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Datasets:
electricsheepafrica
/
africa-synth-microbiology-culture-sensitivity-senegal

Tasks:
Tabular Classification
Modalities:
Tabular
Text
Formats:
csv
Languages:
English
Size:
10K - 100K
Tags:
laboratory
microbiology
culture
antimicrobial-resistance
AMR
ESBL
Libraries:
Datasets
pandas
Polars
License:
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id
int64
age
int64
sex
string
facility_level
string
hiv_positive
int64
inpatient
int64
specimen_type
string
indication
string
culture_performed
int64
empirical_treatment_started
int64
culture_positive
int64
contaminated
int64
organism
string
ast_performed
int64
esbl_positive
int64
mrsa
int64
mdr
int64
carbapenem_resistant
int64
id_method
string
gram_stain_done
int64
antibiotic_changed_post_culture
int64
appropriate_empirical
int64
tat_hours
float64
tat_within_target
int64
reagent_stockout
int64
specimen_rejected
int64
eqa_participating
int64
result_communicated
int64
year
int64
1
37
male
health_centre
0
1
other
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
63
1
1
0
0
0
2,023
2
41
male
district
1
0
wound_swab
diarrhea
0
0
0
0
none
0
0
0
0
0
na
0
0
0
89
0
0
0
0
0
2,019
3
40
female
health_centre
0
1
urine
pneumonia
1
1
0
0
none
0
0
0
0
0
na
1
0
0
133
0
0
0
0
0
2,021
4
18
female
district
0
0
blood
uti
1
1
0
0
none
0
0
0
0
0
na
0
0
0
76
0
0
0
1
0
2,022
5
59
female
health_centre
0
0
sputum
uti
1
1
1
0
klebsiella
0
0
0
0
0
manual_biochemical
1
0
1
103
0
0
0
0
0
2,021
6
41
male
tertiary
1
0
urine
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
120
0
0
0
0
0
2,022
7
9
male
tertiary
0
0
wound_swab
uti
0
1
0
0
none
0
0
0
0
0
na
0
0
0
139
0
0
0
1
0
2,023
8
54
male
regional
0
1
stool
diarrhea
0
1
0
0
none
0
0
0
0
0
na
0
0
0
97
0
0
0
1
0
2,021
9
34
female
regional
0
1
sputum
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
48
1
0
1
0
0
2,021
10
37
male
district
0
0
sputum
pneumonia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
78
0
0
1
0
0
2,023
11
26
female
tertiary
0
1
wound_swab
diarrhea
0
1
0
0
none
0
0
0
0
0
na
0
0
0
75
0
1
1
0
0
2,021
12
16
female
regional
0
1
sputum
uti
0
1
0
0
none
0
0
0
0
0
na
0
0
0
76
0
0
0
0
0
2,022
13
33
female
district
0
0
wound_swab
pneumonia
1
1
0
0
none
0
0
0
0
0
na
0
0
0
48
1
1
0
0
0
2,020
14
83
female
regional
0
0
other
wound_infection
1
1
1
0
s_aureus
0
0
0
0
0
manual_biochemical
1
0
0
52
1
1
0
0
0
2,020
15
21
male
district
0
0
urine
other
1
1
0
0
none
0
0
0
0
0
na
1
0
0
100
0
0
0
0
0
2,023
16
24
male
health_centre
1
1
csf
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
56
1
0
0
0
0
2,021
17
65
female
health_centre
0
1
blood
diarrhea
0
1
0
0
none
0
0
0
0
0
na
0
0
0
53
1
0
0
0
0
2,021
18
25
female
regional
0
1
blood
sepsis_bacteremia
1
1
1
0
salmonella_typhi
0
0
0
0
0
manual_biochemical
1
0
0
67
1
1
0
0
0
2,022
19
39
male
district
0
1
csf
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
153
0
0
0
0
0
2,023
20
31
female
tertiary
0
1
stool
pneumonia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
111
0
1
0
0
0
2,020
21
10
male
regional
0
0
urine
other
0
1
0
0
none
0
0
0
0
0
na
0
0
0
173
0
0
0
0
0
2,023
22
24
female
regional
0
1
wound_swab
fever_unknown
1
1
1
0
acinetobacter
1
0
0
0
0
manual_biochemical
0
0
0
68
1
0
0
0
1
2,022
23
19
female
district
0
1
wound_swab
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
71
1
1
0
1
0
2,022
24
54
female
district
0
0
wound_swab
uti
0
1
0
0
none
0
0
0
0
0
na
0
0
0
89
0
1
0
0
0
2,021
25
84
female
health_centre
0
1
urine
other
0
0
0
0
none
0
0
0
0
0
na
0
0
0
127
0
0
0
1
0
2,022
26
21
male
district
0
1
urine
pneumonia
0
0
0
0
none
0
0
0
0
0
na
0
0
0
110
0
1
0
0
0
2,020
27
41
male
health_centre
0
0
blood
fever_unknown
1
1
0
0
none
0
0
0
0
0
na
1
0
0
79
0
0
1
1
0
2,019
28
7
female
regional
0
1
csf
other
0
1
0
0
none
0
0
0
0
0
na
0
0
0
186
0
1
0
1
0
2,022
29
77
female
health_centre
0
0
blood
uti
0
0
0
0
none
0
0
0
0
0
na
0
0
0
48
1
1
0
1
0
2,023
30
8
male
tertiary
0
0
urine
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
115
0
0
0
0
0
2,022
31
23
female
tertiary
0
1
sputum
sepsis_bacteremia
1
1
0
0
none
0
0
0
0
0
na
1
0
0
113
0
0
0
0
0
2,020
32
7
male
tertiary
0
1
blood
wound_infection
0
1
0
0
none
0
0
0
0
0
na
0
0
0
83
0
0
0
0
0
2,022
33
13
female
district
0
0
stool
other
0
1
0
0
none
0
0
0
0
0
na
0
0
0
65
1
1
0
0
0
2,019
34
47
female
tertiary
0
1
blood
uti
0
1
0
0
none
0
0
0
0
0
na
0
0
0
35
1
0
0
0
0
2,022
35
10
male
health_centre
0
0
urine
diarrhea
0
1
0
0
none
0
0
0
0
0
na
0
0
0
101
0
1
0
0
0
2,020
36
18
female
health_centre
0
0
other
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
199
0
0
0
0
0
2,020
37
15
female
tertiary
0
1
sputum
wound_infection
0
1
0
0
none
0
0
0
0
0
na
0
0
0
41
1
0
0
0
0
2,022
38
26
male
district
0
1
csf
wound_infection
0
0
0
0
none
0
0
0
0
0
na
0
0
0
92
0
0
0
0
0
2,021
39
16
male
health_centre
0
1
urine
uti
1
0
0
0
none
0
0
0
0
0
na
1
0
0
47
1
1
0
0
0
2,022
40
10
female
district
0
0
wound_swab
other
0
0
0
0
none
0
0
0
0
0
na
0
0
0
137
0
0
0
0
0
2,022
41
90
female
regional
0
0
urine
sepsis_bacteremia
1
1
0
0
none
0
0
0
0
0
na
0
0
0
108
0
0
0
0
0
2,019
42
19
female
health_centre
0
1
urine
sepsis_bacteremia
1
1
0
0
none
0
0
0
0
0
na
0
0
0
64
1
0
0
1
0
2,020
43
82
female
tertiary
0
0
blood
pneumonia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
57
1
0
0
0
0
2,020
44
7
male
regional
0
1
blood
uti
0
0
0
0
none
0
0
0
0
0
na
0
0
0
268
0
1
0
1
0
2,022
45
8
male
health_centre
0
1
urine
sepsis_bacteremia
1
1
0
0
none
0
0
0
0
0
na
1
0
0
176
0
0
0
0
0
2,022
46
23
female
regional
0
0
sputum
diarrhea
0
1
0
0
none
0
0
0
0
0
na
0
0
0
67
1
1
0
0
0
2,023
47
39
female
health_centre
0
1
sputum
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0
0
0
0
none
0
0
0
0
0
na
0
0
0
75
0
0
0
0
0
2,019
48
21
female
district
0
1
other
sepsis_bacteremia
1
1
1
0
klebsiella
0
0
0
0
0
manual_biochemical
1
0
1
93
0
1
0
0
0
2,021
49
47
male
tertiary
0
1
sputum
wound_infection
1
1
0
0
none
0
0
0
0
0
na
0
0
0
91
0
1
0
0
0
2,022
50
83
male
health_centre
1
1
wound_swab
sepsis_bacteremia
1
1
0
0
none
0
0
0
0
0
na
1
0
0
142
0
1
0
0
0
2,020
51
68
female
health_centre
1
0
sputum
sepsis_bacteremia
0
0
0
0
none
0
0
0
0
0
na
0
0
0
97
0
0
0
0
0
2,023
52
66
female
regional
0
0
blood
pneumonia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
114
0
1
1
0
0
2,022
53
90
female
regional
0
0
blood
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
99
0
0
1
1
0
2,023
54
56
male
health_centre
0
1
wound_swab
uti
1
1
0
0
none
0
0
0
0
0
na
0
0
0
39
1
1
0
0
0
2,023
55
30
female
district
0
0
wound_swab
wound_infection
0
0
0
0
none
0
0
0
0
0
na
0
0
0
82
0
0
1
0
0
2,022
56
21
male
health_centre
0
0
blood
other
0
1
0
0
none
0
0
0
0
0
na
0
0
0
54
1
0
0
0
0
2,021
57
27
female
health_centre
0
0
blood
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
82
0
1
0
1
0
2,023
58
30
female
health_centre
0
1
sputum
wound_infection
0
1
0
0
none
0
0
0
0
0
na
0
0
0
80
0
0
0
0
0
2,021
59
30
male
district
0
0
blood
sepsis_bacteremia
0
0
0
0
none
0
0
0
0
0
na
0
0
0
68
1
1
0
0
0
2,021
60
29
male
district
0
0
sputum
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
91
0
0
0
0
0
2,023
61
13
male
tertiary
0
0
blood
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
78
0
1
0
0
0
2,022
62
16
male
district
0
0
csf
uti
0
1
0
0
none
0
0
0
0
0
na
0
0
0
86
0
1
0
0
0
2,020
63
39
male
regional
0
0
stool
uti
0
1
0
0
none
0
0
0
0
0
na
0
0
0
37
1
1
0
0
0
2,023
64
26
female
district
0
1
blood
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
219
0
1
0
0
0
2,020
65
57
male
health_centre
0
0
urine
pneumonia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
22
1
0
0
0
0
2,020
66
41
male
tertiary
0
0
wound_swab
diarrhea
0
1
0
0
none
0
0
0
0
0
na
0
0
0
102
0
0
0
1
0
2,023
67
25
male
district
0
1
wound_swab
pneumonia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
57
1
0
0
0
0
2,021
68
41
male
regional
0
0
blood
pneumonia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
130
0
0
0
0
0
2,023
69
90
female
district
0
0
sputum
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
67
1
0
0
1
0
2,019
70
47
female
district
1
1
blood
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
58
1
1
0
1
0
2,020
71
38
female
regional
0
0
other
meningitis
0
1
0
0
none
0
0
0
0
0
na
0
0
0
162
0
0
0
0
0
2,019
72
20
female
district
0
0
stool
uti
0
1
0
0
none
0
0
0
0
0
na
0
0
0
101
0
1
0
0
0
2,023
73
15
female
health_centre
0
0
sputum
pneumonia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
118
0
1
0
0
0
2,020
74
21
female
regional
1
1
csf
fever_unknown
1
1
1
0
klebsiella
0
0
0
0
0
manual_biochemical
1
0
1
391
0
0
0
1
1
2,023
75
31
female
district
1
0
blood
pneumonia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
143
0
0
0
0
0
2,022
76
90
female
health_centre
0
1
urine
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
136
0
0
0
0
0
2,021
77
84
female
district
0
1
stool
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
59
1
1
1
0
0
2,023
78
26
female
health_centre
0
1
stool
fever_unknown
0
0
0
0
none
0
0
0
0
0
na
0
0
0
192
0
1
0
0
0
2,023
79
28
female
district
0
1
blood
diarrhea
1
1
0
0
none
0
0
0
0
0
na
0
0
0
105
0
0
0
0
0
2,021
80
32
female
health_centre
0
1
blood
meningitis
0
1
0
0
none
0
0
0
0
0
na
0
0
0
59
1
0
0
0
0
2,019
81
23
female
district
0
1
wound_swab
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0
1
0
0
none
0
0
0
0
0
na
0
0
0
115
0
0
0
0
0
2,022
82
46
male
regional
0
0
blood
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
84
0
1
0
0
0
2,020
83
15
male
tertiary
0
1
blood
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
67
1
1
0
0
0
2,022
84
21
female
health_centre
1
1
blood
meningitis
0
0
0
0
none
0
0
0
0
0
na
0
0
0
94
0
0
0
0
0
2,019
85
43
male
health_centre
0
0
blood
other
0
1
0
0
none
0
0
0
0
0
na
0
0
0
31
1
1
0
0
0
2,020
86
44
male
tertiary
0
0
urine
pneumonia
1
1
0
0
none
0
0
0
0
0
na
0
0
0
88
0
1
0
0
0
2,021
87
37
female
regional
0
1
blood
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
143
0
0
0
0
0
2,023
88
47
female
district
1
0
urine
other
0
1
0
0
none
0
0
0
0
0
na
0
0
0
71
1
0
0
1
0
2,022
89
6
female
district
1
0
urine
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
105
0
1
0
0
0
2,022
90
54
female
health_centre
0
0
stool
pneumonia
1
0
0
0
none
0
0
0
0
0
na
1
0
0
28
1
0
0
0
0
2,021
91
13
female
health_centre
0
1
stool
sepsis_bacteremia
0
1
0
0
none
0
0
0
0
0
na
0
0
0
174
0
1
0
0
0
2,022
92
35
male
district
0
1
blood
uti
1
0
0
0
none
0
0
0
0
0
na
0
0
0
121
0
0
0
0
0
2,021
93
40
male
district
0
0
blood
diarrhea
0
0
0
0
none
0
0
0
0
0
na
0
0
0
85
0
0
0
1
0
2,019
94
90
male
district
0
0
urine
pneumonia
1
0
0
0
none
0
0
0
0
0
na
1
0
0
116
0
0
0
0
0
2,022
95
10
female
health_centre
0
1
csf
wound_infection
0
0
0
0
none
0
0
0
0
0
na
0
0
0
201
0
0
0
0
0
2,021
96
8
male
tertiary
1
0
urine
other
0
1
0
0
none
0
0
0
0
0
na
0
0
0
121
0
1
0
0
0
2,022
97
44
female
regional
1
1
blood
uti
0
0
0
0
none
0
0
0
0
0
na
0
0
0
133
0
0
0
0
0
2,022
98
10
female
regional
1
1
urine
other
1
1
0
0
none
0
0
0
0
0
na
1
0
0
193
0
0
0
0
0
2,020
99
47
male
health_centre
0
1
sputum
wound_infection
0
1
0
0
none
0
0
0
0
0
na
0
0
0
22
1
0
0
0
0
2,019
100
11
male
district
1
0
urine
fever_unknown
0
1
0
0
none
0
0
0
0
0
na
0
0
0
124
0
0
0
0
0
2,022
End of preview. Expand in Data Studio

⚠️ Synthetic dataset — Parameterized from published SSA literature, not real observations. Not suitable for empirical analysis or policy inference.

Microbiology Culture & Sensitivity

Abstract

Synthetic dataset modeling microbiology laboratory services across three SSA scenarios. Captures culture availability, specimen types, organism identification, antimicrobial susceptibility testing, AMR patterns (ESBL, MRSA), empirical treatment, and quality indicators. Parameterized from SSA microbiology and AMR research.

Parameterization Evidence

Parameter Value Source Year
Blood culture availability <5% district hospitals Nkengasong et al. Lancet 2018
Blood culture positivity 10-15% Musicha et al. BMC Infect Dis 2017
E. coli ESBL SSA 30-70% WHO GLASS 2022
K. pneumoniae ESBL SSA 40-80% WHO GLASS 2022
MRSA SSA 10-50% WHO GLASS 2022
Empirical treatment norm >80% without culture Laxminarayan et al. Lancet 2016

Validation

Validation Report

Usage 

from datasets import load_dataset
ds = load_dataset("electricsheepafrica/microbiology-culture-sensitivity", name="limited_microbiology")
df = ds['train'].to_pandas()

References

  1. Nkengasong JN et al. (2018). Laboratory medicine Africa. Lancet. DOI: 10.1016/S0140-6736(18)30625-8
  2. Musicha P et al. (2017). AMR bloodstream Malawi. BMC Infect Dis. DOI: 10.1186/s12879-017-2810-x
  3. Laxminarayan R et al. (2016). Access to antimicrobials. Lancet. DOI: 10.1016/S0140-6736(15)00474-2
  4. WHO GLASS (2022). Global AMR Surveillance Report

License

CC-BY-4.0
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