biostudies-literatureUnknown10(2)Lozica L<i>Escherichia coli</i> is the main bacterial cause of major economic losses and animal welfare issues in poultry production. In this study, we investigate the effect of an autogenous vaccine on <i>E. coli</i> strains longitudinally isolated from broiler breeder flocks on two farms. In total, 115 <i>E. coli</i> isolates were sequenced using Illumina technologies, and compared based on a single-nucleotide polymorphism (SNP) analysis of the core-genome and antimicrobial resistance (AMR) genes they carried. The results showed that SNP-based phylogeny corresponds to a previous multilocus-sequence typing (MLST)-based phylogeny. Highly virulent sequence types (STs), including ST117-F, ST95-B2, ST131-B2 and ST390-B2, showed a higher level of homogeneity. On the other hand, less frequent STs, suchMicroorganisms377https://www.ebi.ac.uk/biostudies/studies/S-EPMC8879504biostudies-literatureGenomic Analysis of <i>Escherichia coli</i> Longitudinally Isolated from Broiler Breeder Flocks after the Application of an Autogenous Vaccine.PMC8879504Li GVillumsen KRGottstein ZHu XMaljkovic MMLozica LfalseGenomic Analysis of <i>Escherichia coli</i> Longitudinally Isolated from Broiler Breeder Flocks after the Application of an Autogenous Vaccine.<i>Escherichia coli</i> is the main bacterial cause of major economic losses and animal welfare issues in poultry production. In this study, we investigate the effect of an autogenous vaccine on <i>E. coli</i> strains longitudinally isolated from broiler breeder flocks on two farms. In total, 115 <i>E. coli</i> isolates were sequenced using Illumina technologies, and compared based on a single-nucleotide polymorphism (SNP) analysis of the core-genome and antimicrobial resistance (AMR) genes they carried. The results showed that SNP-based phylogeny corresponds to a previous multilocus-sequence typing (MLST)-based phylogeny. Highly virulent sequence types (STs), including ST117-F, ST95-B2, ST131-B2 and ST390-B2, showed a higher level of homogeneity. On the other hand, less frequent STs, such2022-01-01T00:00:00Z2022 Feb2026-04-08T17:33:24.124Z2025-04-04T10:01:53.846ZS-EPMC88795043520883410.3390/microorganisms10020377