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10. Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR

Author

Gotz, A., Pukall, R., Smit, E., Tietze, E., Prager, R., Tschape, H., Elsas, J.D. van, and Smalla, K.

Subjects
Polymerase chain reaction -- Usage, Plasmids -- Genetic aspects, Soil microbiology -- Methods, Manures -- Analysis, Biological sciences
Abstract

The application of PCR primers specific for the plasmid DNA sequences of incompatibility (Inc) groups shows that IncQ and IncP DNA sequences are present in soil and manure slurry while IncN and IncW sequences are present mainly in manure samples. The method offers a good technique for identifying Inc-containing plasmids in nonculturable and culturable bacteria. However, the primers identify only those sequences that are highly similar to their reference sequences. The DNA of plasmids classified on the basis on conventional methods may differ from that of the reference sequences.

Published
1996

20. Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, 2012

Author

Lindstedt, B A, Torpdahl, M, Vergnaud, G, Le Hello, S, Weill, F X, Tietze, E, Malorny, B, Prendergast, D M, Ní Ghallchoir, E, Lista, R F, Schouls, L M, Söderlund, R, Börjesson, Stefan, Åkerström, S, Lindstedt, B A, Torpdahl, M, Vergnaud, G, Le Hello, S, Weill, F X, Tietze, E, Malorny, B, Prendergast, D M, Ní Ghallchoir, E, Lista, R F, Schouls, L M, Söderlund, R, Börjesson, Stefan, and Åkerström, S

Abstract

Genotyping of important medical or veterinary prokaryotes has become a very important tool during the last decades. Rapid development of fragment-separation and sequencing technologies has made many new genotyping strategies possible. Among these new methods is multilocus variable-number tandem repeat analysis (MLVA). Here we present an update on the use of MLVA in eight European countries (Denmark, France, Germany, Ireland, Italy, the Netherlands, Norway and Sweden). Researchers in Europe have been active in developing and implementing a large array of different assays. MLVA has been used as a typing tool in several contexts, from aiding in resolving outbreaks of foodborne bacteria to typing organisms that may pose a bioterrorist threat, as well as in scientific studies.

Published
2013
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21. Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany

Author

Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Grad, Y. H., Lipsitch, M., Griggs, Allison, Haas, Brian J., Shea, T. P., McCowan, C., Montmayeur, A., FitzGerald, M., Wortman, J. R., Krogfelt, K. A., Bingen, E., Weill, F.-X., Tietze, E., Flieger, A., Nusbaum, Chad, Birren, Bruce W., Hung, Deborah T., Hanage, W. P., Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., Grad, Y. H., Lipsitch, M., Griggs, Allison, Haas, Brian J., Shea, T. P., McCowan, C., Montmayeur, A., FitzGerald, M., Wortman, J. R., Krogfelt, K. A., Bingen, E., Weill, F.-X., Tietze, E., Flieger, A., Nusbaum, Chad, Birren, Bruce W., Hung, Deborah T., and Hanage, W. P.

Abstract

In our paper (1), we analyzed isolates from the Escherichia coli O104:H4 outbreaks in Germany and France in May to July 2011. We concluded that, although the German outbreak was larger, the German isolates represent a clade within the greater diversity of the French outbreak. We proposed several hypotheses to explain these findings, including that the lineage leading to the German outbreak went through a narrow bottleneck that purged diversity. Guy et al. (2) report the genomes of eight additional E. coli O104:H4 isolates sampled from the German outbreak. By focusing on the numbers of SNPs in their samples, they suggest that the German outbreak is more diverse than we reported and is similar to the French outbreak. In fact, Guy et al.’s data (2) strongly support our conclusion that the German outbreak represents a clade within the diversity …

Published
2013

23. The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 islated from bacteria of the wheat rhizosphere

Author

Tauch, Andreas, Schneiker-Bekel, Susanne, Selbitschka, Werner, Pühler, Alfred, van Overbeek, LS, Smalla, K, Thomas, CM, Bailey, MJ, Forney, LJ, Weightman, A, Ceglowski, P, Pembroke, T, Tietze, E, Schroder, G, Lanka, E, and van Elsas, JD

Subjects
DNA Replication, DNA, Bacterial, Base Sequence, Amino Acid Motifs, Molecular Sequence Data, Sequence Analysis, DNA, PRI Gewas- en Productie-ecologie, Protein Sorting Signals, plasmid stability, exogenous plasmid isolation, Plant Roots, PRI Crop and Production Ecology, conjugative transfer, horizontal gene spread, Bacterial Proteins, Species Specificity, Chromosome Segregation, Conjugation, Genetic, bacterial genome, plasmid, Amino Acid Sequence, Promoter Regions, Genetic, Soil Microbiology, Triticum, Plasmids
Abstract

Plasmid pIPO2 is a cryptic, conjugative, broad-host-range plasmid isolated from the wheat rhizosphere. It efficiently self-transfers between alpha, beta and gamma Proteobacteria and has a mobilizing/retromobilizing capacity for IncQ plasmids. The complete nucleotide sequence of pIPO2 is presented on the basis of its mini-Tn5::luxABtet-tagged derivative, pIPO2T. The pIPO2 sequence is 39815 bp long and contains at least 43 complete ORFs. Apart from a suite of ORFs with unknown function, all of the genes carried on pIPO2 are predicted to be involved in plasmid replication, maintenance and conjugative transfer. The overall organization of these genes is different from previously described plasmids, but is similar to the genetic organization seen in pSB102, a conjugative plasmid recently isolated from the bacterial community of the alfalfa rhizosphere. The putative conjugative transfer region of pIPO2 covers 23 kb and contains the genes required for DNA processing (Dtr) and mating pair formation (Mpf). The organization of these transfer genes in pIPO2 is highly similar to the genetic organization seen in the environmental plasmid pSB102 and in pXF51 from the plant pathogen Xylella fastidiosa. Plasmids pSB102 and pXF51 have recently been proposed to form a new family of environmental broad-host-range plasmids. Here it is suggested that pIPO2 is a new member of this family. The proposed Mpf system of pIPO2 shares high amino acid sequence similarity with equivalent VirB proteins from the type IV secretion system of Brucella spp. Sequence information was used to design primers specific for the detection of pIPO2. Environmental DNA from a range of diverse habitats was screened by PCR with these primers. Consistently positive signals for the presence of pIPO2 were obtained from a range of soil-related habitats, including the rhizospheres of young wheat plants, of field-grown oats and of grass (all gramineous plants), as well as from the rhizosphere of tomato plants. These data add to the growing evidence that plasmids carry advantageous genes with as yet undefined functions in plant-associated communities.

Published
2002

24. Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, 2012

Author

Lindstedt, B A, primary, Torpdahl, M, additional, Vergnaud, G, additional, Le Hello, S, additional, Weill, F X, additional, Tietze, E, additional, Malorny, B, additional, Prendergast, D M, additional, Ní Ghallchóir, E, additional, Lista, R F, additional, Schouls, L M, additional, Söderlund, R, additional, Börjesson, S, additional, and Åkerström, S, additional

Published
2013
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27. Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany

Author

Grad, Y. H., primary, Lipsitch, M., additional, Griggs, A. D., additional, Haas, B. J., additional, Shea, T. P., additional, McCowan, C., additional, Montmayeur, A., additional, FitzGerald, M., additional, Wortman, J. R., additional, Krogfelt, K. A., additional, Bingen, E., additional, Weill, F.-X., additional, Tietze, E., additional, Flieger, A., additional, Lander, E. S., additional, Nusbaum, C., additional, Birren, B. W., additional, Hung, D. T., additional, and Hanage, W. P., additional

Published
2012
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30. The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 islated from bacteria of the wheat rhizosphere

Author

Tauch, A., Schneiker, S., Selbitschka, W., PÜhler, A., van Overbeek, L.S., Smalla, K., Thomas, C.M., Bailey, M.J., Forney, L.J., Weightman, A., Ceglowski, P., Pembroke, T., Tietze, E., Schröder, G., Lanka, E., van Elsas, J.D., Tauch, A., Schneiker, S., Selbitschka, W., PÜhler, A., van Overbeek, L.S., Smalla, K., Thomas, C.M., Bailey, M.J., Forney, L.J., Weightman, A., Ceglowski, P., Pembroke, T., Tietze, E., Schröder, G., Lanka, E., and van Elsas, J.D.

Abstract

The flood of sequence data resulting from the large number of current genome projects has increased the need for a flexible, open source genome annotation system, which so far has not existed. To account for the individual needs of different projects, such a system should be modular and easily extensible. We present a genome annotation system for prokaryote genomes, which is well tested and readily adaptable to different tasks. The modular system was developed using an object-oriented approach, and it relies on a relational database backend. Using a well defined application programmers interface (API), the system can be linked easily to other systems. GenDB supports manual as well as automatic annotation strategies. The software currently is in use in more than a dozen microbial genome annotation projects. In addition to its use as a production genome annotation system, it can be employed as a flexible framework for the large-scale evaluation of different annotation strategies. The system is open source

Published
2002

39. Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, 2012

Author

Lindstedt, B. A., Torpdahl, M., Gilles Vergnaud, Le Hello, S., Weill, F. X., Tietze, E., Malorny, B., Prendergast, D. M., Ghallchoir, E. Ni, Lista, R. F., Schouls, L. M., Soderlund, R., Borjesson, S., and Akerstrom, S.

Subjects
VDP::Medisinske fag: 700::Helsefag: 800::Epidemiologi medisinsk og odontologisk statistikk: 803, VDP::Midical sciences: 700::Health sciences: 800::Epidemiology, medical and dental statistics: 803

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