Laboratory Characterization

Identification and serogrouping by conventional microbiological methods; confirmation of serogroup and species identification using real-time polymerase chain reaction (PCR)

Whole genome sequencing (WGS)¹ and pulsed field gel electrophoresis as part of special projects

Identification and serotyping (a-f) by conventional microbiological methods

Confirmation of species identification using real-time PCR; confirmation of serotype using real-time PCR as needed

WGS, pulsed field gel electrophoresis as part of special projects

WGS based for all isolates which includes:

1. emm (including subtype level) and T typing
2. Resistance mechanisms and all minimum inhibitory concentrations (MICs) on panel (and others)
3. Multilocus sequence type (MLST², 7 locus genotype useful for identifying major lineages and species verification)
4. Presence/absence of key surface proteins, exotoxins, virulence markers
5. Strategic subset targeted for conventional MIC determination

From select surveillance areas, WGS based for all isolates, which includes:

1. Capsular serotype
2. Resistance mechanisms and all MICs on panel (and others)
3. MLST
4. Strategic subset targeted for conventional MIC determination
5. Penicillin-binding proteins (PBP) type; penicillin-binding protein transpeptidase sequence (PBP type) database for detecting first step beta lactam resistance
6. Presence or absence of various surface proteins, including certain vaccine candidates

Antimicrobial susceptibility testing of all isolates

Serotyping of all isolates

Progressing toward clonal typing of all isolates using MLST

Characterization of resistance mechanisms of selected strains based on phenotypic resistance patterns