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. 2014 Jun 6;9(6):e98739.
doi: 10.1371/journal.pone.0098739. eCollection 2014.

Streptococcus pneumoniae carriage prevalence in Nepal: evaluation of a method for delayed transport of samples from remote regions and implications for vaccine implementation

Sarah Hanieh  1 , Mainga Hamaluba  1 , Dominic F Kelly  2 , Jane A Metz  1 , Kelly L Wyres  3 , Roberta Fisher  3 , Rahul Pradhan  4 , Disuja Shakya  4 , Lochan Shrestha  4 , Amrita Shrestha  4 , Anip Joshi  4 , Jocelyn Habens  4 , Bishnu D Maharjan  4 , Stephen Thorson  4 , Erik Bohler  5 , Ly-Mee Yu  6 , Sarah Kelly  2 , Emma Plested  2 , Tessa John  2 , Anja M Werno  7 , Neelam Adhikari  4 , David R Murdoch  7 , Angela B Brueggemann  3 , Andrew J Pollard  2
Affiliations

Streptococcus pneumoniae carriage prevalence in Nepal: evaluation of a method for delayed transport of samples from remote regions and implications for vaccine implementation

Sarah Hanieh et al. PLoS One. .

Abstract

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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Conflict of interest statement

Competing Interests: AJP conducts clinical trials on behalf of the University of Oxford that are sponsored by manufacturers of pneumococcal conjugate vaccines but does not receive any personal payments from them. The University of Oxford receives unrestricted educational grants for courses and conferences organised by AJP from vaccine manufacturers. DFK has received support to attend scientific meetings from GlaxoSmithKline Biologicals SA and Pfizer and holds research funding through the University of Oxford from GlaxoSmithKline Biologicals SA. We declare that authors AW and DRM are employed by Canterbury Health Laboratories. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. Age-specific pneumococcal carriage rates.
Figure 2
Figure 2. Frequency of pneumococcal serogroups/types in urban STGG samples compared to urban SDP samples.
Figure 3
Figure 3. Serogroup/type concordance between the different swab transport methods.
The size of data points is proportional to the frequency of isolates. Spn = Streptococcus pneumoniae, NT = nontypeable, NG = no growth.
Figure 4
Figure 4. Frequency of pneumococcal serogroups/types in urban SDP compared to rural SDP samples.
Figure 5
Figure 5. Clonal complexes (CCs) found in only one geographical location, or in both locations.
Colors indicate different serogroups/types. The size of each circle is drawn in proportion to the number of isolates within that CC.
See this image and copyright information in PMC

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