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Background   Clostridium perfringens  is a key pathogen in poultry-associated necrotic enteritis (NE). To date there are limited Whole Genome Sequencing based studies describing broiler-associated  C. perfringens  in healthy and diseased birds. Moreover, changes in the caecal microbiome during NE is currently not well characterised. Thus, the aim of this present study was to investigate  C. perfringens  virulence factors linked to health and diseased chickens, including identifying putative caecal microbiota signatures associated with NE.    Results  We analysed 88 broiler chicken  C. perfringens  genomes (representing 66 publicly available genomes and 22 newly sequenced genomes) using different phylogenomics approaches and identified a potential hypervirulent and globally-distributed clone spanning 20-year time-frame (1993–2013). These isolates harbored a greater number of virulence genes (including toxin and collagen adhesin genes) when compared to other isolates. Further genomic analysis indicated exclusive and overabundant presence of important NE-linked toxin genes including  netB  and  tpeL  in NE-associated broiler isolates. Secondary virulence genes including  pfoA ,  cpb2 , and collagen adhesin genes  cna ,  cnaA  and  cnaD  were also enriched in the NE-linked  C. perfringens  genomes. Moreover, an environmental isolate obtained from farm animal feeds was found to encode  netB , suggesting potential reservoirs of NetB-positive  C. perfringens  strains (toxinotype G). We also analysed caecal samples from a small sub-set of 11 diseased and healthy broilers for exploratory microbiome investigation using 16S rRNA amplicon sequencing, which indicated a significant and positive correlation in genus  Clostridium  within the wider microbiota of those broilers diagnosed with NE, alongside reductions in beneficial microbiota members.    Conclusions  These data indicate a positive association of virulence genes including  netB, pfoA, cpb2 ,  tpeL  and  cna  variants linked to NE-linked isolates. Potential global dissemination of specific hypervirulent lineage, coupled with distinctive microbiome profiles, highlights the need for further investigations, which will require a large worldwide sample collection from healthy and NE-associated birds.

animal microbiome

Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis