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1 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 S_bld Blood obtained? Open ended Numeric S_csf CSF obtained? Numeric S_liv Liver sample obtained? Numeric S_lk Left kidney sample obtained? Numeric S_rk Right kidney sample obtained? Numeric S_ll Left lung sample obtained? Numeric S_rl Right lung sample obtained? Numeric S_np Naso/oropharyngeal aspirate obtained? Numeric S_spl Splenic sample obtained? Numeric S_ur Urine obtained? Numeric S_o Other sample obtained? Open ended String TB_gxpval Xpert MTB/RIF valid? Numeric 1
2 Not a GeneXpert sample TB_gxpres Xpert MTB/RIF result Numeric MTB NOT 0 detected 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 TB_znres1BAL BAL: ZN result (1) Numeric TB_blagarresBAL BAL: Blood agar result Numeric TB_hainothBAL BAL: Hain result Open ended String TB_mgitresCSF CSF: MGIT result Numeric TB_znres1CSF CSF: ZN result (1) Numeric TB_blagarresCSF CSF: Blood agar result Numeric TB_hainothCSF CSF: Hain result Open ended String TB_mgitresLIV Liver: MGIT result Numeric TB_znres1LIV Liver: ZN result (1) Numeric TB_blagarresLIV Liver: Blood agar result Numeric 2
3 TB_hainothLIV Liver: Hain result Open ended String TB_mgitresLNG Lungs: MGIT result Numeric TB_znres1LNG Lungs: ZN result (1) Numeric TB_blagarresLNG Lungs: Blood agar result Numeric TB_hainothLNG Lungs: Hain result Open ended String TB_mgitresSPL Spleen: MGIT result Numeric TB_znres1SPL Spleen: ZN result (1) Numeric TB_blagarresSPL Spleen: Blood agar result Numeric TB_hainothSPL Spleen: Hain result Open ended String TB_mgitresURI Urine: MGIT result Numeric TB_znres1URI Urine: ZN result (1) Numeric TB_blagarresURI Urine: Blood agar result Numeric TB_hainothURI Urine: Hain result Open ended String MICRO_aerocyn_BAL BAL: Bact culture positive? Numeric 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 3
4 MICRO_fungcoth_BAL BAL: Fungal culture, other Open ended String MICRO_aerocyn_BLD Blood: Bact culture positive? Numeric 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 MICRO_fungcoth_BLD Blood: Fungal culture, other Open ended String MICRO_aerocyn_CSF CSF: Bact culture positive? Numeric 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 MICRO_fungcoth_CSF CSF: Fungal culture, other Open ended String MICRO_aerocyn_LIV Liver: Bact culture positive? Numeric 4
5 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 MICRO_fungcoth_LIV Liver: Fungal culture, other Open ended String MICRO_aerocyn_LNG Lungs: Bact culture positive? Numeric 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 MICRO_fungcoth_LNG Lungs: Fungal culture, other Open ended String MICRO_aerocyn_SPL Spleen: Bact culture positive? Numeric 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 5
6 MICRO_fungcoth_SPL Spleen: Fungal culture, other Open ended String OTHER_pcpifa_BAL BAL: PCP IFA Numeric Possible 2 Not a PCP result OTHER_crag_BLD Blood: CrAg Numeric CrAg negative 0 CrAg positive 1 No CrAg result OTHER_crag_CSF CSF: CrAg Numeric CrAg negative 0 CrAg positive 1 No CrAg result HIST_diag1 Histology diagnosis 1 Numeric Diss mycob inf, 1 likely TB Diss mycob inf, 2 likely atypical Diss mycob inf, 3 Local mycob inf 4 Evid mycob 5 infect,?treated Bact pneumonia, 6 G-ve bacilli Bact pneumonia, 7 G+ve bacilli Bact pneumonia, 8 G+ve cocci Bacterial pneumonia, G-ve cocci Pneumonia, 10 likely bacterial Disseminated 11 cryptococcosis Local crypto 12 Pneumonitis, 13?viral Pneumonitis, 14 6
7 Steatosis (give 15 details) Steatohepatitis 16 Chronic hepatitis 17 Acute hepatitis 18 Liver cirrhosis 1 Acute tubular 20 necrosis Nephritis 21 Other pulmonary 31 Other cardiac 32 Other hepatic 33 Other renal 34 Other splenic 35 Other infectious 36 Other 6 No other 7 diagnoses HIST_diag2 Histology diagnosis 2 Numeric Diss mycob inf, 1 likely TB Diss mycob inf, 2 likely atypical Diss mycob inf, 3 Local mycob inf 4 Evid mycob 5 infect,?treated Bact pneumonia, 6 G-ve bacilli Bact pneumonia, 7 G+ve bacilli Bact pneumonia, 8 G+ve cocci Bacterial pneumonia, G-ve cocci Pneumonia, 10 likely bacterial Disseminated 11 cryptococcosis Local crypto 12 Pneumonitis, 13?viral 7
8 Pneumonitis, 14 Steatosis (give 15 details) Steatohepatitis 16 Chronic hepatitis 17 Acute hepatitis 18 Liver cirrhosis 1 Acute tubular 20 necrosis Nephritis 21 Other pulmonary 31 Other cardiac 32 Other hepatic 33 Other renal 34 Other splenic 35 Other infectious 36 Other 6 No other 7 diagnoses HIST_diag3 Histology diagnosis 3 Numeric Diss mycob inf, 1 likely TB Diss mycob inf, 2 likely atypical Diss mycob inf, 3 Local mycob inf 4 Evid mycob 5 infect,?treated Bact pneumonia, 6 G-ve bacilli Bact pneumonia, 7 G+ve bacilli Bact pneumonia, 8 G+ve cocci Bacterial pneumonia, G-ve cocci Pneumonia, 10 likely bacterial Disseminated 11 cryptococcosis Local crypto 12 8
9 Pneumonitis, 13?viral Pneumonitis, 14 Steatosis (give 15 details) Steatohepatitis 16 Chronic hepatitis 17 Acute hepatitis 18 Liver cirrhosis 1 Acute tubular 20 necrosis Nephritis 21 Other pulmonary 31 Other cardiac 32 Other hepatic 33 Other renal 34 Other splenic 35 Other infectious 36 Other 6 No other 7 diagnoses HIST_diag4 HIstology diagnosis 4 Numeric Diss mycob inf, 1 likely TB Diss mycob inf, 2 likely atypical Diss mycob inf, 3 Local mycob inf 4 Evid mycob 5 infect,?treated Bact pneumonia, 6 G-ve bacilli Bact pneumonia, 7 G+ve bacilli Bact pneumonia, 8 G+ve cocci Bacterial pneumonia, G-ve cocci Pneumonia, 10 likely bacterial Disseminated 11 cryptococcosis
10 Local crypto 12 Pneumonitis, 13?viral Pneumonitis, 14 Steatosis (give 15 details) Steatohepatitis 16 Chronic hepatitis 17 Acute hepatitis 18 Liver cirrhosis 1 Acute tubular 20 necrosis Nephritis 21 Other pulmonary 31 Other cardiac 32 Other hepatic 33 Other renal 34 Other splenic 35 Other infectious 36 Other 6 No other 7 diagnoses HIST_diag5 Hsitology diagnosis 5 Numeric Diss mycob inf, 1 likely TB Diss mycob inf, 2 likely atypical Diss mycob inf, 3 Local mycob inf 4 Evid mycob 5 infect,?treated Bact pneumonia, 6 G-ve bacilli Bact pneumonia, 7 G+ve bacilli Bact pneumonia, 8 G+ve cocci Bacterial pneumonia, G-ve cocci Pneumonia, 10 likely bacterial 10
11 Disseminated 11 cryptococcosis Local crypto 12 Pneumonitis, 13?viral Pneumonitis, 14 Steatosis (give 15 details) Steatohepatitis 16 Chronic hepatitis 17 Acute hepatitis 18 Liver cirrhosis 1 Acute tubular 20 necrosis Nephritis 21 Other pulmonary 31 Other cardiac 32 Other hepatic 33 Other renal 34 Other splenic 35 Other infectious 36 Other 6 No other 7 diagnoses 11
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