Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis
| Autor: | Ronald A. Dixon, Gordon Dougan, Derek Pickard, Harley Bedwell, Joseph Brown, Lindsay J. Hall, Charlotte Leclaire, Shabhonam Caim, Raymond Kiu |
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| Přispěvatelé: | Hall, Lindsay J [0000-0001-8938-5709], Apollo - University of Cambridge Repository |
| Rok vydání: | 2019 |
| Předmět: |
Clostridium perfringens
lcsh:QR1-502 Virulence Biology medicine.disease_cause Genome lcsh:Microbiology Poultry 03 medical and health sciences medicine Microbiome Pathogen 030304 developmental biology 2. Zero hunger Genetics Whole genome sequencing Necrotic enteritis 0303 health sciences lcsh:Veterinary medicine 030306 microbiology 16S rRNA analysis Phylogenomics General Medicine Bacterial adhesin D320 Animal Health Caecal microbiome lcsh:SF600-1100 Sample collection Toxin C520 Medical and Veterinary Microbiology |
| Zdroj: | Animal Microbiome, Vol 1, Iss 1, Pp 1-14 (2019) |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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