Description of database fields

Provenance/primary metadata

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field namecommentsdata typeallowed valuesrequiredmaximum length (characters)
idid - primary key integer - yes 6
isolatestrain name text - yes 20
aliasesalternative names for isolatetext (multiple)-no-
referencesPubMed ids that link to publications that describe or include recordinteger (multiple)-no-
countrycountry where strain was isolated text
Afghanistan
Åland Islands
Albania
Algeria
American Samoa
Andorra
Angola
Anguilla
Antarctica
Antigua and Barbuda
Argentina
Armenia
Aruba
Australia
Austria
Azerbaijan
Bahamas
Bahrain
Bangladesh
Barbados
Belarus
Belgium
Belize
Benin
Bermuda
Bhutan
Bolivia
Bonaire, Sint Eustatius and Saba
Bosnia and Herzegovina
Botswana
Bouvet Island
Brazil
British Indian Ocean Territory
British Virgin Islands
Brunei
Bulgaria
Burkina Faso
Burundi
Cambodia
Cameroon
Canada
Cape Verde
Cayman Islands
Central African Republic
Chad
Chile
China
China [Hong Kong]
China [Macao]
Christmas Island
Cocos (Keeling) Islands
Colombia
Comoros
Congo [DRC]
Congo [Republic]
Cook Islands
Costa Rica
Croatia
Cuba
Curaçao
Cyprus
Czech Republic
Denmark
Djibouti
Dominica
Dominican Republic
East Timor
Ecuador
Egypt
El Salvador
Equatorial Guinea
Eritrea
Estonia
Ethiopia
Falkland Islands (Malvinas)
Faroe Islands
Fiji
Finland
France
French Guiana
French Polynesia
French Southern Territories
Gabon
Georgia
Germany
Ghana
Gibraltar
Greece
Greenland
Grenada
Guadeloupe
Guam
Guatemala
Guernsey
Guinea
Guinea-Bissau
Guyana
Haiti
Heard Island and McDonald Islands
Holy See
Honduras
Hungary
Iceland
India
Indonesia
Iran
Iraq
Ireland
Isle of Man
Israel
Italy
Ivory Coast
Jamaica
Japan
Jersey
Jordan
Kazakhstan
Kenya
Kiribati
Kuwait
Kyrgyzstan
Laos
Latvia
Lebanon
Lesotho
Liberia
Libya
Liechtenstein
Lithuania
Luxembourg
Madagascar
Malawi
Malaysia
Maldives
Mali
Malta
Marshall Islands
Martinique
Mauritania
Mauritius
Mayotte
Mexico
Micronesia
Moldova
Monaco
Mongolia
Montenegro
Montserrat
Morocco
Mozambique
Myanmar
Namibia
Nauru
Nepal
New Caledonia
New Zealand
Nicaragua
Niger
Nigeria
Niue
Norfolk Island
North Korea
North Macedonia
Northern Mariana Islands
Norway
Oman
Pakistan
Palau
Palestinian territories
Panama
Papua New Guinea
Paraguay
Peru
Philippines
Pitcairn
Poland
Portugal
Puerto Rico
Qatar
Réunion
Romania
Russia
Russia [Asia]
Russia [Europe]
Rwanda
Saint Barthélemy
Saint Helena
Saint Kitts and Nevis
Saint Lucia
Saint Martin (French Part)
Saint Pierre and Miquelon
Saint Vincent and the Grenadines
Samoa
San Marino
São Tomé and Príncipe
Sark
Saudi Arabia
Senegal
Serbia
Seychelles
Sierra Leone
Singapore
Sint Maarten (Dutch part)
Slovakia
Slovenia
Solomon Islands
Somalia
South Africa
South Georgia and the South Sandwich Islands
South Korea
South Sudan
Spain
Sri Lanka
Sudan
Suriname
Svalbard and Jan Mayen Islands
Swaziland
Sweden
Switzerland
Syria
Taiwan
Tajikistan
Tanzania
Thailand
The Gambia
The Netherlands
Togo
Tokelau
Tonga
Trinidad and Tobago
Tunisia
Turkey
Turkmenistan
Turks and Caicos Islands
Tuvalu
Uganda
UK
UK [England]
UK [Northern Ireland]
UK [Scotland]
UK [Wales]
Ukraine
United Arab Emirates
Uruguay
US Minor Outlying Islands
US Virgin Islands
USA
Uzbekistan
Vanuatu
Venezuela
Vietnam
Wallis and Futuna Islands
Western Sahara
Yemen
Zambia
Zimbabwe
Unknown
yes -
regionregion of country (state/county) text - no 50
town_or_citythis 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
originhospital name or other origin text - no 40
yearyear of isolation integer min: 1900; max: 2023 expected 4
speciesAcinetobacter species text
ACB complex
Acinetobacter albensis
Acinetobacter apis
Acinetobacter baumannii
Acinetobacter baylyi
Acinetobacter beijerinckii
Acinetobacter bereziniae
Acinetobacter bohemicus
Acinetobacter boissieri
Acinetobacter bouvetii
Acinetobacter brisouii
Acinetobacter calcoaceticus
Acinetobacter calcoaceticus (A. oleivorans DR1)
Acinetobacter calcoaceticus genomovar rhizosphaerae
Acinetobacter celticus
Acinetobacter chengduensis
Acinetobacter chinensis
Acinetobacter colistiniresistens
Acinetobacter courvalinii
Acinetobacter cumulans
Acinetobacter defluvii
Acinetobacter dispersus
Acinetobacter equi
Acinetobacter gandensis
Acinetobacter genospecies 3
Acinetobacter genospecies 13BJ
Acinetobacter genospecies 13TU
Acinetobacter genospecies 15BJ
Acinetobacter gerneri
Acinetobacter guerrae
Acinetobacter guillouiae
Acinetobacter gyllenbergii
Acinetobacter haemolyticus
Acinetobacter halotolerans
Acinetobacter harbinensis
Acinetobacter indicus
Acinetobacter johnsonii
Acinetobacter junii
Acinetobacter kookii
Acinetobacter kyonggiensis
Acinetobacter lactucae
Acinetobacter lanii
Acinetobacter larvae
Acinetobacter lwoffii
Acinetobacter marinus
Acinetobacter modestus
Acinetobacter nectaris
Acinetobacter nosocomialis
Acinetobacter oleivorans
Acinetobacter parvus
Acinetobacter piscicola
Acinetobacter pittii
Acinetobacter populi
Acinetobacter portensis
Acinetobacter pragensis
Acinetobacter proteolyticus
Acinetobacter pseudolwoffii
Acinetobacter pullicarnis
Acinetobacter pullorum
Acinetobacter puyangensis
Acinetobacter qingfengensis
Acinetobacter radioresistens
Acinetobacter rongchengensis
Acinetobacter rudis
Acinetobacter schindleri
Acinetobacter seifertii
Acinetobacter shaoyimingii
Acinetobacter sichuanensis
Acinetobacter soli
Acinetobacter stercoris
Acinetobacter tandoii
Acinetobacter tianfuensis
Acinetobacter tjernbergiae
Acinetobacter towneri
Acinetobacter ursingii
Acinetobacter variabilis
Acinetobacter venetianus
Acinetobacter vivianii
Acinetobacter wanghuae
Acinetobacter wuhouensis
Acinetobacter sp.
Acinetobacter sp. close to 13TU
yes -
species_id_methodmethod used to identify species on initial submission; biochemical means the use of API for example. text
biochemical
MALDI-ToF
presence of OXA-51
gyrB gene sequence
rpoB gene sequence
MLST sequences
genome sequence
other
unknown
yes -
sourcesource of isolate; assume human if not animal/environment/food unless stated otherwise. Please add source to detailed_source is 'other' is selected. text
abdominal fluid
abscess
animal
bile
blood
CSF
environment
environment (medical)
food
IV catheter
lower respiratory tract
skin
sputum
stool/rectal swab
upper respiratory tract
urine
wound
other
no -
detailed_source text - no 30
age_yrage in years integer min: 0; max: 120 no -
age_mthmonth part of age (0-11) for patients under 1 year old integer min: 0; max: 11 no -
sexsex of patient/carrier text
male
female
no -
PFGEPFGE type text - no 12
AFLPAFLP type text - no 12
amikacin_mic_signindicate if MIC result is greater than, less than, or equal the set value text
<
>
=
no -
amikacin_micMIC in mg/l float - no -
amikacin_SIRS: 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_signindicate if MIC result is greater than, less than, or equal the set value text
<
>
=
no -
gentamicin_micMIC in mg/l float - no -
gentamicin_SIRS: 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_signindicate if MIC result is greater than, less than, or equal the set value text
<
>
=
no -
cefotaxime_micMIC in mg/l float - no -
cefotaxime_SIRS: 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_signindicate if MIC result is greater than, less than, or equal the set value text
<
>
=
no -
cefepime_micMIC in mg/l float - no -
cefepime_SIRS: 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_signindicate if MIC result is greater than, less than, or equal the set value text
<
>
=
no -
levofloxacin_micMIC in mg/l float - no -
levofloxacin_SIRS: 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_signindicate if MIC result is greater than, less than, or equal the set value text
<
>
=
no -
tetracycline_micMIC in mg/l float - no -
tetracycline_SIRS: 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_signindicate if MIC result is greater than, less than, or equal the set value text
<
>
=
no -
imipenem_micMIC in mg/l float - no -
imipenem_SIRS: 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_signindicate if MIC result is greater than, less than, or equal the set value text
<
>
=
no -
meropenem_micMIC in mg/l float - no -
meropenem_SIRS: 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_signindicate if MIC result is greater than, less than, or equal the set value text
<
>
=
no -
colistin_micMIC in mg/l float - no -
colistin_SIRS: 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_profileresistance 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_accessionGenbank accession number text - no 30
bioproject_accessionENA/SRA bioproject accession number text (multiple) - no 20
biosample_accessionENA/SRA biosample accession number text (multiple) - no 20
ENA_run_accessionENA/SRA accession number to access short read data. This should start either ERR, SRR, or DRR. text - no 15
commentsany other comments text - no 1000
sendersender unique name, link to users integer Click for list of sender ids yes 4
curatorcurator who entered data,link to users integer Click for list of curator ids yes 4
date_entereddate first entered date - yes 10
datestampdate last modified date - yes 10

Secondary metadata

Biofilm

field namecommentsdata typeallowed valuesrequiredmaximum length (characters)
OD_neg_controlmean OD for negative control (no cells). float min: -10; max: 10 no -
OD_neg_control_SDstandard deviation of negative control replicates float min: 0; max: 5 no -
OD_samplemean OD for sample. float min: -10; max: 10 no -
biofilm_productionbiofilm production using the classification described by Stepanović et al. (2007) text
none
low
medium
high
no -

Efflux pump overexpression

field namecommentsdata typeallowed valuesrequiredmaximum 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 -