Molecular Methods Show PCV Vaccine May Reduce Colony Density, Not Acquisition

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The PCV-13 demonstrated an association with the detection of low-density colonization and resulted in vaccine efficacy against colonization acquisition.

The 13-valent pneumococcal conjugate vaccine (PCV-13) demonstrated an association with the detection of low-density colonization and resulted in vaccine efficacy against colonization acquisition, according to data published in Vaccine.

The original trial, conducted in 2012, used the Experimental Human Pneumococcal Challenge model: Investigators vaccinated 96 healthy volunteers, in a 1:1 ratio, with either PCV-13 or a control group using the hepatitis A vaccine, and then inoculated all volunteers with 6B Streptococcus pneumonia. They found that PCV-13 conferred 78% protection against colonization acquisition and reduced bacterial intensity measured by classical culture. However, with the recent increase in interest in molecular detection methods, because of their ability to detect pneumococcus colonization at low densities, investigators reassessed the volunteers in this study using the multiplex quantitative polymerase chain reaction (qPCR) approach.

The qPCR for the autolysin, lytA, gene is the current World Health Organization-recommended culture-independent method of detection. Because S pneumoniae has the capacity to exchange genes with other streptococci, investigators opted for the multiplex approach.

Samples from 90 volunteers from the original double-blind, randomized control trial were available and analyzed using a multiplex qPCR assay targeting lytA and pneumococcal serotype 6A/6B cpsA to determine experimental colonization of 6B pneumococcus. Investigators found that all volunteers who were colony-positive by culture were also positive by molecular methods. However, comparing classic culture and qPCR results demonstrated that positivity at any day of the study increased from 4 to 22 of the 45 volunteers in the PCV-13 group. In the control group, there was an increase from 23 to 31 volunteers. The risk ratio by culture was 0.17 (95% CI, 0.07-0.46; P = .0005), and increased to 0.71 (95% CI, 0.50-1.01; P = .06) using molecular methods. In addition, the percentage of protection conferred by PCV-13 against experimental pneumococcal colonization dropped from 83% in the original study to 29%. The PCV-13 did have a pronounced effect on decreasing colonization density in the experimentally colonized volunteers.

Although it is possible that qPCR detects DNA from dead bacteria, investigators do not believe this was a major contributor to the findings because they did not see higher colonization rates at day 2 than day 7. This would have been the expected result, were the method detecting remains of pneumococcal inoculum given at day 0. Another drawback is that the Experimental Human Pneumococcal Challenge model required the ethical imperative to use adult volunteers, rather than children. It is possible that PCV-13 colonization density differs in children, and these findings therefore need to be validated in a younger cohort.

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Colonization density is believed to play an underestimated but pivotal role in the development of disease and transmission dynamics. According to investigators, “our results further support the hypothesis that colonisation density is a determining factor for the clinical outcome and spread of S. pneumoniae.”

Further, the reported 29% protection conferred by PCV -13 against experimental colony acquisition indicates that the main protective mechanism of the vaccine is colony density reduction. Investigators concluded that this reduction leads to decreased risk for disease to vaccinated individuals and transmission, which contributes to the observed herd effects in vaccinated populations.


German EL, Solórzano C, Sunny S, et al. Protective effect of PCV vaccine against experimental pneumococcal challenge in adults is primarily mediated by controlling colonisation density. Vaccine. 2019;37:3953-3956.