TY - JOUR AU - Bernard, K. PY - 2012 DA - 2012// TI - The genus Corynebacterium and other medically relevant coryneform-like bacteria JO - J Clin Microbiol VL - 50 UR - https://doi.org/10.1128/JCM.00796-12 DO - 10.1128/JCM.00796-12 ID - Bernard2012 ER - TY - CHAP AU - Graevenitz, A. AU - Bernard, K. ED - Dworkin, M. ED - Falkow, S. ED - Rosenberg, E. ED - Schleifer, K. -. H. ED - Stackebrandt, E. PY - 2006 DA - 2006// TI - The genus Corynebacterium - medical BT - The prokaryotes: volume 3: archaea Bacteria: Firmicutes, Actinomycetes PB - Springer New York CY - New York UR - https://doi.org/10.1007/0-387-30743-5_31 DO - 10.1007/0-387-30743-5_31 ID - Graevenitz2006 ER - TY - JOUR AU - Leggett, B. A. AU - Zoysa, A. AU - Abbott, Y. E. AU - Leonard, N. AU - Markey, B. AU - Efstratiou, A. PY - 2010 DA - 2010// TI - Toxigenic Corynebacterium diphtheriae isolated from a wound in a horse JO - Vet Rec VL - 166 UR - https://doi.org/10.1136/vr.b4846 DO - 10.1136/vr.b4846 ID - Leggett2010 ER - TY - JOUR AU - Poor, A. P. AU - Moreno, L. Z. AU - Matajira, C. E. C. AU - Parra, B. M. AU - Gomes, V. T. M. AU - Silva, A. P. S. PY - 2017 DA - 2017// TI - Characterization of Corynebacterium diphtheriae, C. confusum and C. amycolatum isolated from sows with genitourinary infection JO - Vet Microbiol VL - 207 UR - https://doi.org/10.1016/j.vetmic.2017.06.008 DO - 10.1016/j.vetmic.2017.06.008 ID - Poor2017 ER - TY - JOUR AU - Meinel, D. M. AU - Kuehl, R. AU - Zbinden, R. AU - Boskova, V. AU - Garzoni, C. AU - Fadini, D. PY - 2016 DA - 2016// TI - Outbreak investigation for toxigenic Corynebacterium diphtheriae wound infections in refugees from Northeast Africa and Syria in Switzerland and Germany by whole genome sequencing JO - Clin Microbiol Infect VL - 22 UR - https://doi.org/10.1016/j.cmi.2016.08.010 DO - 10.1016/j.cmi.2016.08.010 ID - Meinel2016 ER - TY - STD TI - UNICEF Supply Division. Diphtheria Tetanus and Pertussis Vaccine Supply Update October 2016. 2016. Available online at: https://www.unicef.org/supply/index_67674.html. UR - https://www.unicef.org/supply/index_67674.html ID - ref6 ER - TY - JOUR AU - Meinel, D. M. AU - Margos, G. AU - Konrad, R. AU - Krebs, S. AU - Blum, H. AU - Sing, A. PY - 2014 DA - 2014// TI - Next generation sequencing analysis of nine Corynebacterium ulcerans isolates reveals zoonotic transmission and a novel putative diphtheria toxin-encoding pathogenicity island JO - Genome Med VL - 6 UR - https://doi.org/10.1186/s13073-014-0113-3 DO - 10.1186/s13073-014-0113-3 ID - Meinel2014 ER - TY - JOUR AU - Hacker, E. AU - Antunes, C. A. AU - Mattos-Guaraldi, A. L. AU - Burkovski, A. AU - Tauch, A. PY - 2016 DA - 2016// TI - Corynebacterium ulcerans, an emerging human pathogen JO - Future Microbiol VL - 11 UR - https://doi.org/10.2217/fmb-2016-0085 DO - 10.2217/fmb-2016-0085 ID - Hacker2016 ER - TY - JOUR AU - Trost, E. AU - Blom, J. AU - Soares Sde, C. AU - Huang, I. H. AU - Al-Dilaimi, A. AU - Schroder, J. PY - 2012 DA - 2012// TI - Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia JO - J Bacteriol VL - 194 UR - https://doi.org/10.1128/JB.00183-12 DO - 10.1128/JB.00183-12 ID - Trost2012 ER - TY - JOUR AU - DiRita, V. J. PY - 2016 DA - 2016// TI - Classic spotlight: phage bring punch to the party JO - J Bacteriol VL - 198 UR - https://doi.org/10.1128/JB.00644-15 DO - 10.1128/JB.00644-15 ID - DiRita2016 ER - TY - JOUR AU - Collier, R. J. PY - 1975 DA - 1975// TI - Diphtheria toxin: mode of action and structure JO - Bacteriol Rev VL - 39 ID - Collier1975 ER - TY - JOUR AU - Holmes, R. K. PY - 2000 DA - 2000// TI - Biology and molecular epidemiology of diphtheria toxin and the tox gene JO - J Infect Dis VL - 181 UR - https://doi.org/10.1086/315554 DO - 10.1086/315554 ID - Holmes2000 ER - TY - JOUR AU - Chen, C. L. AU - Pan, T. Y. AU - Kan, S. C. AU - Kuan, Y. C. AU - Hong, L. Y. AU - Chiu, K. R. PY - 2008 DA - 2008// TI - Genome sequence of the lytic bacteriophage P1201 from Corynebacterium glutamicum NCHU 87078: evolutionary relationships to phages from Corynebacterineae JO - Virology VL - 378 UR - https://doi.org/10.1016/j.virol.2008.05.027 DO - 10.1016/j.virol.2008.05.027 ID - Chen2008 ER - TY - STD TI - Mansfield MJ, Sugiman-Marangos S, Melnyk RA, Doxey AC. Identification of a diphtheria toxin-like gene family beyond the Corynebacterium genus. FEBS Lett. 2018. Epub 31 July 2018. https://doi.org/10.1002/1873-3468.13208. ID - ref14 ER - TY - JOUR AU - Sing, A. AU - Hogardt, M. AU - Bierschenk, S. AU - Heesemann, J. PY - 2003 DA - 2003// TI - Detection of differences in the nucleotide and amino acid sequences of diphtheria toxin from Corynebacterium diphtheriae and Corynebacterium ulcerans causing extrapharyngeal infections JO - J Clin Microbiol VL - 41 UR - https://doi.org/10.1128/JCM.41.10.4848-4851.2003 DO - 10.1128/JCM.41.10.4848-4851.2003 ID - Sing2003 ER - TY - JOUR AU - Wittchen, M. AU - Busche, T. AU - Gaspar, A. H. AU - Lee, J. H. AU - Ton-That, H. AU - Kalinowski, J. PY - 2018 DA - 2018// TI - Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation JO - BMC Genomics VL - 19 UR - https://doi.org/10.1186/s12864-018-4481-8 DO - 10.1186/s12864-018-4481-8 ID - Wittchen2018 ER - TY - JOUR AU - Dangel, A. AU - Berger, A. AU - Konrad, R. AU - Bischoff, H. AU - Sing, A. PY - 2018 DA - 2018// TI - Geographically diverse clusters of nontoxigenic Corynebacterium diphtheriae infection, Germany, 2016-2017 JO - Emerg Infect Dis VL - 24 UR - https://doi.org/10.3201/eid2407.172026 DO - 10.3201/eid2407.172026 ID - Dangel2018 ER - TY - JOUR AU - Subedi, R. AU - Kolodkina, V. AU - Sutcliffe, I. C. AU - Simpson-Louredo, L. AU - Hirata, R. AU - Titov, L. PY - 2018 DA - 2018// TI - Genomic analyses reveal two distinct lineages of Corynebacterium ulcerans strains JO - New Microbes New infect VL - 25 UR - https://doi.org/10.1016/j.nmni.2018.05.005 DO - 10.1016/j.nmni.2018.05.005 ID - Subedi2018 ER - TY - STD TI - Konrad R, Berger A, Huber I, Boschert V, Hormansdorfer S, Busch U, et al. Matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry as a tool for rapid diagnosis of potentially toxigenic Corynebacterium species in the laboratory management of diphtheria-associated bacteria. Euro Surveill. 2010;15(43) Epub 23 Nov 2010. ID - ref19 ER - TY - JOUR AU - Schuhegger, R. AU - Lindermayer, M. AU - Kugler, R. AU - Heesemann, J. AU - Busch, U. AU - Sing, A. PY - 2008 DA - 2008// TI - Detection of toxigenic Corynebacterium diphtheriae and Corynebacterium ulcerans strains by a novel real-time PCR JO - J Clin Microbiol VL - 46 UR - https://doi.org/10.1128/JCM.01010-08 DO - 10.1128/JCM.01010-08 ID - Schuhegger2008 ER - TY - JOUR AU - Engler, K. H. AU - Glushkevich, T. AU - Mazurova, I. K. AU - George, R. C. AU - Efstratiou, A. PY - 1997 DA - 1997// TI - A modified Elek test for detection of toxigenic corynebacteria in the diagnostic laboratory JO - J Clin Microbiol VL - 35 ID - Engler1997 ER - TY - STD TI - Illumina Inc. Sequencing Analysis Viewer Software. Available from: http://emea.support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.html. UR - http://emea.support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.html ID - ref22 ER - TY - BOOK AU - Andrews, S. PY - 2010 DA - 2010// TI - FastQC: A quality control tool for high throughput sequence data ID - Andrews2010 ER - TY - JOUR AU - Wood, D. E. AU - Salzberg, S. L. PY - 2014 DA - 2014// TI - Kraken: ultrafast metagenomic sequence classification using exact alignments JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/gb-2014-15-3-r46 DO - 10.1186/gb-2014-15-3-r46 ID - Wood2014 ER - TY - JOUR AU - Bolger, A. M. AU - Lohse, M. AU - Usadel, B. PY - 2014 DA - 2014// TI - Trimmomatic: a flexible trimmer for Illumina sequence data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu170 DO - 10.1093/bioinformatics/btu170 ID - Bolger2014 ER - TY - JOUR AU - Bankevich, A. AU - Nurk, S. AU - Antipov, D. AU - Gurevich, A. A. AU - Dvorkin, M. AU - Kulikov, A. S. PY - 2012 DA - 2012// TI - SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing JO - J Comput Biol VL - 19 UR - https://doi.org/10.1089/cmb.2012.0021 DO - 10.1089/cmb.2012.0021 ID - Bankevich2012 ER - TY - JOUR AU - Gurevich, A. AU - Saveliev, V. AU - Vyahhi, N. AU - Tesler, G. PY - 2013 DA - 2013// TI - QUAST: quality assessment tool for genome assemblies JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt086 DO - 10.1093/bioinformatics/btt086 ID - Gurevich2013 ER - TY - JOUR AU - Darling, A. E. AU - Mau, B. AU - Perna, N. T. PY - 2010 DA - 2010// TI - ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0011147 DO - 10.1371/journal.pone.0011147 ID - Darling2010 ER - TY - JOUR AU - Seemann, T. PY - 2014 DA - 2014// TI - Prokka: rapid prokaryotic genome annotation JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu153 DO - 10.1093/bioinformatics/btu153 ID - Seemann2014 ER - TY - BOOK AU - Ehrlich, R. PY - 2016 DA - 2016// TI - Prokka database maker script ID - Ehrlich2016 ER - TY - JOUR AU - Arndt, D. AU - Grant, J. R. AU - Marcu, A. AU - Sajed, T. AU - Pon, A. AU - Liang, Y. PY - 2016 DA - 2016// TI - PHASTER: a better, faster version of the PHAST phage search tool JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw387 DO - 10.1093/nar/gkw387 ID - Arndt2016 ER - TY - STD TI - Leimbach A. Collection of scripts for bacterial genomics. Zenodo. https://doi.org/10.5281/zenodo.215824.2016 [12 Nov 2018]; Available online at: https://github.com/aleimba/bac-genomics-scripts/blob/master/cds_extractor/cds_extractor.pl. UR - https://github.com/aleimba/bac-genomics-scripts/blob/master/cds_extractor/cds_extractor.pl ID - ref32 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: a multiple sequence alignment method with reduced time and space complexity JO - BMC bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-113 DO - 10.1186/1471-2105-5-113 ID - Edgar2004 ER - TY - JOUR AU - Price, M. N. AU - Dehal, P. S. AU - Arkin, A. P. PY - 2010 DA - 2010// TI - FastTree 2--approximately maximum-likelihood trees for large alignments JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0009490 DO - 10.1371/journal.pone.0009490 ID - Price2010 ER -