Comparative genomic analysis of Escherichia coli isolated from cases of bovine clinical mastitis and the dairy farm environment

<i>Escherichia coli</i> is a major causative agent of environmental bovine mastitis, and this disease causes significant economic losses for the dairy industry. There is still debate in the literature as to whether mammary pathogenic <i>E. coli</i> (MPEC) is indeed a unique <i>E. coli</i> pathotype or if this infection is merely an opportunistic infection caused by any <i>E. coli</i> isolate being displaced from the bovine gastrointestinal tract to the environment and then into the udder. In this study, we conducted a thorough genomic analysis of 113 MPEC isolates from clinical mastitis cases and 100 environmental <i>E. coli</i> isolates from the environment of dairy farms around the world. A phylogenomic analysis indicated that MPEC and the environmental <i>E. coli</i> isolates formed clades based on common sequence types and O antigens but did not cluster based on mammary pathogenicity. The comparison of core and soft-core genes of each set of isolates identified the three genes of the ferric dicitrate uptake system (Fec), <i>fecI</i>, <i>fecR</i> and <i>fecA</i>, as soft-core genes of MPEC (<i>n</i>=110). These genes were also present in 27 <i>E. coli</i> isolates from environmental sources. Rather than being a virulence gene cluster, it is likely that the Fec system provides a competitive advantage to <i>E. coli</i> in the mammary gland - an iron-poor environment. Using this cluster as a marker for MPEC may offer an opportunity to develop novel treatments for <i>E. coli</i> mastitis, based on its presence.