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Laboratory Characterization

Download ABCs Isolate Characterization [1 pages]

Pathogens Tests
Neisseria meningitidis Whole genome sequencing (WGS)1 for isolate species confirmation, capsular genotyping, and molecular typing. Conventional microbiological methods, real-time polymerase chain reaction (rt-PCR), and slide agglutination may be performed as needed to resolve any discrepancies.
Haemophilus influenzae rt-PCR for confirmation of isolate species and capsular genogrouping. Conventional microbiological methods, slide agglutination, and whole genome sequencing may be performed as needed to resolve any discrepancies. Whole genome sequencing for molecular typing of isolates as part of special projects or requests.
group A Streptococcus WGS based for all isolates which includes deduction of:
  1. emm types and T types
  2. Resistance mechanisms and all minimum inhibitory concentrations (MICs) on panel (and others). PBP2x amino acid sequence types to monitor for possible emergence of beta lactam nonsusceptibility.
  3. Multilocus sequence type (MLST)2
  4. Presence/absence of key surface proteins, exotoxins, virulence markers
  5. Strategic subset targeted for conventional MIC determination
  6. Phylogenetic clustering within clonal types to detect potential ongoing disease clusters.
group B Streptococcus From select surveillance areas, WGS based for all isolates, which includes deduction of:
  1. Capsular serotype
  2. MIC predictions, including PBP2x typing to detect decreased beta lactam susceptibility
  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
  7. Conventional MIC testing of selected isolates
Streptococcus pneumoniae WGS based characterization of all isolates, which includes deduction of:
  1. Capsular serotype
  2. MIC predictions, including PBP typing system for determining beta lactam antibiotic MICs
  3. MLST
  4. Pilus types
  5. Conventional MIC testing of selected strains

1 WGS: Whole genome sequencing – a process that determines the complete DNA sequence of an organism’s genome at one time. Used as part of CDC’s AMD initiative: www.cdc.gov/amd/project-summaries/pneumococcal-vaccines.html

2 Multilocus sequence type- 7 locus genotype useful for both identifying major lineages and for species verification

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