Complete genome sequences of three commensal and two avian pathogenic Escherichia coli strains isolated from farm animals in Russia

ABSTRACT Farm animals are a natural reservoir of commensal and pathogenic Escherichia coli strains with high zoonotic potential. Here, we present five complete genomes of E. coli strains isolated from healthy animals and animals with colisepticemia from farms in Russia. The strains contain diverse virulence-associated and antibiotic resistance genes and multiple plasmids.

F arm animals are a reservoir of highly diverse commensal and pathogenic Escheri chia coli, which are frequently multidrug resistant.E. coli antibiotic resistance and virulence-associated genes (ARGs and VAGs, respectively) are often carried by transpos able elements and plasmids, pointing to the role of horizontal gene transfer in the emergence of virulent multidrug-resistant strains (1).
Five E. coli strains were isolated from animals from industrial and private farms in Russia between 2019 and 2021.Three strains were obtained from fecal samples of healthy birds (Ch1) and cows (C25 and C51), and two strains (APEC20/16 and APEC37) were obtained from internal organs of birds with typical lesions of colisepticemia (2,3).The research was carried out in accordance with the International Guiding Principles for Biomedical Research Involving Animals.
Biosynthetic gene clusters (BGCs) and bacteriocins were predicted using antiSMASH (8), PRISM4 (9), and BAGEL4 (10).Several non-ribosomal peptide synthetase and polyketide synthase BGCs for siderophore biosynthesis (yersiniabactin, aerobactin, and enterobactin) and two ribosomally synthesized and post-translationally modified peptide (RiPP) BGCs for microcin B17 and C7 were identified in the sequenced genomes (Table 1).Siderophore BGCs were typically chromosomal, except for the aerobactin BGCs  located on plasmids in strains C51 and APEC37.BGCs of RiPPs were predominantly plasmid borne.Six out of 12 identified colicin clusters were found in the C51 strain, which harbors an especially rich set of plasmids (nine plasmids), carrying five out of its colicin clusters (Fig. 1).Multiple ARGs were predicted with Abricate (11) using the NCBI AMRFinderPlus database (12).Strains C51 and APEC contained a wide range of ARGs which confer resistance to up to eight classes of antibiotics (Table 1) and are frequently organized in resistance islands (Fig. 1).VAGs were predicted using VRprofile2 (13).A diverse repertoire of gene clusters related to cell adhesion (encoding curli, common pilus, type-1, F1C, and P fimbriae) and other genes linked to pathogenicity (hemoglobin protease, hemolysin, and K1 capsule biosynthesis) was detected (Table 1).Interestingly, strains isolated from animals with colisepticemia did not have an increased diversity of VAGs and ARGs compared with isolates from healthy animals, indicating that healthy farm animals can serve as a reservoir of pathogenic and antibiotic-resistant E. coli.

TABLE 1
Accession numbers, sequencing and assembly statistics, and genomic features of the sequenced E. coli strains a

TABLE 1
Accession numbers, sequencing and assembly statistics, and genomic features of the sequenced E. coli strains a a Chr indicates chromosomal position of a gene or a gene cluster.