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Core/Whole Genome Multilocus Sequence Typing and Core Genome SNP-Based Typing of OXA-48-Producing Klebsiella pneumoniae Clinical Isolates From Spain.

Miro E, Rossen JWA, Chlebowicz MA, Harmsen D, Brisse S, Passet V, Navarro F, Friedrich AW, García-Cobos S.

Front Microbiol. 2020 Jan 31;10:2961. doi: 10.3389/fmicb.2019.02961. eCollection 2019.


Integration of target analyses, non-target screening and effect-based monitoring to assess OMP related water quality changes in drinking water treatment.

Brunner AM, Bertelkamp C, Dingemans MML, Kolkman A, Wols B, Harmsen D, Siegers W, Martijn BJ, Oorthuizen WA, Ter Laak TL.

Sci Total Environ. 2020 Feb 25;705:135779. doi: 10.1016/j.scitotenv.2019.135779. Epub 2019 Nov 27.


No differences in microbiome changes between anti-adhesive and antibacterial ingredients in toothpastes during periodontal therapy.

Hagenfeld D, Prior K, Harks I, Jockel-Schneider Y, May TW, Harmsen D, Schlagenhauf U, Ehmke B.

J Periodontal Res. 2019 Aug;54(4):435-443. doi: 10.1111/jre.12645. Epub 2019 Mar 9.


Clinical benefits of systemic amoxicillin/metronidazole may depend on periodontitis severity and patients' age: An exploratory sub-analysis of the ABPARO trial.

Eickholz P, Koch R, Kocher T, Hoffmann T, Kim TS, Meyle J, Kaner D, Schlagenhauf U, Harmsen D, Harks I, Ehmke B.

J Clin Periodontol. 2019 Apr;46(4):491-501. doi: 10.1111/jcpe.13096. Epub 2019 Apr 12.


A Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis.

Neumann B, Prior K, Bender JK, Harmsen D, Klare I, Fuchs S, Bethe A, Zühlke D, Göhler A, Schwarz S, Schaffer K, Riedel K, Wieler LH, Werner G.

J Clin Microbiol. 2019 Feb 27;57(3). pii: e01686-18. doi: 10.1128/JCM.01686-18. Print 2019 Mar.


Harmonized Genome Wide Typing of Tubercle Bacilli Using a Web-Based Gene-By-Gene Nomenclature System.

Kohl TA, Harmsen D, Rothgänger J, Walker T, Diel R, Niemann S.

EBioMedicine. 2018 Aug;34:131-138. doi: 10.1016/j.ebiom.2018.07.030. Epub 2018 Aug 13.


Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections.

Janowicz A, De Massis F, Ancora M, Cammà C, Patavino C, Battisti A, Prior K, Harmsen D, Scholz H, Zilli K, Sacchini L, Di Giannatale E, Garofolo G.

J Clin Microbiol. 2018 Aug 27;56(9). pii: e00517-18. doi: 10.1128/JCM.00517-18. Print 2018 Sep.


Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis.

Hagenfeld D, Koch R, Jünemann S, Prior K, Harks I, Eickholz P, Hoffmann T, Kim TS, Kocher T, Meyle J, Kaner D, Schlagenhauf U, Ehmke B, Harmsen D.

PLoS One. 2018 Apr 18;13(4):e0195534. doi: 10.1371/journal.pone.0195534. eCollection 2018.


Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile.

Bletz S, Janezic S, Harmsen D, Rupnik M, Mellmann A.

J Clin Microbiol. 2018 May 25;56(6). pii: e01987-17. doi: 10.1128/JCM.01987-17. Print 2018 Jun.


The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany.

Häsler R, Kautz C, Rehman A, Podschun R, Gassling V, Brzoska P, Sherlock J, Gräsner JT, Hoppenstedt G, Schubert S, Ferlinz A, Lieb W, Laudes M, Heinsen FA, Scholz J, Harmsen D, Franke A, Eisend S, Kunze T, Fickenscher H, Ott S, Rosenstiel P, Schreiber S.

Microbiome. 2018 Feb 20;6(1):37. doi: 10.1186/s40168-018-0414-7.


Epidemiological information is key when interpreting whole genome sequence data - lessons learned from a large Legionella pneumophila outbreak in Warstein, Germany, 2013.

Petzold M, Prior K, Moran-Gilad J, Harmsen D, Lück C.

Euro Surveill. 2017 Nov;22(45). doi: 10.2807/1560-7917.ES.2017.22.45.17-00137.


Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii.

Higgins PG, Prior K, Harmsen D, Seifert H.

PLoS One. 2017 Jun 8;12(6):e0179228. doi: 10.1371/journal.pone.0179228. eCollection 2017.


High Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial.

Mellmann A, Andersen PS, Bletz S, Friedrich AW, Kohl TA, Lilje B, Niemann S, Prior K, Rossen JW, Harmsen D.

J Clin Microbiol. 2017 Mar;55(3):908-913. doi: 10.1128/JCM.02242-16. Epub 2017 Jan 4.


Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting.

Mellmann A, Bletz S, Böking T, Kipp F, Becker K, Schultes A, Prior K, Harmsen D.

J Clin Microbiol. 2016 Dec;54(12):2874-2881. Epub 2016 Aug 24.


Confirming Legionnaires' Disease Outbreak by Genome-Based Method, Germany, 2012.

Burckhardt F, Brion A, Lahm J, Koch HU, Prior K, Petzold M, Harmsen D, Lück C.

Emerg Infect Dis. 2016 Jul;22(7):1303-4. doi: 10.3201/eid2207.151738. No abstract available.


Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men.

Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U.

PLoS One. 2016 May 11;11(5):e0154047. doi: 10.1371/journal.pone.0154047. eCollection 2016.


Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium.

de Been M, Pinholt M, Top J, Bletz S, Mellmann A, van Schaik W, Brouwer E, Rogers M, Kraat Y, Bonten M, Corander J, Westh H, Harmsen D, Willems RJ.

J Clin Microbiol. 2015 Dec;53(12):3788-97.


Is progression of periodontitis relevantly influenced by systemic antibiotics? A clinical randomized trial.

Harks I, Koch R, Eickholz P, Hoffmann T, Kim TS, Kocher T, Meyle J, Kaner D, Schlagenhauf U, Doering S, Holtfreter B, Gravemeier M, Harmsen D, Ehmke B.

J Clin Periodontol. 2015 Sep;42(9):832-842. doi: 10.1111/jcpe.12441. Epub 2015 Sep 22.


Highly Virulent Non-O157 Enterohemorrhagic Escherichia coli (EHEC) Serotypes Reflect Similar Phylogenetic Lineages, Providing New Insights into the Evolution of EHEC.

Eichhorn I, Heidemanns K, Semmler T, Kinnemann B, Mellmann A, Harmsen D, Anjum MF, Schmidt H, Fruth A, Valentin-Weigand P, Heesemann J, Suerbaum S, Karch H, Wieler LH.

Appl Environ Microbiol. 2015 Oct;81(20):7041-7. doi: 10.1128/AEM.01921-15. Epub 2015 Jul 31.


Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents.

Moran-Gilad J, Prior K, Yakunin E, Harrison TG, Underwood A, Lazarovitch T, Valinsky L, Luck C, Krux F, Agmon V, Grotto I, Harmsen D.

Euro Surveill. 2015 Jul 16;20(28). pii: 21186.


Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes.

Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL, Allerberger F, Harmsen D, Mellmann A.

J Clin Microbiol. 2015 Sep;53(9):2869-76. doi: 10.1128/JCM.01193-15. Epub 2015 Jul 1.


The impact of zoonotic MRSA colonization and infection in Germany.

Köck R, Ballhausen B, Bischoff M, Cuny C, Eckmanns T, Fetsch A, Harmsen D, Goerge T, Oberheitmann B, Schwarz S, Selhorst T, Tenhagen BA, Walther B, Witte W, Ziebuhr W, Becker K.

Berl Munch Tierarztl Wochenschr. 2014 Sep-Oct;127(9-10):384-98.


Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+").

Antwerpen MH, Prior K, Mellmann A, Höppner S, Splettstoesser WD, Harmsen D.

PLoS One. 2015 Apr 9;10(4):e0123298. doi: 10.1371/journal.pone.0123298. eCollection 2015.


Degradation of pharmaceuticals in UV (LP)/H₂O₂ reactors simulated by means of kinetic modeling and computational fluid dynamics (CFD).

Wols BA, Harmsen DJ, Wanders-Dijk J, Beerendonk EF, Hofman-Caris CH.

Water Res. 2015 May 15;75:11-24. doi: 10.1016/j.watres.2015.02.014. Epub 2015 Feb 18.


Influence of process conditions and water quality on the formation of mutagenic byproducts in UV/H2O2 processes.

Hofman-Caris RC, Harmsen DJ, Puijker L, Baken KA, Wols BA, Beerendonk EF, Keltjens LL.

Water Res. 2015 May 1;74:191-202. doi: 10.1016/j.watres.2015.01.035. Epub 2015 Feb 7.


State-wide surveillance of antibiotic resistance patterns and spa types of methicillin-resistant Staphylococcus aureus from blood cultures in North Rhine-Westphalia, 2011-2013.

Cuny C, Layer F, Werner G, Harmsen D, Daniels-Haardt I, Jurke A, Mellmann A, Witte W, Köck R.

Clin Microbiol Infect. 2015 Aug;21(8):750-7. doi: 10.1016/j.cmi.2015.02.013. Epub 2015 Feb 20.


Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing.

Bletz S, Mellmann A, Rothgänger J, Harmsen D.

Clin Microbiol Infect. 2015 Apr;21(4):347.e1-4. doi: 10.1016/j.cmi.2014.11.005. Epub 2014 Nov 25.


GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers.

Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D.

PLoS One. 2014 Sep 8;9(9):e107014. doi: 10.1371/journal.pone.0107014. eCollection 2014. Erratum in: PLoS One. 2015;10(3):e0118741.


Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach.

Kohl TA, Diel R, Harmsen D, Rothgänger J, Walter KM, Merker M, Weniger T, Niemann S.

J Clin Microbiol. 2014 Jul;52(7):2479-86. doi: 10.1128/JCM.00567-14. Epub 2014 Apr 30.


Bacterial whole-genome sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes.

Leopold SR, Goering RV, Witten A, Harmsen D, Mellmann A.

J Clin Microbiol. 2014 Jul;52(7):2365-70. doi: 10.1128/JCM.00262-14. Epub 2014 Apr 23.


Degradation of 40 selected pharmaceuticals by UV/H2O2.

Wols BA, Hofman-Caris CH, Harmsen DJ, Beerendonk EF.

Water Res. 2013 Oct 1;47(15):5876-88. doi: 10.1016/j.watres.2013.07.008. Epub 2013 Jul 16.


Updating benchtop sequencing performance comparison.

Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D.

Nat Biotechnol. 2013 Apr;31(4):294-6. doi: 10.1038/nbt.2522. No abstract available. Erratum in: Nat Biotechnol. 2013 Dec;31(12):1148.


Phylogenetic and molecular analysis of food-borne shiga toxin-producing Escherichia coli.

Hauser E, Mellmann A, Semmler T, Stoeber H, Wieler LH, Karch H, Kuebler N, Fruth A, Harmsen D, Weniger T, Tietze E, Schmidt H.

Appl Environ Microbiol. 2013 Apr;79(8):2731-40. doi: 10.1128/AEM.03552-12. Epub 2013 Feb 15.


Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response.

Aarestrup FM, Brown EW, Detter C, Gerner-Smidt P, Gilmour MW, Harmsen D, Hendriksen RS, Hewson R, Heymann DL, Johansson K, Ijaz K, Keim PS, Koopmans M, Kroneman A, Lo Fo Wong D, Lund O, Palm D, Sawanpanyalert P, Sobel J, Schlundt J.

Emerg Infect Dis. 2012 Nov;18(11):e1. doi: 10.3201/eid/1811.120453.


Quantitative assessment of the efficacy of spiral-wound membrane cleaning procedures to remove biofilms.

Hijnen WA, Castillo C, Brouwer-Hanzens AH, Harmsen DJ, Cornelissen ER, van der Kooij D.

Water Res. 2012 Dec 1;46(19):6369-81. doi: 10.1016/j.watres.2012.09.013. Epub 2012 Sep 13.


Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.

Jünemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J, Harmsen D.

PLoS One. 2012;7(8):e41606. doi: 10.1371/journal.pone.0041606. Epub 2012 Aug 1.


Identification of intermediate in evolutionary model of enterohemorrhagic Escherichia coli O157.

Jenke C, Leopold SR, Weniger T, Rothgänger J, Harmsen D, Karch H, Mellmann A.

Emerg Infect Dis. 2012 Apr;18(4):582-8. doi: 10.3201/eid1804.111414.


Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.

Vogel U, Szczepanowski R, Claus H, Jünemann S, Prior K, Harmsen D.

J Clin Microbiol. 2012 Jun;50(6):1889-94. doi: 10.1128/JCM.00038-12. Epub 2012 Mar 29.


Online tools for polyphasic analysis of Mycobacterium tuberculosis complex genotyping data: now and next.

Weniger T, Krawczyk J, Supply P, Harmsen D, Niemann S.

Infect Genet Evol. 2012 Jun;12(4):748-54. doi: 10.1016/j.meegid.2012.01.021. Epub 2012 Feb 10.


Water recovery from sewage using forward osmosis.

Lutchmiah K, Cornelissen ER, Harmsen DJ, Post JW, Lampi K, Ramaekers H, Rietveld LC, Roest K.

Water Sci Technol. 2011;64(7):1443-9. doi: 10.2166/wst.2011.773.


The innovative osmotic membrane bioreactor (OMBR) for reuse of wastewater.

Cornelissen ER, Harmsen D, Beerendonk EF, Qin JJ, Oo H, de Korte KF, Kappelhof JW.

Water Sci Technol. 2011;63(8):1557-65.


Comparison of multilocus variable-number tandem-repeat analysis and multilocus sequence typing for differentiation of hemolytic-uremic syndrome-associated Escherichia coli (HUSEC) collection strains.

Jenke C, Lindstedt BA, Harmsen D, Karch H, Brandal LT, Mellmann A.

J Clin Microbiol. 2011 Oct;49(10):3644-6. doi: 10.1128/JCM.05035-11. Epub 2011 Aug 10.


Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.

Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, Rico A, Prior K, Szczepanowski R, Ji Y, Zhang W, McLaughlin SF, Henkhaus JK, Leopold B, Bielaszewska M, Prager R, Brzoska PM, Moore RL, Guenther S, Rothberg JM, Karch H.

PLoS One. 2011;6(7):e22751. doi: 10.1371/journal.pone.0022751. Epub 2011 Jul 20.


Formation and removal of genotoxic activity during UV/H(2)O(2)-GAC treatment of drinking water.

Heringa MB, Harmsen DJ, Beerendonk EF, Reus AA, Krul CA, Metz DH, Ijpelaar GF.

Water Res. 2011 Jan;45(1):366-74. doi: 10.1016/j.watres.2010.08.008. Epub 2010 Aug 14.


MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria.

Weniger T, Krawczyk J, Supply P, Niemann S, Harmsen D.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W326-31. doi: 10.1093/nar/gkq351. Epub 2010 May 10.


Phylogenetic analysis of enterohemorrhagic Escherichia coli O157, Germany, 1987-2008.

Jenke C, Harmsen D, Weniger T, Rothganger J, Hyytia-Trees E, Bielaszewska M, Karch H, Mellmann A.

Emerg Infect Dis. 2010 Apr;16(4):610-6. doi: 10.3201/eid1604.091361.


Comparison of traditional phenotypic identification methods with partial 5' 16S rRNA gene sequencing for species-level identification of nonfermenting Gram-negative bacilli.

Cloud JL, Harmsen D, Iwen PC, Dunn JJ, Hall G, Lasala PR, Hoggan K, Wilson D, Woods GL, Mellmann A.

J Clin Microbiol. 2010 Apr;48(4):1442-4. doi: 10.1128/JCM.00169-10. Epub 2010 Feb 17.


Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis.

Grundmann H, Aanensen DM, van den Wijngaard CC, Spratt BG, Harmsen D, Friedrich AW; European Staphylococcal Reference Laboratory Working Group.

PLoS Med. 2010 Jan 12;7(1):e1000215. doi: 10.1371/journal.pmed.1000215.


Phylogeny and disease association of Shiga toxin-producing Escherichia coli O91.

Mellmann A, Fruth A, Friedrich AW, Wieler LH, Harmsen D, Werber D, Middendorf B, Bielaszewska M, Karch H.

Emerg Infect Dis. 2009 Sep;15(9):1474-7. doi: 10.3201/eid1509.090161.


High interlaboratory reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry-based species identification of nonfermenting bacteria.

Mellmann A, Bimet F, Bizet C, Borovskaya AD, Drake RR, Eigner U, Fahr AM, He Y, Ilina EN, Kostrzewa M, Maier T, Mancinelli L, Moussaoui W, Prévost G, Putignani L, Seachord CL, Tang YW, Harmsen D.

J Clin Microbiol. 2009 Nov;47(11):3732-4. doi: 10.1128/JCM.00921-09. Epub 2009 Sep 23.

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