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