TY  - JOUR
A1  - Zdziarski, Jaroslaw
A1  - Brzuszkiewicz, Elzbieta
A1  - Wullt, Bjorn
A1  - Liesegang, Heiko
A1  - Biran, Dvora
A1  - Voigt, Birgit
A1  - Gronberg-Hernandez, Jenny
A1  - Ragnarsdottir, Bryndis
A1  - Hecker, Michael
A1  - Ron, Eliora Z.
A1  - Daniel, Rolf
A1  - Gottschalk, Gerhard
A1  - Hacker, Joerg
A1  - Svanborg, Catharina
A1  - Dobrindt, Ulrich
T1  - Host Imprints on Bacterial Genomes-Rapid, Divergent Evolution in Individual Patients
N2  - Bacteria lose or gain genetic material and through selection, new variants become fixed in the population. Here we provide the first, genome-wide example of a single bacterial strain’s evolution in different deliberately colonized patients and the surprising insight that hosts appear to personalize their microflora. By first obtaining the complete genome sequence of the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its descendants after therapeutic bladder colonization of different patients, we identified 34 mutations, which affected metabolic and virulence-related genes. Further transcriptome and proteome analysis proved that these genome changes altered bacterial gene expression resulting in unique adaptation patterns in each patient. Our results provide evidence that, in addition to stochastic events, adaptive bacterial evolution is driven by individual host environments. Ongoing loss of gene function supports the hypothesis that evolution towards commensalism rather than virulence is favored during asymptomatic bladder colonization.
KW  - Proteomanalyse
KW  - Bakterien
Y1  - 2010
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-68594
ER  - 
TY  - JOUR
A1  - Friedrich, Torben
A1  - Rahmann, Sven
A1  - Weigel, Wilfried
A1  - Rabsch, Wolfgang
A1  - Fruth, Angelika
A1  - Ron, Eliora
A1  - Gunzer, Florian
A1  - Dandekar, Thomas
A1  - Hacker, Joerg
A1  - Mueller, Tobias
A1  - Dobrindt, Ulrich
T1  - High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis
N2  - The Enterobacteriaceae comprise a large number of clinically relevant species with several individual subspecies. Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. Array technology offers a fast, reproducible and standardisable means for bacterial typing and thus provides many advantages for bacterial diagnostics, risk assessment and surveillance. The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens. Results: We developed a DNA microarray for strain typing and detection of major antimicrobial resistance genes of clinically relevant enterobacteria. For this purpose, we applied a global genome-wide probe selection strategy on 32 available complete enterobacterial genomes combined with a regression model for pathogen classification. The discriminative power of the probe set was further tested in silico on 15 additional complete enterobacterial genome sequences. DNA microarrays based on the selected probes were used to type 92 clinical enterobacterial isolates. Phenotypic tests confirmed the array-based typing results and corroborate that the selected probes allowed correct typing and prediction of major antibiotic resistances of clinically relevant Enterobacteriaceae, including the subspecies level, e.g. the reliable distinction of different E. coli pathotypes. Conclusions: Our results demonstrate that the global probe selection approach based on longest common factor statistics as well as the design of a DNA microarray with a restricted set of discriminative probes enables robust discrimination of different enterobacterial variants and represents a proof of concept that can be adopted for diagnostics of a wide range of microbial pathogens. Our approach circumvents misclassifications arising from the application of virulence markers, which are highly affected by horizontal gene transfer. Moreover, a broad range of pathogens have been covered by an efficient probe set size enabling the design of high-throughput diagnostics.
KW  - Mikroarray
KW  - Enterobacteriaceae
Y1  - 2010
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-67936
ER  -