococcal pneumonia is complicated by the lack of a diagnostic reference standard that is highly sensitive and specific. Latent class analysis (LCA) is a mathematical technique that relates an unobserved ("latent") infection to multiple diagnostic test results by use of a statistical model. We used classical analysis and LCA to evaluate the sensitivity and specificity of blood culture, sputum Gram stain, sputum polymerase chain reaction (PCR), and urine antigen testing for diagnosing pneumococcal pneumonia among 149 adults with community-acquired pneumonia. On the basis of LCA models, sensitivity of autolysin PCR and pneumolysin PCR was 82% and 89%, respectively, but specificity was low, 38% and 27%, respectively. For urine antigen testing, sensitivity was 77%-78%, and specificity was 67%-71%. Results of the LCA models were comparable with those obtained from classical analysis. LCA may be useful for diagnostic test evaluation and for determining the prevalence of pneumococcal infection in epidemiological studies of community-acquired pneumonia and in vaccine efficacy trials.

Epidemiologic studies of pneumococcal pneumonia, including vaccine efficacy trials, are hampered by a lack of sensitive and specific diagnostic tests. Pneumococcal surface adhesin A (PsaA) is a genetically conserved, surface-expressed protein common to all serotypes of Streptococcus pneumoniae and is highly immunogenic. Detection of anti-PsaA immunoglobulin G by recombinant PsaA enzyme-linked immunosorbent assay was evaluated for diagnosis of pneumococcal pneumonia in paired serum samples from 4 adult populations: 47 healthy control subjects, 56 clinic control subjects without pneumococcal disease syndromes, 109 patients with pneumococcal pneumonia, and 93 pneumonia patients with no evidence of pneumococcal etiology. By considering a 2-fold increase in antibody concentration as positive, sensitivity was 0.70, and specificity was 0.98. With a 1.3-fold increase, these were 0.89 and 0.98, respectively. The test's performance was not affected by the patients' human immunodeficiency virus status or by the pneumococcal serotype. The combination of high sensitivity and high specificity makes this an ideal assay for epidemiologic studies of pneumococcal pneumonia.

In a prospective study, the etiology of community-acquired pneumonia (CAP) was investigated among consecutive patients admitted to an academic, urban public hospital in Seattle. The study population was uniquely young, was predominantly male, and had high rates of homelessness, cigarette smoking, alcoholism, injection drug use, and human immunodeficiency virus (HIV) infection. Leading causes of CAP among HIV-negative patients were aspiration, followed by Streptococcus pneumoniae, Legionella species, and Mycoplasma pneumoniae. Among HIV-positive patients, Pneumocystis carinii, Mycobacterium tuberculosis, S. pneumoniae, and M. pneumoniae were the most common etiologic agents. Severe CAP was associated with typical bacterial infections and aspiration pneumonia but not Legionella infection among HIV-negative patients and with Pseudomonas aeruginosa infections among HIV-positive patients. These findings emphasize the need to tailor empirical antibiotic therapy according to local patient populations and individual risk factors and highlight the importance of recognizing underlying HIV infection in patients who are hospitalized with CAP.

A polymerase chain reaction (PCR) assay based on the amplification of pneumolysin gene fragments in patient sera was developed for the etiologic diagnosis of acute pneumococcal pneumonia. Two pairs of oligonucleotide primers were designed to amplify a 348-bp and a 208-bp fragment of the pneumolysin gene. Amplified products were analyzed by agarose gel electrophoresis and hybridization using a 24-mer probe internal to the amplified DNA. The nested PCR could detect 10 organisms as determined by serial dilutions of DNA from Streptococcus pneumoniae. All 20 serum samples from patients with acute pneumococcal pneumonia (confirmed by blood culture) were positive. Among 100 serum samples from healthy elderly controls, 94 were negative and 6 were positive by PCR. Thus, PCR may be a novel diagnostic method for pneumococcal pneumonia.

To improve diagnostic options for pneumococcal pneumonia, an ELISA system was developed that can detect less than or equal to 6 ng/ml capsular polysaccharide in serum. The test was limited to 39 serotypes causing greater than 95% of pneumococcal infections. In clinical evaluation the test identified 14 of 15 cases (missing one serotype not included). No false-positive reaction occurred. However, the duration and level of antigenemia were variable (greater than or equal to 500-2.5 ng/ml) and seemed not to depend solely on the severity of infection. Therefore, the question of whether the extent of antigenemia was determined by a serotype-dependent variation in the elimination rates of polysaccharides was investigated. Clearance rates for 12 serotypes varied in rabbits and rats by a factor of greater than 250. This remarkable variability appeared to affect the extent of clinical antigenemia. Thus, only very sensitive systems can detect circulating antigen from rapidly cleared polysaccharide serotypes. Furthermore, the question arises whether slow polysaccharide clearance contributes to the virulence of some pneumococcal serotypes.

In a prospective study of the etiology of pneumonia 196 adult patients were included. One of the following criteria was required for diagnosis of pneumococcal pneumonia: isolation of pneumococci from blood; isolation from transtracheal aspirate; isolation from sputum or nasopharynx or detection of capsular antigen in sputum in combination with a significant increase in antibodies against at least one pneumococcal antigen (type-specific capsular polysaccharide, C-polysaccharide, pneumolysin); or increase in antibodies against two pneumococcal antigens. Pneumococcal pneumonia was diagnosed in 63 patients (32%). Other diagnoses were nonencapsulated Haemophilus influenzae isolated from transtracheal aspirates, 9; Mycoplasma pneumoniae diagnosed by serology, 17; Chlamydia psittaci, 6; and viral infections, 42. Twenty-two patients (11%) had evidence of infection with more than one agent. The pathogen could not be determined in 70 (36%). Many patients were given antibiotics before admittance to the study, and in some cases a convalescent serum sample was not available.

The opsonization of type 1 and type 25 pneumococci in the rabbit lung early in the course of experimental pneumonia was studied. Bacteria washed from the lungs of animals with type 1 pneumonia were coated with IgG, IgA, and complement within 24 hr of infection; these bacteria were not phagocytized. Both type 1 and type 25 pneumococci, when incubatd in concentrates of nonimmune bronchopulmonary washings (BPC), adsorbed IgG, IgA, and C3, but neither type of pneumococci was opsonized. Killing of pneumococci by surface phagocytosis, with or without the use of nonimmune BPC, was not demonstrated. When nonimmune serum was used, opsonization of type 25 pneumococci depended on the presence of heat-labile adsorbable factors, and when immune serum and immune BPC were used, opsonization was dependent on adsorbable factors. Depletion of serum complement with cobra venom factor before infection with type 25 pneumococci resulted in severe bacteremic pneumonia in the rabbit, but immunization before complement depletion allowed animals to clear type 25 pneumococci from the blood and lungs within 24 hr. Thus, opsonization is required for efficient clearance of pneumococci from the lung, and in the nonimmune animal, complement is also required for clearance.

The diagnostic reliability of the Quellung reaction of sputum and the gram stain-directed sputum culture (SC) for bacteriologic diagnosis of pneumonia due to Streptococcus pneumoniae was determined. Detection of pneumococcal polysaccharide in sputum by counterimmunoelectrophoresis (CIE) or isolation of pneumococci from blood or pleural fluid (BPF-positive) was considered indicative of definite pneumococcal infection. Specimens were obtained from 211 patients with community-acquired bacterial pneumonia. Of 119 CIE-positive specimens, the Quellung reaction was positive for 117 and the SC was positive for 96. However, 35 CIE-negative specimens were positive by QR, SC, or both, a result suggesting that CIE is a less sensitive indicator of pneumococcal infection than originally assumed. CIE, QR, and SC were positive in similar numbers of BPF-positive cases. All BPF-positive and CIE-positive cases were detected by both QR and SC. Use of both the QR and directed SC offers a rapid, accurate bacteriologic diagnosis of pneumococcal pneumonia.