Volume 29, Number 8—August 2023
Research
Genome-Based Epidemiologic Analysis of VIM/IMP Carbapenemase-Producing Enterobacter spp., Poland
Radosław Izdebski
, Marta Biedrzycka, Paweł Urbanowicz, Dorota Żabicka, and Marek Gniadkowski
, Marta Biedrzycka, Paweł Urbanowicz, Dorota Żabicka, and Marek Gniadkowski
Table
Clonal diversity of Enterobacter spp. with blaVIM or blaIMP genes, integrons, and SNP scores within individual genotypes, Poland, 2006–2019*
| Species/subspecies and clonal status† | ST | blaVIM/IMP gene | Integron‡ | SNPs within the ST |
|---|---|---|---|---|
| E. hormaechei subsp. steigerwaltii, n = 244 | ||||
| CG45, 13 SLVs | ST45, n = 9 | blaVIM–4, n = 7 | In238 | 0–8 |
| blaVIM-1, n = 2 | In916 | 592 | ||
| ST80–ST116–ST582, DLV of ST45 | ST116, n = 1 | blaVIM-1 | In2240 | – |
| ST62–ST421–ST1924 | ST62, n = 1 | blaVIM-1 | In916 | – |
| Singleton | ST89, n = 74 | blaVIM-1, n = 48 | In916 | 0–75 |
| blaVIM-20, n = 12 | In1444 | 0–49 | ||
| blaVIM-40, n = 7 | In1445 | 4–12 | ||
| blaVIM-4, n = 5 | In238, n = 3 | 162–347 | ||
| In1654, n = 1 | – | |||
| In2238, n = 1 | – | |||
| blaVIM-2, n = 2 | In1008 | 0 | ||
| CC90, 10 SLVs | ST90, n = 117 | blaVIM-4, n = 112 | In238, n = 107 | 0–1,692 |
| 238a, n = 5 | 36–61 | |||
| blaVIM-4; blaIMP-19, n = 2 | In238a; In2241 | 3 | ||
| blaVIM-1, n = 3 | In916, n = 1 | – | ||
| In2240, n = 1 | – | |||
| In237a, n = 1 | – | |||
| CC90, SLV of ST90 | ST91, n = 6 | blaVIM-1, n = 4 | In70, n = 3 | 4–73 |
| In916, n = 1 | – | |||
| blaVIM-2, n = 2 | In1008 | 7 | ||
| CC90, SLV of ST90 | ST1762, n = 2 | blaVIM-4, n = 2 | In238 | 70 |
| CG93, 11 SLVs | ST93, n = 3 | blaVIM-4, n = 2 | In238 | 60 |
| blaVIM-2, n = 1 | In1008 | – | ||
| CG106, 7 SLVs | ST106, n = 3 | blaVIM-1 | In916 | 0–1 |
| ST110–ST226–ST656 | ST110, n = 1 | blaVIM-1 | In916 | – |
| ST134–ST1250–ST1901 | ST134, n = 13 | blaVIM-4, n = 11 | In238, n = 9 | 6–24 |
| In238a, n = 2 | 4 | |||
| blaVIM-1, n = 2 | In916 | 0 | ||
| CG175, 3 SLVs | ST175, n = 3 | blaVIM-4, n = 2 | In238a | 109 |
| blaVIM-1, n = 1 | In916 | – | ||
| CG175, SLV of ST175 | ST1755, n = 1 | blaVIM-1 | In916 | – |
| CG184, 5 SLVs | ST184, n = 1 | blaVIM-1 | In916 | – |
| ST517–ST1443 | ST517, n = 1 | blaVIM-20 | In1444 | – |
| ST48–ST533–ST541 | ST533, n = 1 | blaVIM-1 | In916 | – |
| ST494–ST953 | ST953, n = 1 | blaVIM-4 | In238a | – |
| ST535–ST537–ST1758 |
ST1758, n = 6 |
blaVIM-1, n = 6 |
In916 |
1–101 |
| E. hormaechei subsp. xiangfangensis, n = 71 | ||||
| CG66, 11 SLVs | ST66, n = 18 | blaVIM-1 | In916 | 0–404 |
| CG66, SLV of ST66 | ST1754, n = 1 | blaVIM-1 | In916 | – |
| Singleton | ST92, n = 2 | blaVIM-4 | In238 | 1 |
| CG114, 17 SLVs | ST114, n = 3 | blaVIM-4, n = 2 | In238 | 557 |
| blaVIM-1, n = 1 | In916 | – | ||
| CC121, 5 SLVs | ST121, n = 36 | blaVIM-1, n = 24 | In916 | 0–47 |
| blaVIM-4, n = 10 | In238a, n = 6 | 2–10 | ||
| In238, n = 3 | 54–92 | |||
| In2016–like, n = 1 | – | |||
| blaVIM-2, n = 2 | In2242 | 64 | ||
| CC121, SLV of ST121 | ST1756, n = 3 | blaVIM-1 | In916 | 5–15 |
| ST407–ST511–ST552 | ST407, n = 4 | blaVIM-1, n = 2 | In916 | 23 |
| blaVIM-4, n = 2 | In238 | 87 | ||
| Singleton | ST527, n = 1 | blaVIM-1 | In611-like | – |
| ST1348–ST1757 |
ST1757, n = 3 |
blaVIM-1 |
In916 |
5–14 |
| E. hormaechei subsp. hoffmannii, n = 35 | ||||
| CC78, 18 SLVs | ST78, n = 4 | blaIMP-19, n = 2 | In2241 | 41 |
| blaVIM-1, n = 1 | In110 | – | ||
| blaVIM-4, n = 1 | In238 | – | ||
| ST97–ST754–ST761 | ST97, n = 1 | blaVIM-1 | In916 | – |
| ST102–ST343–ST1004 | ST102, n = 2 | blaVIM-1, n = 1 | In916 | – |
| blaVIM-4, n = 1 | In238a | – | ||
| ST104–ST345–ST1018 | ST104, n = 7 | blaVIM-1 | In916 | 3–334 |
| CG145, 5 SLVs; SLV of ST145 | ST118, n = 1 | blaVIM-1 | In916 | – |
| CG145, 12 SLVs; SLV of ST118, ST316, ST381 | ST145, n = 1 | blaVIM-4 | In238 | – |
| CG145, SLV of ST145 | ST316, n = 4 | blaVIM-4, n = 3 | In238 | 3–72 |
| blaVIM-1, n = 1 | In916 | – | ||
| CG145, SLV of ST145 | ST381, n = 1 | blaVIM-1 | In916 | – |
| ST128–ST161–ST135 | ST135, n = 1 | blaVIM-4 | In238 | – |
| ST173–ST1619 | ST173, n = 4 | blaVIM-1, n = 2 | In916 | 90 |
| blaVIM-4, n = 2 | In238, n = 1 | – | ||
| In238a, n = 1 | – | |||
| Singleton | ST485, n = 2 | blaVIM-4 | In238 | 216 |
| ST363–ST764 | ST764, n = 1 | blaVIM-1 | In916 | – |
| CG1641, 4 SLVs | ST1641, n = 1 | blaVIM-1 | In916 | – |
| ST961–ST1417–ST1753 | ST1753, n = 3 | blaVIM-1 | In916 | 13–22 |
| ST419–ST1759 |
ST1759, n = 2 |
blaVIM-1 |
In916 |
1 |
| E. hormaechei subsp. oharae, n = 11 | ||||
| CC68, 3 SLVs | ST68, n = 1 | blaVIM-4 | In238 | – |
| ST94–ST471 | ST94, n = 2 | blaVIM-4 | In238, n = 1 | – |
| In70, n = 1 | – | |||
| CC108, 12 SLVs |
ST108, n = 8 |
blaVIM-2 |
In1008 |
1–11 |
| E. hormaechei subsp. hormaechei, n = 1 | ||||
| ST262–ST269–ST528 |
ST528 |
blaVIM-4 |
In238 |
– |
| E. roggenkampii, n = 8 | ||||
| CC96, 3 SLVs | ST96, n = 4 | blaVIM-4 | In238 | 37–49 |
| ST95–ST515 | ST95, n = 1 | blaVIM-4 | In238 | – |
| ST166–ST433 | ST166, n = 1 | blaVIM-1 | In916 | – |
| ST523–ST823–ST1398 | ST523, n = 1 | blaVIM-4 | In238 | – |
| Singleton |
ST1761, n = 1 |
blaVIM-4 |
In238 |
– |
| E. asburiae, n = 2 | ||||
| Singleton | ST23, n = 1 | blaVIM-4 | In238 | – |
| ST25–ST915–ST1407 |
ST25, n = 1 |
blaVIM-4 |
In238a |
– |
| E. kobei, n = 1 | ||||
| Singleton |
ST99 |
blaVIM-4 |
In238 |
– |
| E. ludwigii, n = 1 | ||||
| ST257–ST1306 | ST1306 | blaVIM-1 | In916 | – |
| E. mori, n = 1 | ||||
| Singleton | ST1760 | blaVIM-4 | In238a | – |
*Bold indicates STs originally identified in this study. CC, clonal complex; CG, clonal group; SLV, single locus variant; SNP, single-nucleotide polymorphism; ST, sequence type; –, not calculated. †Clonal status of an ST is defined against the entire multilocus sequence type database (https://pubmlst.org/ecloacae) as of September 20, 2022. STs are classified into CCs (separate groups of >4 closely related STs with a central genotype), CGs (groups of >4 closely related STs being parts of bigger straggly structures), groups of 2–3 closely related STs for which no central genotype may be currently distinguished, or as singletons. ‡New integron structures are bolded.
Page created: June 12, 2023
Page updated: July 20, 2023
Page reviewed: July 20, 2023
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