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Table 8 Comparisons of STs as identified by INH (MLST-CGE) and 1928

From: Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis

ST

No. of isolates determined by

Discordant across methods [n (%)]

Both INH and 1928

INH only

1928 only

1

5

0

0

0 (0)

5

12

0

1

1 (7.7)

7

2

0

0

0 (0)

8

12

0

0

0 (0)

12

6

0

0

0 (0)

15

30

0

0

0 (0)

20

2

0

0

0 (0)

22

8

0

0

0 (0)

25

3

0

0

0 (0)

26

3

0

0

0 (0)

30

39

0

0

0 (0)

34

2

0

0

0 (0)

39

1

0

1

1 (50.0)

45

51

0

0

0 (0)

46

4

0

0

0 (0)

50

8

0

1

1 (11.1)

97

3

0

0

0 (0)

146

3

0

0

0 (0)

291

2

0

0

0 (0)

375

5

0

0

0 (0)

425

3

0

0

0 (0)

1181

2

0

0

0 (0)

1633

2

0

0

0 (0)

1693

3

0

0

0 (0)

6674

0

2

0a

2 (100.0)

Other STsb

20

0

0

0 (0)

Total (% of 236)c

231 (97.9)

2 (0.8)

3 (1.3)

5 (2.1)

  1. CGE: Center for Genomic Epidemiology, INH: in-house pipeline, MLST: multi-locus sequencing typing, and ST: sequence type
  2. a1928 identified same alleles as INH but assigned no ST
  3. bOther STs include one isolate each of ST6, ST27, ST59, ST101, ST109, ST121, ST123, ST130, ST182, ST188, ST398, ST942, ST1021, ST1035, ST1150, ST1218, ST1675, ST2975, ST4554, and ST6363
  4. cFor 19 isolates, the ST profile could not be determined either by INH (MLST-CGE) or 1928. These isolates are not included in the table