Probiotics limit the spread of drug-resistant genes in preemies

By Dr. Sanchari Sinha Dutta, Ph.D.Reviewed by Lauren HardakerAug 26 2025

New research reveals how probiotic supplementation helps fragile preterm babies build healthier gut microbiomes and lowers the spread of dangerous, drug-resistant bacteria in neonatal intensive care units.

Study: Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants. Image credit: Iryna Inshyna/Shutterstock.com

A new study published in Nature Communications highlights the significance of probiotic supplementation in shaping early-life gut microbiota and restricting multidrug-resistant pathogen load in preterm infants with very-low birth weight.  

Background

Preterm birth is defined as gestation of less than 37 weeks. More than 10% of infants are born prematurely worldwide each year. Over 1% are born with very low birth weight (below 1500 grams). These infants are at higher risk of developing severe, often life-threatening, infections with antibiotic-resistant bacteria due to underdeveloped immune systems.   

Preterm infants are routinely administered broad-spectrum antibiotics, typically benzylpenicillin and gentamicin or derivatives, in their early life to avoid adverse outcomes associated with severe infection. However, this early-life exposure to antibiotics potentially impairs gut microbiota development and triggers the enrichment of antibiotic resistance genes.

Antibiotic resistance genes in the neonatal gut bacterial communities can rapidly spread to other bacteria or other microbial species through horizontal gene transfer. Multidrug-resistant bacteria, such as Staphylococcus and Escherichia, are frequently detected in the preterm infant gut, and their presence is associated with prolonged hospitalization, late-onset blood infections, and secondary infections acquired from hospitals.

The World Health Organization (WHO) has recommended probiotic supplementation specifically for very preterm (<32 weeks), human-milk-fed infants to counteract the consequences of broad-spectrum antibiotic use. Probiotics are live microorganisms in food intended to provide beneficial bacteria and restore microbial balance in the gut.

In the current study, researchers investigated the effects of probiotics and antibiotics on the gut microbiota and antibiotic resistance genes in two groups of breastmilk-fed preterm infants with very-low birth weight.

The study

The study included 34 preterm infants who were divided into two groups. One group received probiotic supplementation (Bifidobacterium bifidum and Lactobacillus acidophilus); the other did not. Within each group, some infants received empirical antibiotic treatment with benzylpenicillin and gentamicin, and the other served as controls with no antibiotic exposure.

Fecal samples collected from the infants during the first three weeks of life were analyzed to characterize gut microbiota. The researchers also reconstructed over 300 bacterial genomes and conducted an ex vivo neonatal gut model experiment to directly test plasmid-mediated horizontal gene transfer of resistance genes in Enterococcus.

Key findings

The study found significant differences in gut microbiota diversity and composition between probiotic-supplemented and non-supplemented infants. Specifically, the comparative analysis revealed a high abundance of Bifidobacterium and a lower abundance of microorganisms with pathogenic potential in the guts of probiotic-supplemented infants.

Bifidobacterium is the major component of the probiotic formulation provided to infants. It was found to restore early-life infant gut microbiota by breaking down complex carbohydrates, including breastmilk oligosaccharides. Other Bifidobacterium species, such as B. breve and B. longum, which are typically associated with healthy term infants, appeared earlier and were more abundant in supplemented infants.

On the other hand, the gut microbiota of non-supplemented infants showed higher abundance of microorganisms with pathogenic potential, including Klebsiella, Enterobacter, Escherichia, Enterococcus, and Staphylococcus.

Notably, the study found the persistent presence of frequently multidrug-resistant pathogens with high horizontal gene transfer potential, like Enterococcus, in both groups of infants, highlighting the need for continued surveillance. Strain-level analysis further showed the circulation of identical Enterococcus and Escherichia coli strains among unrelated infants in the same hospitals, highlighting the role of nosocomial transmission.

The analysis of gut microbiota of infants treated with benzylpenicillin and gentamicin revealed a significantly higher abundance of antibiotic resistance genes in non-supplemented infants during the first three weeks of life, indicating a potential role of probiotics in suppressing antimicrobial resistance in the preterm gut.

The study found that a higher abundance of Bifidobacterium is associated with lower antibiotic resistance genes, justifying the observed benefits of probiotic supplementation in preterm infants. In contrast, a higher abundance of Enterococcus and Staphylococcus was associated with higher antibiotic resistance genes.

The study identified ten antibiotic resistance gene classes, with Enterococcus, Escherichia, Klebsiella, and Staphylococcus identified as the most resistant pathogens. Although differences at the strain level were often trends rather than statistically significant, a reduction in multidrug-resistant strains of Escherichia and Klebsiella was observed in the probiotic group.

The researchers also detected the colistin-resistance gene mcr-9.1 in a preterm infant sample predating its discovery in 2019, highlighting hidden reservoirs of last-resort antibiotic resistance genes in the neonatal gut.

Study significance

The study demonstrates that probiotic supplementation with Bifidobacterium bifidum and Lactobacillus acidophilus in preterm infants is beneficial in terms of increasing the abundance of commensal bacteria in the gut, reducing the abundance of multidrug-resistant bacteria, and reducing overall antibiotic resistance gene carriage.

The study reveals that short-term antibiotic therapy in early life did not show major effects on gut microbiota diversity within the three-week sampling window. Longer-term impacts were not assessed. However, such treatment can significantly increase the abundance of multidrug-resistant microorganisms with horizontal gene transfer potential, including Enterococcus. The ex vivo plasmid transfer experiment confirmed that Enterococcus can pass resistance plasmids between strains within a simulated infant gut environment.  

The observed abundance of Bifidobacterium in probiotic-supplemented preterm infants seems to have a protective effect by reducing the abundance of Enterococcus. This protective effect may be associated with Bifidobacterium-mediated depletion of carbon sources, which prevents the colonization and growth of microorganisms with pathogenic potential.

However, the persistence of bacterial species like Enterococcus in probiotic-supplemented and non-supplemented infants highlights the need for continued surveillance and targeted intervention strategies in neonatal intensive care units to reduce the risk of multidrug-resistant bacterial infection. The study also showed distinct functional pathways in supplemented infants, such as sucrose degradation and enhanced use of breastmilk oligosaccharides, supporting restoration of a more typical infant gut ecosystem.

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