Description of database fields
Provenance/primary metadata
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| field name | comments | data type | allowed values | required | maximum length (characters) |
|---|---|---|---|---|---|
| id | id - primary key | integer | - | yes | 6 |
| isolate | strain name | text | - | yes | 20 |
| aliases | alternative names for isolate | text (multiple) | - | no | - |
| references | PubMed ids that link to publications that describe or include record | integer (multiple) | - | no | - |
| country | country where strain was isolated | text | yes | - | |
| region | region of country (state/county) | text | - | no | 50 |
| town_or_city | this field is used in mapping so please try to ensure correct or most common spelling to facilitate GPS coordinates lookup. For US place names, please suffix 2-letter state code in square brackets, e.g. 'Dallas [TX]', to resolve ambiguities. | text | - | no | 50 |
| origin | hospital name or other origin | text | - | no | 40 |
| year | year of isolation | integer | min: 1900; max: 2023 | expected | 4 |
| species | Acinetobacter species | text | yes | - | |
| species_id_method | method used to identify species on initial submission; biochemical means the use of API for example. | text | yes | - | |
| source | source of isolate; assume human if not animal/environment/food unless stated otherwise. Please add source to detailed_source is 'other' is selected. | text | no | - | |
| detailed_source | text | - | no | 30 | |
| age_yr | age in years | integer | min: 0; max: 120 | no | - |
| age_mth | month part of age (0-11) for patients under 1 year old | integer | min: 0; max: 11 | no | - |
| sex | sex of patient/carrier | text |
male
female |
no | - |
| PFGE | PFGE type | text | - | no | 12 |
| AFLP | AFLP type | text | - | no | 12 |
| amikacin_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| amikacin_mic | MIC in mg/l | float | - | no | - |
| amikacin_SIR | S: susceptible; I: intermediate; R: resistant. Based on CLSI defined breakpoints: Nm (S: <=16; I: >16-<64; R: >=64). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| gentamicin_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| gentamicin_mic | MIC in mg/l | float | - | no | - |
| gentamicin_SIR | S: susceptible; I: intermediate; R: resistant. Based on CLSI defined breakpoints: Nm (S: <=4; I: >4-<16; R: >=16). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| cefotaxime_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| cefotaxime_mic | MIC in mg/l | float | - | no | - |
| cefotaxime_SIR | S: susceptible; I: intermediate; R: resistant. Based on CLSI defined breakpoints: Nm (S: <=8; I: >8-<64; R: >=64). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| cefepime_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| cefepime_mic | MIC in mg/l | float | - | no | - |
| cefepime_SIR | S: susceptible; I: intermediate; R: resistant. Based on CLSI defined breakpoints: Nm (S: <=8; I: >8-<32; R: >=32). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| levofloxacin_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| levofloxacin_mic | MIC in mg/l | float | - | no | - |
| levofloxacin_SIR | S: susceptible; I: intermediate; R: resistant. Based on CLSI defined breakpoints: Nm (S: <=2; I: >2-<8; R: >=8). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| tetracycline_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| tetracycline_mic | MIC in mg/l | float | - | no | - |
| tetracycline_SIR | S: susceptible; I: intermediate; R: resistant. Based on CLSI defined breakpoints: Nm (S: <=4; I: >4-<16; R: >=16). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| imipenem_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| imipenem_mic | MIC in mg/l | float | - | no | - |
| imipenem_SIR | S: susceptible; I: intermediate; R: resistant. Based on CLSI defined breakpoints: Nm (S: <=2; I: >2-<8; R: >=8). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| meropenem_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| meropenem_mic | MIC in mg/l | float | - | no | - |
| meropenem_SIR | S: susceptible; I: intermediate; R: resistant. Based on CLSI defined breakpoints: Nm (S: <=2; I: >2-<8; R: >=8). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| colistin_mic_sign | indicate if MIC result is greater than, less than, or equal the set value | text |
<
> = |
no | - |
| colistin_mic | MIC in mg/l | float | - | no | - |
| colistin_SIR | S: susceptible; R: resistant. Based on EUCAST defined breakpoints: Nm (S: <=2; R: >2). Field value will be populated automatically if MIC value is provided. | text |
S
I R |
no | - |
| resistance_profile | resistance profile using the classification described by Magiorakos et al. (2012) | text |
PDR
XDR MDR not MDR sensitive |
no | - |
| OXA_family | text (multiple) | - | no | - | |
| OXA_class | text (multiple) | - | no | - | |
| OXA_betalactamase | text (multiple) | - | no | - | |
| MBL_family | text (multiple) | - | no | - | |
| MBL_class | text (multiple) | - | no | - | |
| MBL_betalactamase | text (multiple) | - | no | - | |
| class_B_D_betalactamase | text (multiple) | - | no | - | |
| Genbank_accession | Genbank accession number | text | - | no | 30 |
| bioproject_accession | ENA/SRA bioproject accession number | text (multiple) | - | no | 20 |
| biosample_accession | ENA/SRA biosample accession number | text (multiple) | - | no | 20 |
| ENA_run_accession | ENA/SRA accession number to access short read data. This should start either ERR, SRR, or DRR. | text | - | no | 15 |
| comments | any other comments | text | - | no | 1000 |
| sender | sender unique name, link to users | integer | Click for list of sender ids | yes | 4 |
| curator | curator who entered data,link to users | integer | Click for list of curator ids | yes | 4 |
| date_entered | date first entered | date | - | yes | 10 |
| datestamp | date last modified | date | - | yes | 10 |
Secondary metadata
Biofilm
| field name | comments | data type | allowed values | required | maximum length (characters) |
|---|---|---|---|---|---|
| OD_neg_control | mean OD for negative control (no cells). | float | min: -10; max: 10 | no | - |
| OD_neg_control_SD | standard deviation of negative control replicates | float | min: 0; max: 5 | no | - |
| OD_sample | mean OD for sample. | float | min: -10; max: 10 | no | - |
| biofilm_production | biofilm production using the classification described by Stepanović et al. (2007) | text |
none
low medium high |
no | - |
Efflux pump overexpression
| field name | comments | data type | allowed values | required | maximum length (characters) |
|---|---|---|---|---|---|
| amikacin_efflux | - | text |
true
false |
no | - |
| cefepime_efflux | - | text |
true
false |
no | - |
| cefotaxime_efflux | - | text |
true
false |
no | - |
| colistin_efflux | - | text |
true
false |
no | - |
| gentamicin_efflux | - | text |
true
false |
no | - |
| imipenem_efflux | - | text |
true
false |
no | - |
| levofloxacin_efflux | - | text |
true
false |
no | - |
| meropenem_efflux | - | text |
true
false |
no | - |
| tetracycline_efflux | - | text |
true
false |
no | - |