Temporal dynamics & determinants of antibiotic resistance gene profiles in the infant gut during the first year of life

Background & objectives: To evaluate the progressive changes in the antibiotic resistance gene (ARG) profile by investigating their presence at different time points in the gut of infants during early life. Methods: Stool samples of 54 full-term healthy infants at birth at 6, 14, and 36 wk were processed to examine the presence of 20 antibiotic-resistance genes. McNemar’s test was used to check the statistical significance of the change in prevalence of genes across various time points. Chi-square test and logical regression were performed to evaluate the influence of clinical and demographic factors on the carriage of ARGs during early life. Results: Infants predominantly carried genes that conferred resistance to beta-lactams (80.6%), macrolides (MSL_B ) (70%), and the sulphonamide (61%) class of antibiotics. ARG carriage peaked at 6 wk and 14 wk with a significant increase in the proportion of genes like bla_TEM, catB, oqxA, sul1, ermB, tet, bla_SHV (P: <0.05) from birth to 6 wk. Caesarean-section [P = 0.001; odds ratio (OR): 6.93; confidence interval (CI): 2.06-23.26] and maternal exposure to cephalosporins postpartum (P value = 0.013; OR: 4.16; CI: 1.31-13.17) had a significant influence on the increased carriage of the bla_CTX-M gene at 6 wk of life. Interpretation & conclusions: Our findings demonstrate that infants carry a diverse range of ARGs, with peak prevalence observed at 6 and 14 wk. Delivery mode and maternal antibiotic exposure significantly impact ARG carriage, emphasising the need for targeted interventions to reduce antibiotic resistance in early life.