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

Research output: Contribution to journalArticleResearchpeer-review

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.

Original languageEnglish
Article numbere98739
Number of pages9
JournalPLoS ONE
Volume9
Issue number6
DOIs
Publication statusPublished - 6 Jun 2014
Externally publishedYes

Cite this

Hanieh, Sarah ; Hamaluba, Mainga ; Kelly, Dominic F. ; Metz, Jane A. ; Wyres, Kelly L. ; Fisher, Roberta ; Pradhan, Rahul ; Shakya, Disuja ; Shrestha, Lochan ; Shrestha, Amrita ; Joshi, Anip ; Habens, Jocelyn ; Maharjan, Bishnu D. ; Thorson, Stephen ; Bohler, Erik ; Yu, Ly Mee ; Kelly, Sarah ; Plested, Emma ; John, Tessa ; Werno, Anja M. ; Adhikari, Neelam ; Murdoch, David R. ; Brueggemann, Angela B. ; Pollard, Andrew J. / Streptococcus pneumoniae carriage prevalence in Nepal : Evaluation of a method for delayed transport of samples from remote regions and implications for vaccine implementation. In: PLoS ONE. 2014 ; Vol. 9, No. 6.
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title = "Streptococcus pneumoniae carriage prevalence in Nepal: Evaluation of a method for delayed transport of samples from remote regions and implications for vaccine implementation",
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.",
author = "Sarah Hanieh and Mainga Hamaluba and Kelly, {Dominic F.} and Metz, {Jane A.} and Wyres, {Kelly L.} and Roberta Fisher and Rahul Pradhan and Disuja Shakya and Lochan Shrestha and Amrita Shrestha and Anip Joshi and Jocelyn Habens and Maharjan, {Bishnu D.} and Stephen Thorson and Erik Bohler and Yu, {Ly Mee} and Sarah Kelly and Emma Plested and Tessa John and Werno, {Anja M.} and Neelam Adhikari and Murdoch, {David R.} and Brueggemann, {Angela B.} and Pollard, {Andrew J.}",
year = "2014",
month = "6",
day = "6",
doi = "10.1371/journal.pone.0098739",
language = "English",
volume = "9",
journal = "PLoS ONE",
issn = "1932-6203",
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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 2014, 'Streptococcus pneumoniae carriage prevalence in Nepal: Evaluation of a method for delayed transport of samples from remote regions and implications for vaccine implementation' PLoS ONE, vol. 9, no. 6, e98739. https://doi.org/10.1371/journal.pone.0098739

Streptococcus pneumoniae carriage prevalence in Nepal : Evaluation of a method for delayed transport of samples from remote regions and implications for vaccine implementation. / Hanieh, Sarah; Hamaluba, Mainga; Kelly, Dominic F.; Metz, Jane A.; Wyres, Kelly L.; Fisher, Roberta; Pradhan, Rahul; Shakya, Disuja; Shrestha, Lochan; Shrestha, Amrita; Joshi, Anip; Habens, Jocelyn; Maharjan, Bishnu D.; Thorson, Stephen; Bohler, Erik; Yu, Ly Mee; Kelly, Sarah; Plested, Emma; John, Tessa; Werno, Anja M.; Adhikari, Neelam; Murdoch, David R.; Brueggemann, Angela B.; Pollard, Andrew J.

In: PLoS ONE, Vol. 9, No. 6, e98739, 06.06.2014.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Streptococcus pneumoniae carriage prevalence in Nepal

T2 - Evaluation of a method for delayed transport of samples from remote regions and implications for vaccine implementation

AU - Hanieh, Sarah

AU - Hamaluba, Mainga

AU - Kelly, Dominic F.

AU - Metz, Jane A.

AU - Wyres, Kelly L.

AU - Fisher, Roberta

AU - Pradhan, Rahul

AU - Shakya, Disuja

AU - Shrestha, Lochan

AU - Shrestha, Amrita

AU - Joshi, Anip

AU - Habens, Jocelyn

AU - Maharjan, Bishnu D.

AU - Thorson, Stephen

AU - Bohler, Erik

AU - Yu, Ly Mee

AU - Kelly, Sarah

AU - Plested, Emma

AU - John, Tessa

AU - Werno, Anja M.

AU - Adhikari, Neelam

AU - Murdoch, David R.

AU - Brueggemann, Angela B.

AU - Pollard, Andrew J.

PY - 2014/6/6

Y1 - 2014/6/6

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84902579143&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0098739

DO - 10.1371/journal.pone.0098739

M3 - Article

VL - 9

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 6

M1 - e98739

ER -