Use of a rapid test of pneumococcal colonization density to diagnose pneumococcal pneumonia

Abstract

Background: There is major need for a more sensitive assay for the diagnosis of pneumococcal community-acquired pneumonia (CAP). We hypothesized that pneumococcal nasopharyngeal (NP) proliferation may lead to microaspiration followed by pneumonia. We therefore tested a quantitative lytA real-time polymerase chain reaction (rtPCR) on NP swab samples from patients with pneumonia and controls.

Methods: In the absence of a sensitive reference standard, a composite diagnostic standard for pneumococcal pneumonia was considered positive in South African human immunodeficiency virus (HIV)-infected adults hospitalized with radiographically confirmed CAP, if blood culture, induced good-quality sputum culture, Gram stain, or urinary Binax demonstrated pneumococci. Results of quantitative lytA rtPCR in NP swab samples were compared with quantitative colony counts in patients with CAP and 300 HIV-infected asymptomatic controls.

Results: Pneumococci were the leading pathogen identified in 76 of 280 patients with CAP (27.1%) using the composite diagnostic standard. NP colonization density measured by lytA rtPCR correlated with quantitative cultures (r = 0.67; P < .001). The mean lytA rtPCR copy number in patients with pneumococcal pneumonia was 6.0 log(10) copies/mL, compared with patients with CAP outside the composite standard (2.7 log(10) copies/mL; P < .001) and asymptomatic controls (0.8 log(10) copies/mL; P < .001). A lytA rtPCR density ≥8000 copies/mL had a sensitivity of 82.2% and a specificity of 92.0% for distinguishing pneumococcal CAP from asymptomatic colonization. The proportion of CAP cases attributable to pneumococcus increased from 27.1% to 52.5% using that cutoff.

Conclusions: A rapid molecular assay of NP pneumococcal density performed on an easily available specimen may significantly increase pneumococcal pneumonia diagnoses in adults.

Figure 1.

Quantitative colonization densities in human immunodeficiency virus–infected patients with community-acquired pneumonia. Pneumococcal colonization densities are shown as colony counts, obtained with nasopharyngeal (NP) swab cultures and lytA real-time polymerase chain reaction (rtPCR) of NP swab samples. Counts are depicted after logarithmic transformation for those who had Streptococcus pneumoniae identified by the composite diagnostic standard and those who did not. Plus signs represent means; lengths of boxes, interquartile ranges between 25th and 75th percentiles; horizontal lines in boxes, medians; and whiskers, minimum and maximum values (t test, P < .001 for NP counts from cultures and for lytA rtPCR; Wilcoxon rank sum test [used after assignment of value 1 to the colony count for those who were not colonized], P < .001 for NP counts and lytA rtPCR). Abbreviations: CFU, colony-forming units; NP, nasopharyngeal; rtPCR, real-time polymerase chain reaction.

Figure 2.

Nasopharyngeal (NP) colonization densities in human immunodeficiency virus (HIV)–infected patients with pneumococcal community-acquired pneumonia (CAP) and HIV-infected asymptomatic controls. Pneumococcal colonization densities were measured as colony counts, obtained with NP swab cultures and lytA real-time polymerase chain reaction (rtPCR) of NP swab samples. Pluses represent means; lengths of boxes, interquartile ranges between 25th and 75th percentiles; horizontal lines in boxes, medians; and whiskers, minimum and maximum values (t test, P < .001 for NP counts from cultures and for lytA rtPCR; Wilcoxon rank sum test [used after assignment of value 1 to colony count to those who were not colonized], P < .001 for NP counts and lytA rtPCR). Abbreviations: CAP, community-acquired pneumonia; CFU, colony-forming units; HIV, human immunodeficiency virus; NP, nasopharyngeal; rtPCR, real-time polymerase chain reaction.

Figure 3.

Correlation between quantitative lytA real-time polymerase chain reaction and quantitative colony counts from nasopharyngeal swabs in human immunodeficiency virus–infected persons with community-acquired pneumonia and asymptomatic controls (Pearson’s correlation coefficient r = .67; P < .001). Abbreviation: rtPCR, real-time polymerase chain reaction.