Molecular surveillance on Streptococcus pneumoniae carriage in non-elderly adults; little evidence for pneumococcal circulation independent from the reservoir in children

Abstract

Carriage of Streptococcus pneumoniae in adults is rarely detected by the gold standard culture method. With molecular tests of high sensitivity now available, we analysed upper respiratory tract samples collected during autumn/winter 2012/2013 from parents of PCV7-vaccinated infants and from childless adults, directly comparing culture and qPCR-based S. pneumoniae detection. As compared to the gold standard of testing nasopharyngeal swabs, qPCR-based analysis of oral samples significantly improved detection of pneumococcal carriage (5% versus 20%, p < 0.0001) with higher carriage rates in parents compared to childless adults (34% versus 7%; p < 0.001). Molecular methods also increased the number of serotype-carriage events detected with higher carriage frequencies of serotypes 3 and 7A/F and lower of serotypes 6C/D and 15A/B/C in parents compared to their infant children. We provide evidence that culture-based methods severely underestimate adult carriage rates and for the superiority of testing oral samples over nasopharyngeal swabs. The substantial circulation of pneumococci in parents is however, not representative for the entire adult population. While age-associated differences in serotype carriage suggests reservoirs outside infants as potential sources of vaccine-serotypes contributing to weakening of vaccine herd effects, we find no evidence for reservoirs in adults contributing to serotype replacement in carriage.

Minimally Invasive Nasal Sampling in Children Offers Accurate Pneumococcal Colonization Detection

“…Possible explanations for this discrepancy are differences in anatomy, physiology, and nasal/oral microbiome between both groups and the possible change of colonization niche from the nasopharynx to oropharynx in adults. 5 Our findings are in agreement with decreasing sensitivity of nasal swabs, when compared with NPSs, to detect pneumococcal carriage in adults compared with children. 10 The increased presence of pneumococcus in the anterior parts of the nose in children compared with adults could offer an explanation as to why children are transmitting more than adults.…”

“…Saliva sampling, which is painless to collect, has been successfully used to detect pneumococcus in children instead of NPS or oropharyngeal swabs; however, due to its polymicrobial nature might give false-positive results when using molecular methods. 5 On the other hand, sampling of nasal lining fluid using synthetic absorptive matrices (SAM) does not cause discomfort and has been used to detect respiratory syncytial virus infection in a pediatric intensive care unit setting. 6 Whether such minimally invasive samples could detect bacteria, including pneumococcus, has not been assessed yet, and there is a lack of evidence on whether nasal sampling is as sensitive as nasopharyngeal sampling for detection of carriage.…”

Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species

“…While targeting other serotype-specific genes has demonstrated a lack of specificity due to homologous sequences in non-pneumococcal Mitis group streptococci [ 11 , 71 ], sequencing a wzh gene fragment of the capsular locus was highly specific, supporting its potential as a reliable alternative to culture-dependent pneumococcal serotyping or to molecular methods requiring multiple assays. However, despite the specificity of molecular methods when applied to pure pneumococcal isolates [ 25 , 49 , 68 ], their reliability when applied to polymicrobial samples must be carefully monitored, due to reports of false positive signals from non-pneumococcal species [ 24 , 33 , 34 , 42 ]. In this study, comparatively few non-pneumococcal strains generated signal in serotype-specific assays.…”

High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions

“…Additionally, LRTIs are the second principal cause for loss of healthy life (disability-adjusted life years, a combination of mortality and morbidity, (2). Furthermore, the pneumococcus is part of the typical microbiota of the respiratory tract (3)(4)(5), with four in five young children (< 5 years, 6) and one in three adults (7) carrying the bacterium.…”