Phylogenetic Analysis and PCR-Restriction Fragment Length Polymorphism Identification of
            <i>Campylobacter</i>
            Species Based on Partial
            <i>groEL</i>
            Gene Sequences

Kärenlampi, R.; Tolvanen, T. P.; Hänninen, Marja‐Liisa

doi:10.1128/jcm.42.12.5731-5738.2004

Cited by 56 publications

(17 citation statements)

References 43 publications

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“…This result is consistent with that by a previous study, in which the phylogeny was inferred from rpoB or SSU rRNA sequences [47]. However, C. jejuni is clearly different from C. coli in the groEL -based tree [49]. Furthermore, the Campylobacter genus can split into two main lineages, i.e., the jejuni lineage, which includes C. jejuni , C. coli, C. lari , and C. upsaliensis ; and the non-jejuni lineage, which includes C. fetus , Campylobacter concisus , Campylobacter gracilis , Campylobacter hominis , C. curvus , C. rectus , and Campylobacter showae .…”

Section: Resultssupporting

confidence: 93%

Comprehensive Genomic Characterization of Campylobacter Genus Reveals Some Underlying Mechanisms for its Genomic Diversification

Zhou

Guo

et al. 2013

PLoS ONE

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Campylobacter species.are phenotypically diverse in many aspects including host habitats and pathogenicities, which demands comprehensive characterization of the entire Campylobacter genus to study their underlying genetic diversification. Up to now, 34 Campylobacter strains have been sequenced and published in public databases, providing good opportunity to systemically analyze their genomic diversities. In this study, we first conducted genomic characterization, which includes genome-wide alignments, pan-genome analysis, and phylogenetic identification, to depict the genetic diversity of Campylobacter genus. Afterward, we improved the tetranucleotide usage pattern-based naïve Bayesian classifier to identify the abnormal composition fragments (ACFs, fragments with significantly different tetranucleotide frequency profiles from its genomic tetranucleotide frequency profiles) including horizontal gene transfers (HGTs) to explore the mechanisms for the genetic diversity of this organism. Finally, we analyzed the HGTs transferred via bacteriophage transductions. To our knowledge, this study is the first to use single nucleotide polymorphism information to construct liable microevolution phylogeny of 21 Campylobacter jejuni strains. Combined with the phylogeny of all the collected Campylobacter species based on genome-wide core gene information, comprehensive phylogenetic inference of all 34 Campylobacter organisms was determined. It was found that C. jejuni harbors a high fraction of ACFs possibly through intraspecies recombination, whereas other Campylobacter members possess numerous ACFs possibly via intragenus recombination. Furthermore, some Campylobacter strains have undergone significant ancient viral integration during their evolution process. The improved method is a powerful tool for bacterial genomic analysis. Moreover, the findings would provide useful information for future research on Campylobacter genus.

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Section: Resultssupporting

confidence: 93%

Comprehensive Genomic Characterization of Campylobacter Genus Reveals Some Underlying Mechanisms for its Genomic Diversification

Zhou

Guo

et al. 2013

PLoS ONE

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“…Therefore, PCR-based methods have been developed for detection of Campylobacter spp. in different specimens, including fecal samples (11,13,14). The main source of Campylobacter disease outbreaks is associated with consumption of contaminated water or milk and consumption of undercooked food; in particular, poultry products are the main cause of sporadic Campylobacteriosis cases (1)(2)(3)(4)(5)(6)(7)(8).…”

Section: Discussionmentioning

confidence: 99%

“…In this step, positive PCR products of 23S rRNA were digested using two restriction enzymes, AluI and TasI (Thermo Scientific) in order to differentiate Campylobacter species (11,13,14). The RFLP mixture for a final AluI volume of 32 µL contained: 10 µL PCR product of 23S rRNA, 1 µL restriction enzyme AluI, 2 µL (10×) tango buffer, and 18 µL nuclease-free water.…”

Section: Pcr-rflp Conditionsmentioning

confidence: 99%

“…All extracted DNA from specimens was checked by genus-specific cadF primer, then positive samples were analyzed with hipo and asp primers to differentiate jejuni and coli species ( Figure 1). All cadf positive samples were tested by PCR using 23S rRNA (another Campylobacter genus-specific gene) primer, and the products were digested with AluI and TasI enzymes using the RFLP method (9)(10)(11)(12)(13)(14). The PCR mixture in a total volume of 25 µL for each primer contained: 12.5 µL Taq Mix (2×) with 1× final concentration (DELTA life sciences), 1 µL reverse primer (10 µM), 1 µL forward primer (10 µM), 5.5 µL sterile water, and 5 µL template DNA.…”

Section: Polymerase Chain Reactionmentioning

confidence: 99%

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Comparative Study of Campylobacter spp. Isolated from Children With Gastroenteritis in Bahonar Hospital, Karaj, Using PCR and RFLP

Abdi¹,

Harzandi²,

Kalantar³

2016

Int J Enteric Pathog

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Background: Campylobacter species are responsible for the majority of cases of food-borne gastroenteritis. The sources of the disease outbreaks are often contaminated water or milk, and consumption of undercooked poultry product is the main cause of sporadic campylobacteriosis cases. Objectives: The aims of this study were to determine the prevalence of Campylobacter gastroenteritis in children and to differentiate the interfering species using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) methods at the Bahonar hospital in Karaj, Iran. Patients and Methods: A total of 150 stool samples were collected from children under 10 years old during the summer of 2014. PCR was performed using genus-and species-specific primers and RFLP was done using AluI and TasI enzymes. Results:The results showed the amplification of 400 and 491 bp segments and Campylobacter contamination in 30 (20%) samples; 5 out of 30 Campylobacter positive samples (16.66%) were identified as C. jejuni, 20 (66.66%) as C. coli, 3 (10%) as C. jejuni and C. coli (mixed infection), and 2 (6.66%) were identified as non-jejuni, non-coli Campylobacter using the PCR method. Following the evaluation of RFLP results, 7 positive samples (23.33%) showed the electrophoretic pattern of C. jejuni, 21 (70%) showed the electrophoretic pattern of C. coli, and 2 (6.6%) showed both of the patterns and mixed contamination with jejuni and coli species. The results of digestion with TasI did not show any C. lari or C. upsaliensis patterns. Conclusions:The results of this study showed high percentage of Campylobacter contamination in the tested stool samples. The other surprising finding was the high rate of Campylobacter coli positive samples; the difference between the results of PCR using species-specific primers (hipo and asp) and the RFLP method (electrophoretic patterns) in some of the positive samples confirms the hypothesis of variations in nucleotide sequences of the hipo primer binding site in some Iranian isolates of Campylobacters.

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“…Most of the methods described target only the most common species i.e. A. butzleri [10,11], A. cryaerophilus [12] and/or A. skirrowii [13,14]. Even the most recently proposed identification method, m-PCR, described by Douidah et al .…”

Section: Introductionmentioning

confidence: 99%

Updated 16S rRNA-RFLP method for the identification of all currently characterised Arcobacter spp

2012

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BackgroundArcobacter spp. (family Campylobacteraceae) are ubiquitous zoonotic bacteria that are being increasingly recognised as a threat to human health. A previously published 16S rRNA-RFLP Arcobacter spp. identification method produced specific RFLP patterns for the six species described at that time, using a single endonuclease (MseI). The number of characterised Arcobacter species has since risen to 17. The aim of the present study was to update the 16S rRNA-RFLP identification method to include all currently characterised species of Arcobacter.ResultsDigestion of the 16S rRNA gene with the endonuclease MseI produced clear, distinctive patterns for 10 of the 17 species, while the remaining species shared a common or very similar RFLP pattern. Subsequent digestion of the 16S rRNA gene from these species with the endonucleases MnlI and/or BfaI generated species-specific RFLP patterns.Conclusions16S rRNA-RFLP analysis identified 17 Arcobacter spp. using either polyacrylamide or agarose gel electrophoresis. Microheterogeneities within the 16S rRNA gene, which interfered with the RFLP identification, were also documented for the first time in this genus, particularly in strains of Arcobacter cryaerophilus isolated from animal faeces and aborted foetuses.

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Phylogenetic Analysis and PCR-Restriction Fragment Length Polymorphism Identification of Campylobacter Species Based on Partial groEL Gene Sequences

Cited by 56 publications

References 43 publications

Comprehensive Genomic Characterization of Campylobacter Genus Reveals Some Underlying Mechanisms for its Genomic Diversification

Comprehensive Genomic Characterization of Campylobacter Genus Reveals Some Underlying Mechanisms for its Genomic Diversification

Comparative Study of Campylobacter spp. Isolated from Children With Gastroenteritis in Bahonar Hospital, Karaj, Using PCR and RFLP

Updated 16S rRNA-RFLP method for the identification of all currently characterised Arcobacter spp

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