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

Hanieh S, Hamaluba M, Kelly DF, Metz JA, Wyres KL, Fisher R, Pradhan R, Shakya D, Shrestha L, Shrestha A, Joshi A, Habens J, Maharjan BD, Thorson S, Bohler E, Yu LM, Kelly S, Plested E, John T, Werno AM, Adhikari N, Murdoch DR, Brueggemann AB, Pollard AJ - PLoS ONE (2014)

Bottom Line: 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.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).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.

View Article: PubMed Central - PubMed

Affiliation: Oxford 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.

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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Frequency of pneumococcal serogroups/types in urban SDP compared to rural SDP samples.
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pone-0098739-g004: Frequency of pneumococcal serogroups/types in urban SDP compared to rural SDP samples.

Mentions: Carriage was significantly higher in the rural population compared to the urban population (69.2% vs 40.9%; P<0.001; using SDP) and was highest in the >12 to 24 month age group (75.4%, 138/183; P = 0.03; Figure 1). Following transport to the University of Oxford, UK, only 350 isolates collected using the SDP method in the rural area contributed to serogroup/type data as several cultures were non-viable and therefore were unable to be typed. The distribution of serogroups/types from SDP in urban versus rural samples is presented in Figure 4. The five most prevalent rural serotypes constituted 41% of total isolates and three were shared with the urban group (6, NT and 15B/C). The fifteen most prevalent rural serotypes constituted 72% of isolates and ten were also in the top fifteen for the urban group. Of the remaining five serogroups/types not shared with urban group the mean difference in serogroup/type rank between rural and urban distributions was 21 positions (range 13–28 positions).


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

Hanieh S, Hamaluba M, Kelly DF, Metz JA, Wyres KL, Fisher R, Pradhan R, Shakya D, Shrestha L, Shrestha A, Joshi A, Habens J, Maharjan BD, Thorson S, Bohler E, Yu LM, Kelly S, Plested E, John T, Werno AM, Adhikari N, Murdoch DR, Brueggemann AB, Pollard AJ - PLoS ONE (2014)

Frequency of pneumococcal serogroups/types in urban SDP compared to rural SDP samples.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4048273&req=5

pone-0098739-g004: Frequency of pneumococcal serogroups/types in urban SDP compared to rural SDP samples.
Mentions: Carriage was significantly higher in the rural population compared to the urban population (69.2% vs 40.9%; P<0.001; using SDP) and was highest in the >12 to 24 month age group (75.4%, 138/183; P = 0.03; Figure 1). Following transport to the University of Oxford, UK, only 350 isolates collected using the SDP method in the rural area contributed to serogroup/type data as several cultures were non-viable and therefore were unable to be typed. The distribution of serogroups/types from SDP in urban versus rural samples is presented in Figure 4. The five most prevalent rural serotypes constituted 41% of total isolates and three were shared with the urban group (6, NT and 15B/C). The fifteen most prevalent rural serotypes constituted 72% of isolates and ten were also in the top fifteen for the urban group. Of the remaining five serogroups/types not shared with urban group the mean difference in serogroup/type rank between rural and urban distributions was 21 positions (range 13–28 positions).

Bottom Line: 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.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).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.

View Article: PubMed Central - PubMed

Affiliation: Oxford 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.

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.

Show MeSH