Data supporting "Prevalence of subclinical pulmonary tuberculosis and its association with HIV in household contacts of tuberculosis in two South African provinces: analysis of a cluster-randomised trial" – Data codebook

Permanent identifier

10.17037/DATA.00003373

Description

This dataset and accompanying R code contains the data and analysis that was used to produce the results reported in the manuscript "Prevalence of subclinical pulmonary tuberculosis and its association with HIV in household contacts of tuberculosis in two South African provinces: analysis of a cluster-randomised trial".

Data access procedure

Applications for the dataset will be reviewed by Professor Emily Webb (Emily.Webb@lshtm.ac.uk) and Professor Neil Martinson (info@phru.co.za), in conjunction with the University of the Witwatersrand Institutional Review Board.

Applicants are requested to provide the following information when applying for access:

Applications will be assessed on the basis of the following criteria:

  1. The proposed analysis is compatible with the consent agreement that the study participant signed.
  2. The proposed analysis can be performed using the fully de-identified dataset.
  3. The applicant is able to complete and comply with a Data Transfer Agreement (DTA), which outlines conditions of storage and use.

Data codebook

The TB dataset contains 43 variables, outlined below.

Variable Name Variable Label Answer Label Answer Code Variable Type
hhid Household ID Open ended   Numeric
study_id Study ID Open ended   Numeric
study_site Study Site     String
    Capricorn Capricorn  
    Mangaung Mangaung  
hhmembers Number of household members     Numeric
i_sex Index patient sex     String
      Female  
      Male  
i_age Index patient age (years) Open ended   Numeric
i_agp Index patient age group     String
    0 to 4 years 0-4 years  
    5 to 9 years 5-9 years  
    10 to 15 years 10-15 years  
    16 to 24 years 16-24 years  
    25 to 34 years 25-34 years  
    35 to 44 years 35-44 years  
    45 to 54 years 45-54 years  
    55 to 64 years 55-64 years  
    65 or over 65+ years  
i_hiv Index patient HIV status     String
    Negative Negative  
    Positive Positive  
    Not applicable NA  
i_art Index patient taking anti-retroviral therapy or not (if HIV positive)     String
    Negative Negative  
    Positive Positive  
    Not applicable NA  
h_sex Household contact sex     String
    Female Female  
    Male Male  
h_age Household contact age     Numeric
h_smk Household contact smoking status     String
    Never smoked Never smoked  
    No (previously smoked) No (previously smoked)  
    Yes (currently smoke) Yes (currently smoke)  
h_alc Household contact drinks alcohol     String
    Yes Yes  
    No No  
    Not applicable NA  
h_hiv Household contact HIV status     String
    Positive Positive  
    Negative Negative  
    Not applicable NA  
h_art Household contact taking anti-retroviral therapy or not (if HIV positive)     Numeric
    Yes Yes  
    No No  
    Not applicable NA  
h_cgh Household contact history of cough (number of days or 0 if not present) Open ended   Numeric
h_spt Household contact history of sputum (number of days or 0 if not present) Open ended   Numeric
h_hpt Household contact history of haemoptysis (number of days or 0 if not present) Open ended   Numeric
h_lwt Household contact history of weight loss (number of days or 0 if not present) Open ended   Numeric
h_nsw Household contact history of night sweats (number of days or 0 if not present) Open ended   Numeric
h_fev Household contact history of fever (number of days or 0 if not present) Open ended   Numeric
h_xpt Household contact sputum Xpert nucleic acid amplification test (NAAT) result     String
    M Tuberculosis detected M Tuberculosis detected  
    M Tuberculosis not detected M Tuberculosis not detected  
    Not applicable NA  
h_smr Household contact sputum smear for TB microscopy result     String
    1+ 1+  
    2+ 2+  
    3+ 3+  
    Scanty Scanty  
    Negative/Not seen Negative/Not seen  
    Not applicable NA  
h_cul Household contact sputum culture for TB result     String
    Positive for M tuberculosis Positive for M tuberculosis  
    Negative Negative  
    Contaminated or lab problem Contaminated or lab problem  
    Not applicable NA  
h_mtb History of TB     Numeric
    No 0  
    Yes 1  
employment Household contact employment status     String
    Currently employed Currently employed  
    Not employed Not employed  
    Student Student  
    Other Other  
    Not applicable NA  
cd4 Household contact CD4 count Open ended   Numeric
cd4_date Date of CD4 count Open ended   Date
h_dm Household contact history of diabetes     String
    No Diabetes No Diabetes  
    Diabetes - Oral treatment only Diabetes - Oral treatment only  
    Diabetes - Insulin injection Diabetes - Insulin injection  
    Diabetes - Not treated Diabetes - Not treated  
h_agegrp Household contact age group     String
    5 to 9 years 5-9 years  
    10 to 15 years 10-15 years  
    16 to 24 years 16-24 years  
    25 to 34 years 25-34 years  
    35-44 years 35-44 years  
    45 to 54 years 45-54 years  
    55 to 64 years 55-64 years  
    65 or over 65+ years  
cd4_cat CD4 count categorical groupings      
    Under 200 <200  
    200 to 499 200-499  
    500 or over 500+  
    Not applicable NA  
cum_symp Household contact history of cough, weight loss, night sweats, and fever (h_cgh+h_lwt+h_nsw+h_fev)     String
    Yes yes  
    No no  
    Not applicable NA  
Symptomatic At least one of cough, fever, weight loss or night sweats (any duration) indicates symptomatic     String
    Yes yes  
    No no  
    Not applicable NA  
scTB Household contact categorised as subclinical TB     Numeric
    No 0  
    Yes 1  
activeTB Household contact categorised as active TB     Numeric
    No 0  
    Yes 1  
microTB_status Microbiological TB status     String
    scTB scTB  
    Active TB activeTB  
    No TB noTB  
cgh_binary Household contact presence of cough (any duration)     String
    Yes yes  
    No no  
    Not applicable NA  
spt_binary Household contact presence of sputum (any duration)     String
    Yes yes  
    No no  
    Not applicable NA  
hpt_binary Household contact presence of haemoptysis (any duration)     String
    Yes yes  
    No no  
    Not applicable NA  
lwt_binary Household contact presence of weight loss (any duration)     String
    Yes yes  
    No no  
    Not applicable NA  
nsw_binary Household contact presence of night sweats (any duration)     String
    Yes yes  
    No no  
    Not applicable NA  
fev_binary Household contact presence of fever (any duration)     String
    Yes yes  
    No no  
    Not applicable NA  
binaryHIV Household contact HIV-positive status     String
    No 0  
    Yes 1  
    Not applicable NA