Description of database fields

Order columns by clicking their headings. Reset default order.

field namecommentsdata typeallowed valuesrequiredmaximum length (characters)
idprimary key integer - yes 6
isolateisolate 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
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/city etc inside country text - no 30
yearyear of isolation integer min: 1900; max: 2020 no 4
date_sampleddate sample was taken date max: 2020-09-27 no 10
isoyear_sampledISO year (this may be different from the Gregorian year recorded in the year field) - value is determined automatically from the contents of the date_sampled field. This cannot be updated manually integer - no -
week_sampledweek of the year - value is determined automatically from the contents of the date_sampled field. This cannot be updated manually integer - no -
date_receiveddate received by laboratory (may be approximate) date max: 2020-09-27 no 10
non_cultureresult comes from non-culture diagnosis bool - no -
serotype text
a
b
c
d
e
f
non-b
NT
ND
yes -
serotype_by_serology text
a
b
c
d
e
f
non-b
NT
no -
serotype_by_PCR text
a
b
c
d
e
f
non-b
NT
no -
genotype text
a
b
c
d
e
f
no -
biotype text
I
II
III
IV
V
VI
VII
VIII
no -
ribotype integer min: 1; max: 100 no 3
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 -
sourcebiological source of sample - add source details to comments if source is 'other' text
blood
brain tissue
bronchoalveolar lavage
CSF
ear
eye
joint aspirate
nasal swab
sputum
throat swab
other
no -
diseaseadd other diseases to comments text
bacteraemia
bronchitis
carriage
chronic obstructive pulmonary disease
invasive (unspecified/other)
meningitis
meningitis and septicaemia
otitis media
pneumonia
other
no -
epidemiology text
cluster case
commununity acquired
sporadic case
surveillance
no -
MLEE_lineage text - no 10
MLEE_ET text - no 10
beta_lactamase text - no 12
AMX_MICamoxicillin MIC text - no 10
AMX_SIRamoxicillin interpretation text
S
I
R
no -
AMC_MICamoxicillin-clavulanic acid MIC text - no 10
AMC_SIRamoxicillin-clavulanic acid interpretation text
S
I
R
no -
CTX_MICcefotaxime MIC text - no 10
CTX_SIRcefotaxime interpretation text
S
I
R
no -
CRO_MICceftriaxone MIC text - no 10
CRO_SIRceftriaxone interpretation text
S
I
R
no -
ENA_accessionENA SRA accession number to access short read data text - no 30
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