Antibiotics after birth affects gut microbes of babies

Treating babies with antibiotics in the first week of life is linked to a decrease in healthy bacteria necessary, among others, to digest milk and an increase in antimicrobial resistance, research suggests.

According to experts, clinicians should consider using antibiotics in a way that causes least harm to the newborns microbiome — the community of microbes that live in our body.

Under current guidelines, antibiotics directed at a wide range of bacteria are prescribed to four to 10 per cent of all newborns for suspected infections.

However, experts say that in most cases the antibiotics are prescribed unnecessarily as only a small proportion of those who receive the drugs are eventually diagnosed with an infection.

This overprescription is to ensure early treatment for those who are ultimately found to have an infection as any delay may quickly become life-threatening.

The study, published in Nature Communications, found a change in 251 of 695 different bacteria after treatment, changing the balance between good and bad bacteria in favour of more potentially harmful microbes.

Though gradually recovering over time, the changes to the microbiome and to antimicrobial resistance genes persisted for at least 12 months and did not improve with breastfeeding, which is known to help a baby’s immune system.

“We were surprised with the magnitude and duration of the effects of broad spectrum antibiotics on the infants’ microbiome when compared to effects of those same antibiotics on adults’ microbiota,” said lead author Professor Debby Bogaert, Chair of Paediatric Medicine at the University of Edinburgh.

“This is likely because the antibiotic treatment is given at a time that infants have just received their first microbes from their mother and have not yet developed a resilient microbiome,”Bogaert added.

Researchers conducted a clinical trial involving 227 babies to analyse how antibiotics affect a newborn’s microbiome.

The samples were analysed for the microbes that made up their newly forming microbiome and for bacterial genes related to antimicrobial resistance.

For newborns that had been prescribed antibiotics, there was found to be a significant decrease in the levels of different Bifidobacterium species compared with babies who had no antibiotic treatment.

These microbes aid in the digestion of human breast milk and promote gut health, while also supporting the immune defence against infection.

The team also found an increase in potentially disease-causing bacteria and in the number and abundance of genes related to antimicrobial resistance in the group that received antibiotics.

Further, of the three antibiotic treatment regimens tested, the combination of penicillin and gentamicin, was found to have the least detrimental effect on a baby’s gut microbiome and the number of antimicrobial resistance genes that emerge.


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