Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.

Among 80 patients receiving ceftriaxone, 12 (15%) acquired ESBL-E colonization by day 30.

• Prospective study of patients with suspected bacterial infections receiving ceftriaxone.
• Rectal samples were collected before antibiotic administration, during treatment, and 30 days after initiation.
• Samples were analyzed by shotgun metagenomic sequencing.
• The acquisition rate of ESBL-E colonization was 15% (12/80 patients).

Ceftriaxone exposure induced a profound and sustained reduction in microbial richness and diversity across all patients.

• The reduction in microbial richness and diversity was observed across all 80 patients.
• The disruption was sustained throughout the study period.
• This effect was observed regardless of whether patients subsequently acquired ESBL-E colonization.
• Analysis was conducted using shotgun metagenomic sequencing of rectal samples at multiple time points.

No specific taxonomic signature at baseline predicted subsequent ESBL-E colonization.

• Despite profound microbiome disruption across all patients, taxonomic composition did not differentiate those who acquired ESBL-E from those who did not.
• This finding suggests that taxonomic composition is less important than functional resistome features in predicting colonization risk.
• Baseline rectal samples were analyzed by shotgun metagenomic sequencing prior to antibiotic administration.

Patients who did not acquire ESBL-E displayed a significantly richer and more diverse repertoire of β-lactamase-encoding genes at baseline compared to those who acquired ESBL-E.

• The β-lactamase gene repertoire (termed 'β-lactamasome') was assessed from baseline rectal samples prior to ceftriaxone administration.
• Greater β-lactamasome richness and diversity at baseline was associated with protection against subsequent ESBL-E colonization.
• This association was independently associated with protection against colonization in multivariate analysis.
• This represents the first real-world evidence linking pre-existing β-lactamasome diversity to colonization resistance.

Patients exposed to multiple antibiotics experienced greater and more sustained microbiome disruption compared with those receiving ceftriaxone alone.

• The comparison was made between patients receiving ceftriaxone as monotherapy versus those receiving ceftriaxone plus additional antibiotics.
• Multi-antibiotic exposure led to both greater magnitude and longer duration of microbiome disruption.
• This finding highlights the additive impact of broad-spectrum antibiotic combinations on gut microbiome ecology.

Functional resistome diversity, rather than taxonomic composition, was the key microbiome feature associated with protection against ESBL-E colonization.

• Pre-existing β-lactamasome diversity was independently associated with protection against antibiotic-driven colonization by ESBL-E.
• Taxonomic composition did not predict colonization risk, whereas functional resistome diversity did.
• The authors highlight 'the importance of functional resistome diversity over taxonomic composition in colonization resistance.'
• These findings suggest a novel ecological mechanism by which the resident gut resistome may competitively exclude or suppress incoming resistant organisms.