Fig 1.
Genomic phylogeny of S. enterica isolates sampled in Brazil and imported chicken meat from Brazil.
Maximum likelihood phylogeny of core genome alignment (253,248 informative sites) from 495 genomes of S. enterica isolated from Brazilian poultry production (tips—green) or known UK imports (tips—brown). Inner ring indicates sequence type (MLST) according to the key. Outer ring indicates serovar, predicted by SISTR. An interactive version of this figure with supporting metadata is available at https://microreact.org/project/brch-figure1.
Fig 2.
Phylogeny of global Salmonella Heidelberg including Brazil and UK (domestic/imported food/travel) isolates.
(A) Maximum likelihood phylogenetic tree of Salmonella Heidelberg genomes, including isolates from Brazil, imported chicken meat from Brazil, domestic UK poultry, and representatives from the rest of the world. Nodes are coloured by country of origin as indicated in the key. An interactive version of this figure with supporting metadata is available at https://microreact.org/project/brch-fig2a (B) Maximum likelihood phylogenetic tree of genomes highlighted in lilac in part A. Tips were colour coded according to sample origin. Inner ring indicates the source lab. Outer ring indicates the collection year. An interactive version of this figure with supporting metadata is available at https://microreact.org/project/brch-fig2b.
Fig 3.
Phylogeny of Salmonella Minnesota.
(A) Maximum likelihood phylogenetic tree of Salmonella Minnesota genomes, including isolates from Brazil, imported chicken meat from Brazil, and representatives from the rest of the world. Nodes are coloured by country of origin as indicated in the key. An interactive version of this figure with supporting metadata is available at https://microreact.org/project/brch-3a (B) Maximum likelihood phylogenetic tree of genomes highlighted in lilac in part A. Tips were colour coded according to sample origin. Inner ring indicates the source niche. Outer ring indicates the collection year. An interactive version of this figure with supporting metadata is available at https://microreact.org/project/brch3b.
Fig 4.
UKHSA Salmonella Heidelberg and Salmonella Minnesota trends in human salmonellosis cases in England and Wales.
(A) Percentage over time of Salmonella Heidelberg and Salmonella Minnesota. (B) Percentage over time of four serovars causing salmonellosis in England and Wales.
Fig 5.
Phylogeny of sul2, tetA and/or blaCMY-2 carrying IncC plasmids in selected isolates.
Selected isolates from imported Brazilian raw chicken and food products tested in the UK and chicken obtained in Brazil. (A) Maximum likelihood phylogenetic tree of 67 genomes identified with an IncC plasmid. Genomes were selected from Brazilian samples collected from poultry. Nodes are coloured by predicted serovar as indicated in the key. (B) Maximum likelihood phylogenetic tree of 39 genomes identified with an IncI1 plasmid. Genomes were selected from Brazilian samples collected from poultry. Nodes are coloured by predicted serovar as indicated in the key.