DOI: 10.5061/dryad.34hp52d
title: Data from: Using routinely collected laboratory data to identify high rifampicin-resistant tuberculosis burden communities in the Western Cape Province, South Africa: a retrospective spatiotemporal analysis

description: Background: South Africa has the highest tuberculosis incidence globally
 (781/100,000), with an estimated 4.3% of cases being rifampicin resistant
 (RR). Control and elimination strategies will require detailed spatial
 information to understand where drug-resistant tuberculosis exists and why
 it persists in those communities. We demonstrate a method to enable
 drug-resistant tuberculosis monitoring by identifying high-burden
 communities in the Western Cape Province using routinely collected
 laboratory data. Methods and findings: We retrospectively identified cases
 of microbiologically confirmed tuberculosis and RR-tuberculosis from all
 biological samples submitted for tuberculosis testing (n = 2,219,891) to
 the Western Cape National Health Laboratory Services (NHLS) between
 January 1, 2008, and June 30, 2013. Because the NHLS database lacks unique
 patient identifiers, we performed a series of record-linking processes to
 match specimen records to individual patients. We counted an individual as
 having a single disease episode if their positive samples came from within
 two years of each other. Cases were aggregated by clinic location (n =
 302) to estimate the percentage of tuberculosis cases with rifampicin
 resistance per clinic. We used inverse distance weighting (IDW) to produce
 heatmaps of the RR-tuberculosis percentage across the province. Regression
 was used to estimate annual changes in the RR-tuberculosis percentage by
 clinic, and estimated average size and direction of change was mapped. We
 identified 799,779 individuals who had specimens submitted from mappable
 clinics for testing, of whom 222,735 (27.8%) had microbiologically
 confirmed tuberculosis. The study population was 43% female, the median
 age was 36 years (IQR 27–44), and 10,255 (4.6%, 95% CI: 4.6–4.7) cases had
 documented rifampicin resistance. Among individuals with microbiologically
 confirmed tuberculosis, 8,947 (4.0%) had more than one disease episode
 during the study period. The percentage of tuberculosis cases with
 rifampicin resistance documented among these individuals was 11.4% (95%
 CI: 10.7–12.0). Overall, the percentage of tuberculosis cases that were
 RR-tuberculosis was spatially heterogeneous, ranging from 0% to 25% across
 the province. Our maps reveal significant yearly fluctuations in
 RR-tuberculosis percentages at several locations. Additionally, the
 directions of change over time in RR-tuberculosis percentage were not
 uniform. The main limitation of this study is the lack of unique patient
 identifiers in the NHLS database, rendering findings to be estimates
 reliant on the accuracy of the person-matching algorithm. Conclusions: Our
 maps reveal striking spatial and temporal heterogeneity in RR-tuberculosis
 percentages across this province. We demonstrate the potential to monitor
 RR-tuberculosis spatially and temporally with routinely collected
 laboratory data, enabling improved resource targeting and more rapid
 locally appropriate interventions.
description: geospatial_tb_south_africa_tab-delimTab-delimited text file containing: Location, City, Age, Sex, Year.first.tested, Latitude, Longitude, ID RIF.test INH.test.