Skip to main content

Table 1 An example of the Global Pneumococcal Sequencing (GPS) project metadata

From: Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics

Categories Fields Example
ID Public name GPS_ZA_0001
Geographical location Country South Africa
Region Gauteng
City Johannesburg
Facility where collected Hospital A
Submitting institute NICD
Time Year 2010
Month Aug
Clinical data Gender F
Age (years) 0
Age (months) 1
Age (days) 0
Clinical manifestation Meningitis
Source Cerebrospinal fluid
HIV status Negative
Other underlying conditions No
Microbiological data Phenotypic serotype method Quellung
Phenotypic serotype 19A
Multilocus sequence type ST81
Antimicrobial susceptibilitya Method Broth dilution
Antimicrobial (e.g. penicillin) 2 mg/L
Selection Random selection Y
  1. aAntimicrobial susceptibility profile of 17 antimicrobials including penicillin, amoxicillin, cefotaxime, ceftriaxone, cefuroxime, meropenem, chloramphenicol, cotrimoxazole, erythromycin, clindamycin, linezolid, levofloxacin, ciprofloxacin, synercid, tetracycline, rifampin and vancomycin