PubMLST Database home Contents
Log in

Description of database fields

Order columns by clicking their headings. Reset default order.

field namecommentsdata typeallowed valuesrequired
idprimary keyint - yes
isolateisolate nametext - yes
countrycountry where strain was isolatedtext 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
Northern Mariana Islands
North Korea
North Macedonia
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
Ukraine
United Arab Emirates
Uruguay
USA
US Minor Outlying Islands
US Virgin Islands
Uzbekistan
Vanuatu
Venezuela
Vietnam
Wallis and Futuna Islands
Western Sahara
Yemen
Zambia
Zimbabwe
Unknown
yes
regionRegion/city etc inside countrytext - no
yearyear of isolationint min: 1900; max: 2019 no
age_yrage in years if age over 12 monthsint - no
age_monthsage in months if age less than 1 yearint min: 0; max: 11 no
age_daysday part of age 0-120int min: 0; max: 120 no
sextext male
female
no
disease1please put up to 3 diagnosestext carrier
bacteraemia
cellulitis
meningitis
osteomyelitis
endophthalmitis
endocarditis
lower respiratory tract infection
native joint infection
prosthetic joint infection
chorioamnionitis
endometritis
surgical site infection
urinary tract infection
no focus
other
no
disease2please put up to 3 diagnosestext carrier
bacteraemia
cellulitis
meningitis
osteomyelitis
endophthalmitis
endocarditis
lower respiratory tract infection
native joint infection
prosthetic joint infection
chorioamnionitis
endometritis
surgical site infection
urinary tract infection
no focus
other
no
disease3please put up to 3 diagnosestext carrier
bacteraemia
cellulitis
meningitis
osteomyelitis
endophthalmitis
endocarditis
lower respiratory tract infection
native joint infection
prosthetic joint infection
chorioamnionitis
endometritis
surgical site infection
urinary tract infection
no focus
other
no
sourceplease put detail in comments fieldtext blood
cerebrospinal fluid
rectovaginal swab
vaginal swab
joint fluid
bone biopsy
swab of bone or joint
ear swab
umbilical swab
throat swab
bronchoalveolar lavage
other swab
sputum
urine
other human
cattle
cows milk
other animal
no
epidemiologytext hospital acquired
community acquired
no
speciesSpecies name in multiple species databases where permittedtext Streptococcus agalactiae
yes
capsular_serotypeserotypetext Ia
Ib
II
III
IV
V
VI
VII
VIII
NT
no
capsular_genotypeserotypetext Ia
Ib
II
III
IV
V
VI
VII
VIII
IX
no
erythromycin_disc_testingDisc testingtext susceptible
intermediate
resistant
no
erythromycin_micMIC in microgram/mltext - no
tetracycline_disc_testingDisc testingtext susceptible
intermediate
resistant
no
tetracycline_micMIC in microgram/mltext - no
clindamycin_disc_testingDisc testingtext susceptible
intermediate
resistant
no
clindamycin_micMIC in microgram/mltext - no
penicillin_disc_testingDisc testingtext susceptible
intermediate
resistant
no
penicillin_micMIC in microgram/mltext - no
commentsany other commentstext - no
ENA_accessionENA SRA accession number to access short read datatext - no
private_projectLeave this blank unless you know what you are doing - entering anything here will hide your data in the public interfacetext - no
sendersender unique name, link to usersint Click for list of sender ids yes
curatorcurator who entered data,link to usersint Click for list of curator ids yes
date_entereddate first entereddate - yes
datestampdate last modifieddate - yes