DOI: 10.5061/dryad.051h0
title: Data from: Delays and loss to follow up before treatment of drug-resistant TB following implementation of Xpert MTB/RIF in South Africa: a retrospective cohort study

description: Background: South Africa has a large burden of rifampicin-resistant
 tuberculosis (RR-TB), with 18,734 patients diagnosed in 2014. The number
 of diagnosed patients has increased substantially with the introduction of
 the Xpert MTB/RIF test, used for TB diagnosis for all patients with
 presumptive TB. Routine aggregate data suggest a large treatment gap
 (pre-treatment loss to follow up) between the numbers of laboratory
 confirmed RR-TB patients and those reported to have started second-line
 treatment. We aimed to assess the impact of Xpert MTB/RIF implementation
 on the delay to treatment initiation and loss to follow-up before
 second-line treatment for RR-TB across South Africa. Methods and findings:
 A nationwide retrospective cohort study was conducted to assess
 second-line treatment initiation and treatment delay among laboratory
 diagnosed RR-TB patients. Cohorts, including approximately 300
 sequentially diagnosed RR-TB patients per South African province, were
 drawn from 2011 and 2013, before and after Xpert implementation. Patients
 with prior laboratory RR-TB diagnoses within 6 months and currently
 treated patients were excluded. Treatment initiation was determined
 through data linkage with national and local treatment registers, medical
 record review, interviews with healthcare staff, and direct contact with
 patients or household members. Additional laboratory data were used to
 track cases. National estimates of percentage treatment initiation and
 time to treatment were weighted to account for the sampling design. There
 were 2,508 and 2,528 eligible patients in the 2011 and 2013 cohorts
 respectively; 92% were newly diagnosed with RR-TB (new RR-TB, no prior
 RR-TB diagnoses). Nationally, among 2,340 and 2,311 new RR-TB patients in
 the 2011 and 2013 cohorts, 55% (95% CI 53-57) and 63% (95% CI 61-65)
 respectively started treatment within 6 months of their diagnostic
 specimen being sent (p&lt;0.001). However, in 2013, there was no
 difference in the percentage of patients who initiated treatment at six
 months between the 1,368174 new RR-TB patients diagnosed by Xpert (62%,
 95% CI 59-65) and the 943ose diagnosed by other methods (64%, 95% CI
 61-67) (p=0.39). The median time to treatment decreased from 44 (IQR
 20-69) days in 2011 to 22 (IQR 2-43) days in 2013 (p&lt;0.001). In
 2013, across the nine provinces, there were substantial variations in both
 treatment initiation (range 51-73% by six months) and median time to
 treatment (range 15-36 days, N=1,450), and only 53% of 1,448 new RR-TB who
 received treatmented patients were recorded on the national RR-TB
 register. This retrospective study is limited by the lack of information
 to assess reasons for non-initiation of treatment, particularly
 pre-treatment mortality data. Other limitations include the use of names
 and dates of birth to locate patient-level data, potentially resulting in
 missed treatment initiation among some patients. Conclusions: In 2013,
 there was a large treatment gap for RR-TB in South Africa which varied
 significantly across provinces. Xpert implementation, while reducing
 treatment delay, had not contributed substantially to reducing the
 treatment gap in 2013. However, given improved case detection with Xpert,
 overall a larger proportion of the total RR-TB burden has received
 treatment, with reduced delays. Nonetheless, strategies to further improve
 linkage to treatment for all diagnosed RR-TB patients are urgently
 required.
description: Data from: Delays and
 loss to follow up before treatment of drug-resistant TB following
 implementation of Xpert MTB/RIF in South Africa: a retrospective cohort
 studyData
 for submission Jan 2017.xlsx