Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation
Open accessAbstract
Background: Probiotic use in preterm infants can mitigate the impact of antibiotic exposure and reduce rates of certain illnesses; however, the benefit on the gut resistome, the collection of antibiotic resistance genes, requires further investigation. We hypothesized that probiotic supplementation of early preterm infants (born < 32-week gestation) while in hospital reduces the prevalence of antibiotic resistance genes associated with pathogenic bacteria in the gut. We used a targeted capture approach to compare the resistome from stool samples collected at the term corrected age of 40 weeks for two groups of preterm infants (those that routinely received a multi-strain probiotic during hospitalization and those that did not) with samples from full-term infants at 10 days of age to identify if preterm birth or probiotic supplementation impacted the resistome. We also compared the two groups of preterm infants up to 5 months of age to identify persistent antibiotic resistance genes. Results: At the term corrected age, or 10 days of age for the full-term infants, we found over 80 antibiotic resistance genes in the preterm infants that did not receive probiotics that were not identified in either the full-term or probiotic-supplemented preterm infants. More genes associated with antibiotic inactivation mechanisms were identified in preterm infants unexposed to probiotics at this collection time-point compared to the other infants. We further linked these genes to mobile genetic elements and Enterobacteriaceae, which were also abundant in their gut microbiomes. Various genes associated with aminoglycoside and beta-lactam resistance, commonly found in pathogenic bacteria, were retained for up to 5 months in the preterm infants that did not receive probiotics. Conclusions: This pilot survey of preterm infants shows that probiotics administered after preterm birth during hospitalization reduced the diversity and prevented persistence of antibiotic resistance genes in the gut microbiome. The benefits of probiotic use on the microbiome and the resistome should be further explored in larger groups of infants. Due to its high sensitivity and lower sequencing cost, our targeted capture approach can facilitate these surveys to further address the implications of resistance genes persisting into infancy without the need for large-scale metagenomic sequencing.
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PS infants harboured significantly fewer ARGs than NPS infants.
“our results also showed that PS infants harboured significantly fewer ARGs than NPS infants29.”
From Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants. (2025) · cites this paper as [29]
The Results section reports significantly fewer *unique* ARGs per PS infant than per NS infant at several visits. But the Results and Discussion also state that the overall number of ARGs did not differ significantly between groups. The claim omits the distinction between unique ARGs and ARGs overall. (LLM, conf=0.88)
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- Authors
- Guitor, A. K., Yousuf, E. I., Raphenya, A. R., Hutton, E. K., Morrison, K. M., McArthur, A. G., Wright, G. D., & Stearns, J. C.
- Affiliations
- Michael G. DeGroote Institute for Infectious Disease Research (CA)
- McMaster University (CA)
- CanChild Centre for Childhood-onset Disability Research (CA)
- Corresponding author
- Stearns, Jennifer C.
- ORCID
- Venue
- Microbiome
- Published
- 2022-08-26
- Volume
- 10
- Issue
- 1
- Pages
- 136-136
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC9414150
- OpenAlex
- W4293106355
- Cited by
- 44
- References
- 78
- Citations by year
- 2026: 11 · 2025: 12 · 2024: 7 · 2023: 12 · 2022: 2
- FWCI
- 2.70
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Microbiome (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- McMaster University
- Canadian Institutes of Health Research (PJT156214, 164145_1, 148463_1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- antibiotic resistance genes, resistome, preterm infants, probiotic supplementation, gut microbiota, antibiotic exposure, mobile genetic elements, Enterobacteriaceae, aminoglycoside resistance, beta-lactam resistance, targeted capture sequencing
- MeSH terms
- Anti-Bacterial Agents, Bacteria, Female, Humans, Infant, Infant, Newborn, Infant, Premature, Dietary Supplements, Probiotics, Premature Birth
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