Complete Genome Sequence of Clostridium perfringens LLY_N11, a Necrotic Enteritis-Inducing Strain Isolated from a Healthy Chicken Intestine

Li, Charles; Yan, Xianghe; Lillehoj, Hyun S.

doi:10.1128/genomea.01225-17

Cited by 9 publications

(10 citation statements)

References 14 publications

(14 reference statements)

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“…In this study, we also analysed C. perfringens isolates obtained from healthy or asymptomatic birds, with several isolates (LLY_N11 and T18) encoding comparable numbers of virulence genes when compared to broiler-NE isolates (n > 10). Importantly, healthy-broiler isolate LLY_N11 (netB-negative strain, encoded pfoA and cpb2) has previously been shown to successfully induce NE in an experimental model [4,50]. These data highlight the important role other host factors may play in prevention of overt disease e.g.…”

Section: Discussionmentioning

confidence: 85%

“…Twenty-two C. perfringens genomes were sequenced and assembled specific to this study and the remaining isolates were publicly available. Broiler isolates Del1 and LLY_N11 were publicly available complete genomes sequenced using long-read sequencing and were included in analyses [4,19]. A Maximum Likelihood (ML) phylogenetic tree was assembled using 88 isolates from 20,194 SNPs identified from the alignment of 1810 core genes ( Fig.…”

Section: Phylogenetic Analysis Reveals a Potentially Important Intercmentioning

confidence: 99%

“…As broilers reach slaughter weight at a young age (4-7 weeks) they are susceptible to several welfare and infection issues. Importantly, poultry Necrotic Enteritis (NE), an inflammatory gut infection in chickens, is responsible for a loss of US$6 billion per annum in the poultry industry, with C. perfringens reported to be the main causative agent [2][3][4][5].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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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 subset 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.

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Section: Discussionmentioning

confidence: 85%

Section: Phylogenetic Analysis Reveals a Potentially Important Intercmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2019

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“…In this study, we also analysed C. perfringens isolates obtained from healthy or asymptomatic birds, with several isolates (LLY_N11 and T18) encoding comparable numbers of virulence genes when compared to broiler-NE isolates (n>10). Importantly, healthy-broiler isolate LLY_N11 ( netB- negative strain, encoded pfoA and cpb2 ) has previously been shown to successfully induced NE in an experimental model [4, 50]. These data highlight the important role other host factors that may play a role in prevention of overt disease e.g.…”

Section: Discussionmentioning

confidence: 91%

“…Twenty-two C. perfringens genomes were sequenced and assembled specific to this study and the remaining isolates were publicly available. Broiler isolates Del1 and LLY_N11 were publicly available complete genomes sequenced using long-read sequencing and were included in analyses [4, 19]. A Maximum Likelihood (ML) phylogenetic tree was assembled using 88 isolates from 20194 SNPs identified from the alignment of 1810 core genes (Fig.…”

Section: Resultsmentioning

confidence: 99%

Genomic analysis on broiler-associated Clostridium perfringens strains and caecal microbiome profiling reveals key factors linked to poultry Necrotic Enteritis

Kiu¹,

Brown

Bedwell³

et al. 2019

Preprint

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BackgroundClostridium 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 caecal microbiota signatures associated with NE.ResultsWe 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 sub-set of 11 diseased and healthy broilers 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.ConclusionsThese 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.

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Molecular Biology Perspective of Susceptibility and Resistance in Main Target Pathogens in the Respective Species and Antimicrobials of Concern

Pokludová

2020

Antimicrobials in Livestock 1: Regulation, Science, Practice

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Complete Genome Sequence of Clostridium perfringens LLY_N11, a Necrotic Enteritis-Inducing Strain Isolated from a Healthy Chicken Intestine

Cited by 9 publications

References 14 publications

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

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

Genomic analysis on broiler-associated Clostridium perfringens strains and caecal microbiome profiling reveals key factors linked to poultry Necrotic Enteritis

Molecular Biology Perspective of Susceptibility and Resistance in Main Target Pathogens in the Respective Species and Antimicrobials of Concern

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