Antibiotic Resistance Genes Found in Newborns Within Hours of Birth

Meconium, the first stool passed by infants, was long considered sterile, yet recent molecular studies have detected microbial genetic material in these samples. Early microbial exposure has also been proposed as a contributor to resistance development. Researchers now present data showing that multiple antibiotic resistance genes can be detected in newborns within hours of birth.

Aristotle University of Thessaloniki led a multidisciplinary study that screened meconium collected from 105 infants admitted to a neonatal intensive care unit (NICU) within the first 72 hours of life. Conducted between July 2024 and July 2025, the analysis targeted 56 resistance genes associated with commonly used antibiotics. The work was presented at ESCMID Global 2026.

The approach focused on identifying antibiotic resistance genes (ARGs)—segments of DNA that enable bacteria to withstand antimicrobial treatment—and characterizing their early presence in the neonatal gut. Prior findings referenced by the investigators indicate that meconium can harbor microbial genetic material, suggesting exposure may occur during pregnancy. The team notes that ARG carriage at this stage may facilitate dissemination through horizontal gene transfer among bacteria, underscoring the relevance of early-life resistome profiling.

Results showed a high prevalence of specific ARGs. The oqxA gene was detected in 98% of samples and qnrS in 96%. Genes encoding beta-lactamases, enzymes that degrade widely used beta-lactam antibiotics, were also frequent, including blaCTXM (55%), blaCMY (51%), and blaSHV (39%). Genes associated with carbapenem resistance—a last-line antibiotic class—were present in 21% of samples. Each meconium specimen contained a median of eight resistance genes.

Analyses further linked ARG detection with maternal and early neonatal factors. Presence of the msrA gene, which confers macrolide-streptogramin resistance, was associated with maternal hospitalization during pregnancy. A higher total number of ARGs correlated with central venous catheter placement within 24 hours of life, while resuscitation shortly after birth was unexpectedly associated with fewer ARGs, a finding the team advises interpreting cautiously. Overall, the investigators conclude that both maternal transmission and early hospital exposures may contribute to establishing ARGs in the neonatal gut and emphasize the importance of surveillance and infection prevention and control in neonatal care.

"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 lead author Dr. Argyro Ftergioti. "Although some ARGs were expected, their high prevalence across the majority of samples was striking—particularly for clinically critical genes offering carbapenem resistance."

Related Links
ESCMID Global