Genome-Wide Analysis of Escherichia coli Isolated from Dairy Animals Identifies Virulence Factors and Genes Enriched in Multidrug-Resistant Strains

Abstract

The gastrointestinal tracts of dairy calves and cows are reservoirs of antimicrobial-resistant bacteria (ARB), which are present regardless of previous antimicrobial therapy. Young calves harbor a greater abundance of resistant bacteria than older cows, but the factors driving this high abundance are unknown. Here, we aimed to fully characterize the genomes of multidrug-resistant (MDR) and antimicrobial-susceptible Escherichia coli strains isolated from pre-weaned calves, post-weaned calves, dry cows, and lactating cows and to identify the accessory genes that are associated with the MDR genotype to discover genetic targets that can be exploited to mitigate antimicrobial resistance in dairy farms. Results indicated that both susceptible and resistant E. coli isolates recovered from animals on commercial dairy operations were highly diverse and encoded a large pool of virulence factors. In total, 838 transferrable antimicrobial resistance genes (ARGs) were detected, with genes conferring resistance to aminoglycosides being the most common. Multiple sequence types (STs) associated with mild to severe human gastrointestinal and extraintestinal infections were identified. A Fisher’s Exact Test identified 619 genes (ARGs and non-ARGs) that were significantly enriched in MDR isolates and 147 genes that were significantly enriched in susceptible isolates. Significantly enriched genes in MDR isolates included the iron scavenging aerobactin synthesis and receptor genes (iucABCD-iutA) and the sitABCD system, as well as the P fimbriae pap genes, myo-inositol catabolism (iolABCDEG-iatA), and ascorbate transport genes (ulaABC). The results of this study demonstrate a highly diverse population of E. coli in commercial dairy operations, some of which encode virulence genes responsible for severe human infections and resistance to antibiotics of human health significance. Further, the enriched accessory genes in MDR isolates (aerobactin, sit, P fimbriae, and myo-inositol catabolism and ascorbate transport genes) represent potential targets for reducing colonization of antimicrobial-resistant bacteria in the calf gut.

Virulome analysis of Escherichia coli ST117 from bovine sources identifies similarities and differences with strains isolated from other food animals

“…Dairy calves are often born anemic and for the first eight weeks of life are predominantly fed a milk/milk-replacer diet, which is low in iron compared to the forages of older post-weaned animals [ 32 ]. We have previously hypothesized that this low-iron environment selects for strains that encode accessory siderophores, such as those strains with iucABCD-iutA and sitABCD [ 11 , 12 ]. These two iron-scavenging operons are frequently located on an IncFIB plasmid that can simultaneously encodes ARGs [ 33 , 34 ].…”

“…Multidrug-resistant E. coli ST117 can be found in the bovine calf gut, which is an iron-poor environment because of the low iron levels in colostrum and milk [11,12,29]. Previous research has identified a positive association between the presence of iron-scavenging genes and the MDR genotype in E. coli collected from young calves [11,12].…”

“…Multidrug-resistant E. coli ST117 can be found in the bovine calf gut, which is an iron-poor environment because of the low iron levels in colostrum and milk [11,12,29]. Previous research has identified a positive association between the presence of iron-scavenging genes and the MDR genotype in E. coli collected from young calves [11,12]. In this study, 81% of the bovine-associated genomes encoded iucABCD-iutA, 97% encoded fyuA, 99% encoded chuA, and 71% encoded sitABCD, all of which are involved in iron transport from the extracellular environment into the E. coli cell.…”

“…Dairy calves typically shed a greater ratio of resistant bacteria to susceptible bacteria, and the mechanisms for this are not yet elucidated [5,9]. Previous research has suggested that diet is related to this difference in resistance carriage by animal age [10][11][12]. The iron content of milk is relatively low and this has been hypothesized to select for strains that encode accessory iron scavenging genes (siderophores) which are often colocated on plasmids carrying ARGs [11,12].…”

“…Previous research has suggested that diet is related to this difference in resistance carriage by animal age [10][11][12]. The iron content of milk is relatively low and this has been hypothesized to select for strains that encode accessory iron scavenging genes (siderophores) which are often colocated on plasmids carrying ARGs [11,12].…”