The ribosomal RNA operon ( rrn ) of Campylobacter concisus supports molecular typing to genomospecies level

Huq, M. I.; Van, Thi Thu Hao; Gürtler, Volker; Elshagmani, Eltaher; Allemailem, Khaled S.; Smooker, Peter M.; Istivan, Taghrid

doi:10.1016/j.genrep.2016.10.008

Cited by 7 publications

(13 citation statements)

References 41 publications

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“…The phylogenetic trees generated from 15 rrn operons and 23S rRNA genes also demonstrated sequence differences between strains within the rrn. Hence, the study confirmed that C. concisus can be classified into two genomospecies (A& B) based on the presence of the indels in the rrn operon and the 23S rRNA gene is a more reliable target for C. concisus typing than the 16S rRNA gene [80].…”

Section: Typing By Rrn Analysissupporting

confidence: 63%

“…The diversity of the ribosomal RNA (rrn) operon (5S rRNA, 16S rRNA, 23S rRNA genes, and the ITS regions) is considered a useful tool for differentiation of the heterogeneous C. concisus species [80]. The sequences of C. concisus rrn operons were used in a recent study for the purpose of strain typing and delineation of phylogenetic relationships within these operons.…”

Section: Typing By Rrn Analysismentioning

confidence: 99%

“…The study also reported novel genomic islands that contain type IV secretion system and putative effector proteins, in addition to other new genomic features. A study by our team investigated the rrn operon (5S rRNA, 16S rRNA, 23S rRNA genes, and the ITS regions) for four newly sequenced whole genomes extracted from intestinal and oral C. concisus strains, along with eight available WGSs online and established a clear correlation between the rrn operons and genomospecies [80].…”

Section: Whole Genome Sequencingmentioning

confidence: 99%

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Conventional and Molecular Detection Methods of the Opportunistic Bacterial Pathogen Campylobacter concisus

Huq¹,

Istivan²

2022

Campylobacter

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Campylobacter concisus is an emerging pathogen that causes gastroenteritis and is a suspected cause of inflammatory bowel diseases. Its importance is enhanced by the chronic sequela that results from acute infection. This bacterium has been under-diagnosed in intestinal infectious diseases, and its clinical importance has not been determined yet. In order to establish the implication of this emerging bacterial species in human gastroenteritis and other infections, different approaches and procedure have been performed, where molecular typing methods have played a central role. The chapter provides a comprehensive past and recent updates on the detection of C. concisus by biochemical and molecular methods.

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Section: Typing By Rrn Analysissupporting

confidence: 63%

Section: Typing By Rrn Analysismentioning

confidence: 99%

Section: Whole Genome Sequencingmentioning

confidence: 99%

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Conventional and Molecular Detection Methods of the Opportunistic Bacterial Pathogen Campylobacter concisus

Huq¹,

Istivan²

2022

Campylobacter

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“…To determine whether the C. concisus plasmids found in this study are associated with different types of gastrointestinal disease, their prevalence in a total of 239 strains in the public databases was compared using NCBI nucleotide blast [35]. These strains included 58 strains from 29 patients with CD, 62 strains from 28 patients with UC, 64 strains from 42 healthy individuals, 54 strains from 46 patients with diarrhoea and 1 strain from a patient with IBD (unknown if CD or UC) [13,14,19,22,[38][39][40]. Of the C. concisus strains isolated from patients with UC, 40 strains were from 15 patients who have undergone ileal pouch-anal anastomosis (UC-IPAA) due to their severe disease, and they were referred to as severe UC [41].…”

Section: Examination Of the Association Between The Newly Identifiedmentioning

confidence: 99%

Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis

et al. 2020

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Campylobacter concisus is an emerging enteric pathogen that is associated with several gastrointestinal diseases, such as inflammatory bowel disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC). Currently, only three complete C. concisus genomes are available and more complete C. concisus genomes are needed in order to better understand the genomic features and pathogenicity of this emerging pathogen. DNA extracted from 22 C . concisus strains were subjected to Oxford Nanopore genome sequencing. Complete genome assembly was performed using Nanopore genome data in combination with previously reported short-read Illumina data. Genome features of complete C. concisus genomes were analysed using bioinformatic tools. The enteric disease associations of C. concisus plasmids were examined using 239 C . concisus strains and confirmed using PCRs. Proteomic analysis was used to examine T6SS secreted proteins. We successfully obtained 13 complete C. concisus genomes in this study. Analysis of 16 complete C. concisus genomes (3 from public databases) identified multiple novel plasmids. pSma1 plasmid was found to be associated with severe UC. Sec-SRP, Tat and T6SS were found to be the main secretion systems in C. concisus and proteomic data showed a functional T6SS despite the lack of ClpV. T4SS was found in 25% of complete C. concisus genomes. This study also found that GS2 strains had larger genomes and higher GC content than GS1 strains and more often had plasmids. In conclusion, this study provides fundamental genomic data for understanding C. concisus plasmids, genomospecies features, evolution, secretion systems and pathogenicity.

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“…C. concisus strains can be separated into two major genomospecies (GS), consistently defined by the analysis of core genomes and housekeeping genes (Istivan, 2005 ; Miller et al, 2012 ; Mahendran et al, 2015 ; Chung et al, 2016 ; Nielsen et al, 2016 ). C. concisus 23S rRNA gene has polymorphisms, which was also used to define the genomospecies by comparison of the entire 23S rRNA gene sequence or PCR amplification of 23S rRNA gene fragments (Engberg et al, 2005 ; Kalischuk and Inglis, 2011 ; On et al, 2013 ; Huq et al, 2017 ; Wang et al, 2017 ).…”

Section: Concisusmentioning

confidence: 99%

The Clinical Importance of Campylobacter concisus and Other Human Hosted Campylobacter Species

Liu

Wang

et al. 2018

Front. Cell. Infect. Microbiol.

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Historically, Campylobacteriosis has been considered to be zoonotic; the Campylobacter species that cause human acute intestinal disease such as Campylobacter jejuni and Campylobacter coli originate from animals. Over the past decade, studies on human hosted Campylobacter species strongly suggest that Campylobacter concisus plays a role in the development of inflammatory bowel disease (IBD). C. concisus primarily colonizes the human oral cavity and some strains can be translocated to the intestinal tract. Genome analysis of C. concisus strains isolated from saliva samples has identified a bacterial marker that is associated with active Crohn's disease (one major form of IBD). In addition to C. concisus, humans are also colonized by a number of other Campylobacter species, most of which are in the oral cavity. Here we review the most recent advancements on C. concisus and other human hosted Campylobacter species including their clinical relevance, transmission, virulence factors, disease associated genes, interactions with the human immune system and pathogenic mechanisms.

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The ribosomal RNA operon ( rrn ) of Campylobacter concisus supports molecular typing to genomospecies level

Cited by 7 publications

References 41 publications

Conventional and Molecular Detection Methods of the Opportunistic Bacterial Pathogen Campylobacter concisus

Conventional and Molecular Detection Methods of the Opportunistic Bacterial Pathogen Campylobacter concisus

Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis

The Clinical Importance of Campylobacter concisus and Other Human Hosted Campylobacter Species

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