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Table 1 List of CRhvKp clusters. In some assemblies carbapenemase genes (CR), iuc and iro (hypervirulence; HV) loci were located on the same assembly contig or chromosome. The underlying data is available in Additional file 2: Data S2, S3 and S4

From: Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains

Cluster

Is robust*

N

Main STs (N)

Total STs

Species

Collection dates

Main replicons**

Main countries

Main siderophores

Main carbapenemases

Contig with CR and replicon

Contig with HV and replicon

Contig with CR and HV

A

Yes (0%)

560

ST11 (499), ST23 (35), ST268 (13)

11

K. pneumoniae, K. quasipneumoniae

2012–2021

ColRNAI (943), repB (555), IncFII(pHN7A8) (501), IncHI1B(pNDM-MAR) (489), IncR (486)

China (517), Russia (12), Missing (8), Singapore (6)

iuc 1 (554), iro 1 (90), iro 1 (incomplete) (truncated) (22), iro 1 (incomplete) (55)

OXA-48 (16), KPC-2 (516), IMP-4 (8)

74

341

2

B

No (99%)

83

ST11 (74)

5

K. pneumoniae

2012–2021

ColRNAI (139), IncFII(pHN7A8) (74), IncR (60)

China (81)

iuc 1 (78)

KPC-2 (79)

20

11

0

C

Yes (0%)

82

ST147 (32), ST395 (24), ST383 (10)

15

K. aerogenes, K. pneumoniae

2012–2020

Col(pHAD28) (91), IncHI1B(pNDM-MAR) (80), IncFIB(pNDM-Mar)(79)

Russia (32), China (16), Egypt (9), Germany (8)

iuc 1 (76)

OXA-48 (51), NDM-1 (23)

16

11

3

D

Yes (0%)

61

ST231 (60)

2

K. pneumoniae

2013–2019

Col440I (73), IncFIB(pQil) (61), IncFII(K) (61), IncFIA (60), IncFII(pAMA1167-NDM-5) (60), ColKP3 (59), Col(pHAD28) (55)

Thailand (24), India (17), Pakistan (8)

iuc 5 (60)

OXA-232 (59)

60

8

0

E

No (88%)

50

ST86 (16), ST65 (14)

10

K. pneumoniae

2013–2019

repB (50), IncHI1B(pNDM-MAR) (49)

China (16), Singapore (14), Thailand (13)

iuc 1 (44), iro 1 (40)

KPC-2 (32), OXA-232 (13)

19

32

0

F

Yes (0%)

34

ST290 (7), ST15 (6)

12

K. pneumoniae

2012–2020

IncFII(K) (35), IncFIB(K) (32)

China (23), Russia (7)

iuc 3 (truncated) (16), iuc 1 (14)

NDM-5 (8), NDM-1 (14), KPC-2 (8)

8

19

2

G

Yes (0%)

32

ST15 (26)

6

K. pneumoniae

2015–2020

repB (31), ColRNAI (31), IncHI1B(pNDM-MAR) (30), IncFIB(pKPHS1) (28), IncFII(K) (28), ColKP3 (28), Col(pHAD28) (28), Col440I (25), IncFIB(pQil) (21)

China (25)

iuc 1 (32)

OXA-232 (27)

32

7

0

H

Yes (0%)

31

ST512 (9)

6

K. aerogenes, K. pneumoniae

2008–2021

IncFII(K) (23), ColRNAI (22), IncFIB(pQil) (20)

Italy (11), USA (6)

iuc 1 (16), iro unknown (13)

KPC-3 (15)

18

2

0

I

Yes (0%)

16

ST395 (16)

1

K. pneumoniae

2015–2017

IncHI1B(pNDM-MAR) (16), IncFIB(K) (16), Col440II (16), Col(pHAD28) (16), IncFII(K) (16), IncFIB(pNDM-Mar) (15)

Italy (16)

iuc 1 (15)

KPC-3 (14)

2

5

0

Unassigned

Yes (0%)

79

ST101 (8), ST2096 (6), ST218 (6)

25

K. aerogenes, K. variicola subsp. variicola, K. pneumoniae

2011–2021

Col(pHAD28) (45), IncFII(K) (40), ColRNAI (38), IncHI1B(pNDM-MAR) (30), IncFIB(pNDM-Mar) (28)

China (16), USA (11), Germany (8), Russia (7)

iuc 1 (38), iuc 5 (7), iro unknown (29), iro 1 (11)

KPC-3 (9), KPC-2(19), OXA-48 (13), OXA-232 (8), OXA-244 (6)

32

17

1

  1. HV hypervirulent Kp, CRKp carbapenemase-resistant Kp
  2. * Cluster is considered robust if <1% of -log10 (chi-squared p-value) are <20, see the “Methods” section for detail
  3. ** Different clusters with the same main replicons may have different variants