Among 157 collected fecal samples from domestic animals (dogs and cats), a total of 218 bacterial isolates were obtained from selective medium agar LBJMR (Vancomycin and colistin). As already reported, the gastrointestinal tract of animals can harbor a highly complex mixture of organisms that help maintain intestinal flora and overall health [31]. Indeed, the study of fecal samples depends upon the natural composition of the microorganisms and is specific to each animal. According to the literature, most studies have been performed on the general microorganism composition and most data have been derived from the analysis of feces from healthy laboratory animals [32,33]. In our study, the composition of microorganisms in the feces samples was described in terms of naturally colistin-resistant bacteria and those with acquired colistin resistance via mcr genes. Identification of colistin-resistant bacteria in cats revealed 150 bacteria, as represented in Figure 1. Identification encompassed 23 different bacterial species. Eighty percent (n = 120) of all identified bacteria were Gram-positive and 20% (n = 30) were Gram-negative. The dominant strains were naturally colistin-resistant for all GPB: Bacillus cereus, B. vallismortis, Enterococcus durans, E. faecalis, E. faecium, E. hirae, Leuconostoc citreum, L. mesenteroides, and Pediococcus pentosacens. A high proportion of Lactobacillus species were identified: L. curvatus, L. brevis, L. fructivorans, L. murinus, L. paracasei, L. planetarium, L. reuteri, L. sakei, and L. salivarius. In contrast, the GNB that were isolated were believed to have acquired resistance to colistin via mcr genes or other mechanisms. Here, 13% (n = 4) of colistin-resistant GNB were screened as being mcr carriers: E. coli (n = 3) and Rahnella aquatilis (n = 1). In addition, 87% (n = 26) of GNB strains were naturally resistant to colistin: Sphingomonas paucimobilis, Providencia heimbachae, and Hafnia alvei (Figure 1).

The selective bacterial culture of dogs’ feces allowed us to isolate a total of 68 bacterial strains, divided into 14 different species. Fifty percent (n = 34) of the isolated strains were Gram-negative and 50% (n = 34) were Gram-positive. The isolated GPB in dogs’ feces were: L. brevis, L. coryniformis, L. murinus, L. paracasei, L. planetarium, L. reuteri, L. saerimmeri, L. sakei and P. pentosacens. The Gram-negative strains corresponded to E. coli, Moellerella wisconsensis and Brevundimonas diminuta. Sixty-five percent (n = 22) of the GNB were naturally resistant to colistin: H. alvei and Morganella morganii (Figure 2). Colistin-resistant bacteria differ widely from one animal to another. As mentioned previously, bacteria in fecal samples from dogs exhibited broad variability [34]. Generally, colistin is used orally, with low bioavailability, so the gastrointestinal microorganisms are directly exposed to colistin [35]. In 2016, the polymyxin family was the fifth best-selling antibiotic in Europe, and among polymyxins, colistin accounted for more than 99.9% of sales [36]. This uncontrollable use accelerated the dissemination of colistin resistance in animals and, subsequently, human beings [37]. Consequently, in 2016 the European Medicines Agency (EMA) updated its guidelines to minimize the use of colistin in animals to reduce its impact on human health [36,38]. The restricted colistin use in cats and dogs in France has not prevented the abundance of colistin-resistant bacteria in their microbiome composition. These findings highlight a topic that requires more research on the sources of colistin resistance.

Cats and dogs, on the other hand, share certain bacterial species; however, as shown in Figure 3, colistin-resistant bacteria in cat and dog feces are variable. In cats, we isolated a variety of species of the genera: Lactobacillus, Bacillus, and Enterococcus, whereas in dogs Lactobacillus was the most abundant genus, with seven different species. Moreover, GNB isolated in cats and dogs are different and do not belong to the same bacterial genera. In addition, cats and dogs also share certain bacterial species. The bacterial cross-link between cats and dogs corresponds to the following bacteria: GNB (E. coli, H. alvei, P. heimbachae and S. paracaseimobilis); and GPB (L. murinus, L. plantarum, L. sakei, L. reuteri, L. paracasei, L. brevis and P. pentosaceus). In colistin-resistant bacteria, natural colistin resistance is stronger than acquired resistance. It is interesting to note that both humans and animals can have a cross-link of identical bacterial species in their stools, which could lead to bacterial exchanges between the two species [39].