Exposure to antibiotics with anaerobe coverage is associated with higher rates of enteric pathobiont carriage and relative abundance in long-term residential aged care residents, even where pathobiont species are sensitive to the administered antibiotic.
The vast majority of long-term care residents carried at least one enteric pathobiont.
Treatment with antibiotics that cover anaerobes (EAC) was associated with higher rates of pathobiont carriage compared to those with no prior antibiotic exposure.
Exposure to antibiotics with anaerobe coverage (EAC) was associated with higher overall pathobiont relative abundance.
Antibiotics with limited anaerobe coverage (LAC) showed no significant associations with pathobiont carriage or relative abundance.
Amoxicillin-clavulanate (a commonly prescribed EAC antibiotic) was specifically associated with higher pathobiont detection and relative abundance.
Pathobionts with greater representation in amoxicillin-clavulanate recipients included both antibiotic-resistant and antibiotic-sensitive species.
The study concluded that off-target disruption of commensal anaerobes should be considered when selecting antibiotic treatments in long-term care populations.
This research suggests that the type of antibiotic prescribed to elderly residents in long-term care facilities matters beyond just treating the immediate infection. Specifically, antibiotics that kill anaerobic bacteria — a group of beneficial gut microbes — were associated with a significantly higher likelihood of residents harboring potentially dangerous gut bacteria called pathobionts. In contrast, antibiotics that spare these anaerobic bacteria were not linked to increased pathobiont presence. Over 84% of the 164 residents studied already carried at least one such pathobiont, highlighting how common this phenomenon is in this population. A particularly notable finding was that even pathobionts that should be killed by the antibiotic being used (such as Klebsiella pneumoniae being sensitive to amoxicillin-clavulanate) were found at higher levels in people who received that antibiotic. This suggests the problem is not simply that antibiotics wipe out susceptible bacteria and leave resistant ones to flourish. Instead, the research points to a broader ecological disruption: when beneficial anaerobic bacteria in the gut are depleted, they can no longer keep potentially harmful bacteria in check — a protective function known as colonisation resistance. This research suggests that when doctors choose antibiotics for elderly people in care homes, the impact on the broader gut bacterial community — particularly anaerobic commensals — should be factored into the decision, not just the antibiotic's effectiveness against the target infection. Selecting antibiotics that preserve gut anaerobes where clinically appropriate may help reduce the risk of subsequent infections caused by opportunistic gut bacteria in this vulnerable population.
Vasil E, Papanicolas L, Miller S, Shoubridge A, Taylor S, Rogers G. (2026). Exposure to antibiotics with anaerobe coverage in later life is associated with higher enteric pathobiont carriage.. The Journal of infection. https://doi.org/10.1016/j.jinf.2026.106774