Autopsy Prevalence of Tuberculosis and Other Potentially Treatable Infections among Adults with Advanced HIV Enrolled in Out-Patient Care in South Africa: Lesedi Kamoso study data – Data codebook

Persistent identifier

10.17037/DATA.122

Description

Early mortality among HIV-positive adults starting antiretroviral therapy (ART) remains high in resource-limited settings, with tuberculosis (TB) the leading cause of death. However, current methods to estimate TB-related deaths are inadequate and most autopsy studies do not adequately represent those attending primary health clinics (PHCs). The TB Fast Track study aimed to determine the autopsy prevalence of TB and other infections in adults enrolled at South African PHCs in the context of a pragmatic trial of empiric TB treatment.

This dataset contains basic demographic information and lab investigation results of 34 HIV-positive individuals who died after study enrolment. This includes MGIT culture and Xpert MTB/RIF; aerobic and fungal cultures; and histological findings

Data codebook

The MIA_Data_Summary dataset may be requested for the purpose of research verification. Researchers wishing to access the data should complete a request form, outlining the proposed analysis and variables that they wish to use. This application will be reviewed by the study access committee to ensure it complies with the ethical conditions of the original study.

The table below lists variables contained within the raw dataset. To protect the confidentiality of patients and their family, it may be necessary to process information for the purpose of anonymisation.

Variable Name Variable Label Answer Label Answer Code Variable Type
id ID Open ended   Numeric
sex Gender     Numeric
    Male 1  
    Female 2  
denrol Date of enrolment Open ended   Numeric
dtbtx Date started TB treatment Open ended   Integer
dart Date started ART Open ended   Integer
dod Date of death Open ended   Numeric
agedeath Age at death Open ended   Numeric
dmia Date of NA Open ended   Integer
S_bal BAL obtained?     Numeric
    No 0  
    Yes 1  
S_bld Blood obtained? Open ended   Numeric
S_csf CSF obtained?     Numeric
    No 0  
    Yes 1  
S_liv Liver sample obtained?     Numeric
    No 0  
    Yes 1  
S_lk Left kidney sample obtained?     Numeric
    No 0  
    Yes 1  
S_rk Right kidney sample obtained?     Numeric
    No 0  
    Yes 1  
S_ll Left lung sample obtained?     Numeric
    No 0  
    Yes 1  
S_rl Right lung sample obtained?     Numeric
    No 0  
    Yes 1  
S_np Naso/oropharyngeal aspirate obtained?     Numeric
    No 0  
    Yes 1  
S_spl Splenic sample obtained?     Numeric
    No 0  
    Yes 1  
S_ur Urine obtained?     Numeric
    No 0  
    Yes 1  
S_o Other sample obtained? Open ended   String
TB_gxpval Xpert MTB/RIF valid?     Numeric
    No 0  
    Yes 1  
    Not a GeneXpert sample 9  
TB_gxpres Xpert MTB/RIF result     Numeric
    MTB NOT detected 0  
    MTB detected 1  
TB_gxprif Xpert MTB/RIF resistance     Numeric
    Resistant 1  
    Susceptible 2  
    Indeterminate 3  
    Not applicable 7  
TB_mgitresBAL BAL: MGIT result     Numeric
    Negative 0  
    Positive 1  
    Contaminated 2  
TB_znres1BAL BAL: ZN result (1)     Numeric
    Negative 0  
    Positive 1  
TB_blagarresBAL BAL: Blood agar result     Numeric
    Negative 0  
    Positive 1  
TB_hainothBAL BAL: Hain result Open ended   String
TB_mgitresCSF CSF: MGIT result     Numeric
    Negative 0  
    Positive 1  
    Contaminated 2  
TB_znres1CSF CSF: ZN result (1)     Numeric
    Negative 0  
    Positive 1  
TB_blagarresCSF CSF: Blood agar result     Numeric
    Negative 0  
    Positive 1  
TB_hainothCSF CSF: Hain result Open ended   String
TB_mgitresLIV Liver: MGIT result     Numeric
    Negative 0  
    Positive 1  
    Contaminated 2  
TB_znres1LIV Liver: ZN result (1)     Numeric
    Negative 0  
    Positive 1  
TB_blagarresLIV Liver: Blood agar result     Numeric
    Negative 0  
    Positive 1  
TB_hainothLIV Liver: Hain result Open ended   String
TB_mgitresLNG Lungs: MGIT result     Numeric
    Negative 0  
    Positive 1  
    Contaminated 2  
TB_znres1LNG Lungs: ZN result (1)     Numeric
    Negative 0  
    Positive 1  
TB_blagarresLNG Lungs: Blood agar result     Numeric
    Negative 0  
    Positive 1  
TB_hainothLNG Lungs: Hain result Open ended   String
TB_mgitresSPL Spleen: MGIT result     Numeric
    Negative 0  
    Positive 1  
    Contaminated 2  
TB_znres1SPL Spleen: ZN result (1)     Numeric
    Negative 0  
    Positive 1  
TB_blagarresSPL Spleen: Blood agar result     Numeric
    Negative 0  
    Positive 1  
TB_hainothSPL Spleen: Hain result Open ended   String
TB_mgitresURI Urine: MGIT result     Numeric
    Negative 0  
    Positive 1  
    Contaminated 2  
TB_znres1URI Urine: ZN result (1)     Numeric
    Negative 0  
    Positive 1  
TB_blagarresURI Urine: Blood agar result     Numeric
    Negative 0  
    Positive 1  
TB_hainothURI Urine: Hain result Open ended   String
MICRO_aerocyn_BAL BAL: Bact culture positive?     Numeric
    No 0  
    Yes 1  
MICRO_aeroc1_BAL BAL: Bact. culture 1 Open ended   String
MICRO_aeroc2_BAL BAL: Bact. culture 2 Open ended   String
MICRO_aeroc3_BAL BAL: Bact. culture 3 Open ended   String
MICRO_aeroc4_BAL BAL: Bact. culture 4 Open ended   String
MICRO_aeroc5_BAL BAL: Bact. culture 5 Open ended   String
MICRO_fungcult_BAL BAL: Fungal culture     Numeric
    Candida albicans 1  
    Cryptococcus neoformans 2  
    Aspergillus fumigatus 3  
    Other 6  
    No fungal growth 7  
    No fungal culture 9  
MICRO_fungcoth_BAL BAL: Fungal culture, other Open ended   String
MICRO_aerocyn_BLD Blood: Bact culture positive?     Numeric
    No 0  
    Yes 1  
MICRO_aeroc1_BLD Blood: Bact. culture 1 Open ended   String
MICRO_aeroc2_BLD Blood: Bact. culture 2 Open ended   String
MICRO_aeroc3_BLD Blood: Bact. culture 3 Open ended   String
MICRO_aeroc4_BLD Blood: Bact. culture 4 Open ended   String
MICRO_aeroc5_BLD Blood: Bact. culture 5 Open ended   String
MICRO_fungcult_BLD Blood: Fungal culture     Numeric
    Candida albicans 1  
    Cryptococcus neoformans 2  
    Aspergillus fumigatus 3  
    Other 6  
    No fungal growth 7  
    No fungal culture 9  
MICRO_fungcoth_BLD Blood: Fungal culture, other Open ended   String
MICRO_aerocyn_CSF CSF: Bact culture positive?     Numeric
    No 0  
    Yes 1  
MICRO_aeroc1_CSF CSF: Bact. culture 1 Open ended   String
MICRO_aeroc2_CSF CSF: Bact. culture 2 Open ended   String
MICRO_aeroc3_CSF CSF: Bact. culture 3 Open ended   String
MICRO_aeroc4_CSF CSF: Bact. culture 4 Open ended   String
MICRO_aeroc5_CSF CSF: Bact. culture 5 Open ended   String
MICRO_fungcult_CSF CSF: Fungal culture     Numeric
    Candida albicans 1  
    Cryptococcus neoformans 2  
    Aspergillus fumigatus 3  
    Other 6  
    No fungal growth 7  
    No fungal culture 9  
MICRO_fungcoth_CSF CSF: Fungal culture, other Open ended   String
MICRO_aerocyn_LIV Liver: Bact culture positive?     Numeric
    No 0  
    Yes 1  
MICRO_aeroc1_LIV Liver: Bact. culture 1 Open ended   String
MICRO_aeroc2_LIV Liver: Bact. culture 2 Open ended   String
MICRO_aeroc3_LIV Liver: Bact. culture 3 Open ended   String
MICRO_aeroc4_LIV Liver: Bact. culture 4 Open ended   String
MICRO_aeroc5_LIV Liver: Bact. culture 5 Open ended   String
MICRO_fungcult_LIV Liver: Fungal culture     Numeric
    Candida albicans 1  
    Cryptococcus neoformans 2  
    Aspergillus fumigatus 3  
    Other 6  
    No fungal growth 7  
    No fungal culture 9  
MICRO_fungcoth_LIV Liver: Fungal culture, other Open ended   String
MICRO_aerocyn_LNG Lungs: Bact culture positive?     Numeric
    No 0  
    Yes 1  
MICRO_aeroc1_LNG Lungs: Bact. culture 1 Open ended   String
MICRO_aeroc2_LNG Lungs: Bact. culture 2 Open ended   String
MICRO_aeroc3_LNG Lungs: Bact. culture 3 Open ended   String
MICRO_aeroc4_LNG Lungs: Bact. culture 4 Open ended   String
MICRO_aeroc5_LNG Lungs: Bact. culture 5 Open ended   String
MICRO_fungcult_LNG Lungs: Fungal culture     Numeric
    Candida albicans 1  
    Cryptococcus neoformans 2  
    Aspergillus fumigatus 3  
    Other 6  
    No fungal growth 7  
    No fungal culture 9  
MICRO_fungcoth_LNG Lungs: Fungal culture, other Open ended   String
MICRO_aerocyn_SPL Spleen: Bact culture positive?     Numeric
    No 0  
    Yes 1  
MICRO_aeroc1_SPL Spleen: Bact. culture 1 Open ended   String
MICRO_aeroc2_SPL Spleen: Bact. culture 2 Open ended   String
MICRO_aeroc3_SPL Spleen: Bact. culture 3 Open ended   String
MICRO_aeroc4_SPL Spleen: Bact. culture 4 Open ended   String
MICRO_aeroc5_SPL Spleen: Bact. culture 5 Open ended   String
MICRO_fungcult_SPL Spleen: Fungal culture     Numeric
    Candida albicans 1  
    Cryptococcus neoformans 2  
    Aspergillus fumigatus 3  
    Other 6  
    No fungal growth 7  
    No fungal culture 9  
MICRO_fungcoth_SPL Spleen: Fungal culture, other Open ended   String
OTHER_pcpifa_BAL BAL: PCP IFA     Numeric
    Negative 0  
    Positive 1  
    Possible 2  
    Not a PCP result 9  
OTHER_crag_BLD Blood: CrAg     Numeric
    CrAg negative 0  
    CrAg positive 1  
    No CrAg result 9  
OTHER_crag_CSF CSF: CrAg     Numeric
    CrAg negative 0  
    CrAg positive 1  
    No CrAg result 9  
HIST_diag1 Histology diagnosis 1     Numeric
    Diss mycob inf, likely TB 1  
    Diss mycob inf, likely atypical 2  
    Diss mycob inf, other (specify) 3  
    Local mycob inf (specify) 4  
    Evid mycob infect, ?treated 5  
    Bact pneumonia, G-ve bacilli 6  
    Bact pneumonia, G+ve bacilli 7  
    Bact pneumonia, G+ve cocci 8  
    Bacterial pneumonia, G-ve cocci 9  
    Pneumonia, likely bacterial 10  
    Disseminated cryptococcosis 11  
    Local crypto (specify) 12  
    Pneumonitis, ?viral 13  
    Pneumonitis, other (specify) 14  
    Steatosis (give details) 15  
    Steatohepatitis (give details) 16  
    Chronic hepatitis (give details) 17  
    Acute hepatitis (give details) 18  
    Liver cirrhosis 19  
    Acute tubular necrosis 20  
    Nephritis 21  
    Other pulmonary 31  
    Other cardiac 32  
    Other hepatic 33  
    Other renal 34  
    Other splenic 35  
    Other infectious 36  
    Other 96  
    No other diagnoses 97  
HIST_diag2 Histology diagnosis 2     Numeric
    Diss mycob inf, likely TB 1  
    Diss mycob inf, likely atypical 2  
    Diss mycob inf, other (specify) 3  
    Local mycob inf (specify) 4  
    Evid mycob infect, ?treated 5  
    Bact pneumonia, G-ve bacilli 6  
    Bact pneumonia, G+ve bacilli 7  
    Bact pneumonia, G+ve cocci 8  
    Bacterial pneumonia, G-ve cocci 9  
    Pneumonia, likely bacterial 10  
    Disseminated cryptococcosis 11  
    Local crypto (specify) 12  
    Pneumonitis, ?viral 13  
    Pneumonitis, other (specify) 14  
    Steatosis (give details) 15  
    Steatohepatitis (give details) 16  
    Chronic hepatitis (give details) 17  
    Acute hepatitis (give details) 18  
    Liver cirrhosis 19  
    Acute tubular necrosis 20  
    Nephritis 21  
    Other pulmonary 31  
    Other cardiac 32  
    Other hepatic 33  
    Other renal 34  
    Other splenic 35  
    Other infectious 36  
    Other 96  
    No other diagnoses 97  
HIST_diag3 Histology diagnosis 3     Numeric
    Diss mycob inf, likely TB 1  
    Diss mycob inf, likely atypical 2  
    Diss mycob inf, other (specify) 3  
    Local mycob inf (specify) 4  
    Evid mycob infect, ?treated 5  
    Bact pneumonia, G-ve bacilli 6  
    Bact pneumonia, G+ve bacilli 7  
    Bact pneumonia, G+ve cocci 8  
    Bacterial pneumonia, G-ve cocci 9  
    Pneumonia, likely bacterial 10  
    Disseminated cryptococcosis 11  
    Local crypto (specify) 12  
    Pneumonitis, ?viral 13  
    Pneumonitis, other (specify) 14  
    Steatosis (give details) 15  
    Steatohepatitis (give details) 16  
    Chronic hepatitis (give details) 17  
    Acute hepatitis (give details) 18  
    Liver cirrhosis 19  
    Acute tubular necrosis 20  
    Nephritis 21  
    Other pulmonary 31  
    Other cardiac 32  
    Other hepatic 33  
    Other renal 34  
    Other splenic 35  
    Other infectious 36  
    Other 96  
    No other diagnoses 97  
HIST_diag4 HIstology diagnosis 4     Numeric
    Diss mycob inf, likely TB 1  
    Diss mycob inf, likely atypical 2  
    Diss mycob inf, other (specify) 3  
    Local mycob inf (specify) 4  
    Evid mycob infect, ?treated 5  
    Bact pneumonia, G-ve bacilli 6  
    Bact pneumonia, G+ve bacilli 7  
    Bact pneumonia, G+ve cocci 8  
    Bacterial pneumonia, G-ve cocci 9  
    Pneumonia, likely bacterial 10  
    Disseminated cryptococcosis 11  
    Local crypto (specify) 12  
    Pneumonitis, ?viral 13  
    Pneumonitis, other (specify) 14  
    Steatosis (give details) 15  
    Steatohepatitis (give details) 16  
    Chronic hepatitis (give details) 17  
    Acute hepatitis (give details) 18  
    Liver cirrhosis 19  
    Acute tubular necrosis 20  
    Nephritis 21  
    Other pulmonary 31  
    Other cardiac 32  
    Other hepatic 33  
    Other renal 34  
    Other splenic 35  
    Other infectious 36  
    Other 96  
    No other diagnoses 97  
HIST_diag5 Hsitology diagnosis 5     Numeric
    Diss mycob inf, likely TB 1  
    Diss mycob inf, likely atypical 2  
    Diss mycob inf, other (specify) 3  
    Local mycob inf (specify) 4  
    Evid mycob infect, ?treated 5  
    Bact pneumonia, G-ve bacilli 6  
    Bact pneumonia, G+ve bacilli 7  
    Bact pneumonia, G+ve cocci 8  
    Bacterial pneumonia, G-ve cocci 9  
    Pneumonia, likely bacterial 10  
    Disseminated cryptococcosis 11  
    Local crypto (specify) 12  
    Pneumonitis, ?viral 13  
    Pneumonitis, other (specify) 14  
    Steatosis (give details) 15  
    Steatohepatitis (give details) 16  
    Chronic hepatitis (give details) 17  
    Acute hepatitis (give details) 18  
    Liver cirrhosis 19  
    Acute tubular necrosis 20  
    Nephritis 21  
    Other pulmonary 31  
    Other cardiac 32  
    Other hepatic 33  
    Other renal 34  
    Other splenic 35  
    Other infectious 36  
    Other 96  
    No other diagnoses 97