Meta-analysis of Pandemic Escherichia coli ST131 Plasmidome Proves Restricted Plasmid-clade Associations

Abstract

extraintestinal multidrug resistant Escherichia coli sequence type (ST) 131 is a worldwide pandemic pathogen and a major cause of urinary tract and bloodstream infections. the role of this pandemic lineage in multidrug resistance plasmid dissemination is still scarce. We herein performed a metaanalysis on E. coli ST131 whole-genome sequence (WGS) databases to unravel ST131 plasmidome and specifically to decipher CTX-M encoding plasmids-clade associations. We mined 880 ST131 WGS data and proved that CTX-M-27-encoding IncF[F1:A2:B20] (Group1) plasmids are strictly found in clade C1, whereas CTX-M-15-encoding IncF[F2:A1:B-] (Group2) plasmids exist only in clade C2 suggesting strong plasmid-clade adaptations. Specific Col-like replicons (Col156, Col(MG828), and Col8282) were also found to be clade C1-associated. BLAST-based search revealed that Group1 and Group2 plasmids are narrow-host-range and restricted to E.coli. Among a collection of 20 newly sequenced Israeli ST131 CTX-M-encoding plasmids (2003-2016), Group1 and Group2 plasmids were dominant and associated with the expected clades. We found, for the first time in ST131, a CTX-M-15-encoding phage-like plasmid group (Group3) and followed its spread in the WGS data. This study offers a comprehensive way to decipher plasmid-bacterium associations and demonstrates that the CTX-M-encoding ST131 Group1 and Group2 plasmids are clade-restricted and presumably less transmissible, potentially contributing to ST131 clonal superiority. Multidrug resistant ESBL-producing Escherichia coli ST131 is a high-risk extraintestinal pathogenic E. coli (ExPEC) lineage that has spread explosively throughout the world 1-4 , mostly by patient-to-patient spread and contaminated food 5. This lineage may colonize healthy humans and animals 6 and is the causative pathogen of urinary tract and bloodstream infections 7-9. E. coli ST131 nowadays is recognized as the major E. coli lineage responsible for the spread of multidrug resistance (MDR) 3 and in specific CTX-M ESBL genes 10. The global expansion of this lineage is driven by spread of two major fluoroquinolone-resistance clades which possess fimH30 allele-H30R/C1 and H30Rx/C2, where the later harbors bla CTX-M-15 ESBL gene 4,11-13. Plasmid-bacterium associations in ST131 clades connected CTX-M-15-encoding IncF[F2:A1:B-] (FAB formula) plasmids to clade C2 11,12,14,15 , and non-CTX-M-15-encoding IncF[F1:A2:B20] plasmids to clade C1 4,11. The major CTX-M genes described in clade С1 were CTX-M-14 and −27 alleles of the CTX-M-9 group 16 , with this later allele-C1-M27 16 , recognized recently as a new subclade with global occurrence 17,18. MDR often disseminates in bacteria through horizontal gene transfer of mobile genetic elements, especially plasmid transmission 19,20. However, if there are highly adaptive plasmid-bacterium associations within ST131 lineage, the main driving force for MDR spread related to this pandemic clone is due to clonal expansion rather than to horizontal plasmid spread 11,12,15. The existence of successful plasmid-S...

Genomic Surveillance of Ceftriaxone-Resistant Escherichia coli in Western New York Suggests the Extended-Spectrum β-Lactamase blaCTX-M-27 Is Emerging on Distinct Plasmids in ST38

“…In these studies and others, the bla CTX-M-27 gene has been associated with fimH30 and fluoroquinolone resistance as part of clade C1-M27. Here, we found the same, as well as noting that the bla CTX-M-27 gene was often embedded in plasmids of pMLST IncF[F1:A2:B20] which was almost exclusively restricted to the C1-M27 clade, as reported by others (Ghosh et al, 2017;Kondratyeva et al, 2020). Interestingly, An IncF[F1:A2:B20] plasmid was also found in a single ST38 strain (URMC_96; Figure 3C).…”

Trends in Population Dynamics ofEscherichia coliSequence Type 131, Calgary, Alberta, Canada, 2006–20161

“…Using IncF plasmid replicons (FII_1, FIA_2, FIB_20, FII_2, and FIA_1) and a plasmid classification system published recently ( 26 ), we found that group 1 plasmids (combination of FII_1, FIA_2, and FIB_20) were in clades A, B, C1-nonM27, and C1-M27, and group 2 plasmids (combination of FII_2 and FIA_1) were in clades C0 and C2 ( Table 1 ). Group 1 plasmids were common among C1 clades, and group 2 plasmids were common among C2 isolates.…”

Editorial Comment to Differential effects of chromosome and plasmid blaCTX‐M‐15 genes on antibiotic susceptibilities in extended‐spectrum beta‐lactamase‐producing Escherichia coli isolates from patients with urinary tract infection

“…ST131 E. coli strains are of worldwide importance as a quinolone-resistant and ESBL-producing bacteria, the spread of which is attributed to the plasmid. 4 This study shows both the importance of ST410 and that the antimicrobial-resistant pattern of these strains might be different if it spreads. Thus, it is necessary to be aware of the latest epidemiology.…”