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Description of database fields

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field namecommentsdata typeallowed valuesrequired
idprimary keyint - yes
isolateisolate nametext - yes
countryCountry where strain was isolatedtext Afghanistan
Albania
Algeria
Andorra
Angola
Antigua & Barbuda
Argentina
Armenia
Australia
Austria
Azerbaijan
Bahamas
Bahrain
Bangladesh
Barbados
Belarus
Belgium
Belize
Benin
Bhutan
Bolivia
Bosnia & Herzegovina
Botswana
Brazil
Brunei
Bulgaria
Burkina Faso
Burma
Burundi
Cambodia
Cameroon
Canada
Cape Verde
Central African Republic
Chad
Chile
China
Colombia
Comoros
Congo
Costa Rica
Croatia
Cuba
Cyprus
Czech Republic
Denmark
Djibouti
Dominica
Dominican Republic
East Timor
Ecuador
Egypt
El Salvador
Equatorial Guinea
Eritrea
Estonia
Ethiopia
Fiji
Finland
France
Gabon
Georgia
Germany
Ghana
Greece
Grenada
Guadeloupe
Guatemala
Guinea
Guinea Bissau
Guyana
Haiti
Honduras
Hungary
Iceland
India
Indonesia
Iran
Iraq
Ireland
Isle of Man
Israel
Italy
Ivory Coast
Jamaica
Japan
Jordan
Kazakhstan
Kenya
Kiribati
Kuwait
Kyrgyzstan
Laos
Latvia
Lebanon
Lesotho
Liberia
Libya
Liechtenstein
Lithuania
Luxembourg
Macedonia
Madagascar
Malawi
Malaysia
Maldives
Mali
Malta
Marshall Islands
Martinique
Mauritania
Mauritius
Mayotte
Mexico
Micronesia
Moldavia
Moldova
Monaco
Mongolia
Montenegro
Morocco
Mozambique
Namibia
Nauru
Nepal
New Caledonia
New Zealand
Nicaragua
Niger
Nigeria
North Korea
Norway
Oman
Pakistan
Palau
Palestinian territories
Panama
Papua New Guinea
Paraguay
Peru
Philippines
Poland
Portugal
Qatar
Reunion
Romania
Russia
Rwanda
Samoa
San Marino
Saudi Arabia
Senegal
Serbia
Seychelles
Sierra Leone
Singapore
Slovakia
Slovenia
Solomon Islands
Somalia
South Africa
South Korea
Spain
Sri Lanka
St. Kitts & Nevis
St. Lucia
Sudan
Suriname
Swaziland
Sweden
Switzerland
Syria
Tahiti
Taiwan
Tajikistan
Tanzania
Thailand
The Gambia
The Netherlands
Togo
Tonga
Trinidad & Tobago
Tunisia
Turkey
Turkmenistan
Tuvalu
UK
USA
Uganda
Ukraine
United Arab Emirates
Uruguay
Uzbekistan
Vanuatu
Vatican City
Venezuela
Vietnam
Yemen
Zambia
Zimbabwe
Unknown
yes
regionRegion/city etc inside countrytext - no
yearyear of isolationint min: 1900; max: 2017 no
age_yrage in yearsint min: 0; max: 120 no
age_categorytext infant
child
adult, young
adult
adult, elderly
adult, NOS
child, NOS
no
gendersex of patient/carriertext male
female
other
no
primary_diseaseadd other diseases to commentstext abscess
APSGN
ARF
arthritis
bacteremia
carriage
cellulitis
erysipelas
impetigo
invasive, NOS
meningitis
necrotizing fasciitis
osteomyelitis
otitis media
pharyngitis and/or tonsillitis
pneumonia
puerperal fever
scarlet fever
sepsis
skin/soft tissue infection, NOS
streptococcal toxic shock syndrome
wound, NOS
no
tissue_sourcebiological source of sampletext abscess
blood
CSF
impetigo lesion
lung
middle ear fluid
necropsy
nonsterile site, NOS
purulent exudate, NOS
skin, NOS
skin/soft tissue, NOS
sputum
sterile site, NOS
synovial fluid
URT
wound
no
disease_other_1biological source of sampletext abscess
arthritis
bacteremia
cellulitis
endocarditis
erysipelas
impetigo
meningitis
multiorgan failure
necrotizing fasciitis
osteomyelitis
pharyngitis and/or tonsillitis
pneumonia
puerperal fever
scarlet fever
sepsis
septic arthritis
septic shock
skin/soft tissue infection
wound, NOS
no
disease_other_2text - no
epidemiology_1text community
hospital
institution, other
no
epidemiology_2text outbreak
surveillance
no
emm_typetext - no
emm_subtypeenter in emm##.# formattext - no
emm_pattern_predictedtext A-C
D
E
REA
no
emm_cluster_predictedtext - no
T_typetext - no
FCT_typeenter in FCT-# formattext - no
macrolide_phenotype_1text S
R
R (assumed)
I
no
macrolide_phenotype_2text S
R
R (assumed)
I
cMLS
iMLS
M
MLS
no
macrolide_resistance_genotypetext erm
ermA
ermA, ermB
ermA, mefA
ermB
ermB, mefA
mef/mefA
no
erythromycin_MICtext - no
clindamycin_MICtext - no
tetracycline_resistance_phenotypetext S
R
R (assumed)
I
no
tetracycline_resistance_genotypetext tetM
tetO
tetT
no
tetracycline_MICtext - no
ENA_accessionENA SRA accession number to access short read datatext - no
commentsany other commentstext - no
original_strain_sourcetext - 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