Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli
Abstract
:1. Introduction
2. CC/ST131, the Worldwide Predominant High-Risk Clone
3. ST1193, a Recently Emerging Pandemic MDR Clone from Phylogroup B2
4. ST69 and CC10, the Second and Third Most Common High-Risk Clones
5. ST405 and High-Risk CC/ST38 Clones from Phylogenetic Group D
6. ST457, a Novel Emerging Clone from Phylogroup F
7. Further Potential ExPEC High-Risk Clones
8. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sequence Type | Accession Numbers (Bioproject, Biosample, SRA, European Nucleotide Archive, EMBL-EBI Database Project) | Reference |
---|---|---|
ST131-B | JAENHI000000000.1 (E. coli strain S802) | [56] |
VEWQ00000000 (E. coli strain UPEC U34) | [57] | |
ST131-C | JSXN00000000 (E. coli strain NA101) JSXO00000000 (E. coli strain NA112) | [38] |
JACHQR000000000.1 (E. coli strain LMLEEc001) JACHQP000000000.1 (E. coli strain LMLEEc003) JACHQO000000000.1 (E. coli strain LMLEEc010) JACHQK000000000.1 (E. coli strain LMLEEc025) | [39] | |
JAJPAL000000000.1 (E. coli strain ECO112) | [20] | |
NCVZ00000000.1 (E. coli strain EcMO) | [47] | |
PRJEB46895 (E. coli strain EC-119) | [58] | |
ST1193 | CP030111 (E. coli strain MCJCHV-1) | [59] |
JACHQB000000000.1 (E. coli strain LMLEEc041) | [39] | |
ST69 | SAMN11246379 (E. coli strain EC81) SAMN11246556 (E. coli strain EC369) SAMN11246590 (E. coli strain EC801) SAMN11246609 (E. coli strain EC820) | [60] |
CC10 (ST617) | PIZJ00000000 (E. coli strain ECCO2) | [61] |
CC10 (ST167) | CP074120 (E. coli strain EC16) | [7] |
QLNK00000000 (E. coli strain ECWJ1) | [62] | |
ST405 | AP019803 (E. coli strain KY1497) | [63] |
ERS4552076 (E. coli strain SSM100) | [64] | |
NGUU00000000 (E. coli strain WCHEC96200) | [65] | |
NXEQ00000000 (E. coli strain 2009-30) NXER00000000 (E. coli strain 2009-27) | [66] | |
ST38 | NCWA00000000.1 (E. coli strain Ec6M) | [67] |
SAMN17315482 (strain URMC_401_E_coli) | [68] | |
RZGB00000000 (E. coli strain URMC_9) RZBC00000000 (E. coli strain URMC_13) | [69] | |
NCWA00000000.1 (E. coli strain Ec6M) | [47] | |
MVIO00000000 (E. coli strain NA090) | [38] | |
ST457 | NDBC00000000 (E. coli strain EM1CRO) | [70] |
CC23 | NBCL00000000 (E. coli strain 13B) LYPE00000000 (E. coli strain Ec47VL) | [71] |
ST95 | CP012625 (E. coli strain SF-468) CP012631 (E. coli strain SF-173) CP012633 (E. coli strain SF-166) CP012635 (E. coli strain SF-88) | [72] |
ST73 | JACHPD000000000.1 (E. coli strain LMLEEc115) | [39] |
ST410 | VFBH01000000 (E. coli strain A240) | [73] |
ST648 | PEDQ00000000.1 (E. coli strain ICBECG2) PEDR00000000.1 (E. coli strain ICBECG4) | [74] |
ST393 | QGIF00000000 (E. coli strain 77H) QHCX00000000 (E. coli strain 51H) | [75] |
ST58 | SRX10825685 (E. coli strain IBIS_39) | [76] |
ST101 | VYQD00000000 (E. coli strain EC121) | [77] |
Resistance Markers of ExPEC High-Risk Clones | ||||||
---|---|---|---|---|---|---|
Sequence Type (ST) [References] | Beta-Lactamases | Resistance to Fluoroquinolones | Resistance to Colistin | Inc Plasmid Types | ||
ESBL | AmpC | Carbapenemases (Ambler Class A, B, D) | ||||
ST-131-A [46,54,55] | blaCTX-M-14, blaCTX-M-15, blaCTX-M-27+, | blaDHA-1 | blaKPC-3, blaOXA-48 | mutations in gyrA, parC, parE, double alteration of gyrA +, qnrB4, qnrB66, aac(6′)Ib-cr | No data available | FI, FII, A1, B1, B10 |
ST-131-B (*) + [38,46,56,57] | blaCTX-M-15+ | No data available | qnrA1, * qnrB19+ | mcr-1,(*) mcr-3,(*) mcr-5, * mcr-9* | F-ColV like lineage, FIB-like, FII, HI2, HI2A | |
ST-131-C1-M27 [20,46,83] | blaCTX-M-27, blaCTX-M−2, blaTEM | No data available | blaNDM-1, blaOXA-232 | No data available | FI:A2:B20 | |
ST-131-C1-non-M27 [58] | blaCTX-M-14,
blaTEM | No data available | blaKPC-2, blaKPC-3, and blaKPC-18 | No data available | ||
ST-131-C2 (*) [40,58] | blaCTX-M-15, (*) blaCTX-M-G-1, blaCTX-M-G-2, blaCTX-M-G-8, blaCTX-M-G-9, blaCTX-M-G-25, blaTEM (*) blaSHV-12 | blaFOX−5, | blaNDM-1, blaNDM-5, blaVIM-1, blaKPC-2, blaKPC-3, blaKPC-18, blaOXA-48, blaOXA-181, blaOXA-232, co-expression of blaNDM-1 and blaVIM-1 | qnrB19, (*) qnrS1, mutations in gyrA, parC, parE | mutations in pmrA and pmrB, mcr-3 | FII:A1:B-, F36:A4:B1 |
ST1193 [39,40,59,84,102] | blaCTX-M-9, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, blaTEM-1B | blaCMY-2 | blaNDM-1, blaKPC-2 | mutations in gyrA, parC or parE, aac(6′)Ib-cr | mutations in pmrA and pmrB | FII, FIB, I1 |
ST69 (*) [20,40,60,100,105] | blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaTEM-1B, (*) blaTEM-1C | blaCMY-6 (co-carriage with blaNDM-1) | blaNDM-1, blaKPC-2 | mutations in gyrA and parC (*) | mcr-1,+ mcr-3+ | FIIB |
CC10 (containing ST10, ST44, ST48, ST167 and ST617) (+) [7,61,62,112,113] | blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, blaTEM-1B, blaTEM-169, blaTEM-206, blaTEM-214 blaSHV-12 | blaCMY-42, | blaNDM-1, blaNDM-5, blaNDM-9, blaIMP-8, blaKPC-2, blaKPC-3, blaOXA-181, (co-expressed with blaNDM-5) blaOXA-48 (co-expressed with blaNDM-5) | mutations in gyrA and parC, qnrS1, (*) qnrB19, qepA4, aac(6′)-Ib-cr | mcr-1 (co-expressed with blaNDM-1) | IncFIA, Col-like, I1 |
ST405 (+) [63,64,65,66] | blaCTX-M-14, blaCTX-M-15, blaCTX-M-88, blaTEM-1, blaTEM-12 | No data available | blaNDM-4, blaNDM-5, blaKPC-2, blaOXA-48 | mutations in gyrA, parC, and parE, qnrS1, aac(6′)-Ib-cr | mcr-1+ | FIB, FII, F1A, Col-like, F1:A1:B49 |
ST38 (*) [38,40,67,68,69,70] | blaCTX-M-2, blaCTX-M-3, blaCTX-M -9, blaCTX-M -14, (*) blaCTX-M-15, (*) blaCTX-M-27, blaTEM-1B | blaCMY-12, blaDHA-1 | blaNDM-1, blaNDM-6, blaOXA-48, blaOXA-244 | mutations in gyrA, parC | mcr-5 (*) | FII:A-:B10, FI:A2:B20 |
ST457 (*) [19,70] | blaCTX-M-1, blaCTX-M-2, blaCTX-M-3, blaCTX-M-8; blaCTX-M-12, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, blaTEM-1 | blaCMY-2 | blaNDM-5, blaNDM-9, blaIMP-4, blaKPC-2, blaKPC-3, blaOXA-23 | mutations in gyrA and parC, qnrB19 * | mcr-1 (*), mcr-3 (*), mcr-5 (*) | F64:A:B:27, I1 |
Linkage between ExPEC Clones and Colistin, Fosfomycin, Nitrofurantoin Resistance Determinants | ||||||
---|---|---|---|---|---|---|
Colistin Resistance | Fosfomycin Resistance | Nitrofurantion Resistance | ||||
pmrA and pmrB Mutations | mcr-1 | mcr-3 | mcr-5 | mcr-9 | fosA3 Enzymatic Activity | Nitroreductase (nfsA, nfsB) Enzymatic Activity |
ST131 ST1193 | ST131 ST69 CC10 ST405 ST457 ST410 ST48 ST58 ST88 ST57 ST156 ST224 ST345 ST354 ST393 ST744 ST850 ST3024 ST8900 ST12657 | ST69 ST457 ST101 ST155 ST206 ST443 ST1081 ST1638 ST5038 | ST131-B ST38 ST457 ST57 ST93 ST113 ST165 ST189 ST224 ST366 ST580 ST641 ST752 ST2705 ST6853 ST8061 | ST131-B | ST131 ST1193 ST69 CC10 ST38 ST457 ST95 ST12 ST117 ST307 ST648 ST744 ST746 ST1730 ST2646 | ST131 ST38 |
Resistance Genes and Mechanisms | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
Clones | blaCTX-M-14-Variants (e.g., CTX-M-2) | blaCTX-M-15 | blaCTX-M-27 | blaKPC-Variants | blaOXA-48-Variants (e.g., OXA-244) | blaIMP-Variants | blaNDM-Variants | blaVIM-Variants | Fluoro-Quinolones | Colistin |
ST131 (including A, B, C1, C2 clades) | 2004 | 2005 | 2004 | 2011 | 2012 | 2010 | 2015-2017 (2022) 1 | 2004 | 2014 | |
ST1193 | 2013 | 2017 | 2022 | 2022 | 2012 | 2021 | ||||
ST69 | 2014–2017 (2020) 2 | 2014–2017 (2020) 2 | 2014–2017 (2020) 2 | 2015–2017 (2022) 1 | 2022 | 2017 | 2018 | |||
CC10 (ST10 with its variants, namely ST167, ST617, ST410) | 2015 | 2015 | 2017 | 2016 | 2015 | 2022 | 2015 | 2017 | 2022 | |
ST405 | 2012 | 2012 | 2016 | 2016 | 2013 (2020), 2016 3 | 2012 | 2020 | |||
ST38 | 2011 | 2020 | 2020 | 2011 | 2011 | 2013 (2015) 4 | 2019 | |||
ST457 | 2016 | 2016 | 2012 | 2014 | 2020 | 2019 | 2014 | 2008 | 2012 (2020) 5 |
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Kocsis, B.; Gulyás, D.; Szabó, D. Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli. Life 2022, 12, 2077. https://doi.org/10.3390/life12122077
Kocsis B, Gulyás D, Szabó D. Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli. Life. 2022; 12(12):2077. https://doi.org/10.3390/life12122077
Chicago/Turabian StyleKocsis, Béla, Dániel Gulyás, and Dóra Szabó. 2022. "Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli" Life 12, no. 12: 2077. https://doi.org/10.3390/life12122077