Comparative genomic analyses of Escherichia coli from meat processing environment in relation to their biofilm formation and persistence

We investigated the phylogeny of biofilm forming (BF) and non-biofilm forming (NBF) Escherichia coli (n = 114) from beef processing environment and genetic elements in their BF and persistence, by comparative genomic analysis. Phylogroup B1 made up the largest proportion of both BF (73.8%) and NBF (50.9%) groups. E. coli from all sources examined had mixed phylogroups except for those recovered from equipment after cleaning which were exclusively phylogroup B1. Both core genome and gene content trees showed a tree-wide spread of BF strains, with clusters including both BF and NBF strains. Genome wide association studies (GWAS) by Scoary or Pyseer did not find any genes/mutations overrepresented in the BF group. Retrospective analysis of phenotypes found significant correlation (P < 0.05) between BF ability and curli production, cellulose synthesis, and/or mobility. However, the BF group also included strains negative for curli and cellulose and/or missing encoding genes for the two traits. All curli and cellulose encoding genes were present in most genomes, regardless of their BF status. The degree of motility was correlated with both curli and cellulose production, and 80 common genes were overrepresented in all three trait positive groups. A PTS enzyme II and a subsidiary gluconate catabolism pathway, and an iron-dicitrate transport system were more abundant in the persisting E. coli group. These findings suggest gene function redundancy in E. coli for biofilm formation and additional substrate utilization and iron acquisition in its persistence.