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

Abstract

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.

Bifidobacterium breveUCC2003 induces a distinct global transcriptomic programme in neonatal murine intestinal epithelial cells

“…Genomic DNA extraction of mouse caecal samples on day 4 was performed with FastDNA Spin Kit for Soil following manufacturer’s instructions and extending the bead-beating step to 3 min as described previously [56]. Extracted DNA was quantified, normalised and sequenced on Illumina MiSeq platform using a read length of 2 × 300 bp, sequencing reads were analysed using OTU clustering methods (QIIME v1.9.1) to assign bacterial taxonomy and visualised as described previously [57, 58]. PCA was performed via R package ggfotify function autoplot and prcomp , while diversity index was computed via package vegan [59-61].…”

Cannabis-derived cannabidiol and nanoselenium improve gut barrier function and affect bacterial enzyme activity in chickens subjected to C. perfringens challenge

“…The major site of Clostridium perfringens- host interactions in chickens is the gastrointestinal tract (GIT). Thus, this environment is an important anatomical region in which to investigate mechanisms involved in the response to Clostridium perfringens challenge and for the development of agents that may potentially regulate this response [ 12 ]. Identifying the mechanisms by which NE can be limited may provide new insights into biosecurity.…”

Characterization of Clostridium Perfringens Isolates Collected from Three Agricultural Biogas Plants over a One-Year Period

“…In another study, they were detected in 26% and 22% of isolates of environmental origin (soils, water, and sewage) [8]. The proportion of isolates carrying the erm(Q) gene (13.6%) in the digestates of the two BGPs fed with pig manure was also higher than that previously observed in isolates that were collected from broiler chickens (4.5%) and in environmental samples (1%) [8,14].…”

“…Their prevalence in digestates was slightly higher than that reported in other matrices. Indeed, Kiu et al [14] observed a frequency of detection of tetA(P) alone and of the tetA(P)-tetB(P) gene of 14.8% and 35.2% in isolates from broiler chickens, respectively. In another study, they were detected in 26% and 22% of isolates of environmental origin (soils, water, and sewage) [8].…”

“…C. perfrin gens is a Gram-positive anaerobic spore forming bacterium that is responsible for various diseases, including food poisoning, gas gangrene, enteritis necroticans, and enterotoxemia [ 14 ]. It is also involved in antibiotic-associated diarrhea [ 15 ].…”