Fig 1.
Phylogeny and AMR profile of C. jejuni isolates from this study.
Core genome maximum likelihood phylogeny of C. jejuni isolates visualised in the interactive Tree of life tool (iTol) [23]. The tree was rooted on isolate 2445 to facilitate comparison with the SNP-based phylogeny shown in S1 Fig. Clustering of isolates was found to be in accordance between core genome and SNP-based phylogenies (S1 Fig). Clustering of isolates belonging to the same ST was consistent. Shown for each isolate are: isolate identifier, the geographic location of isolation, presence of AMR determinants and ST.
Fig 2.
Phylogeny and AMR profile of C. coli isolates from this study.
Core genome maximum likelihood phylogeny of C. coli isolates visualised in the iTol [23]; the tree was rooted with isolate B15 as an outgroup. Clustering of isolates was found to be in accordance between core genome and SNP-based phylogenies (S2 Fig). Isolates belonging to the same ST clustered together. Shown for each isolate are: isolate identifier, the geographic location os isolation, presence of AMR determinants and ST.
Fig 3.
MLST of C. jejuni isolates from this study and other African C. jejuni isolates.
Minimum spanning tree generated from C. jejuni allelic profiles visualised in GrapeTree [25], which included African C. jejuni isolates that were available in the PubMLST database [24] (accessed in January 2017). Isolates are colour-coded according to country and labelled with STs. The number of isolates per node (ST) are indicated through pie-charts. The number of nucleotide differences between STs is depicted at the branches. If STs differ by more than 2 nucleotides, branches are truncated (dashed lines). More details can be found in S1 Table and in the text.
Fig 4.
MLST of C. coli isolates from this study and other African C. coli isolates.
Minimum spanning tree generated from C. coli allelic profiles visualised in GrapeTree [25], which included African C. coli isolates that were available in the PubMLST database [24] (accessed in January 2017). Isolates are colour-coded according to country and labelled with STs. The number of isolates per node (ST) are indicated through pie-charts. The number of nucleotide differences between STs is depicted at the branches. If STs differ by more than 2 nucleotides, branches are truncated (dashed lines). More details can be found in S1 Table and in the text.
Table 1.
Frequency of antimicrobial resistance genes (tetO, gyrA-T86I and blaOXA-61) in C. jejuni and C. coli from broiler, free-range chickens and human clinical isolates.