BackgroundAntibiotic resistance, an increasing challenge, is not only a national threat but also a global threat. Carriage of resistance genes is not limited to adults alone, various microbiota niches present in the body system of children have been found to harbor bacteria carrying resistant genes, especially, their gut microbiota. This study aims to identify selected antibiotic-resistant genes from the fecal samples of infants and the association of antibiotics use with the occurrence of resistant genes in the infant’s gut.MethodsA total number of 172 metagenomic DNA samples previously extracted from stool samples of 28 Nigerian babies longitudinally within their first year of life were screened for the presence of ESBL genes (blaSHV,blaTEM, andblaCTX-M), PMQR genes (qnrA,qnrB,qnrS,qepA), ribosomal protection protein tetracycline resistance gene, (RPP) β-lactamase (blaZ), macrolide (ermA,ermB,mefA/E), aminoglycoside modifying enzymes gentR(aac(6′)/aph(2″)) anddfrAgenes by PCR. Nineteen (19) of the 28 babies used antibiotics during the study. The association between antibiotic use by the babies within the first year of life and occurrence of resistant genes were analyzed by Spearman rank correlation.ResultsOne hundred and twenty-two (122) samples (71%) out of the 172 isolates had antibiotic-resistance genes. PMQR genes were absent in all the samples. Three isolates hadblaTEM gene, nine isolates hadblaSHV gene, six isolates hadblaCTX-M gene and 19 isolates haddfrAgene, 31 samples hadtetgene, 29 samples hadmefgene, 27 samples hadermBgene, four samples hadermAgene, 13 samples hadblaZgene and 16 samples hadaacgene. The babies whose samples had resistant genes used antibiotics in the same months the samples were collected. Interestingly, the 11 babies whose samples had thedfrA gene all used antibiotics in the same months their samples were collected but none of them used trimethoprim/sulfamethoxazole antibiotic. The overall correlation matrix of the babies showed a strong association between antibiotic use (AU) and antibiotic use presence of resistance genes (AUPRG) with a coefficient of 0.89. Antibiotic-resistant genes are present in the gut of infants and their occurrence is strongly connected with antibiotic use by infants.