Preliminary Data on Escherichia coli, Yersinia enterocolitica, and Other Bacteria, as Well as Absent African Swine Fever Virus in the Gut Microbiota of Wild Mice and Voles from Bulgaria

Abstract

Small mammals are bioindicator organisms, and, through their gut microbiota (GM), could be carriers of pathogens and resistant bacteria. Also, wild GM composition has been suggested to have large implications for conservation efforts. Seventeen bacterial species were obtained from intestinal samples of Bulgarian yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) via classic microbiological cultivation and biochemical identification. Twelve Gram-negative—Escherichia coli, Yersinia enterocolitica, Yersinia kristensenii, Hafnia alvei, Serratia liquefaciens, Serratia marcescens, Serratia proteamaculans, Pseudescherichia vulneris, Klebsiella pneumoniae ssp. ozaenae, Enterobacter cloacea, Pantoea agglomerans, Pseudomonas fluorescens group—and five Gram-positive bacteria, Enterococcus faecium, Enterococcus faecalis, Enterococcus hirae, Bacillus thuringiensis, and Lysinibacillus sphaericus, were discovered. Enterobacteriaceae was the most abundant family. The isolates belonged to one of the major reported taxa in rodents, Firmicutes (the Gram-positive species) and to the less abundant, but still among the first, phyla, Proteobacteria (the Gram-negative strains). We did not find any members of the other major phylum, Bacteroidetes, likely due to lack of metagenomic techniques. E. coli and Y. enterocolitica were confirmed with polymerase chain reaction. Almost all strains had pathogenic potential, but the good condition of the test animals suggests their commensal role. The Y. enterocolitica strains did not have the ail pathogenicity gene. There was high prevalence of multi-drug resistance (MDR), but for the expected species with high level of intrinsic resistance, such as the enterococci and S. marcescens. E. coli and some other species had very low antimicrobial resistance (AMR), in line with other studies of wild rodents. Many of the strains had biotechnological potential; e.g., B. thuringiensis is the most used biological insecticide, with its proteins incorporated into the Bt genetically modified maize. The GM of the tested wild mice and voles from Bulgaria proved to be a source of bacterial diversity; many of the strains were promising in terms of biotechnology, and, in addition, the samples did not contain the African swine fever virus.