Outbreak of amoxicillin-resistant Haemophilus influenzae type b: variable number of tandem repeats as novel molecular markers

Belkum, Alex van; Melchers, W.J.G.; IJsseldijk, C.; Nohlmans, L; Verbrugh, Henri A.; Meis, Jacques F.

doi:10.1128/jcm.35.6.1517-1520.1997

Cited by 38 publications

(11 citation statements)

References 24 publications

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“…To assess the intraspecies diversity of these homogeneous species, alternative genomic methods have been developed. In variable number tandem repeat (VNTR) analysis, the variation in copy number of short nucleotide sequences that are repeated multiple times (resulting in length polymorphisms), is detected by PCR [173][174][175]. The resolution of this technique can even further be improved by simultaneously studying multiple loci (multiple-locus VNTR analysis, MLVA) [175][176][177].…”

Section: Detection Of Intraspecies Diversitymentioning

confidence: 99%

Towards a prokaryotic genomic taxonomy

Coenye¹,

Gevers²,

Peer³

et al. 2005

FEMS Microbiology Reviews

129

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One of the most interesting developments in the field of modern-day microbiology is the ever increasing number of whole-genome sequences that is publicly available. There is an increasing interest in the use of these genome sequences to assess evolutionary relationships among microbial taxa, as it is anticipated that much additional taxonomic information can be extracted from these sequences. In a first part of the present review, mechanisms that are responsible for the evolution of genomes will be discussed. Subsequently, we will give an overview of approaches that are presently available to assess the taxonomic relationships between prokaryotic species based on complete genome sequences, followed by a brief discussion of the potential implications of these novel approaches for bacterial taxonomy in general and our thinking about the bacterial species concept in particular.

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Section: Detection Of Intraspecies Diversitymentioning

confidence: 99%

Towards a prokaryotic genomic taxonomy

Coenye¹,

Gevers²,

Peer³

et al. 2005

FEMS Microbiology Reviews

129

View full text Add to dashboard Cite

show abstract

“…The presence of simple sequence repeats (SSR) in prokaryotes is well documented (Gur-Arie et al, 2000), and some SSRs show extensive length polymorphisms (Yang et al, 2003;Sreenu et al, 2006). Successful use of PCR-based SSR amplification followed by amplicon size determination to analyze the spread of microbial pathogens has been reported for Haemophilus influenzae and Candida albicans (Bretagne et al, 1997;van Belkum et al, 1997). Inter simple sequence repeat-PCR (ISSR-PCR) technique also exploits the genome-wide distribution of SSRs.…”

Section: Introductionmentioning

confidence: 99%

Genetic characterization ofVibrio choleraestrains by inter simple sequence repeat-PCR

Kumar

Sathish

Nair

et al. 2007

FEMS Microbiology Letters

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The utility of inter simple sequence repeat-PCR (ISSR-PCR) assay in the characterization and elucidation of the phylogenetic relationship between the pathogenic and nonpathogenic isolates of Vibrio cholerae is demonstrated. A total of 45 V. cholerae strains including 15 O1 El Tor, nine O139 and 21 non-O1/non-O139 strains were analyzed using eight ISSR primers. These primers, which are essentially simple sequence repeats (SSR) with additional nonrepeat bases at the 5' or 3' end, amplify genomic regions interspersed between closely spaced SSRs. Neighbor-joining analysis showed that the strains belonging to the same serogroup clustered together with the exception of one O1 and two O139 strains. The absence of pathogenicity islands in these strains, as confirmed by PCR, suggested their non-O1/non-O139 origin. Thus the ISSR-PCR-based phylogeny was consistent with the classification of V. cholerae based on serological methods. A finer resolution of the clustering of the toxinogenic O1 El Tor and toxinogenic O139 subtypes was obtained by ISSR-PCR analysis as compared with the Enterobacterial Repetitive Intergenic Consensus sequences-based PCR analysis for the same set of strains. Thus, it is proposed that ISSR-PCR is an efficient tool in phylogenetic classification of prokaryotic genomes in general and diagnostic genotyping of microbial pathogens in particular.

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“…The length of the VNTRs was a stable genetic marker for separate colonies derived from a single clinical specimen or strains passaged in the microbiology laboratory for several weeks on chocolate agar plates. When several strains isolated from di¡erent patients during an outbreak of lung disease caused by H. in£uenzae were analysed [15], increased but limited variation was encountered in the four-nucleotide unit VNTR sites [19]. It appeared that the tri-, penta-or hexanucleotide VNTRs were more stable in nature and consequently more suited for epidemiological studies.…”

Section: Discussionmentioning

confidence: 99%

Variable numbers of tandem repeat loci in genetically homogeneous Haemophilus influenzae strains alter during persistent colonisation of cystic fibrosis patients

Renders¹

1999

FEMS Microbiology Letters

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Serial sputum isolates of Haemophilus influenzae (n = 69) were obtained from eight patients suffering from cystic fibrosis. For two of these patients all strains were analysed for polymorphism in the major outer membrane protein profile. For all patients the strains were genetically characterised by random amplification of polymorphic DNA analysis. All strains were included in a survey for polymorphism in regions containing moieties of repetitive DNA as well. A single locus containing trinucleotide repeat units, three loci harbouring tetranucleotides, one region comprising pentanucleotide units and two hexanucleotide repeat unit-containing loci were analysed for repeat number variability. Most of the regions were previously shown to be directly adjacent to or even within virulence genes. All regions behaved as genuine variable number of tandem repeat loci in the sense that genetic polymorphism based on the presence of varying numbers of repeat units could be demonstrated among different strains. Interestingly, several of the repeats showed variation in the absence of the variability as assessed by major outer membrane protein or random amplification of polymorphic DNA analysis. These observations indicate that the repeat loci may vary independently from major chromosomal polymorphism. Consequently, H. influenzae appears to modify its virulence gene regions of the chromosome during persistent colonisation of the lung in cystic fibrosis patients. z 1999 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

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Outbreak of amoxicillin-resistant Haemophilus influenzae type b: variable number of tandem repeats as novel molecular markers

Cited by 38 publications

References 24 publications

Towards a prokaryotic genomic taxonomy

Towards a prokaryotic genomic taxonomy

Genetic characterization ofVibrio choleraestrains by inter simple sequence repeat-PCR

Variable numbers of tandem repeat loci in genetically homogeneous Haemophilus influenzae strains alter during persistent colonisation of cystic fibrosis patients

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