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DNA-Microarray-based Genotyping of Clostridium difficile.

Gawlik D, Slickers P, Engelmann I, Müller E, Lück C, Friedrichs A, Ehricht R, Monecke S - BMC Microbiol. (2015)

Bottom Line: Tested isolates were assigned to 37 distinct profiles that clustered mainly according to MLST-defined clades.Three additional profiles were predicted from published genome sequences, although they were not found experimentally.Overall hybridization profiles correlated with MLST-derived clades.

View Article: PubMed Central - PubMed

Affiliation: Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany. darius.gawlik@web.de.

ABSTRACT

Background: Clostridium difficile can cause antibiotic-associated diarrhea and a possibility of outbreaks in hospital settings warrants molecular typing. A microarray was designed that included toxin genes (tcdA/B, cdtA/B), genes related to antimicrobial resistance, the slpA gene and additional variable genes.

Results: DNA of six reference strains and 234 clinical isolates from South-Western and Eastern Germany was subjected to linear amplification and labeling with dUTP-linked biotin. Amplicons were hybridized to microarrays providing information on the presence of target genes and on their alleles. Tested isolates were assigned to 37 distinct profiles that clustered mainly according to MLST-defined clades. Three additional profiles were predicted from published genome sequences, although they were not found experimentally.

Conclusions: The microarray based assay allows rapid and high-throughput genotyping of clinical C. difficile isolates including toxin gene detection and strain assignment. Overall hybridization profiles correlated with MLST-derived clades.

No MeSH data available.


Related in: MedlinePlus

SplitsTree graph based on hybridization profiles, showing the clustering of profiles into different clades as defined by MLST. For the issue of the tcd-negatives, see Discussion.
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Fig1: SplitsTree graph based on hybridization profiles, showing the clustering of profiles into different clades as defined by MLST. For the issue of the tcd-negatives, see Discussion.

Mentions: Applying this approach, tested isolates and reference strains clustered into 37 distinct hybridization profiles (HPs; Table 1 and Fig. 1). Three additional profiles were predicted from published genome sequences, although they were not found experimentally. If several isolates with identical hybridization profiles were subjected to MLST, they yielded identical or related sequence types. Occasionally, several ribotypes (RTs) were observed within one cluster and some ribotypes were present in different, although similar or related, clusters.Fig. 1


DNA-Microarray-based Genotyping of Clostridium difficile.

Gawlik D, Slickers P, Engelmann I, Müller E, Lück C, Friedrichs A, Ehricht R, Monecke S - BMC Microbiol. (2015)

SplitsTree graph based on hybridization profiles, showing the clustering of profiles into different clades as defined by MLST. For the issue of the tcd-negatives, see Discussion.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4526300&req=5

Fig1: SplitsTree graph based on hybridization profiles, showing the clustering of profiles into different clades as defined by MLST. For the issue of the tcd-negatives, see Discussion.
Mentions: Applying this approach, tested isolates and reference strains clustered into 37 distinct hybridization profiles (HPs; Table 1 and Fig. 1). Three additional profiles were predicted from published genome sequences, although they were not found experimentally. If several isolates with identical hybridization profiles were subjected to MLST, they yielded identical or related sequence types. Occasionally, several ribotypes (RTs) were observed within one cluster and some ribotypes were present in different, although similar or related, clusters.Fig. 1

Bottom Line: Tested isolates were assigned to 37 distinct profiles that clustered mainly according to MLST-defined clades.Three additional profiles were predicted from published genome sequences, although they were not found experimentally.Overall hybridization profiles correlated with MLST-derived clades.

View Article: PubMed Central - PubMed

Affiliation: Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany. darius.gawlik@web.de.

ABSTRACT

Background: Clostridium difficile can cause antibiotic-associated diarrhea and a possibility of outbreaks in hospital settings warrants molecular typing. A microarray was designed that included toxin genes (tcdA/B, cdtA/B), genes related to antimicrobial resistance, the slpA gene and additional variable genes.

Results: DNA of six reference strains and 234 clinical isolates from South-Western and Eastern Germany was subjected to linear amplification and labeling with dUTP-linked biotin. Amplicons were hybridized to microarrays providing information on the presence of target genes and on their alleles. Tested isolates were assigned to 37 distinct profiles that clustered mainly according to MLST-defined clades. Three additional profiles were predicted from published genome sequences, although they were not found experimentally.

Conclusions: The microarray based assay allows rapid and high-throughput genotyping of clinical C. difficile isolates including toxin gene detection and strain assignment. Overall hybridization profiles correlated with MLST-derived clades.

No MeSH data available.


Related in: MedlinePlus