Communications medicine · 2025
Variants of β-lactamase-encoding genes are disseminated by multiple genetically distinct lineages of bloodstream Escherichia coli.
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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
Аннотация
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.
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.