Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates of Escherichia coli

Abstract

Blood stream invasion by Escherichia coli is the commonest cause of bacteremia in the UK and elsewhere with an attributable mortality of about 15–20 %; antibiotic resistance to multiple agents is common in this microbe and is associated with worse outcomes. Genes conferring antimicrobial resistance, and their frequent location on horizontally transferred genetic elements is well-recognised, but the origin of these determinants, and their ability to be maintained and spread within clinically-relevant bacterial populations is unclear. Here, we set out to examine the distribution of antimicrobial resistance genes in chromosomes and plasmids of 16 bloodstream isolates of E. coli from patients within Scotland, and how these genes are maintained and spread. Using a combination of short and long-read whole genome sequencing methods, we were able to assemble complete sequences of 44 plasmids, with 16 Inc group F and 20 col plasmids; antibiotic resistance genes located almost exclusively within the F group. bla CTX-M15 genes had re-arranged in some strains into the chromosome alone (five strains), while others contained plasmid copies alone (two strains). Integrons containing multiple antibiotic genes were widespread in plasmids, notably many with a dfrA7 gene encoding resistance to trimethoprim, thus linking trimethoprim resistance to the other antibiotic resistance genes within the plasmids. This will allow even narrow spectrum antibiotics such as trimethoprim to act as a selective agent for plasmids containing antibiotic resistance genes mediating much broader resistance, including blaCTX-M15. To our knowledge, this is the first analysis to provide complete sequence data of chromosomes and plasmids in a collection of pathogenic human bloodstream isolates of E. coli . Our findings reveal the interplay between plasmids and integrative and conjugative elements in the maintenance and spread of antibiotic resistance genes within pathogenic E. coli .

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

“…IncI1 plasmids are common in ExPEC and are associated with different ESBL genes [67, 128–130]. Given that backbone plasmid genes may determine fitness effects more than ESBL genes [131] and long-term IncF plasmid persistence in ST131 [62], plasmids pEK204, (pEK516,) and pEK499 proteins’ higher interaction rates with chromosomally-encoded proteins relative to other relevant plasmids could be due to co-evolution. Measuring the indirect connectivity as PPI network loops per interaction showed evidence of this long-term retention, and may help identify plasmids compatible with E.…”

“…Some plasmids in ST131 encode genes for post-segregation killing and stable inheritance to ensure their propagation, but these genes can be lost or may recombine with other plasmids [58][59][60]. As a result of this mixing and their extensive array of MGEs, plasmids may rearrange extensively even within a clonal radiation [61,62]. Plasmids may also impair cell reproduction due to the energetic cost of their replication and maintenance, so conjugation and recombination could allow gene dosage optimisation and gene expression coordination.…”

Plasmids Shape the Diverse Accessory Resistomes of Escherichia coli ST131

“…Given that backbone plasmid genes may determine fitness effects more than ESBL genes [131] and long-term IncF plasmid persistence in ST131 [62], plasmids pEK204, (pEK516,) and pEK499 proteins' higher interaction rates with chromosomally-encoded proteins relative to other relevant plasmids could be due to co-evolution. Measuring the indirect connectivity as PPI network loops per interaction showed evidence of this long-term retention, and may help identify plasmids compatible with E. coli chromosomes.…”

Plasmids shape the diverse accessory resistomes ofEscherichia coliST131

“…IncI1 plasmids are common in ExPEC and are associated with different ESBL genes [67,[129][130][131]. Given that backbone plasmid genes may determine fitness effects more than ESBL genes [132] and long-term IncF plasmid persistence in ST131 [62], plasmids pEK204, (pEK516,) and pEK499 proteins' higher interaction rates with chromosomally-encoded proteins relative to other relevant plasmids could be due to co-evolution. Measuring the indirect connectivity as PPI network loops per interaction showed evidence of this longterm retention, and may help identify plasmids compatible with E. coli chromosomes.…”

“…Some plasmids in ST131 encode genes for post-segregation killing and stable inheritance to ensure their propagation, but these genes can be lost or may recombine with other plasmids [58][59][60]. As a result of this mixing and their extensive array of MGEs, plasmids may rearrange extensively even within a clonal radiation [61][62]. Plasmids may also impair cell reproduction due to the energetic cost of their replication and maintenance, so conjugation and recombination could allow gene dosage optimisation and gene expression coordination.…”