Genome analysis of Clostridium perfringens isolates from healthy and necrotic enteritis infected chickens and turkeys

Ronco, Troels; Stegger, Marc; Ng, Kim Lee; Lilje, Berit; Lyhs, Ulrike; Andersen, Paal Skytt; Pedersen, Karl

doi:10.1186/s13104-017-2594-9

Cited by 22 publications

(25 citation statements)

References 23 publications

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“…Adhesin is an important virulence factor in broiler-linked NE [14, 18], and in this study we found that adhesin genes (at least one variant) were overall enriched (P<0.0001) in NE-linked isolates (58/62; 93.5%) vs healthy isolates (9/20; 45%). Among all related adhesin variants, cna, cnaA and cnaD genes were significantly enriched in NE-associated C. perfringens isolates (P<0.05), linking these genes to NE-disease development (Additional file 2: Fig.…”

Section: Resultssupporting

confidence: 51%

“…At present there are only two smaller scale WGS-based studies on broiler-associated C. perfringens [14, 18]. Thus, to further our understanding on C. perfringens dissemination and virulence profiles in the context of broiler-NE, we performed phylogenetics and in-depth comparative genomics on 88 chicken-associated C. perfringens isolates, (strains from public genome databases, alongside 22 newly isolated and sequenced strains).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Resultssupporting

confidence: 51%

Section: Introductionmentioning

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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“…Birds raised on litter as was the case in the present study, are more likely to be colonized than birds reared on a wire floor. As long as our knowledge about the prevalence of virulent environmental turkey Clostridium perfringens strains is insufficient [15,16], a role of environmental Clostridium perfringens strains in lesion induction cannot be ruled out.…”

Section: Colonization Of the Small Intestine By Environmentalmentioning

confidence: 99%

“…The causative agent [1,2], pathogenesis [3,4], role of host immunity [5] and intestinal microbiota [6,7], epidemiology [8,9] and experimental reproduction [10] of this disease in broiler chickens have been extensively investigated. Necrotic enteritis occurs in turkeys and Clostridium perfringens has been implicated in the aetiology [11][12][13][14][15], but little information exists concerning the pathogenesis [16], immunity, microbiota or experimental reproduction of turkey necrotic enteritis.…”

Section: Introductionmentioning

confidence: 99%

Developing an experimental necrotic enteritis model in turkeys - the impact of Clostridium perfringens, Eimeria meleagrimitis and host age on frequency of severe intestinal lesions

et al. 2020

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Background: Necrotic enteritis is a significant problem to the poultry industry globally and, in Norway up to 30% of Norwegian turkey grow-outs can be affected. However, despite an awareness that differences exist between necrotic enteritis in chickens and turkeys, little information exists concerning the pathogenesis, immunity, microbiota or experimental reproduction of necrotic enteritis in turkeys. In particular, it is important to determine the appearance of the gross lesions, the age dependency of the disease and the role of netB toxin of Clostridium perfringens. To this end, we report our findings in developing an in vivo experimental model of necrotic enteritis in turkeys. Results: A four tier (0-3) scoring system with clearly defined degrees of severity of macroscopic intestinal lesions was developed, based on 2312 photographic images of opened intestines from 810 B.U.T. 10 or B.U.T. Premium turkeys examined in nine experiments. Loss of macroscopically recognizable villi in the anterior small intestine was established as the defining lesion qualifying for a score 3 (severe intestinal lesions). The developed scoring system was used to identify important factors in promoting high frequencies of turkeys with severe lesions: a combined Eimeria meleagrimitis and Clostridium perfringens challenge, challenge at five rather than 3 weeks of age, the use of an Eimeria meleagrimitis dose level of at least 5000 oocysts per bird and finally, examination of the intestines of 5-week-old turkeys at 125 to 145 h after Eimeria meleagrimitis inoculation. Numbers of oocysts excreted were not influenced by Clostridium perfringens inoculation or turkey age. Among three different lesion score outcomes tested, frequency of severe lesions proved superior in discriminating between impact of four combinations of Clostridium perfringens inoculation and turkey age at challenge. Conclusions: This study provides details for the successful establishment of an in vivo model of necrotic enteritis in turkeys.

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“…This potent pore-forming toxin is reported to disrupt intestinal tight junction barriers, which is associated with intestinal disease symptoms (19). C. perfringens , and associated encoded toxins, have been extensively studied with respect to disease pathogenesis, with a strong focus on animal infections (20–24). Recent studies analysing a range of diverse C. perfringens strains (from both animal and human-associated infections) indicates a plastic and divergent pangenome, with a significant proportion of accessory genes predicted to be involved in virulence mechanisms and metabolisms, linked to enhanced host colonisation and disease initiation (3, 25).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analysis ofClostridium perfringensidentifies isogenic strains in gastroenteritis outbreaks, and novel virulence-related features

Kiu

Caim

Pickard

et al. 2019

Preprint

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Clostridium perfringens is a major enteric pathogen known to cause gastroenteritis in human adults. Although major outbreak cases are frequently reported, limited Whole Genome Sequencing (WGS) based studies have been performed to understand the genomic epidemiology and virulence gene content of C. perfringens-associated outbreak strains. We performed both genomic and phylogenetic analysis on 109 C. perfringens strains (human and food) isolated from disease cases in England and Wales between 2011-2017. Initial findings highlighted the enhanced discriminatory power of WGS in profiling outbreak C. perfringens strains, when compared to the current Public Health England referencing laboratory technique of Fluorescent Amplified Fragment Length Polymorphism (fAFLP). Further analysis identified that isogenic C. perfringens strains were associated with nine distinct care home-associated outbreaks over the course of a 5-year interval, indicating a potential common source linked to these outbreaks or transmission over time and space. As expected the enterotoxin CPE gene was encoded in all but 4 isolates (96.4%; 105/109), with virulence plasmids encoding cpe (particularly pCPF5603- and pCPF4969-family plasmids) extensively distributed (82.6%;90/109). Genes encoding accessory virulence factors, such as beta-2 toxin, were commonly detected (46.7%; 50/109), and genes encoding phage proteins were also frequently identified, with additional analysis indicating their contribution to increased virulence determinants within the genomes of gastroenteritis-associated C. perfringens. Overall this large-scale genomic study of gastroenteritis-associated C. perfringens suggested that 3 major sub-types underlie these outbreaks: strains carrying (1) pCPF5603 plasmid, (2) pCPF4969 plasmid, and (3) strains carrying cpe on transposable element Tn5565(usually integrated into chromosome). Our findings indicate that further studies will be required to fully probe this enteric pathogen, particularly in relation to developing intervention and prevention strategies to reduce food poisoning disease burden in vulnerable patients, such as the elderly.

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Genome analysis of Clostridium perfringens isolates from healthy and necrotic enteritis infected chickens and turkeys

Cited by 22 publications

References 23 publications

Genomic analysis on broiler-associated Clostridium perfringens strains and caecal microbiome profiling 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

Developing an experimental necrotic enteritis model in turkeys - the impact of Clostridium perfringens, Eimeria meleagrimitis and host age on frequency of severe intestinal lesions

Phylogenomic analysis ofClostridium perfringensidentifies isogenic strains in gastroenteritis outbreaks, and novel virulence-related features

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