Prevalence and genetic analysis of mcr-3-positive aeromonas species from humans, retail meat, and environmental water samples

Abstract

The mobile colistin resistance gene mcr-3 is globally disseminated in both Enterobacteriaceae and Aeromonas species, with the latter potentially serving as a reservoir for this gene. Here, we investigated the prevalence of mcr-3 in rectal swabs from humans, in food-producing animals and their products, and in the aquatic environment, and we investigated the genetic relationships between the mcr-3-positive isolates. An enriched broth screening method was used to detect mcr-3 in samples, and species identification of isolates from positive samples was carried out by matrix-assisted laser desorption ionization–time of flight mass spectrometry and shotgun sequencing. All mcr-3-positive isolates were subjected to antimicrobial susceptibility testing, conjugation, and whole-genome sequencing. Ten Aeromonas isolates, including 2 from human rectal swabs, 1 from pork, 3 from chicken meat, and 4 from the aquatic environment, were positive for mcr-3, but only 2 showed resistance to colistin. In addition to the mcr-3 variants identified previously (the novel variants were termed mcr-3.13 to mcr-3.18), all isolates harbored mcr-3-like genes downstream of the mcr-3 variants. The MCR-3.13 to MCR-3.18 proteins exhibited only 89.2% to 96.1% amino acid identity to the original MCR-3 protein. Whole-genome sequence analysis indicated diversity within the genetic environments of mcr-3-positive Aeromonas isolates and possible transmission between different sources in China and even worldwide. Close relationships between mcr-3-positive and mcr-3-negative Aeromonas isolates suggested that mcr-3 might be common in Aeromonas species, which are not inherent hosts of mcr-3 but may act as an important reservoir of this mobile colistin resistance gene.