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Updated: Apr 28, 2026
Experimental Human Pneumococcal Carriage
Published on: February 15, 2013
Streptococcus pneumoniae carriage prevalence in Nepal: evaluation of a method for delayed transport of samples from
Sarah Hanieh1, Mainga Hamaluba1, Dominic F Kelly2
1Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom; Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
Insights
Pneumococcal carriage prevalence in Nepali children is underestimated by delayed sample transport. Novel genotypes and limited vaccine coverage highlight the need for ongoing surveillance.
Area of Science:
- Microbiology
- Epidemiology
- Vaccinology
Background:
- Pneumococcal disease poses a significant health burden in young children in Nepal.
- Current pneumococcal conjugate vaccines provide limited coverage for prevalent disease isolates.
Purpose of the Study:
- To determine pneumococcal nasopharyngeal carriage prevalence in urban and rural Nepal.
- To analyze serogroup/type distribution and isolate genotypes.
- To compare sample transport methods for pneumococcal carriage studies.
Main Methods:
- A prevalence study involving 1101 children aged 1.5 to 24 months in Nepal.
- Nasopharyngeal swabs were transported using silica desiccant packages (SDP) with delayed processing or skim-milk-tryptone-glucose-glycerin (STGG) with immediate processing.
- Pneumococcal carriage, serogroup/type, and genotypes were determined using multilocus sequence typing.
Main Results:
- Overall carriage prevalence was 58.7% with STGG versus 40.9% with SDP.
- Pneumococcal carriage prevalence was higher in rural (69.2%) than urban (40.9%) populations using SDP.
- Serogroup/type distribution varied geographically, and over half of identified genotypes were novel.
Conclusions:
- Delayed transport methods like SDP underestimate pneumococcal carriage prevalence but may be useful in remote settings.
- The presence of novel genotypes and limited vaccine serotype coverage complicates vaccine impact prediction.
- Continued surveillance of pneumococcal isolates is essential following vaccine introduction in Nepal.
Background:
Pneumococcal disease is a significant cause of morbidity and mortality in young children in Nepal, and currently available pneumococcal conjugate vaccines offer moderate coverage of invasive disease isolates.
Methods:
A prevalence study of children aged 1.5 to 24 months in urban and rural Nepal was conducted. In the urban group, nasopharyngeal swabs (NPS) were transported using silica desiccant packages (SDP) with delayed processing (2 weeks), or skim-milk-tryptone-glucose-glycerin (STGG) with immediate processing (within 8 hours). Pneumococcal nasopharyngeal carriage prevalence, serogroup/type distribution and isolate genotypes (as defined by multilocus sequence typing) were determined.
Results:
1101 children were enrolled into the study: 574 in the urban group and 527 in the rural group. Overall carriage prevalence based on culture from specimens transported and stored in STGG was 58.7% (337/574), compared to 40.9% (235/574) in SDP. There was concordance of detection of pneumococcus in 67% of samples. Using the SDP method, pneumococcal carriage prevalence was higher in the rural population (69.2%; 364/526) compared to the urban population (40.9%; 235/574). Serogroup/type distribution varied with geographical location. Over half of the genotypes identified in both the urban and rural pneumococcal populations were novel.
Conclusion:
The combination of delayed culture and transport using SDP underestimates the prevalence of pneumococcal carriage; however, in remote areas, this method could still provide a useful estimate of carriage prevalence and serogroup/type distribution. Vaccine impact is unpredictable in a setting with novel genotypes and limited serotype coverage as described here. Consequently, continued surveillance of pneumococcal isolates from carriage and disease in Nepali children following the planned introduction of pneumococcal conjugate vaccines introduction will be essential.
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