Variants of β-lactamase-encoding genes are disseminated by multiple genetically distinct lineages of bloodstream Escherichia coli.

BACKGROUND

Escherichia coli is a major cause of bloodstream infections (BSI), which can lead to life-threatening organ dysfunction. We determined the genomic characteristics of E. coli implicated in BSI and the spread of antimicrobial resistance (AMR).

METHODS

We carried out in vitro antimicrobial susceptibility testing and whole genome sequencing of 557 E. coli isolates recovered from BSI at Dartmouth-Hitchcock Medical Center, USA.

RESULTS

We identify at least 119 previously recognized sequence types (ST), of which five STs (ST69, ST73, ST95, ST127, ST131) altogether represent 50% of the bloodstream E. coli population. Of the 142 distinct serotypes detected, the most common are O25:H4 and O1:H7. A total of 62 acquired genes are associated with resistance to at least 13 antimicrobial classes. These include the β-lactamase gene families blaTEM, blaSHV, blaOXA, blaCTX-M, and blaCMY, which together can be further classified into 15 variants, including seven genes encoding extended-spectrum β-lactamases (ESBL). A total of 210/557 genomes carry at least one bla gene, with blaTEM-1 being the most prevalent variant. ESBL-related genes are frequently detected in ST131 genomes. Four virulence operons related to iron uptake are differentially distributed among the five dominant STs. The putative IncF-type plasmid is often associated with genes related to AMR and iron uptake. Estimation of core and accessory genome similarity identifies 12 presumptive epidemiological linkages that span anywhere between 2-18 months.

CONCLUSIONS

Multiple but genetically distinct E. coli lineages similarly cause BSI and shape AMR dissemination, emphasizing the opportunistic nature of E. coli in invasive infections.