TABLE 1

Summary statistics of sequencing results, turnaround times, and reasons for sequencing failures during interval I

OrganismNo. of isolatesMean % of successfully extracted cgMLST targetsNo. (%) of isolates that required repeated sequencingMean (SD)a turnaround time (in days) for all samples without repeatersMean (SD) turnaround time (in days) for all samples, including failed samplesReasons for sequencing failure (no. of samples)b
S. aureus41298.538 (9.2)4.4 (1.6)5.0 (2.6)Low coverage (22), sequencing run failure (12), primary base-calling failure (4)
E. coli10299.211 (10.8)4.4 (1.4)5.3 (3.0)Low coverage (10), sequencing run failure (1)
E. faecium7997.220 (25.3)4.1 (1.5)6.2 (4.6)Low coverage (14), mixed culture (5), sequencing run failure (1)
P. aeruginosa5297.815 (28.8)4.8 (1.8)6.8 (4.0)Low coverage (10), sequencing run failure (5)
Total64598.484 (13.0)4.4 (1.5)5.3 (3.2)Low coverage (56), sequencing run failure (19), mixed culture (5), primary base-calling failure (4)
  • a SD, standard deviation.

  • b The low coverage led to a failure to achieve at least 95% successfully extracted cgMLST targets.