Evaluating patient data quality in South Africa’s National Health Laboratory Service Data Warehouse, 2017-2020: implications for monitoring child health programmes

Abstract Background South Africa’s National Health Laboratory Service (NHLS), the only clinical laboratory service in the country’s public health sector, is an important resource for monitoring public health programmes. Objectives We describe NHLS data quality, particularly patient demographics among infants, and the effect this has on linking multiple test results to a single patient. Methods Retrospective descriptive analysis of NHLS data from 1st January 2017—1st September 2020 was performed. A validated probabilistic record-linking algorithm linked multiple results to individual patients in lieu of a unique patient identifier. Paediatric HIV PCR data was used to illustrate the effect on monitoring and evaluating a public health programme. Descriptive statistics including medians, proportions and inter quartile ranges are reported, with Chi-square univariate tests for independence used to determine association between variables. Results During the period analysed, 485 300 007 tests, 98 217 642 encounters and 35 771 846 patients met criteria for analysis. Overall, 15.80% (n = 15 515 380) of all encounters had a registered national identity (ID) number, 2.11% (n = 2 069 785) were registered without a given name, 63.15% (n = 62 020 107) were registered to women and 32.89% (n = 32 304 329) of all folder numbers were listed as either the patient’s date of birth or unknown. For infants tested at