Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus

Abstract

Staphylococcus aureus are globally disseminated among farmed chickens causing skeletal muscle infections, dermatitis, and septicaemia. The emergence of poultry-associated lineages has involved zoonotic transmission from humans to chickens but questions remain about the specific adaptations that promote proliferation of chicken pathogens. We characterized genetic variation in a population of genome-sequenced S. aureus isolates of poultry and human origin. Genealogical analysis identified a dominant poultry-associated sequence cluster within the CC5 clonal complex. Poultry and human CC5 isolates were significantly distinct from each other and more recombination events were detected in the poultry isolates. We identified 44 recombination events in 33 genes along the branch extending to the poultry-specific CC5 cluster, and 47 genes were found more often in CC5 poultry isolates compared with those from humans. Many of these gene sequences were common in chicken isolates from other clonal complexes suggesting horizontal gene transfer among poultry associated lineages. Consistent with functional predictions for putative poultry-associated genes, poultry isolates showed enhanced growth at 42 °C and greater erythrocyte lysis on chicken blood agar in comparison with human isolates. By combining phenotype information with evolutionary analyses of staphylococcal genomes, we provide evidence of adaptation, following a human-to-poultry host transition. This has important implications for the emergence and dissemination of new pathogenic clones associated with modern agriculture.

Keywords: Staphylococcus; evolution; genomics; poultry infection; recombination.

Fig. 1.—

Samples were collected from infected breeder chickens across the UK (n = 161), USA (n = 25), and the Netherlands (n = 5). Grouped bar charts show the relative proportion of isolates belonging to CC5 by country (1a), year of collection (1b), and disease site (1c). MLST clonal complexes were assigned based on shared sequence at five or more MLST house-keeping loci.

Fig. 2.—

Genetic relatedness of S. aureus isolates from different hosts. (a) Host origin of all S. aureus isolates from chicken (blue), human (red), and other species (yellow). Clonal complex (CC) designations are based on shared MLST housekeeping loci. Chicken isolates were found in five sequence clusters, corresponding to CCs 1, 5, 30, 358, and 398 which are highlighted. The tree was constructed from a core genome alignment (2,789,909 bp) of 1,700 genes using an approximation of the maximum likelihood algorithm. (b) Reconstruction of the clonal frame with putative recombination regions removed of CC5, including 20 chicken (blue) and 26 human (red) isolates (2,302,773 bp alignment in ClonalFrame).

Fig. 3.—

Genes and recombination regions identified as poultry-associated in ClonalFrame analysis mapped to the ED98 reference genome and three plasmids (pAVX, pAVY, and pT181). The frequency of these genes (red circles) and recombination regions (black crosses) in chicken and human isolate genomes is shown for CC5, CC398, CC1, and CC385 (chicken only). The relative abundance of these genes/recombination regions was calculated as presence in chicken minus presence in human isolates. 0 score denotes equal presence in poultry and human isolates. The majority of poultry-association in the core and accessory genome is colocalized in three chromosomal regions, which are labeled.

Fig. 4.—

Genome positions of colocalized poultry-associated genes and recombination regions. (a) Poultry-associated genes (blue) and recombination regions (red) mapped to the ED98 reference chromosome. Hot spots of colocalization of poultry-associated elements are numbered. (b) Schematic diagrams of each hot spot showing gene content, including poultry-associated genes and genes containing recombination regions. Genes with no poultry-association in the same regions are also shown (grey). Poultry-associated genes and genes containing recombination regions are labeled, including S. aureus pathogenicity island genes (1), transposon-related genes (2), hypothetical proteins (3), and phage-related genes (4). More details of putative gene function can be found in supplementary table S2, Supplementary Material online.

Fig. 5.—

Growth of S. aureus isolates from poultry (red) and human (black) in TSB medium. Curves represent growth levels in vitro (OD₆₀₀) over a period of 20 h at 37 °C (dashed lines) and 42 °C (solid lines) in medium. Mean growth levels and standard deviation (dotted lines) was calculated for 12 poultry and four human clinical samples.