In Silico Analysis of the cadF Gene and Development of a Duplex Polymerase Chain Reaction for Species-Specific Identification of Campylobacter jejuni and Campylobacter coli

Shams, Saeed; Moghadam, Tahereh Tohidi

doi:10.5812/jjm.29645

Cited by 23 publications

(23 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There are various other PCR assays published for species differentiation of C. jejuni and C. coli with and without detection of further Campylobacter spp 12,[24][25][26][27][28][29] . Thus, the whole-genome sequences of the strains leading to ambiguous species differentiation with mapA/ceuE targets 3,5 and the correctly identified C. coli hybrids with high C. jejuni content were further assessed in silico ( Supplementary Fig.…”

Section: Are the Strains With Ambiguous Qpcr Results Typable By Other mentioning

confidence: 99%

“…The sequence data revealed that also cpn60 detection 24 would lead to false species identification of all C. coli hybrid strains but would identify C. coli correctly in the "half hybrids", in which mapA/ceuE were no reliable targets. Besides, strain BfR-CA-17110 harboured a C. jejuni sequence in the target cadF 28,29 , leading to false C. jejuni identification of this C. coli strain. All other targets hipO, glyA, lpxA and ccoN displayed either no or low C. jejuni introgression.…”

Section: Are the Strains With Ambiguous Qpcr Results Typable By Other mentioning

confidence: 99%

“…In our study we identified in total 37 strains (21 "hybrid" strains and 16 "half hybrid" strains), which were not identifiable in the qPCR using mapA/ceuE targets, including two isolates, which were falsely identified as C. jejuni. All "hybrid" strains failed to be typed using the cpn60 target 24 and one "half-hybrid" would be incorrectly typed as C. jejuni using the cadF target 28,29 .…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential

Golz

Epping

Knüver

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Campylobacter is the major bacterial agent of human gastroenteritis worldwide and represents a crucial global public health burden. Species differentiation of C. jejuni and C. coli and phylogenetic analysis is challenged by inter-species horizontal gene transfer. Routine real-time PCR on more than 4000 C. jejuni and C. coli field strains identified isolates with ambiguous PCR results for species differentiation, in particular, from the isolation source eggs. K-mer analysis of whole genome sequencing data indicated the presence of C. coli hybrid strains with huge amounts of C. jejuni introgression. Recombination events were distributed over the whole chromosome. MLST typing was impaired, since C. jejuni sequences were also found in six of the seven housekeeping genes. cgMLST suggested that the strains were phylogenetically unrelated. Intriguingly, the strains shared a stress response set of C. jejuni variant genes, with proposed roles in oxidative, osmotic and general stress defence, chromosome maintenance and repair, membrane transport, cell wall and capsular biosynthesis and chemotaxis. The results have practical impact on routine typing and on the understanding of the functional adaption to harsh environments, enabling successful spreading and persistence of Campylobacter. Since 2005, Campylobacter is the major zoonotic agent in the European Union, causing 250,161 confirmed campylobacteriosis cases in 2017 1. Around one third of the cases can be directly attributed to handling, preparation and consumption of broiler meat 2. Measures for Campylobacter reduction focus on virulence mechanisms and persistence factors, enabling the pathogen to successfully circulate within the food chain. Typing of Campylobacter by species differentiation methods and by multi-locus sequence typing (MLST) has become key tools for diagnostics and source attribution. Specific gene targets have proven stable and were, therefore, chosen for this purpose. Two of commonly used species differentiation markers 3-5 are mapA, a fitness factor in chicken colonization 6 and ceuE playing a role in iron acquisition 7. For MLST, central enzymatic functions, which are conserved in the genome were defined 8 and are commonly used for phylogenetic analysis. It was shown that high level of interspecies transfer of genetic material can occur between C. jejuni and C. coli 9. Adaptation to hosts can modulate the gene pool and allele variants and was suggested to be of more relevance than geographical location 10. Here we identified extensive interspecies gene transfer from C. jejuni to C. coli, impairing species differentiation and MLST analysis. Whole genome sequencing revealed that these hybrid strains shared C. jejuni gene variants, involved in stress response. Since the hybrids had predominantly been isolated from egg shells, we suggest that gene variations due to C. jejuni sequence introgression might have been a consequence of selection of survivors in a harsh environment.

show abstract

Section: Are the Strains With Ambiguous Qpcr Results Typable By Other mentioning

confidence: 99%

Section: Are the Strains With Ambiguous Qpcr Results Typable By Other mentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential

Golz

Epping

Knüver

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…They can be transmitted to humans through direct contact with animals, consumption of contaminated food and water, and unpasteurized milk [1,4]. Some gastrointestinal problems, called campylobacteriosis, especially in children have observed affected by Campylobacter jejuni [5][6][7]. CadF is one of the important proteins, a 37kDa protein as a conserved and genus-speci c outer membrane protein, that binds to bronectin and the bacterium attaches to the host cell, lead to facilitate colonization.…”

Section: Introductionmentioning

confidence: 99%

In Silico Analysis of CadF Epitope-based Vaccine Design Against Campylobacter Jejuni

Naseri

Shams

Naseri

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Objective: To eradicate infectious diseases, vaccination is an important strategy. CadF protein of Campylo bacter jejuni is one of the important factors in the process of the pathogenesis of the bacterium. So, the purpose of the work was to perform a bioinformatics study for identifying an epitope-based CadF vaccine, as a subunit vaccine. CadF sequences were extracted from the NCBI database. In silico analysis including all ergeni city, antigenicity, epitope conservancy assessment, molecular docking, etc.was done by different servers. Results:The results showed that CadF is an antigenic and non-allergenic protein and provides a suitable structure for vaccine design. Among epitopes, LSDSLALRL has been confirmed to stimulate both B and T cells. This 9-mers peptide is located in 135-143 segment of the CadF protein and interacted with HLA-A0101 and HLA-DRB1 0101 with energies of docking -26.18kcal/mol and -109.89kcal/mol. The peptide is not an allergen and as an antigen, it has the ability for motivating the immune system. Hence, the analyses are performed on that the epitope structure could verify the design of a vaccine against C. jejuni. The obtained theoretical results showed that CadF protein could be used for designing and evaluating a new vaccine in humans.

show abstract

“…They can be transmitted to humans through direct contact with animals, consumption of contaminated food and water, unpasteurized milk or contact with patients [1,3]. Some gastrointestinal diseases are caused by this pathogen, which it has considered as one common bacterial cause of diarrhea, especially in children [1,[4][5][6]. According to researches, more than 229,000 cases of the campylobacteriosis have been reported worldwide [7].…”

Section: Introductionmentioning

confidence: 99%

In silico Analysis of CadF epitope- based vaccine design against Campylobacter jejuni

Mm¹,

Shams²,

Bakhshi³

2019

Preprint

Self Cite

View full text Add to dashboard Cite

Background To eradicate infectious diseases caused by microorganisms, vaccination is a popular strategy against them and can be an effective approach. Among vaccines, subunit vaccines have been used to be more effective against diseases. CadF protein of Campylobacter jejuni is one of the important antigens in the pathogenic process of the bacterium. So, the aim of this work was to do a bioinformatics study for the identification of epitope-based CadF vaccine, as a subunit vaccine. Main body CadF gene sequences were extracted from the NCBI database and suitable physic-chemical properties of CadF were evaluated by Protprom server. Some epitopes of the CadF protein with high affinity were detected by different servers, which were predicted based on MHC-peptide complex and B-cell epitopes. The results indicated that CadF is an antigenic and non-allergenic protein and provided a desirable structure for design vaccine. Among epitopes, LSDSLALRL was confirmed for the simulation of both of B and T cells. This 9-mers peptide was located in 135-143 sequences of CadF protein and interacted with HLA-A0101. The peptide isn’t allergen and has the ability to be an antigen for motivating immune system. Besides, the analysis implied that the epitope structure could allow designing a vaccine against C. jejuni.

show abstract

In Silico Analysis of the cadF Gene and Development of a Duplex Polymerase Chain Reaction for Species-Specific Identification of Campylobacter jejuni and Campylobacter coli

Cited by 23 publications

References 23 publications

Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential

Whole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential

In Silico Analysis of CadF Epitope-based Vaccine Design Against Campylobacter Jejuni

In silico Analysis of CadF epitope- based vaccine design against Campylobacter jejuni

Contact Info

Product

Resources

About