RT Journal
A1 Arimizu, Yoko
A1 Kirino, Yumi
A1 Sato, Mitsuhiko P.
A1 Uno, Koichi
A1 Sato, Toshio
A1 Gotoh, Yasuhiro
A1 Auvray, Frédéric
A1 Brugere, Hubert
A1 Oswald, Eric
A1 Mainil, Jacques G.
A1 Anklam, Kelly S.
A1 Döpfer, Dörte
A1 Yoshino, Shuji
A1 Ooka, Tadasuke
A1 Tanizawa, Yasuhiro
A1 Nakamura, Yasukazu
A1 Iguchi, Atsushi
A1 Morita-Ishihara, Tomoko
A1 Ohnishi, Makoto
A1 Akashi, Koichi
A1 Hayashi, Tetsuya
A1 Ogura, Yoshitoshi
T1 Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains
JF Genome Research 
JO Genome Research 
YR 2019 
FD September 01 
VO 29 
IS 9 
SP 1495 
OP 1505 
DO 10.1101/gr.249268.119 
UL http://genome.cshlp.org/content/29/9/1495.abstract 
AB How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)–producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectively. The locus of enterocyte effacement (LEE)–encoded type 3 secretion system (T3SS) is the major virulence determinant of EPEC and is also possessed by major STEC lineages. Cattle are thought to be the primary reservoir of STEC and EPEC. However, genome sequences of bovine commensal E. coli are limited, and the emerging process of STEC and EPEC is largely unknown. Here, we performed a large-scale genomic comparison of bovine commensal E. coli with human commensal and clinical strains, including EPEC and STEC, at a global level. The analyses identified two distinct lineages, in which bovine and human commensal strains are enriched, respectively, and revealed that STEC and EPEC strains have emerged in multiple sublineages of the bovine-associated lineage. In addition to the bovine-associated lineage-specific genes, including fimbriae, capsule, and nutrition utilization genes, specific virulence gene communities have been accumulated in stx- and LEE-positive strains, respectively, with notable overlaps of community members. Functional associations of these genes probably confer benefits to these E. coli strains in inhabiting and/or adapting to the bovine intestinal environment and drive their evolution to highly virulent human pathogens under the bovine-adapted genetic background. Our data highlight the importance of large-scale genome sequencing of animal strains in the studies of zoonotic pathogens.