Prevalence and Genetic Analysis of <i>mcr-3</i> -Positive Aeromonas Species from Humans, Retail Meat, and Environmental Water Samples

Abstract

The mobile colistin resistance gene <i>mcr-3</i> is globally disseminated in both <i>Enterobacteriaceae</i> and <i>Aeromonas</i> species, with the latter potentially serving as a reservoir for this gene. Here, we investigated the prevalence of <i>mcr-3</i> 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 <i>mcr-3</i>-positive isolates. An enriched broth screening method was used to detect <i>mcr-3</i> 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 <i>mcr-3</i>-positive isolates were subjected to antimicrobial susceptibility testing, conjugation, and whole-genome sequencing. Ten <i>Aeromonas</i> isolates, including 2 from human rectal swabs, 1 from pork, 3 from chicken meat, and 4 from the aquatic environment, were positive for <i>mcr-3</i>, but only 2 showed resistance to colistin. In addition to the <i>mcr-3</i> variants identified previously (the novel variants were termed <i>mcr-3.13</i> to <i>mcr-3.18</i>), all isolates harbored <i>mcr-3</i>-like genes downstream of the <i>mcr-3</i> 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 <i>mcr-3</i>-positive <i>Aeromonas</i> isolates and possible transmission between different sources in China and even worldwide. Close relationships between <i>mcr-3</i>-positive and <i>mcr-3</i>-negative <i>Aeromonas</i> isolates suggested that <i>mcr-3</i> might be common in <i>Aeromonas</i> species, which are not inherent hosts of <i>mcr-3</i> but may act as an important reservoir of this mobile colistin resistance gene.