High-resolution genomic fingerprinting of Campylobacter jejuni and Campylobacter coli by analysis of amplified fragment length polymorphisms

Kokotovic, Branko

doi:10.1016/s0378-1097(99)00034-8

Cited by 44 publications

(69 citation statements)

References 11 publications

(30 reference statements)

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“…Strain 6871 also showed only 94.6 to 96% groEL sequence similarity with C. jejuni, whereas the intraspecies sequence similarities among the other strains ranged from 98 to 100%. Hippurate-negative C. jejuni strains may represent a distinct clonal lineage of C. jejuni, as proposed previously (15).…”

Section: Discussionsupporting

confidence: 61%

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

2004

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The phylogeny of 12 Campylobacter species and reference strains of Arcobacter butzleri and Helicobacter pylori was studied based on partial 593-bp groEL gene sequences. The topology of the phylogenetic neighbor-joining tree based on the groEL gene was similar to that of the tree based on the 16S rRNA gene. However, groEL was found to provide a better resolution for Campylobacter species, with lower interspecies sequence similarities (range, 65 to 94%) compared with those for the 16S rRNA gene (range, 90 to 99%) and high intraspecies sequence similarities (range, 95 to 100%; average, 99%). A new universal reverse primer that amplifies a 517-bp fragment of the groEL gene was developed and used for PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of 68 strains representing 11 Campylobacter species as well as reference strains of A. butzlerii and H. pylori. Digestion with the AluI enzyme discriminated all Campylobacter species included in the study but showed more intraspecies diversity than digestion with the ApoI enzyme. A hippurate-negative variant of Campylobacter jejuni with a high level of groEL sequence similarity to both C. jejuni (96%) and C. coli (94%) gave a unique AluI profile and an ApoI profile identical to those of other C. jejuni strains. In conclusion, groEL gene sequencing and PCR-RFLP analysis are recommended as valuable tools for the identification of Campylobacter species.

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Section: Discussionsupporting

confidence: 61%

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

2004

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“…Recently, this method has been adapted for epidemiological typing of C. jejuni and C. coli. These studies demonstrated the subtyping of individual strains, and have already differentiated between two species (Duim et al, , 2000Kokotovic & On, 1999 ;On & Harrington, 2000). In this study, the value of AFLP analysis was determined for the identification and differentiation, at strain level, of nine Campylobacter species and three subspecies belonging to well-defined taxa and representing Campylobacter species that are very important in a veterinary context.…”

Section: Introductionmentioning

confidence: 93%

Differentiation of Campylobacter species by AFLP fingerprinting

Duim¹,

Vandamme

Rigter³

et al. 2001

Microbiology

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The fluorescent amplified fragment length polymorphism (AFLP) fingerprinting method was tested for its ability to identify and subtype the most important Campylobacter species found in veterinary infections. Sixty-nine reference strains and 19 clinical isolates of Campylobacter jejuni subsp. jejuni, Campylobacter jejuni subsp. doylei, Campylobacter upsaliensis, Campylobacter coli, Campylobacter lari, Campylobacter fetus subsp. fetus, C. fetus subsp. venerealis, Campylobacter hyointestinalis subsp. hyointestinalis, C. hyointestinalis subsp. lawsonii, Campylobacter mucosalis, Campylobacter helveticus and Campylobacter sputorum were subjected to analysis. The topology of the dendrogram obtained by numerical analysis of the AFLP profiles did not reflect the phylogenetic relationships as derived from 16S rDNA sequence comparison. However, except for C. lari, AFLP analysis grouped the strains that belonged to the same genomic species into distinct clusters. C. lari strains were separated into two distinct AFLP groups, which corresponded with nalidixic-acid-sensitive and -resistant variants of C. lari. These results correlated with data from whole-cell protein profiling. Within C. jejuni, C. hyointestinalis and C. fetus, strains could be identified at the subspecies level. AFLP analysis also allowed the subtyping of most species at the strain level. It is concluded that AFLP analysis is a valuable tool for concurrent identification of campylobacters at the species, subspecies and strain levels. In addition, the data confirm and extend previous reports showing that C. lari is a heterogeneous species that may comprise multiple taxa.

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“…Whole-genome fingerprinting by amplified fragment length polymorphisms (AFLP) is a powerful tool for concurrent taxonomic and subtyping analyses of various bacterial species, and it has been shown to accurately identify interstrain relationships at the subspecies, species, and strain levels (8,14,(23)(24)(25)(26). It has been suggested (23) that the use of AFLP profiling could help resolve the complex taxonomic structure of C. concisus and assess the prevalence of diverse genomospecies isolated from clinical samples, thus elucidating more clearly their potential roles in gastrointestinal illness.…”

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confidence: 99%

Delineation of Campylobacter concisus Genomospecies by Amplified Fragment Length Polymorphism Analysis and Correlation of Results with Clinical Data

Aabenhus

Siemer

et al. 2005

J Clin Microbiol

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Campylobacter concisus has been as frequently isolated from human diarrhea as the important enteropathogen Campylobacter jejuni, but it also occurs in the feces of healthy individuals. The role of C. concisus in human disease has been difficult to determine, since the species comprises at least two phenotypically indistinguishable but genetically distinct taxa (i.e., genomospecies) that may vary in pathogenicity. We examined 62 C. concisus strains by amplified fragment length polymorphism (AFLP) profiling and correlated the results with clinical data. All C. concisus strains gave unique AFLP profiles, and numerical analysis of these data distributed the strains among four clusters. The clustering was of taxonomic significance: two clusters contained, respectively, the type strain (of oral origin) and a reference strain (from diarrhea) of each of the known genomospecies. Genomospecies 2 strains were more frequently isolated from immunocompetent patients and/or patients without concomitant infections that presented with fever, chronic diarrhea, and gut inflammation than was genomospecies 1, clustering with the type strain of oral origin. Bloody diarrhea was recorded only with C. concisus genomospecies 2 infections. We identified two additional C. concisus genomospecies: genomospecies 3 comprised a single strain from an immunocompetent patient, and genomospecies 4 contained five isolates from severely immunodeficient patients, i.e., organ transplantation recipients or those with hematological malignancies. All genomospecies 4 strains were of the same protein profile group and failed to react with a C. concisus species-specific PCR assay based on 23S rRNA gene sequences: the taxonomic position of this group requires closer investigation. Campylobacter concisus is genetically and taxonomically diverse and contains at least four distinct genomospecies that may exhibit differences in their spectra of virulence potential.

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High-resolution genomic fingerprinting of Campylobacter jejuni and Campylobacter coli by analysis of amplified fragment length polymorphisms

Cited by 44 publications

References 11 publications

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

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

Differentiation of Campylobacter species by AFLP fingerprinting

Delineation of Campylobacter concisus Genomospecies by Amplified Fragment Length Polymorphism Analysis and Correlation of Results with Clinical Data

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