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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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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.
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pone-0098739-g005: 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.

Mentions: The 307 unique STs clustered into 214 CCs, which included 123 STs that had only one isolate representative (21% of the collection of 585 isolates). 92 CCs were found in Kathmandu only, 69 CCs in Okhaldunga only, and 53 CCs were comprised of pneumococci from both locations (Figure 5). Overall, there were 10 major CCs that were comprised of ≥10 isolates each and another 18 CCs with 5–9 isolates each (Table 2). Two major CCs (4560 and 4908) were comprised of a single ST, i.e. no closely-related variants were detected. Only CC63 was also an internationally-distributed CC, having been found in many countries worldwide (http://spneumoniae.mlst.net/). Isolate representatives of all the major CCs were found in both Kathmandu and Okhaldhunga, although most predominated in one of the two locations (Table 2).


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)

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.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0098739-g005: 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.
Mentions: The 307 unique STs clustered into 214 CCs, which included 123 STs that had only one isolate representative (21% of the collection of 585 isolates). 92 CCs were found in Kathmandu only, 69 CCs in Okhaldunga only, and 53 CCs were comprised of pneumococci from both locations (Figure 5). Overall, there were 10 major CCs that were comprised of ≥10 isolates each and another 18 CCs with 5–9 isolates each (Table 2). Two major CCs (4560 and 4908) were comprised of a single ST, i.e. no closely-related variants were detected. Only CC63 was also an internationally-distributed CC, having been found in many countries worldwide (http://spneumoniae.mlst.net/). Isolate representatives of all the major CCs were found in both Kathmandu and Okhaldhunga, although most predominated in one of the two locations (Table 2).

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