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

• Published in: Communications medicine Vol. 5; no. 1; pp. 260 - 11
• Main Authors: Souza, Stephanie S. R., Piper, Kathryn R., Ikhimiukor, Odion O., Marcovici, Michael M., Zac Soligno, Nicole I., Harmon, Ashley J., Eckhardt, Elissa M., Carreiro, Nisalda, Workman, Adrienne A., Martin, Isabella W., Andam, Cheryl P.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.07.2025; Springer Nature B.V; Nature Portfolio
• Subjects: 45/22; 631/208/212/748; 631/326/107; Antibiotics; Antimicrobial agents; E coli; Fatalities; Genomes; Genomics; Human subjects; Infections; Laboratories; Medicine; Medicine & Public Health; Multidrug resistant organisms; Public health; United States > US; New Hampshire; California
• ISSN: 2730-664X; 2730-664X
• DOI: 10.1038/s43856-025-00972-x

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 bla TEM , bla SHV , bla OXA , bla CTX-M , and bla CMY , 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 bla TEM-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. Souza et al. determine the genomic characteristics of Escherichia coli implicated in bloodstream infection and the spread of antimicrobial resistance. The spread of genes encoding different variants of β-lactamases , including extended-spectrum β-lactamases , is driven by genetically distinct lineages of E. coli. Plain language summary Over time, bacteria such as E. coli develop resistance to multiple antibiotics, making treatment difficult and causing adverse outcomes. Here, we investigate how E. coli from bloodstream infections (BSI) have evolved and spread resistance. The study findings show that five genetically distinct E. coli dominate these infections, each carrying various resistance genes, including those for β-lactamases (enzymes that break down antibiotics) and iron uptake systems, which help bacteria survive in the body. Our genomic monitoring approach may help reduce antimicrobial resistance to existing treatments in BSI and improve surveillance of BSI in future.