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Description of database fields

Provenance/primary metadata

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field namecommentsdata typeallowed valuesrequiredmaximum length (characters)
idprimary key integer - yes 6
isolateisolate name text - yes 30
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 (multiple) - no 30
yearyear of isolation integer min: 1900; max: 2020 no 4
date_sampleddate sample was taken date max: 2020-08-10 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: 2020-08-10 no 10
non_cultureresult comes from non-culture diagnosis bool - no -
epidemiological_yearepidemiological year for study in format mm/yyyy-mm/yyyy text - no 15
age_yrage in years integer min: 0; max: 120 no -
age_rangeage range - this will be populated automatically if you enter a value for age_yr text
<1
1-4
5-14
15-24
25-44
45-64
65+
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 -
diseaseplease put other diseases in comments field text
carrier
meningitis
septicaemia
meningitis and septicaemia
uncomplicated gonorrhoea
disseminated gonococcal infection
invasive (unspecified/other)
other
no -
sourcebiological source of sample - please put other sources in comments field text
blood
CSF
joint fluid
rectal swab
sputum
throat swab
urethral swab
other
no -
epidemiology text
carrier
healthy contact
sporadic case
endemic
epidemic
MSM
MSW
pandemic
no -
species text
Neisseria meningitidis
Neisseria lactamica
Neisseria gonorrhoeae
Neisseria animalis
Neisseria animaloris
Neisseria arctica
Neisseria bacilliformis
Neisseria bergeri
Neisseria canis
Neisseria cinerea
Neisseria dentiae
Neisseria dentrificans
Neisseria dumasiana
Neisseria elongata
Neisseria elongata subsp. elongata
Neisseria elongata subsp. glycolytica
Neisseria elongata subsp. nitroreducens
Neisseria flava
Neisseria flavescens
Neisseria iguanae
Neisseria macacae
Neisseria mucosa
Neisseria mucosa subsp. heidelbergensis
Neisseria musculi
Neisseria oralis
Neisseria perflava
Neisseria polysaccharea
Neisseria shayeganii
Neisseria sicca
Neisseria skkuensis
Neisseria subflava
Neisseria tadorna
Neisseria wadsworthii
Neisseria weaveri
Neisseria zoodegmatis
Neisseria sp.
Non-Neisseria sp.
yes -
serogroupgroup determined by serological means. If you select 'other' please provide further details in the comments field. Values in this field from legacy data may have been determined by genotypic means, but for new data this should only represent values determined by serology. text
A
B
C
E
W
W/Y
X
Y
Z
H
J
K
L
W
NG
other
no -
genogroupgroup determined by genotypic means text
A
B
C
E
W
W/Y
X
Y
Z
H
J
K
L
cnl
NG
no -
genogroup_notesdetails about genogroup prediction text - no 512
capsule_groupcapsular group value is determined automatically from the contents of the serogroup and genogroup fields. This cannot be updated manually text - no -
MLEE_designation text
A4 Cluster
ET-37 Complex
ET-5 Complex
Lineage 3
Lineage IV
Subgroup I
Subgroup II
Subgroup III
Subgroup IV-I
Subgroup IV-II
Subgroup V
Subgroup VI
Subgroup VII
Subgroup VIII
Subgroup IX
Subgroup X
other
no -
serotype text - no 15
sero_subtype text - no 15
ET_no text - no 10
penicillinMIC in mg/l text - no 20
penicillin_rangeMIC value range text
<=0.06 (susceptible)
>0.06 - 1 (intermediate)
>1 (resistant)
no -
amoxicillinMIC in mg/l text - no 20
sulphonamideMIC in mg/l text - no 20
ceftriaxoneMIC in mg/l text - no 20
ceftriaxone_rangeMIC value range text
<=0.06 (susceptible)
>0.06 (not susceptible)
no -
chloramphenicolMIC in mg/l text - no 20
chloramphenicol_rangeMIC value range text
<=2 (susceptible)
>2 - <8 (intermediate)
>=8 (resistant)
no -
cefotaximeMIC in mg/l text - no 20
cefotaxime_rangeMIC value range text
<=0.06 (susceptible)
>0.06 (not susceptible)
no -
rifampicinMIC in mg/l text - no 20
rifampicin_rangeMIC value range text
<=1 (susceptible)
>1 (resistant)
no -
ciprofloxacinMIC in mg/l text - no 20
ciprofloxacin_rangeMIC value range text
<=0.03 (susceptible)
>0.03 - <0.12 (intermediate)
>=0.12 (resistant)
no -
tetracyclineMIC in mg/l text - no 20
cefiximeMIC in mg/l text - no 20
azithromycinMIC in mg/l text - no 20
spectinomycinMIC in mg/l text - no 20
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
private_projectLeave this blank unless you know what you are doing - entering anything here will hide your data in the public interface text - no 30
commentsany other comments text (multiple) - no 500
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

Risk factors

field namecommentsdata typeallowed valuesrequiredmaximum length (characters)
UK_school_yearSchool year that sample subject belonged to (UK) text
12
13
other
not in full-time education
no -
persons_in_householdNumber of people in the subject's household integer min: 1; max: 10 no -
antibiotic_useWhether or not the subject recently took antibiotics text
yes [currently]
stopped [last month]
stopped [last week]
no
no -
current_URTIcurrent cold or sore throat boolean - no -
cigarettes_per_daycigarettes smoked per day text
0
1-5
6-10
11-20
21+
no -
ecigarettes_per_weekNumber of e-cigarettes smoked per week text
0
1-2
3-6
7+
no -
waterpipes_per_monthNumber of water pipes (shisha) smoked per month text
0
1
2
3-4
5+
no -
passive_smokingexposure to passive smoking (inside or outside) text
yes [undefined]
no
yes [inside]
yes [outside]
no -
pubs_clubs_per_weekattendance at pubs or clubs per week text
0
1
2-3
4-5
6-7
no -
persons_kissed_past_weeknumber of persons kissed in the past week text
0
1
2-3
4+
no -
regular_partnerregular girlfriend or boyfriend boolean - no -
regular_partner_smokesregular girlfriend or boyfriend who smokes boolean - no -
ethnicity- text
white
asian
black
mixed
other
no -

Vaccines

field namecommentsdata typeallowed valuesrequiredmaximum length (characters)
Bexsero_reactivityPrediction of Bexsero coverage. This field is automatically populated. text
exact match
cross-reactive
none
insufficient data
no -
Bexsero_notesExplanation of Bexsero_reactivity result. This field is automatically populated. text - no -
Trumenba_reactivityPrediction of Trumenba coverage. This field is automatically populated. text
exact match
cross-reactive
none
insufficient data
no -
Trumenba_notesExplanation of Trumenba_reactivity result. This field is automatically populated. text - no -