Antibiotic resistance genes (ARGs) – segments of DNA that help bacteria escape the effects of antibiotics – may be present in newborns within the first hours of life, according to research presented at ESCMID Global 2026.
The study analyzed meconium samples from 105 infants admitted to the neonatal intensive care unit (NICU) within the first 72 hours of life between July 2024 and July 2025. The study was part of a multidisciplinary research project led by Professor Elias Iosifidis at the Aristotle University of Thessaloniki, involving pediatric infectious disease specialists, neonatologists and molecular microbiology researchers.
Meconium, the first stool passed by newborn babies, was traditionally considered sterile. However, recent molecular studies have detected microbial genetic material in meconium samples, suggesting that the newborn’s gut may be exposed to bacteria during pregnancy. This early microbial exposure has been proposed as a possible contributor to the development of antibiotic resistance. ARGs have been found in meconium samples, And their presence at this early stage may facilitate the spread of resistance through horizontal gene transfer between bacteria. Based on this, the researchers examined the samples for 56 different resistance genes associated with commonly used antibiotics.
This is the largest study of its kind exploring the effect of the hospital environment on the accumulation of ARGs in the newborn intestine. We analyzed meconium samples within the first 72 hours of life to capture an early snapshot of microbial and genetic exposure in newborns. At this stage, the accumulation of resistance genes is primarily shaped by maternal transmission, delivery mode, and very early hospital exposure.”
Dr. Argiro Tergiotti, lead author
Most common genes detected oqxA (in 98% of samples) and QNRS (96%), which are associated with resistance to some commonly used antibiotics. The study also identified several genes encoding beta-lactamases, enzymes that break down widely used antibiotics. The most popular of these were blahCTXM (55%), blahCMY (51%) and blahSHV (39%). Genes associated with resistance to carbapenems, the last class of antibiotics, were found in 21% of the 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 newborn gut has a diverse immune response, and the presence of clinically significant ARGs so early in life is worrisome,” said Dr. Fattergioti.
“Although some ARGs were expected, their high prevalence in most samples was surprising – especially for clinically important genes conferring carbapenem resistance.”
The study also identified relationships between resistance genes and several maternal and neonatal factors. presence of MSRA (macrolide-streptogramin resistance) gene was associated with maternal hospitalization during pregnancy, while a higher number of resistance genes were associated with central venous catheter placement within the first 24 hours of life. Both findings likely reflect exposure to health care-associated germs in the hospital setting.
“Surprisingly, resuscitation soon after birth was associated with fewer resistance genes. We caution that this finding should be interpreted cautiously, however, as it may reflect differences in early microbial exposure or other clinical factors,” said Dr. Fatrigiotti.
Overall, the findings suggest that both maternal transmission and early exposure in the hospital environment may contribute to the establishment of ARGs in the newborn gut.
“Although further research is needed to understand how early transmission of resistance genes affects microbiome development and infection risk, these findings highlight the importance of surveillance, infection prevention and control in neonatal care,” Dr. Fatrigiotti concluded.
