Comparative transcriptome analysis by RNAseq of necrotic enteritis Clostridium perfringens during in vivo colonization and in vitro conditions

Parreira, Valeria R.; Russell, Kay; Athanasiadou, Spiridoula; Prescott, John F.

doi:10.1186/s12866-016-0792-6

Cited by 24 publications

(19 citation statements)

References 40 publications

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“…Previous studies have examined the transcriptomes of regulatory mutants of C. perfringens JIR325 in vitro ( 33 ), of an avian necrotic enteritis strain in chicken intestinal loops ( 34 ), and of a C. perfringens biofilm ( 35 ). We compared the in vivo bacterial gene expression levels with the expression levels from the equivalent in vitro broth cultures, which represents the first time that the transcriptome of C. perfringens cells in a myonecrosis infection has been examined.…”

Section: Resultsmentioning

confidence: 99%

Concurrent Host-Pathogen Transcriptional Responses in a Clostridium perfringens Murine Myonecrosis Infection

Low

Harrison

Gould

et al. 2018

mBio

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To obtain an insight into host-pathogen interactions in clostridial myonecrosis, we carried out comparative transcriptome analysis of both the bacterium and the host in a murine Clostridium perfringens infection model, which is the first time that such an investigation has been conducted. Analysis of the host transcriptome from infected muscle tissues indicated that many genes were upregulated compared to the results seen with mock-infected mice. These genes were enriched for host defense pathways, including Toll-like receptor (TLR) and Nod-like receptor (NLR) signaling components. Real-time PCR confirmed that host TLR2 and NLRP3 inflammasome genes were induced in response to C. perfringens infection. Comparison of the transcriptome of C. perfringens cells from the infected tissues with that from broth cultures showed that host selective pressure induced a global change in C. perfringens gene expression. A total of 33% (923) of C. perfringens genes were differentially regulated, including 10 potential virulence genes that were upregulated relative to their expression in vitro. These genes encoded putative proteins that may be involved in the synthesis of cell wall-associated macromolecules, in adhesion to host cells, or in protection from host cationic antimicrobial peptides. This report presents the first successful expression profiling of coregulated transcriptomes of bacterial and host genes during a clostridial myonecrosis infection and provides new insights into disease pathogenesis and host-pathogen interactions.

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Section: Resultsmentioning

confidence: 99%

Concurrent Host-Pathogen Transcriptional Responses in a Clostridium perfringens Murine Myonecrosis Infection

Low

Harrison

Gould

et al. 2018

mBio

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“…Other virulence factors may additively contribute to the CP pathogenesis in NE induction. Global transcriptomic analysis performed on ligated intestinal loops in chickens following infection with a netB + CP strain revealed that numerous virulence factors were significantly expressed in vivo, such as cpa, netB and sialidase genes [ 19 ]. Del1 strain is a virulent strain isolated from a field disease outbreak to be used as a challenge strain.…”

Section: Resultsmentioning

confidence: 99%

Complete genome sequences of Clostridium perfringens Del1 strain isolated from chickens affected by necrotic enteritis

Yan

Lillehoj

2017

Gut Pathog

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Background Clostridium perfringens is ubiquitous in nature. It is a normal inhabitant in the intestinal tract of animals and humans. As the primary etiological agent of gas gangrene, necrosis and bacteremia, C. perfringens causes food poisoning, necrotic enteritis (NE), and even death. Epidemiology research has indicated that the increasing incidence of NE in poultry is associated with the withdrawal of in-feed antibiotic growth promoters in poultry production in response to government regulations. The recent omics studies have indicated that bacterial virulence is typically linked to highly efficient conjugative transfer of toxins, or plasmids carrying antibiotic-resistance traits. Currently, there is limited information on understanding of host–pathogen interaction in NE caused by virulent strains of C. perfringens. Elucidating such pathogenesis has practical impacts on fighting infectious diseases through adopting strategies of prophylactic or therapeutic interventions. In this report, we sequenced and analyzed the genome of C. perfringens Del1 strain using the hybrid of PacBio and Illumina sequencing technologies.ResultsSequence analysis indicated that Del1 strain comprised a single circular chromosome with a complete 3,559,163 bp and 4 plasmids: pDel1_1 (82,596 bp), pDel1_2 (69,827 bp), pDel1_3 (49,582 bp), and pDel1_4 (49,728 bp). The genome had 3361 predicted coding DNA sequences, harbored numerous genes for pathogenesis and virulence factors, including 6 for antibiotic and antimicrobial resistance, and 3 phage-encoded genes. Phylogenetic analysis revealed that Del1 strain had similar genome and plasmid sequences to the CP4 strain.ConclusionComplete chromosomal and plasmid sequences of Del1 strain are presented in this report. Since Del1 was isolated from a field disease outbreak, this strain is a good source to identify virulent genes that cause many damaging effects of Clostridial infections in chicken gut. Genome sequencing of the chicken pathogenic isolates from commercial farms provides valuable insights into the molecular pathogenesis of C. perfringens as a gastrointestinal pathogen in food animals. The detailed information on gene sequencing of this important field strain will benefit the development of novel vaccines specific for C. perfringens-induced NE in chickens.Electronic supplementary materialThe online version of this article (10.1186/s13099-017-0217-6) contains supplementary material, which is available to authorized users.

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“…p -value or q -value were used to conduct significance analysis. Parameters for classifying significantly DEGs are ≥2-fold differences (|log 2 FC|≥1, FC: the fold change of expressions) in the transcript abundance and q < 0.05 (Parreira et al, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

“…The best matches were selected to annotate the DEGs. Finally, DEGs were subjected to GO functional analysis and KEGG, utilizing default parameters, to annotate the DEGs' major GO, and KEGG categories (Liu et al, 2014 ; Parreira et al, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic Analysis of Oenococcus oeni SD-2a Response to Acid Shock by RNA-Seq

et al. 2017

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Oenococcus oeni can be applied to conduct malolactic fermentation (MLF), but also is the main species growing naturally in wine. Due to the high stress tolerance, it is an interesting model for investigating acid response mechanisms. In this study, the changes in the transcriptome of O.oeni SD-2a during the adaptation period have been studied. RNA-seq was introduced for the transcriptomic analysis of O. oeni samples treated with pH 4.8 and pH 3.0 at 0 and 1 h, respectively. Gene ontology (GO) and Kyoto encyclopedia of genes and genome (KEGG) were performed to compare the transcriptome data between different treatments. From GO analysis, the majority of differentially expressed genes (DEGs) (pH 3.0_1 h-VS-pH 4.8_1 h, pH 3.0_1 h-VS-pH 4.8_0 h, and pH 4.8_1 h-VS-pH 4.8_0 h) were found to be involved in the metabolic process, catalytic activity, cellular process, and binding. KEGG analysis reveals that the most functional gene categories affected by acid are membrane transport, amino acid metabolism and carbohydrate metabolism. Some genes, like the heat shock protein Hsp20, malate transporter and malate permease, were also over-expressed in response to acid stress. In addition, a considerable proportion of gene indicate a significantly different expression in this study, are novel, which needs to be investigated further. These results provide a new viewpoint and crucial resource on the acid stress response in O. oeni.

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Comparative transcriptome analysis by RNAseq of necrotic enteritis Clostridium perfringens during in vivo colonization and in vitro conditions

Cited by 24 publications

References 40 publications

Concurrent Host-Pathogen Transcriptional Responses in a Clostridium perfringens Murine Myonecrosis Infection

Concurrent Host-Pathogen Transcriptional Responses in a Clostridium perfringens Murine Myonecrosis Infection

Complete genome sequences of Clostridium perfringens Del1 strain isolated from chickens affected by necrotic enteritis

Transcriptomic Analysis of Oenococcus oeni SD-2a Response to Acid Shock by RNA-Seq

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