Vaccines in childhood linked to lower drug-resistant bacteria risk

A new study conducted in Guatemala suggests that pneumococcal conjugate vaccination may offer an unexpected benefit: lowering children’s risk of carrying drug-resistant bacteria in their gut. The findings, led by Washington State University (WSU) researchers, indicate that pneumococcal vaccination—specifically PCV13—is associated with reduced colonization of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), a group of bacteria that includes E. coli and is resistant to critical antibiotics used for severe infections.^1,2

The research, published in Vaccine, evaluated whether a pair of routine childhood vaccines, rotavirus (RV) and pneumococcal (PCV13), might indirectly lower ESCrE colonization. Investigators collected vaccination records, stool samples, and questionnaire data from 406 children living in Guatemala’s Western Highlands.

“Most vaccine studies on antimicrobial resistance focus on infection and how vaccines prevent illness and reduce antibiotic use, thereby reducing selection processes of antibiotic resistant bacteria," said Dr. Brooke Ramay, lead author and researcher in WSU’s College of Veterinary Medicine’s Paul G. Allen School for Global Health. "We took a different approach by looking at colonizing bacteria and we found vaccination reduced antimicrobial resistance through a completely different mechanism: vaccination prevented clinic visits and resulted in a lower probability of colonization with antibiotic resistant bacteria. We think this may be because individuals had less exposure to environments where these resistant bacteria are present."

The team’s analysis used an instrumental variables approach to explore connections between vaccination, clinic visits, diarrhea, and bacterial colonization. Children included in the study ranged from 0 to 14 years old: 123 (30.3%) were 0–2 years old, 103 (25.4%) were 3–5 years old, and 180 (44.3%) were 6–14 years old.²

Protection from PCV13

PCV13 vaccination showed a statistically significant indirect negative effect on ESCrE colonization (−0.092, P < 0.01), largely mediated by its strong negative effect on clinic visits (−0.461, P < 0.01).² Clinic visits have previously been linked to higher antimicrobial-resistant colonization in the region, making this pathway notable, according to the researchers.¹

Rotavirus vaccination effects were inconclusive, likely due to the limited number of unvaccinated children and a low number of reported diarrhea cases, which researchers attributed to recall bias.^1,2

Other measured factors also played a role²:

• Yogurt consumption showed protective effects, with negative associations in both models (−0.064, P < 0.01; −0.062, P < 0.01).
• Land used for agriculture increased colonization risk, showing positive associations (0.232, P < 0.01; 0.224, P < 0.01), likely due to environmental exposure to fecal contamination.
• Recent diarrhea increased colonization, demonstrating a direct positive effect in the RV model (0.731, P < 0.01) and indirect positive effects in the PCV13 model (0.090, P < 0.01).
• Antibiotic use showed no direct or indirect association with ESCrE colonization.

"Vaccination for pneumococcal disease was associated with a reduction in colonization with ESCrE bacteria," the study authors concluded. "These findings should be confirmed through studies designed to collect clinical outcomes data. Findings from this and other studies suggest that ESCrE colonization is mediated by a complex interplay of factors."

References:

1. Study links childhood vaccination to lower risk of drug-resistant bacteria. Washington State University. Press release. Published December 2, 2025. Accessed December 9, 2025. https://www.eurekalert.org/news-releases/1108014
2. Ramay BM, Yoder J, Castillo C, et al. Assessing effects of pneumococcal vaccination (Pcv13) and rotavirus vaccination (Rv) on colonization with extended-spectrum cephalosporin-resistant Enterobacterales (Escre) in Guatemalan children. Vaccine. 2025;66:127852. doi:10.1016/j.vaccine.2025.127852