Fig 1.
Demographic overview of S. Agona infections in England and Wales, from 2004–2020.
(A) Population pyramid of age and sex distribution of 2098 cases of infections. (B) Annual case numbers. (C) Neighbour-joining phylogeny categorised by year of isolation (inner ring), travel (second ring), most common HC5 clusters (third ring) and carriage status (outer ring) as denoted by colour. S. Agona strains associated with carriage are distributed throughout the population structure with domestic and travel associated clusters differentiated at the HC5 level.
Fig 2.
Genome structure variations were solely identified in early stages of infection.
(A) Number and distribution of genome structures (GSs) identified from acute/same episode infection (orange) or carriage (blue). (B) All GSs identified in the collection where GS designations are given as X.Y which represent the order (X) and orientation (Y) of the seven genome fragments (coloured blocks labelled 1–7) which are located between the seven ribosomal operons (open arrows) that split Salmonella genomes [29]. GS fragments are labelled numerically clockwise in respect to the Salmonella enterica reference LT2 (GS1.0) and individual inverted fragment orientations are denoted prime (′) with striped colours. Isolate numbers displaying each GS are shown. Dashed and solid black lines show the origin and terminus of replication, respectively.
Fig 3.
Visualisation of gain/loss in metabolic capacity during infection within patients.
Highlighted comparisons of carbon utilisation of original and final isolates of chronic carriers P1 (A), P4 (B-D), P5 (E and F) and P6 (G and H). For P6, carbon source utilisation was also assessed for another two intermediate isolates. Keys are included with each graph showing isolates in chronical order from the original at the top to last. Highlighted carbon source is named below each graph.