SeqSphere+ cgMLST Publications
Ugolotti E, Larghero P, Vanni I, Bandettini R, Tripodi G, Melioli G, Di Marco E, Raso A, Biassoni R. Whole genome sequencing as standard practice for the analysis of clonality in outbreaks of meticillin-resistant Staphylococcus aureus in a paediatric setting. J Hosp Infect. 2016, Apr 16. pii: S0195-6701(16)30014-7 [PubMed].
Graham RM, Doyle CJ, Jennison AV. Epidemiological typing of Neisseria gonorrhoeae and detection of markers associated with antimicrobial resistance directly from urine samples using next generation sequencing. Sex Transm Infect. 2016, Mar 11. pii: sextrans-2015-052422 [PubMed].
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. Evolutionary events associated with an outbreak of meningococcal disease in men who have sex with men. PLoS One. 2016, 11: e0154047 [PubMed].
Shore AC, Lazaris A, Kinnevey PM, Brennan OM, Brennan GI, O'Connell B, Feßler AT, Schwarz S, Coleman DC. First report of cfr-carrying plasmids in the pandemic sequence type 22 methicillin-resistant Staphylococcus aureus staphylococcal cassette chromosome mec type IV clone. Antimicrob Agents Chemother. 2016, 60: 3007-15 [PubMed].
Holmes MA, Harrison EM, Fisher EA, Graham EM, Parkhill J, Foster G, Paterson GK. Genomic analysis of companion rabbit Staphylococcus aureus. PLoS One 2016, 11: e0151458 [PubMed].
Strauß L, Ruffing U, Abdulla S, Alabi A, Akulenko R, Garrine M, Germann A, Grobusch MP, Helms V, Herrmann M, Kazimoto T, Kern W, Mandomando I, Peters G, Schaumburg F, von Müller L, Mellmann A. Detecting Staphylococcus aureus virulence and resistance genes - a comparison of whole genome sequencing and DNA microarray technology. J Clin Microbiol. 2016, 54: 1008-16 [PubMed].
Kinnevey PM, Shore AC, Mac Aogáin M, Creamer E, Brennan GI, Humphreys H, Rogers TR, O'Connell B, Coleman DC. Enhanced tracking of nosocomial transmission of endemic sequence type 22 methicillin-resistant Staphylococcus aureus type IV isolates among patients and environmental sites by use of whole-genome sequencing. J Clin Microbiol. 2016, 54: 445-8 [PubMed].
Ruppitsch W, Prager R, Halbedel S, Hyden P, Pietzka A, Huhulescu S, Lohr D, Schönberger K, Aichinger E, Hauri A, Stark K, Vygen S, Tietze E, Allerberger F, Wilking H. Ongoing outbreak of invasive listeriosis, Germany, 2012 to 2015. Euro Surveill. 2015, 20(50): pii=30094 [PubMed].
Mossong J, Decruyenaere F, Moris G, Ragimbeau C, Olinger CM, Johler S, Perrin M, Hau P, Weicherding P. Investigation of a staphylococcal food poisoning outbreak combining case-control, traditional typing and whole genome sequencing methods, Luxembourg, June 2014. Euro Surveill. 2015, 20(45): pii=30059 [PubMed].
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. A core genome MLST scheme for high- resolution typing of Enterococcus faecium. J Clin Microbiol. 2015, 53: 3788-97 [PubMed].
Nyholm O, Halkilahti J, Wiklund G, Okeke U, Paulin L, Auvinen P, Haukka K, Siitonen A. Comparative Genomics and Characterization of Hybrid Shigatoxigenic and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains. PLoS One. 2015, 10: e0135936 [PubMed].
Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL, Allerberger F, Harmsen D, Mellmann A. Defining and evaluating a core genome MLST scheme for whole genome sequence-based typing of Listeria monocytogenes. J Clin Microbiol. 2015, 53: 2869-76 [PubMed].
Weterings V, Zhou K, Rossen JW, van Stenis D, Thewessen E, Kluytmans J, Veenemans J. An outbreak of colistin-resistant Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae in the Netherlands (July to December 2013) with inter-institutional spread. Eur J Clin Microbiol Infect Dis. 2015, 34: 1647-55 [PubMed].
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. Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents. Euro Surveill. 2015, 20(14): pii=21186 [PubMed].
Azarian T, Cook RL, Johnson JA, Guzman N, McCarter YS, Gomez N, Rathore MH, Morris JG, Salemi M. Whole-genome sequencing for outbreak investigations of methicillin-resistant Staphylococcus aureus in the neonatal intensive care unit: time for routine practice? Infect Control Hosp Epidemiol. 2015, 36: 777-85 [PubMed].
Antwerpen MH, Prior K, Mellmann A, Höppner S, Splettstoesser WD, Harmsen D. Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes. PLoS One. 2015, 10: e0123298 [PubMed].
Bletz S, Mellmann A, Rothgänger J, Harmsen D. Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing. Clin Microbiol Infect. 2015, 21: 347.e1-4 [PubMed].
Toro M, Retamal P, Allard M, Brown EW, Evans P, Gonzalez-Escalona N. Draft genome sequences of 33 Salmonella enterica clinical and wildlife isolates from Chile. Genome Announc. 2015, 3: pii=e00054-15 [PubMed].
Lee Y, Kim BS, Chun J, Yong JH, Lee YS, Yoo JS, Yong D, Hong SG, D'Souza R, Thomson KS, Lee K, Chong Y. Clonality and resistome analysis of KPC-producing Klebsiella pneumoniae strain isolated in Korea using whole genome sequencing. Biomed Res Int. 2014, 2014: 352862 [PubMed].
Kohl TA, Diel R, Harmsen D, Rothgänger J, Walter KM, Merker M, Weniger T, Niemann S. Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach. J Clin Microbiol. 2014, 52: 2479-86 [PubMed].
Leopold SR, Goering RV, Witten A, Harmsen D, Mellmann A. Bacterial whole-genome sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes. J Clin Microbiol. 2014, 52: 2365-70 [PubMed].
Schmid D, Allerberger F, Huhulescu S, Pietzka A, Amar C, Kleta S, Prager R, Preußel K, Aichinger E, Mellmann A. Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011-2013. Clin Microbiol Infect. 2014, 20: 431-6 [PubMed].
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D. Updating benchtop sequencing performance comparison. Nat Biotechnol. 2013, 31: 294-6 [PubMed].
