Abstract
S. pneumoniae is a common colonizer of the human nasopharynx in high income and low-middle income countries. Due to limitations of standard culture methods, the prevalence of concurrent colonization with multiple serotypes is unclear. We evaluated the use of multiplex quantitative PCR (qPCR) to detect multiple pneumococcal serotypes/group colonization in archived nasopharyngeal swabs of pneumococcal conjugate vaccine naive children who had previously been investigated by traditional culture methods. Overall the detection of pneumococcal colonization was higher by qPCR (82%) compared to standard culture (71%; p < 0.001), with a high concordance (kappa = 0.73) of serotypes/groups identified by culture also being identified by qPCR. Also, qPCR was more sensitive in detecting multiple serotype/groups among colonized cases (28.7%) compared to culture (4.5%; p < 0.001). Of the additional serotypes detected only by qPCR, the majority were of lower density (<104 CFU/ml) than the dominant colonizing serotype, with serotype/group 6A/B, 19B/F and 23F being the highest density colonizers, followed by serotype 5 and serogroup 9A/L/N/V being the most common second and third colonizers respectively. The ability of qPCR to detect multiple pneumococcal serotypes at a low carriage density might provide better insight into underlying mechanism for changes in serotype colonization in PCV vaccinated children.
Highlights
Streptococcus pneumoniae is a common colonizer of the human nasopharynx in both high-income and low-middle-income countries, with carriage being a pre-requisite to pathogenesis of pneumococcal disease as well as transmission between hosts[1,2,3,4,5]
In this study we aimed to evaluate the use of multiplex quantitative PCR for the detection and density characterisation of multiple pneumococcal serotypes on nasopharyngeal swabs, from pneumococcal conjugate vaccine (PCV) naive black-African children previously investigated by traditional culture methods
The findings of our study showed that quantitative PCR (qPCR) was more sensitive in detecting concurrent carriage with multiple pneumococcal serotypes, with at least 28.7% of all LytA positive nasopharyngeal samples having multiple serogroups/types identified compared to 4.5% of culture positive cases
Summary
Streptococcus pneumoniae is a common colonizer of the human nasopharynx in both high-income and low-middle-income countries, with carriage being a pre-requisite to pathogenesis of pneumococcal disease as well as transmission between hosts[1,2,3,4,5]. Despite the ubiquitous use of culture based methods for nasopharyngeal colonization studies, detection of concurrent colonization by other serotypes of a lower density are often missed[8]. Molecular detection of pneumococci in the nasopharynx have several potential advantages over culture based methods, including detection of multiple serotypes from a single sample with high sensitivity, as well as quantitative PCR methods being able to measure the density of colonization and relative proportion of colonizing serotypes[9]. In this study we aimed to evaluate the use of multiplex quantitative PCR (qPCR) for the detection and density characterisation of multiple pneumococcal serotypes on nasopharyngeal swabs, from PCV naive black-African children previously investigated by traditional culture methods
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