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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 STGG samples compared to urban SDP samples.
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pone-0098739-g002: Frequency of pneumococcal serogroups/types in urban STGG samples compared to urban SDP samples.

Mentions: Overall carriage prevalence based on culture from specimens transported and stored in STGG was 58.7% (337/574), and in SDP 40.9% (235/574) (chi-squared test P<0.001). For participants in whom any pneumococcus was detected (in STGG and/or SDP) there was concordance of detection of pneumococcus in 67% of samples. The remaining 33% were discordant with 30% being STGG +/ SDP-, and 3% being STGG -/ SDP+. The serogroup/type distribution for urban STGG versus SDP samples is presented in Figure 2. The four most prevalent STGG serogroups/types were shared with those from SDP (6, NT, 15B/C, and 34). The fourteen most prevalent STGG serogroups/types constituted 68% of isolates and twelve were shared with those from SDP. Of the two STGG serogroups/types not shared with SDP the mean difference in rank order was 11 positions (range 9–14 positions). For the 211 participants in whom pneumococci were detected by both STGG and SDP (and serogroup/types were available), discordant serogroups/types were seen in 27.5% (58/211) of individuals (Figure 3).


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 STGG samples compared to urban SDP samples.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0098739-g002: Frequency of pneumococcal serogroups/types in urban STGG samples compared to urban SDP samples.
Mentions: Overall carriage prevalence based on culture from specimens transported and stored in STGG was 58.7% (337/574), and in SDP 40.9% (235/574) (chi-squared test P<0.001). For participants in whom any pneumococcus was detected (in STGG and/or SDP) there was concordance of detection of pneumococcus in 67% of samples. The remaining 33% were discordant with 30% being STGG +/ SDP-, and 3% being STGG -/ SDP+. The serogroup/type distribution for urban STGG versus SDP samples is presented in Figure 2. The four most prevalent STGG serogroups/types were shared with those from SDP (6, NT, 15B/C, and 34). The fourteen most prevalent STGG serogroups/types constituted 68% of isolates and twelve were shared with those from SDP. Of the two STGG serogroups/types not shared with SDP the mean difference in rank order was 11 positions (range 9–14 positions). For the 211 participants in whom pneumococci were detected by both STGG and SDP (and serogroup/types were available), discordant serogroups/types were seen in 27.5% (58/211) of individuals (Figure 3).

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