Colistin, currently regarded as the last‐resort antibiotic for the treatment of infections caused by multidrug‐resistant bacteria, is used in poultry production to treat and prevent infection, and as a growth promoter. Poultry litter is commonly used as organic fertilizer; however, there are no reports on the effect of its application regarding colistin resistance in soils. Thus, the objective of the present study was to compare the abundance of the colistin resistance gene (mcr‐1) in soils from vegetable production areas that received non‐composted poultry litter as organic fertilizer and native vegetation areas. The mcr‐1 gene was detected in all soil samples from both areas. A significant difference (p < 0.05) was observed in the relative abundance of the mcr‐1 gene between soils pertaining to the vegetable production area and the native vegetation area in six of those 10 properties. This is the first report of the presence of the colistin resistance gene in soils from Brazil. The vast majority of antibiotic resistance genes acquired by human pathogens originated in natural environments. Thus, the presence of the mcr‐1 gene in soils treated with poultry litter and from native vegetation areas reinforces the need for studies that minimize potential risks of the development of colistin resistance. Highlights Poultry litter usually is employed as fertilizer; however, there are no reports of its impact in colistin resistance in soils. The mcr‐1 gene was detected in soils from both native vegetation and vegetable production. This is the first report of the presence of colistin resistance gene in soils from Brazil. The presence of mcr‐1 gene in soils can increase risks of the development and spread of colistin resistance.

Poultry litter is widely used worldwide as an organic fertilizer in agriculture. However, poultry litter may contain high concentrations of antibiotics and/or antimicrobial-resistant bacteria (ARB), which can be mobilized through soil erosion to water bodies, contributing to the spread of antimicrobial resistance genes (ARGs) in the environment. To better comprehend this kind of mobilization, the bacterial communities of four ponds used for irrigation in agricultural and poultry production areas were determined in two periods of the year: at the beginning (low volume of rainfall) and at the end of the rainy season (high volume of rainfall). 16S rRNA gene sequencing revealed not only significantly different bacterial community structures and compositions among the four ponds but also between the samplings. When the DNA obtained from the water samples was PCR amplified using primers for ARGs, those encoding integrases (intI1) and resistance to sulfonamides (sul1 and sul2) and β-lactams (blaGES, blaTEM and blaSHV) were detected in three ponds. Moreover, bacterial strains were isolated from CHROMagar plates supplemented with sulfamethoxazole, ceftriaxone or ciprofloxacin and identified as belonging to clinically important Enterobacteriaceae. The results presented here indicate a potential risk of spreading ARB through water resources in agricultural areas with extensive fertilization with poultry litter.