title: Estimating malaria parasite prevalence from community surveys in Uganda: a comparison of microscopy, rapid diagnostic tests and polymerase chain reaction.
abstract: BACKGROUND
  Household surveys are important tools for monitoring the malaria disease burden and measuring impact of malaria control interventions with parasite prevalence as the primary metric. However, estimates of parasite prevalence are dependent on a number of factors including the method used to detect parasites, age of the population sampled, and level of immunity. To better understand the influence of diagnostics, age, and endemicity on estimates of parasite prevalence and how these change over time, community-based surveys were performed for two consecutive years in three settings and the sensitivities of microscopy and immunochromatographic rapid diagnostic tests (RDTs) were assessed, considering polymerase chain reaction (PCR) as the gold standard.
  
  
  METHODS
  Surveys were conducted over the same two-month period in 2012 and 2013 in each of three sub-counties in Uganda: Nagongera in Tororo District (January-February), Walukuba in Jinja District (March-April), and Kihihi in Kanungu District (May-June). In each sub-county, 200 households were randomly enrolled and a household questionnaire capturing information on demographics, use of malaria prevention methods, and proxy indicators of wealth was administered to the head of the household. Finger-prick blood samples were obtained for RDTs, measurement of hemoglobin, thick and thin blood smears, and to store samples on filter paper.
  
  
  RESULTS
  A total of 1200 households were surveyed and 4433 participants were included in the analysis. Compared to PCR, the sensitivity of microscopy was low (65.3% in Nagongera, 49.6% in Walukuba and 40.9% in Kihihi) and decreased with increasing age. The specificity of microscopy was over 98% at all sites and did not vary with age or year. Relative differences in parasite prevalence across different age groups, study sites, and years were similar for microscopy and PCR. The sensitivity of RDTs was similar across the three sites (range 77.2-82.8%), was consistently higher than microscopy (p < 0.001 for all pairwise comparisons), and decreased with increasing age. The specificity of RDTs was lower than microscopy (76.3% in Nagongera, 86.3% in Walukuba, and 83.5% in Kihihi) and varied significantly by year and age. Relative differences in parasite prevalence across age groups and study years differed for RDTs compared to microscopy and PCR.
  
  
  CONCLUSIONS
  Malaria prevalence estimates varied with diagnostic test, age, and transmission intensity. It is important to consider the effects of these parameters when designing and interpreting community-based surveys.
authors.affiliation: Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda. jnankabirwa@yahoo.co.uk.|Infectious Diseases Research Collaboration, Kampala, Uganda. jnankabirwa@yahoo.co.uk.
authors.forename: Joaniter I
authors.initials: JI
authors.lastname: Nankabirwa
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda. yadoke@yahoo.com.|Makerere University School of Public Health, College of Health Sciences, Kampala, Uganda. yadoke@yahoo.com.
authors.forename: Adoke
authors.initials: A
authors.lastname: Yeka
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda. earinaitwe@idrc-uganda.org.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Arinaitwe
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda. kigoziruth@gmail.com.
authors.forename: Ruth
authors.initials: R
authors.lastname: Kigozi
authors.affiliation: London School of Hygiene and Tropical Medicine, London, UK. chris.drakeley@lshtm.ac.uk.
authors.forename: Chris
authors.initials: C
authors.lastname: Drakeley
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda. mkamya@infocom.co.ug.|School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda. mkamya@infocom.co.ug.
authors.forename: Moses R
authors.initials: MR
authors.lastname: Kamya
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, USA. bryan.greenhouse@ucsf.edu.
authors.forename: Bryan
authors.initials: B
authors.lastname: Greenhouse
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, USA. philip.rosenthal@ucsf.edu.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Rosenthal
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, USA. grant.dorsey@ucsf.edu.
authors.forename: Grant
authors.initials: G
authors.lastname: Dorsey
authors.affiliation: Infectious Diseases Research Collaboration, Kampala, Uganda. sarah.staedke@lshtm.ac.uk.|London School of Hygiene and Tropical Medicine, London, UK. sarah.staedke@lshtm.ac.uk.
authors.forename: Sarah G
authors.initials: SG
authors.lastname: Staedke
mesh_terms: D000293:Adolescent; D000328:Adult; D000367:Age Factors; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D002675:Child, Preschool; D003430:Cross-Sectional Studies; D003955:Diagnostic Tests, Routine / Q000379:methods*; D005260:Female; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008288:Malaria / Q000175:diagnosis / Q000453:epidemiology*; D008297:Male; D008853:Microscopy; D008875:Middle Aged; D010961:Plasmodium / Q000166:cytology / Q000235:genetics / Q000302:isolation & purification*; D016133:Polymerase Chain Reaction; D015995:Prevalence; D011795:Surveys and Questionnaires; D014454:Uganda / Q000453:epidemiology; D055815:Young Adult