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.
  
  
  CONCLUSIONS
  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.
authors.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.
authors.forename: Sarah
authors.initials: S
authors.lastname: Hanieh
authors.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.
authors.forename: Mainga
authors.initials: M
authors.lastname: Hamaluba
authors.affiliation: Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
authors.forename: Dominic F
authors.initials: DF
authors.lastname: Kelly
authors.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.
authors.forename: Jane A
authors.initials: JA
authors.lastname: Metz
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Kelly L
authors.initials: KL
authors.lastname: Wyres
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Roberta
authors.initials: R
authors.lastname: Fisher
authors.affiliation: Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
authors.forename: Rahul
authors.initials: R
authors.lastname: Pradhan
authors.affiliation: Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
authors.forename: Disuja
authors.initials: D
authors.lastname: Shakya
authors.affiliation: Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
authors.forename: Lochan
authors.initials: L
authors.lastname: Shrestha
authors.affiliation: Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
authors.forename: Amrita
authors.initials: A
authors.lastname: Shrestha
authors.affiliation: Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
authors.forename: Anip
authors.initials: A
authors.lastname: Joshi
authors.affiliation: Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
authors.forename: Jocelyn
authors.initials: J
authors.lastname: Habens
authors.affiliation: Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
authors.forename: Bishnu D
authors.initials: BD
authors.lastname: Maharjan
authors.affiliation: Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
authors.forename: Stephen
authors.initials: S
authors.lastname: Thorson
authors.affiliation: Okhaldhunga Community Hospital, Okhaldhunga, Nepal.
authors.forename: Erik
authors.initials: E
authors.lastname: Bohler
authors.affiliation: Nuffield Department of Primary Care and Health Sciences, University of Oxford, Oxford, United Kingdom.
authors.forename: Ly-Mee
authors.initials: LM
authors.lastname: Yu
authors.affiliation: Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
authors.forename: Sarah
authors.initials: S
authors.lastname: Kelly
authors.affiliation: Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
authors.forename: Emma
authors.initials: E
authors.lastname: Plested
authors.affiliation: Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
authors.forename: Tessa
authors.initials: T
authors.lastname: John
authors.affiliation: Department of Pathology, University of Otago, Christchurch, New Zealand; Canterbury Health Laboratories, Christchurch, New Zealand.
authors.forename: Anja M
authors.initials: AM
authors.lastname: Werno
authors.affiliation: Patan Academy Paediatric Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
authors.forename: Neelam
authors.initials: N
authors.lastname: Adhikari
authors.affiliation: Department of Pathology, University of Otago, Christchurch, New Zealand; Canterbury Health Laboratories, Christchurch, New Zealand.
authors.forename: David R
authors.initials: DR
authors.lastname: Murdoch
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Angela B
authors.initials: AB
authors.lastname: Brueggemann
authors.affiliation: Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Pollard
mesh_terms: D002353:Carrier State / Q000382:microbiology*; D002675:Child, Preschool; D005260:Female; D060005:Genotyping Techniques; D006801:Humans; D007223:Infant; D008297:Male; D009390:Nepal; D022242:Pneumococcal Vaccines; D015995:Prevalence; D012424:Rural Population; D012703:Serotyping; D013048:Specimen Handling / Q000379:methods*; D013296:Streptococcus pneumoniae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D013997:Time Factors; D014505:Urban Population
chemical_list: D022242:Pneumococcal Vaccines