The effect of antibiotics after birth on gut microbes of babies

The effect of antibiotics after birth on gut microbes of babies
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A new study has uncovered that treating babies with antibiotics in the first week of life affects their gut microbes, the ability to digest milk, and antimicrobial resistance.

The experts have stated that clinicians should consider using antibiotics in a way that causes minimal harm to a newborn’s microbiome, which is the community of the gut microbes that live in our body.

Researchers from the Universities of Edinburgh and Birmingham, and the Spaarne Hospital and University Medical Centre Utrecht, The Netherlands, conducted a clinical trial involving 227 babies to analyse how antibiotics affect the gut microbes in babies.

The findings were published in Nature Communications.

The impact of antibiotics on gut microbes

Current guidelines state that antibiotics can be utilised to target a wide range of bacteria, known specifically as broad-spectrum antibiotics. These are currently prescribed to four to 10% of all newborns for suspected infections. However, experts claim 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 over-prescription is to ensure early treatment for those who are ultimately found to have an infection as any delay may become life-threatening.

The study looked at 147 infants with suspected sepsis who had received one of three standard antibiotic treatments. Their outcomes were compared with those of 80 babies with no suspected infections and those who had not been prescribed an antibiotic.

To analyse the impact, all the babies had a rectal or faecal sample taken before and after treatment, and at one, four and 12 months of age. The samples were analysed for gut microbes that made up their newly forming microbiome and for bacterial genes related to antimicrobial resistance.

For newborn’s that had been prescribed antibiotics, the team of researchers discovered a significant decrease in levels of different Bifidobacterium species compared with babies who had no antibiotic treatment. These specific gut microbes aid in the digestion of human breast milk and promote gut health whilst supporting the immune defence against infection.

Furthermore, 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. A change in 251 of 695 different bacteria investigated was observed after treatment, changing the balance between good and bad bacteria in favour of more potentially harmful gut microbes. The changes to the microbiome and antimicrobial resistance genes persisted for at least 12 months and did not improve with breastfeeding, which is known to support the baby’s immune system.

Professor Debby Bogaert, Chair of Paediatric Medicine at the University of Edinburgh and study lead, said: “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. 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.”

Antibiotic treatments

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

The researchers concluded this particular combination of antibiotics should be preferably prescribed when treating suspected infections in newborns.

Dr Marlies van Houten, general paediatrician at the Spaarne Hospital, the Netherlands, and co-Principal Investigator of the study, said: “The fact that start of antibiotic treatment rather than duration seems to be responsible for the damage to the microbiome underlines we need better biomarkers or biological predictors to more accurately determine which infant will develop an infection and thus require antibiotics, and which will not.”

Prof Willem van Schaik, Professor of Microbiology and Infection at the University of Birmingham, said: ”It is particularly troubling that following antibiotic therapy in newborns we observed a strong increase in Klebsiella and Enterococcus species which are both important multidrug-resistant pathogens.

“This underlines the importance of further studies into balancing the need and effectiveness of these antibiotics and the risk of the emergence of genes linked with resistance. There may also be scope to develop new interventions, like live biotherapeutics – a treatment that is produced by or involving living cells –  to effectively restore the composition of the infant gut microbiome after antibiotic therapy.”


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