Chlorinated water and the infant gut resistome
Even at concentrations compliant with health standards, chlorinated drinking water may enhance antibiotic resistance functions in the infant gut microbiome. A randomized, double-blind trial involving 197 Australian infants revealed a potential risk of selectively favoring resistant bacterial populations.1
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About this article
Antibiotic resistance –a major component of antimicrobial resistance– is a global public health priority and a growing health concern. Between 2018 and 2023, more than 40% of the pathogen–antibiotic combinations monitored by the WHO showed increasing resistance.2 While efforts to combat antibiotic resistance have primarily focused on reducing antibiotic use and promoting vaccination, an Australian study explores a less investigated environmental factor that may impact the gut microbiota: the consumption of chlorinated drinking water. Although chlorination is essential for water disinfection and is subject to regulatory limits (residual chlorine levels ranged from 0.3 to 1.1 mg/L in the study, below the 5 mg/L limit), residual chlorine and other chlorine-related disinfection by-products may exert selective pressure on the infant gut microbiome, potentially favoring resistant bacteria. According to the authors, this is the first randomized, double-blind controlled trial evaluating this hypothesis in a high-income country, where drinking water is subject to treatment and disinfection standards.
Resistome :
The set of antibiotic resistance genes carried by microorganisms within a given environment, in this case, the gut microbiota.4
197 infants followed for 12 months
A total of 197 six-month-old infants from the ORIGINS Project cohort were randomly assigned to two groups for a 12-month intervention: one received conventional chlorinated tap water, while the other received tap water dechlorinated through filtration, which significantly reduced levels of chlorine and certain disinfection by-products. Stool samples were collected at the beginning and end of the study period and analyzed using metagenomic sequencing. This enabled researchers to assess changes in the composition and functional characteristics of the gut microbiota under different levels of exposure to chlorine.
Summary table of key results
Overview: number and variety of bacteria (abundance, diversity).
Observed Result (chlorinated water vs. dechlorinated water):
No significant difference between the two groups.
Detailed view: quantity of certain bacteria (genera and species).
Observed Result (chlorinated water vs. dechlorinated water):
Despite the overall similarity, subtle differences were observed, with considerable variability between infants.
Less abundant in the chlorinated-water group: Bacteroides, Clostridium, and Blautia (taxa associated with a healthy gut microbiome).
More abundant: Streptococcus and Klebsiella pneumoniae (opportunistic pathogens under certain circumstances), as well as Faecalibacterium prausnitzii and Bifidobacterium (beneficial taxa).
Observed Result (chlorinated water vs. dechlorinated water):
Significantly more abundant in the chlorinated-water group;
The specific resistance genes involved were not individually identified.
Observed Result (chlorinated water vs. dechlorinated water):
Greater enrichment of resistance functions was observed among children who had received antibiotics, but the difference was not statistically significant after adjustment. Further investigation is needed.
Gut microbial diversity remained unchanged, but antibiotic resistance functions were enhanced
No significant differences in bacterial richness or overall diversity were observed between the two groups. At the taxonomic level, differences between the two groups were identified in a small subset of bacterial taxa. However, these were rarely detected and showed considerable variability between infants. The main finding concerned the functional potential of the gut microbiota: functions associated with antibiotic resistance, including efflux pumps and antibiotic-degrading enzymes, were significantly enriched in infants exposed to chlorinated drinking water. The authors nevertheless acknowledge an important limitation: the specific antibiotic resistance genes involved were not individually identified. An additional analysis stratified by antibiotic exposure suggested a more pronounced enrichment among infants who had received antibiotics (n=40). However, this trend was not statistically significant after adjustment and requires further investigation. Secondary health outcomes, including allergies, wheezing, and eczema, were available for approximately half of the children. No significant differences were observed between the groups, although a clinical effect cannot be ruled out.
Stratified analysis:
A statistical approach in which analyses are performed separately within subgroups defined by a specific characteristic (in this case, antibiotic exposure) to assess whether an observed effect varies according to that factor.
These findings do not challenge the practice of drinking water chlorination, which has well-established health benefits. However, they highlight the need to investigate, within the broader context of the infant exposome, whether the timing or methods of water introduction could be optimized to minimize exposure to chlorinated disinfectants, alongside the appropriate use of antibiotics in pediatric care. The results should nevertheless be interpreted as exploratory. The COVID-19 pandemic reduced the number of children who completed the study, and the sample size was insufficient to adequately assess the role of antibiotic exposure. Consequently, the study cannot yet establish whether chlorinated drinking water selects for antibiotic-resistant bacterial populations or whether such changes have health consequences.
Exposome:
The totality of environmental exposures an individual experiences from conception onward, including diet, lifestyle, and endogenous factors.5
The study1 was partly funded by Water Corporation WA and received in-kind support from Pure Water Systems. Neither partner was involved in the study design, data analysis, or decision to publish.
What type of water should be used to prepare infant formula? Recommendations from the French Agency for Food, Environmental and Occupational Health & Safety (ANSES)3
ANSES recommendation :
Suitable for use, provided certain precautions are taken: let the water run for a few seconds, use only cold water, and clean the tap aerator regularly.
ANSES recommendation :
Not recommended, as these systems may promote microbial growth.
ANSES recommendation :
Consult your local town hall or competent health authority before use.
1. Parkin K, Christophersen CT, Verhasselt V, et al. Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: a randomized trial. Commun Med. 2026;6:405. doi:10.1038/s43856-026-01626-2.
2. World Health Organization. WHO warns of widespread resistance to common antibiotics worldwide. Geneva: WHO; 13 October 2025.
4. D'Costa VM, McGrann KM, Hughes DW, Wright GD. Sampling the antibiotic resistome. Science. 2006;311(5759):374-377. doi:10.1126/science.1120800
5. Wild CP. Complementing the genome with an "exposome": the outstanding challenge of environmental exposure measurement in molecular epidemiology. Cancer Epidemiol Biomarkers Prev. 2005;14(8):1847-1850. doi:10.1158/1055-9965.EPI-05-0456
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