Radically different
Research presented at ESCMID Global 2026 in Munich has shown that antibiotic resistance genes (ARGs) can be present in newborns within the first hours of life, with the newborn gut becoming colonized before, during, or recently after delivery.
Meconium, the first stool passed by newborns, was traditionally thought to be sterile, explained study lead Elias Iosifidis, MD, PhD, from Aristotle University of Thessaloniki in Greece. However, recent molecular studies have detected microbial genetic material in meconium samples, indicating that the neonatal gut may be exposed to bacteria during pregnancy.
It has been suggested that this early microbial exposure could contribute to the development of antibiotic resistance. Indeed, ARGs have been detected in meconium samples, and their presence at this early stage may facilitate the spread of resistance through horizonal gene transfer between bacteria.
To investigate further, Iosifidis and colleagues screened 105 meconium samples that were collected from newborns admitted to a neonatal intensive care unit within 24 hours of birth for 56 different resistance genes associated with commonly used antibiotics.
“This is the largest study of its kind exploring the effect of hospital environment on the collection of ARGs in the neonatal gut,” said lead author Argyro Ftergioti. “We analyzed 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.”
The most frequently detected ARGs were oqxA, a gene that causes resistance to fluoroquinolones (like ciprofloxacin), olaquindox, chloramphenicol, and tigecycline, and qnrS, which contributes to decreased susceptibility to quinolones. These were found in 98% and 96% of samples, respectively.
The study also identified several genes encoding beta-lactamases, enzymes that cause resistance to beta-lactam antibiotics such as penicillins and cephalosporins. Among these, the most prevalent were blaCTXM (55%), blaCMY (51%), and blaSHV (39%). Genes linked to carbapenem resistance (KPC/NDM/GES/VIM), 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 harbors a diverse resistome, and the presence of clinically important ARGs so early in life is concerning,” said Ftergioti. “Although some ARGs were expected, their high prevalence across the majority of samples was striking—particularly for clinically critical genes offering carbapenem resistance.”
The team also found associations between resistance genes and several maternal and neonatal factors. The presence of the msrA (macrolide-streptogramin resistance) gene was linked with maternal hospitalization during pregnancy, while a higher number of resistance genes was associated with central venous catheter placement 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,” noted Ftergioti. He cautioned, however, that “this finding should be interpreted carefully, as it may reflect differences in early microbial exposure or other clinical factors.”
Overall, the data suggest that both maternal transmissions and early exposure to the hospital environment may contribute to the establishment of ARGs in the neonatal gut.
“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,” Ftergioti concluded.
The post Antibiotic Resistance Genes Established Early in Newborns appeared first on Inside Precision Medicine.
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