MBIRA - Mortality from Bacterial Infections Resistant to Antibiotics study - underlying data – Data codebook

Permanent identifier



Antimicrobial resistance is a major global health concern, but there is limited data linking laboratory resistance testing to clinical outcomes, especially from Low-and-Middle-Income countries, including African nations. This is a project collecting prospective data about bloodstream infections caused by Enterobacterales bacteria in African hospitals in 2020-22. A central focus was the impact of 3rd generation cephalosporin (3GC) resistance on patient mortality. In the main study, n=8 hospitals in eight different countries contributed to this project. Preliminary work involved collection of descriptive information from these 8 hospitals, including access to antibiotics in hospital pharmacies. Information was collected for infected patients and matched non-infected patients in same hospitals.

The MBIRA study collected data about hospitals, patients, bacterial isolates and antibiotic use. The “mbira_hospital” dataset contains information collected as a one-off event as part of the “hospital” form and the “mbira_pharmacy” contains information on antibiotic availability in pharmacies that were collected each month. Further datasets will be made available at a later date.

Hospital-level data

The hospital-level data – this is in the form of two small data tables. One relates to the “hospital form” (a one-off data collection, see Appendix 1) and the second relates to the “antibiotic form” (repeated monthly collection of data about antibiotic availability in pharmacies, see Appendix 2). These are two small data tables (mbira_hospital.xls and mbira_pharmacy.xls) that are in the form of excel spreadsheets.

MBIRA Hospital data

Variable name Variable label Answer label Answer code Variable type
1 Site ID     Numeric
2 Event Name     String
    Hospital profile survey (Arm 1: English)    
3 Repeat Instrument Hospital profile   String
4 Repeat Instance     Numeric
5 Data Access Group     String
6 1. Date of hospital survey started DD/MM/YYYY   Date
7 2. Full physical address     String
8 3. Urban or rural ?     String
    Mixed urban and rural    
9 4. Hospital type ?     String
10 4a.if Other Hospital type please specify describe here.     String
11 5. Hospital level     String
12 6. Hospital total beds + cots total     Numeric
13 Total ICU beds     Numeric
14 ICU beds [total_icu_beds_sa] Level of ICU care     String
15 Total Paediatric ICU beds/cots     String
16 Paediatric ICU beds/cots [total_paediatric_bed_cot_sa] Level of ICU care     String
17 Total NICU cots     String
18 NICU cots [total_nicu_cots_sa] Level of ICU care     String
19 8. Total hospital admissions in 2019 (round 1) or 2020 (round 2) [total_hospital_admissions] from 1st Jan to 31st Dec for relevant year     Numeric
20 8a. Total hospital inpatient-days in 2019 (round 1) or 2020 (round 2) [total_hospital_inpatient_days] from 1st Jan to 31st Dec for relevant year     Numeric
21 Core component 1 total score: IPC programme ( [ipc_programme] / 100 )     Numeric
22 Core component 2 total score: IPC guidelines ( [ipc_guidelines] / 100 )     Numeric
23 Core component 3 total score: IPC education and training ( [ipc_education_training] / 100)     Numeric
24 Core component 4 total score: Health-care Associated Infection surveillance ( [associated_infection_surveillanc] / 100 )     Numeric
25 Core component 5 total score: Multimodal strategies for implementation of IPC interventions ( [ipc_interventions] / 100 )     Numeric
26 Core component 6 total score: Monitoring / audit of IPC practices and feedback ( [ipc_practices_and_feedback] / 100 )     Numeric
27 Core component 7 total score: Workload, staffing and bed occupancy ( [staffing_and_bed_occupancy] / 100 )     Numeric
28 Core component 8 total score: built environment, materials and equipment for IPC at the facility level ( [ipc_at_the_facility_level] / 100 )     Numeric
29 Total score (= sum of all core Components above)     Numeric
30 Note: The completed full version of the IPC Self-assessment framework sheets will need to be scanned and loaded to the REDCap database     String
31 Section 1. Leadership Commitment (Q1-3)     String
32 Section 2. Accountability and Responsibilities (Q4-9b)     String
33 Section 3. AMS Actions (Q10-17b)PL     String
34 Section 4. Education and Training (Q18-20)     String
35 Section 5. Monitoring and Surveillance (Q21-24)     String
36 Section 6. Reporting and Feedback (Q25-28)     String
37 Total of all sections (sum of above scores)     String
38 Note: The completed full version of the Antimicrobial Stewardship assessment will need to be scanned and loaded to the REDCap database.     String
39 Date of hospital survey completed DD/MM/YYYY   Date

MBIRA Pharmacy data

Variable name Variable label Answer label Answer code Variable type
1 Site ID     Numeric
2 Event Name Hospital pharmacy Survey (Arm 1: English)   String
3 Repeat Instance     Numeric
4 Data Access Group     String
5 1. Date of pharmacy survey   DD/MM/YYYY Date
6 amoxicillin     String
7 co-amoxiclav     String
8 gentamicin     String
9 ciprofloxacin     String
10 ceftriaxone     String
11 cefotaxime     String
12 ceftazidime     String
13 amikacin     String
14 meropenem     String
15 imipenem     String
16 chloramphenicol     String
17 piperacillin-tazobactam     String
18 co-trimoxazole     String
19 Group 1 : Other cephalosporins     String
20 Group 2 : Other β-lactam, β-lactamase inhibitors (BLBI)     String
21 Group 3 : Other carbapenem antibiotics     String
22 Group 4 : Tigecycline     String
23 Group 5: Any other agents for resistant Gram-negative infections     String
24 Date survey form was completed   DD/MM/YYYY Date
25 Date data was entered   DD/MM/YYYY Date

Collapsed data for scatter plot

Variable name Variable label Answer label Answer code Variable type
Redcap data access group Country of study hospital     String
Name of antibiotic Name of antibiotic     String
    co-trimoxazole (septrin, eusaprim)    
    piperacillin-tazobactam (tazocin)    
Percent patients Percentage of study patients that received treatment     Numeric
drugavailable Proportion of monthly study surveys where antibiotic described as being available     Numeric