Streptococcus pneumoniae

Streptococcus pneumoniae (pneumococcus) is a leading cause of community-acquired pneumonia, meningitis, otitis media, and invasive pneumococcal disease (IPD), with the highest burden in young children and older adults. Pneumococcal conjugate vaccines (PCV7, PCV10, PCV13, PCV15, PCV20) have reshaped the global serotype landscape, driving declines in vaccine-type disease while enabling replacement by non-vaccine serotypes. Resistance to penicillin, macrolides, tetracyclines, and trimethoprim–sulfamethoxazole remains common, and multidrug-resistant lineages are monitored closely.

The AMRnet S. pneumoniae view summarises genomic surveillance of serotype distribution, Global Pneumococcal Sequence Cluster (GPSC) lineages, and AMR determinants across geography and time.

Note

The S. pneumoniae module is in preparation. This page will be expanded with variable definitions, vaccine-coverage annotations, and the full list of source studies once the first data release is available.

Variable definitions

  • Serotype: capsular polysaccharide type predicted in silico (e.g., by seroBA or PneumoCaT), following the standard nomenclature of >100 known serotypes.

  • Genotypes (MLST): 7-locus sequence types from the S. pneumoniae MLST scheme hosted by PubMLST.

  • GPSC (Global Pneumococcal Sequence Cluster): whole-genome-based lineage definitions from the Global Pneumococcal Sequencing Project, providing a stable global framework for lineage tracking.

  • Vaccine coverage: annotation of whether a serotype is included in PCV7, PCV10, PCV13, PCV15, or PCV20 formulations.

  • AMR determinants: penicillin-binding protein (pbp1a, pbp2b, pbp2x) mosaic alleles and substitutions underlying β-lactam resistance; macrolide resistance (ermB, mefA/E); tetracycline resistance (tetM, tetO); fluoroquinolone resistance (gyrA, parC mutations); trimethoprim (folA I100L) and sulfamethoxazole (folP insertions) resistance; chloramphenicol (cat) resistance.

Abbreviations

  • IPD: invasive pneumococcal disease.

  • PCV7 / PCV10 / PCV13 / PCV15 / PCV20: pneumococcal conjugate vaccines and their serotype compositions.

  • PNSP: penicillin non-susceptible pneumococcus (MIC ≥ 0.12 mg/L by CLSI meningitis breakpoints).

  • MDR: resistant to three or more antimicrobial classes.

  • GPSC: Global Pneumococcal Sequence Cluster.

Data source

Source studies and BioProject accessions will be listed here once the S. pneumoniae data release is published. The Global Pneumococcal Sequencing Project (GPS) is expected to be the primary upstream source.