Data for: "Use of point-of-care C-reactive protein testing for screening of tuberculosis in the community in high-burden settings: a prospective, cross-sectional study in Zambia and South Africa" – Data Codebook

Persistent identifier

10.17037/DATA.00005150

Description

Dataset containing results of an investigation to determine the prevalence of tuberculosis (TB) among enrolled participants of the TREATS study between February 19 and August 11, 2019. Participants were aged 15 years and over and located in one of 3 communities in Zambia or 1 community in South Africa. TB was detected using point-of-care C-reactive protein testing, alone and combined with symptom screening, that covered self-reported symptoms for cough, fever, chest pain, night sweats, and weight loss.

This is the minimal dataset required to conduct the analysis presented in the published paper:

Ruperez M, Shanaube K, Mureithi L, Wapamesa C, Burnett MJ, Kosloff B, de Haas P, Hayes R, Fidler S, Gachie T, Schaap A, Floyd S, Klinkenberg E, Ayles H; TREATS study team. Use of point-of-care C-reactive protein testing for screening of tuberculosis in the community in high-burden settings: a prospective, cross-sectional study in Zambia and South Africa. Lancet Glob Health. 2023 May;11(5):e704-e714. doi: 10.1016/S2214-109X(23)00113-4. Erratum in: Lancet Glob Health. 2023 Jul;11(7):e1011. doi: 10.1016/S2214-109X(23)00222-X. PMID: 37061309.

The study protocol and ICF were approved by LSHTM Ethics Committee (ref: 14905) as well as the University of Zambia Biomedical Research Ethics Committee (ref: 005–02–18) and Pharma-Ethics Ltd in South Africa (ref: 180219727).
Data Codebook

CRP dataset - open

The open dataset contains the following variables.

Variable Name Variable Label Answer Label Answer Code Variable Type
pin Participant ID Open ended   String
symp_cough Self-reported cough     Numeric
    Yes 1  
    No 2  
symp_cough_weeks Duration of self-reported cough     Numeric
    No cough 0  
    < 1 week 1  
    7-13 days 2  
    14-27 days 3  
    >=4 weeks & < 3 months 4  
    >= 3 months 5  
symp_fever Self-reported fever     Numeric
    Yes 1  
    No 2  
symp_fever_weeks Duration of self-reported fever     Numeric
    No fever 0  
    < 1 week 1  
    7-13 days 2  
    14-27 days 3  
    >=4 weeks & < 3 months 4  
    >= 3 months 5  
symp_chestpain self-reported chest pain     Numeric
    Yes 1  
    No 2  
symp_chestpain_weeks Duration of self-reported chest pains     Numeric
    No chest pains 0  
    < 1 week 1  
    7-13 days 2  
    14-27 days 3  
    >=4 weeks & < 3 months 4  
    >= 3 months 5  
symp_nightsweats self-reported night sweats     Numeric
    Yes 1  
    No 2  
symp_nightsweats_weeks Duration of self-reported night sweats     Numeric
    No nightsweats 0  
    < 1 week 1  
    7-13 days 2  
    14-27 days 3  
    >=4 weeks & < 3 months 4  
    >= 3 months 5  
symp_weightlost Self-reported weight loss     Numeric
    Yes 1  
    No 2  
symp_weightlost_weeks Duration of self-reported weight loss     Numeric
    No weight lost 0  
    < 1 week 1  
    7-13 days 2  
    14-27 days 3  
    >=4 weeks & < 3 months 4  
    >= 3 months 5  
crp_testoffer Was C-Reactive Protein (CRP) test offered     Numeric
    No 0  
    Yes 1  
    Not available 2  
cxr_field_taken Was chest X-ray (CXR) done     Numeric
    No 0  
    Yes 1  
    Not available 2  
CAD_score Computer aided detection for TB (CAD4TB) score Open ended   Numeric
mo_cxrreview Chest X-ray (CXR) reviewed by medical officer     Numeric
    No 0  
    Yes 1  
    Unknown 2  
mo_tbreferral Participant referred for TB treatment by medical officer     Numeric
    No 0  
    Yes 1  
    Unknown 2  
mo_cxrreading Medical officer's interpretation of chest X-ray (CXR)     Numeric
    Normal 1  
    Abnormal not suggestive for TB 2  
    Abnormal suggestive for pulmonary TB 3  
    Not interpretable 7  
date_recin Date of enrolment MM/YYYY   Date
sex Participant sex     String
    Female F  
    Male M  
tb_history If self-reported previous TB treatment     String
    No no  
    History of TB treatment history of tb treatment  
    Currently on TB treatment currently on tb treatment  
crp_value C-reactive protein value result Open ended   Numeric
mo_referral If referred to medical officer     String
    No referral no referral  
         
    referred for TB-treatment (bacteriologically) ref. TB-treatment, bacteriologically  
    referred for TB-treatment (clinically) ref. TB-treatment, clinically  
    Referred for other treatment referred for other  
country Country     String
    South Africa SA  
    Zambia Zambia  
culture_eligible Culture eligible for inclusion     String
    No no  
    Yes yes  
cult_final culture outcome     String
    No growth No growth  
    contaminated contaminated  
    NTM NTM  
    MTB MTB  
    sputum not processed sputum not processed  
    non-interpretable non interpretable  
age_group Participant age group categories     Numeric
    15–24 1  
    25–34 2  
    35–44 3  
    45–54 4  
     ≥55 5  
symp_elig TB suggestive symptoms according to TREATS definition     Numeric
    No 0  
    Yes 1  
hsb_tbcurrent_all Current TB treatment at the time of enrolment     Numeric
    No 0  
    Yes 1  
sputum_elig Sputum eligible if either symptoms or CADscore>=40     Numeric
    No 0  
    Yes 1  
s1_gxp_group s1 Xpert result     Numeric
    Not MTB 0  
    Trace 1  
    MTB very low 2  
    MTB low 3  
    MTB medium 4  
    MTB high 5  
s2_gxp_group s2 Xpert result     Numeric
    Not MTB 0  
    Trace 1  
    MTB very low 2  
    MTB low 3  
    MTB medium 4  
    MTB high 5  
s1s2_gxp_group Final result s1s2 Xpert     Numeric
    Not MTB 0  
    Trace 1  
    MTB very low 2  
    MTB low 3  
    MTB medium 4  
    MTB high 5  
crp_positive C-Reactive Protein (CRP) value >=4mg/dl     Numeric
    Negative (<=4mg/dl) 0  
    Positive (>4mg/dl) 1  
    Not recorded -  
crp_testresult_cat5 C-Reactive Protein (CRP) 5 categories     Numeric
    0–4.9mg/dl 0  
    5.0–9.9mg/dl 1  
    10.0–14.9mg/dl 2  
    15.0–19.9mg/dl 3  
    ≥20.0mg/dl 4  
Xpertculture Composite reference standard: Positive if Xpert Ultra final result (from combination of both Xperts in S1 and S2 samples) or culture final results were positive for Mycobacterium tuberculosis and defined as tuberculosis-negative if both Xpert Ultra and culture final results were negative     Numeric
    Negative 0  
    Positive 1  
CRP5 C-Reactive Protein (CRP) value>=5mg/dl     Numeric
    Negative 0  
    Positive 1  
CRP8 C-Reactive Protein (CRP) value>=8mg/dl     Numeric
    Negative 0  
    Positive 1  
CRP10 C-Reactive Protein (CRP) value>=10mg/dl     Numeric
    Negative 0  
    Positive 1  
cxr_date Date chest X-ray (CXR) was taken MM/YYYY   Date
crp_date Date C-Reactive Protein (CRP) test was taken MM/YYYY   Date
mwrd_grade Final result s1s2 Xpert     Numeric
    Not MTB 0  
    Trace 1  
    MTB very low 2  
    MTB low 3  
    MTB medium 4  
    MTB high 5  
mwrd_test Xpert s1 and s2 results available     Numeric
    No 0  
    Yes 1  
mwrd_date Date Xpert sample (s1 and s2) were collected MM/YYYY   Date
mwrd_result Final positive/negative results s1s2 Xpert. Defined as negative if both sputum samples (s1 and S2) provided on the first day were “M tuberculosis not detected”. Xpert Ultra results were defined as positive if either sample was graded as “M tuberculosis detected”—trace, very low, or above     Numeric
    Negative 0  
    Positive 1  
culture_result Final positive/negative culture result. The final culture result was classified as positive if one or more tube result was positive for M tuberculosis. Those that were not culture-positive were classified as culture-negative if one or more tube results were negative for M tuberculosis or one or more tube results were positive for non tuberculosis Mycobacteria, classified as contaminated if both tubes were contaminated, and classified as non interpretable if both tubes were non-interpretable, or one was non-interpretable and one was contaminated. For this study, a valid culture result was one defined as culture-positive or culture-negative and from a batch where the positive control grew, and the negative control did not     Numeric
    Negative 0  
    Positive 1  
s1s2_gxp_group_final Final positive/negative results s1s2 Xpert. Defined as negative if both sputum samples (s1 and S2) provided on the first day were “M tuberculosis not detected”. Xpert Ultra results were defined as positive if either sample was graded as “M tuberculosis detected”—trace, very low, or above     Numeric
    Negative 0  
    Positive 1  

CRP dataset – Full

The full dataset is made available through a controlled access process. This contains the following additional variables. Additionally, continuous dates (day/month/year) are provided for the following - date_recin (Date of enrolment), cxr_date (Date CXR taken), crp_date (Date CRP test was taken), and mwrd_date (Date Xpert sample collected).

Variable Name Variable Label Answer Label Answer Code Variable Type
mo_cxr_comment Medical officer's comments on chest X-ray (CXR) Open ended   String
hiv_status_final Final HIV status. People were asked about HIV status, if they self-reported to be positive they were classified as positive. If they self-reported to have tested within the last 3 months and had negative results they were considered negative. if status was unknown or they had been tested more than three months ago they were offered HIV testing.     Numeric
    Negative 0  
    Positive 1  
    Unknown 2  
hivart_status_final Participant on antiretroviral therapy (ART)     Numeric
    HIV-negative 0  
    HIV+, on ART 1  
    HIV+, not ART 2  
    Unknown 3