Data from: Using routinely collected laboratory data to identify high rifampicin-resistant tuberculosis burden communities in Western Cape Province, South Africa: a retrospective spatiotemporal analysis

Background: South Africa has the highest tuberculosis incidence globally (781/100,000), with an estimated 4.3% of cases being rifampicin-resistant (RR). 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 2008 and June 2013. Since 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 a year 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 to produce heat maps 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, median age was 36 years (IQR 27-44), and 10,255 (4.6%, 95% CI: 4.6-4.7) cases were RR. 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 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. 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.**背景**：南非是全球结核病（tuberculosis, TB）发病率最高的国家，发病率达781/10万，据估计有4.3%的病例为利福平耐药（rifampicin-resistant, RR）结核。本研究提出一种方法，通过利用常规收集的实验室数据，识别西开普省的结核病高负担社区，以实现耐药结核的监测。 **方法与结果**：本研究于2008年1月至2013年6月期间，从提交至西开普省国家卫生实验室服务中心（National Health Laboratory Services, NHLS）的所有结核检测生物样本（n=2,219,891）中，回顾性筛选经微生物学确认的结核及利福平耐药结核病例。由于NHLS数据库缺乏唯一患者标识符，我们开展了一系列记录关联流程，将样本记录匹配至个体患者。若患者的阳性样本采集时间间隔在1年以内，则将其计为单次疾病发作。按临床机构位置（n=302）对病例进行汇总，以估算每家机构的结核病例中利福平耐药病例占比。我们采用逆距离加权法生成全省利福平耐药结核占比的热力图。通过回归分析估算每家机构的利福平耐药结核占比的年度变化，并将估算得到的平均变化幅度与变化方向进行可视化制图。本研究共纳入799,779名来自可定位临床机构并提交检测样本的个体，其中222,735名（27.8%）经微生物学确认患有结核。研究人群中女性占比43%，年龄中位数为36岁（四分位距27~44岁，IQR），共有10,255例（4.6%，95% CI: 4.6~4.7）为利福平耐药结核。在经微生物学确认患有结核的个体中，有8,947名（4.0%）在研究期间出现多次疾病发作。该群体中利福平耐药结核占比为11.4%（95% CI: 10.7~12.0）。总体而言，全省利福平耐药结核占比存在空间异质性，范围为0%至25%。我们的制图结果显示，多个地区的利福平耐药结核占比存在显著的年度波动。此外，不同地区利福平耐药结核占比的时间变化方向并不统一。 **结论**：本研究的制图结果揭示了西开普省利福平耐药结核占比显著的时空异质性。我们证实，利用常规收集的实验室数据可实现利福平耐药结核的时空监测，这有助于优化资源配置，并快速开展符合当地实际情况的干预措施。