Table 4 Core genome sequence clusters (cgSCs), multi-locus sequence types (STs) and serotypes of NSW IPD isolates in pre- and post-vaccine years.

From: Genome-wide analysis of Streptococcus pneumoniae serogroup 19 in the decade after the introduction of pneumococcal conjugate vaccines in Australia

cgSC (cases)

ST (cases)

Serotypes 2004

Serotypes 2008

Serotypes 2014

19F (n = 32)

19A (n = 8)

19F (n = 4)

19A (n = 56)

19F (n = 7)

19A (n = 16)

cgSC1 (6)1

81 (2)

 

1

 

1

  

2417 (2)

   

2

  

242 (1)

1

     

cgSC2 (12)

66 (13)

8

2

2 (VF n = 2)

1

  

cgSC3 (12)

1201 (9)

1

1

 

6

 

1 (VF)

9 (1)

1

     

Newa (2)

2

     

cgSC4 (3)

309 (3)

3

     

cgSC5 (9)

654 (5)

1

   

4 (VF n = 3)

 

3616 (1)

    

1

 

251 (1)

    

1

 

476 (1)

 

1

    

482 (1)

1

     

cgSC6 (1)

695 (1)

     

1(VF)

cgSC7 (31)

199 (15)

2

2

 

9

 

2 (VF n = 1)

1756 (2)

 

1

 

1

  

876 (5)

 

1

 

4

  

416 (4)

   

3

 

1 (VF)

649 (2)

   

2

  

667(1)

     

1

419(1)

     

1

3017(1)

   

1

  

cgSC8 (16)

63(17)

   

15

 

2

cgSC9 (14)

2345 (7)

   

5

 

2 (VF n = 2)

277 (1)

   

1

  

172 (1)

   

1

  

339 (1)

1

     

Newb (2)

   

1

 

1

cgSC10 (3)

162 (3)

3

     

cgSC11 (18)

320 (13)

6

 

1

3

 

3 (VF n = 2)

271 (1)

    

1

 

236 (1)

1

     

352 (1)

1

     

1451 (1)

     

1 (VF)

Undeterminedc (1)

  

1(VF n = 1)

   
  1. Notes:
  2. aContains ATCC Streptococcus pneumoniae strain 49619, isolated in 1992.
  3. bNew - allelic profile not previously recognized or designated as a ST (2 isolates in cgSC3, and 2 isolates in cgSC9).
  4. cUndetermined - STs could not be generated for one isolate because of housekeeping gene deletion in ddl (1 isolate, cgSC11).
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