Background Infants are at a high risk of acquiring fatal infections, and their treatment relies on functioning antibiotics. Antibiotic resistance genes (ARGs) are present in high numbers in antibiotic-naive infants’ gut microbiomes, and infant mortality caused by resistant infections is high. The role of antibiotics in shaping the infant resistome has been studied, but there is limited knowledge on other factors that affect the antibiotic resistance burden of the infant gut. Objectives Our objectives were to determine the impact of early exposure to formula on the ARG load in neonates and infants born either preterm or full term. Our hypotheses were that diet causes a selective pressure that influences the microbial community of the infant gut, and formula exposure would increase the abundance of taxa that carry ARGs. Methods Cross-sectionally sampled gut metagenomes of 46 neonates were used to build a generalized linear model to determine the impact of diet on ARG loads in neonates. The model was cross-validated using neonate metagenomes gathered from public databases using our custom statistical pipeline for cross-validation. Results Formula-fed neonates had higher relative abundances of opportunistic pathogens such as Staphylococcus aureus, Staphylococcus epidermidis, Klebsiella pneumoniae, Klebsiella oxytoca, and Clostridioides difficile. The relative abundance of ARGs carried by gut bacteria was 69% higher in the formula-receiving group (fold change, 1.69; 95% CI: 1.12–2.55; P = 0.013; n = 180) compared to exclusively human milk–fed infants. The formula-fed infants also had significantly less typical infant bacteria, such as Bifidobacteria, that have potential health benefits. Conclusions The novel finding that formula exposure is correlated with a higher neonatal ARG burden lays the foundation that clinicians should consider feeding mode in addition to antibiotic use during the first months of life to minimize the proliferation of antibiotic-resistant gut bacteria in infants.

The global emergence and increased spread of antibiotic resistance threaten the effectiveness of antibiotics and, thus, the health of the entire population. Therefore, understanding the resistomes in different geographical locations is crucial in the global fight against the antibiotic resistance crisis.

Antimicrobial resistance (AMR) is one of the greatest global threats to human health, but substantial gaps in AMR data exist in West African countries. To obtain in-depth data, we explored the presence of antimicrobial resistance genes (ARGs) in the hospital wastewaters (HWW) of nine hospitals in Benin and Burkina Faso and, for comparison, of four hospitals in Finland. The highest total relative abundance of ARGs in HWWs was observed in Benin and the lowest in Finland. HWW resistomes were more similar to each other in Benin and Burkina Faso than in Finland. Different clinically relevant carbapenemases were detected in varying abundances, especially in HWWs from Burkina Faso and Finland. The most widespread carbapenemase gene in the Beninese hospitals, blaGES, was also found in water used for handwashing. blaNDM was present in the HWW of one Beninese hospital and was also detected in the stools of a hospitalized patient. Mobile colistin ARGs were detected in the HWWs of all the three studied countries, with mcr-5 variants being the most common. These and other mcr genes were observed in very high abundance in treated wastewater released into rivers in Burkina Faso. In Benin, only little is done to treat wastewaters, including HWWs. The results provide evidence for public health decision-makers in Benin and Burkina Faso for the dire need to increase wastewater treatment capacity, with particular attention to HWWs.SynopsisMetagenomic analysis of HWWs revealed high abundances of ARGs and their potential transmission to other environments in Benin and Burkina Faso.