Analysis of meconium samples from 105 newborns found microbial genetic material with antibiotic resistance genes(ARGs) present, raising concerns about the impact of maternal hospitalisation and other exposure factors on the neonatal gut.
Via research presented at ESCMID Global 2026, a study of over a hundred newborns admitted to a neonatal intensive care unit (NICU) within the first 72 hours of life between July 2024 and July 2025 and led by Professor Elias Iosifidis at Aristotle University of Thessaloniki, confirmed the presence of antibiotic resistance genes in samples of meconium, the first stool passed by newborns.
Traditionally thought to be sterile, molecular studies have since established that microbial genetic material is present in meconium, which supports the theory that the neonatal gut may be exposed to bacteria during pregnancy.
The presence of microbial genetic material in the gut biome may contribute to the development and spread of antibiotic resistance through horizonal gene transfer between bacteria.
“This is the largest study of its kind exploring the effect of hospital environment on the collection of ARGs in the neonatal gut,” lead author Dr Argyro Ftergioti said. “We analysed meconium samples within the first 72 hours of life to capture the earliest snapshot of microbial and genetic exposure in newborns. At this stage, the collection of resistance genes is mainly shaped by maternal transmission, delivery mode and very early hospital exposures.”
Each sample contained a median of eight resistance genes
The genes associated with commonly used antibiotic resistence most detected were:
- oqxA (in 98% of samples)
- qnrS (96%)
The study also identified several genes encoding beta-lactamases, enzymes that break down widely used antibiotics. Within these, the most prevalent were:
- blaCTXM (55%)
- blaCMY (51%)
- blaSHV (39%)
Genes linked to resistance to carbapenems, a last-line class of antibiotics, were detected in 21% of samples. Each sample contained a median of eight resistance genes.
“This finding suggests that a pattern of ARGs is already established at this stage. The neonatal gut harbours a diverse resistome, and the presence of clinically important ARGs so early in life is concerning,” Dr Ftergioti added.
“Although some ARGs were expected, their high prevalence across the majority of samples was striking – particularly for clinically critical genes offering carbapenem resistance.”
Resistance genes were also associated with maternal and neonatal factors
Maternal hospitalisation during pregnancy was linked with the presence of the msrA (macrolide-streptogramin resistance) gene. The study also identified a higher number of resistance genes in newborns that had a central venous catheter placed within the first 24 hours of life.
Both findings likely reflect exposure to healthcare-associated microbes in hospital settings.
“Surprisingly, resuscitation shortly after birth was associated with fewer resistance genes. We would caution that this finding should be interpreted carefully, however, as it may reflect differences in early microbial exposure or other clinical factors,” Dr Ftergioti noted.
Dr Ftergioti emphasised that further research of the presence of antibiotic resistance genes in newborns would be needed, as well as careful interpretation of the findings. But the early indications suggest that maternal transmission and early hospital exposure may contribute to the issue.
“While further research is needed to understand how early carriage of resistance genes affects microbiome development and infection risk, these findings highlight the importance of surveillance, infection prevention and control in neonatal care,” concluded Dr Ftergioti.
Team Health Accessible
Health & Wellness Editorial Team
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