Table 3 Diagnostic methods and typing results of proven outbreaks

1

n/a

MALDI-TOF, WGS

WGS

20

20

n/a

Isolate difference 4–28 SNPs

2

KPC CHROMagar (rectal swabs n = 6) or n/a (n = 3)

MALDI-TOF, 16 S

WGS

9

8

n/a

3

n/a

MALDI-TOF

RAPD-PCR

20

Cluster 1/2/3: 3

Cluster 4/5/6: 2

> 85% similarity

4

n/a

VITEK-2, 16 S†

Rep-PCR

9

Cluster 1: 3

Cluster 2: 2

Cluster 3: 2

n/a

6

n/a

MALDI-TOF, 16 S

PFGE

40

Cluster V: 25

Cluster VII: 6

Cluster I/III/IV: 2

n/a

Isolates within a cluster were > 88% similar

7

n/a

WGS

PFGE + WGS

11

10

< 60 SNPs distance by WGS

8

n/a

MALDI-TOF, WGS†

WGS

69

66

Subcluster 1: 13

Subcluster 2: 6/69

Subcluster 3: 9/69

Subcluster 4: 3/69

Subcluster 5: 2/69

Subcluster 6: 26/69

n/a

9

n/a

MALDI-TOF, WGS

PFGE + WGS

26 (PFGE),

18 (WGS)

26 (PFGE),

18 (WGS)

> 80% (PFGE)

n/a (WGS)

10

n/a

MALDI-TOF, WGS

WGS

14

2

n/a

11

BA, 36 °C, 48 h

MALDI-TOF, 16 S, WGS†

Rep-PCR, WGS

3

3

n/a

Isolates were > 99% similar (Rep-PCR), or < 30 SNPs distance (WGS)

12

n/a

16 S, species specific PCR

PFGE

34

Cluster A: 8

Cluster H/I: 4

Cluster D: 3

Cluster F/G/J/K/M: 2

n/a

Isolates were > 85% similar

13

n/a

16 S

PFGE

66

Cluster 10: 20

Cluster 1: 16

Cluster 12: 7

Cluster 7: 6

Cluster 11: 3

Cluster 4/6: 2

> 85% similarity

14

n/a

MALDI-TOF, 16 S†

PFGE

17

2‡

n/a

Isolates were 93% similar