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On reliable discovery of molecular signatures
Linköping University, Department of Physics, Chemistry and Biology, Computational Biology . Linköping University, The Institute of Technology.
Karolinska Institute.
Linköping University, Department of Physics, Chemistry and Biology, Computational Biology . Linköping University, The Institute of Technology.
2009 (English)In: BMC BIOINFORMATICS, ISSN 1471-2105 , Vol. 10, no 38Article in journal (Refereed) Published
Abstract [en]

Background: Plasmid encoded (CTX)-C-bla-M enzymes represent an important sub-group of class A beta-lactamases causing the ESBL phenotype which is increasingly found in Enterobacteriaceae including Klebsiella spp. Molecular typing of clinical ESBL-isolates has become more and more important for prevention of the dissemination of ESBL-producers among nosocomial environment.

Methods: Multiple displacement amplified DNA derived from 20 K. pneumoniae and 34 K. oxytoca clinical isolates with an ESBL-phenotype was used in a universal CTX-M PCR amplification assay. Identification and differentiation of (CTX)-C-bla-M and (OXY)-O-bla/K1 sequences was obtained by DNA sequencing of M13-sequence-tagged CTX-M PCR-amplicons using a M13-specific sequencing primer.

Results: Nine out of 20 K. pneumoniae clinical isolates had a (CTX)-C-bla-M genotype. Interestingly, we found that the universal degenerated primers also amplified the chromosomally located K1-gene in all 34 K. oxytoca clinical isolates. Molecular identification and differentiation between (CTX)-C-bla-M and (OXY)-O-bla/K1-genes could only been achieved by sequencing of the PCR-amplicons. In silico analysis revealed that the universal degenerated CTX-M primer-pair used here might also amplify the chromosomally located (OXY)-O-bla and K1-genes in Klebsiella spp. and K1-like genes in other Enterobacteriaceae.

Conclusion: The PCR-based molecular typing method described here enables a rapid and reliable molecular identification of (CTX)-C-bla-M, and (OXY)-O-bla/K1-genes. The principles used in this study could also be applied to any situation in which antimicrobial resistance genes would need to be sequenced.

Place, publisher, year, edition, pages
2009. Vol. 10, no 38
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Medical and Health Sciences
Identifiers
URN: urn:nbn:se:liu:diva-17519DOI: 10.1186/1471-2105-10-38OAI: oai:DiVA.org:liu-17519DiVA: diva2:209915
Note
Original Publication:Roland Nilsson, Johan Bjorkegren and Jesper Tegnér, On reliable discovery of molecular signatures, 2009, BMC BIOINFORMATICS, (10), 38.http://dx.doi.org/10.1186/1471-2105-10-38Licensee: BioMed Centralhttp://www.biomedcentral.com/Available from: 2009-03-28 Created: 2009-03-27 Last updated: 2009-03-28Bibliographically approved

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