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Taxonomic reassessment of the genus Pseudocitrobacter using whole genome sequencing: Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis and description of Pseudocitrobacter vendiensis sp. nov.

Kämpfer P, Fuglsang-Damgaard D, Overballe-Petersen S, Hasman H, Hammerum AM, Fuursted K, Blom J, Glaeser SP, Hansen F.

Int J Syst Evol Microbiol. 2019 Dec 20. doi: 10.1099/ijsem.0.003918. [Epub ahead of print]


Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids.

Sydenham TV, Overballe-Petersen S, Hasman H, Wexler H, Kemp M, Justesen US.

Microb Genom. 2019 Nov;5(11). doi: 10.1099/mgen.0.000312.


PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).

Carattoli A, Hasman H.

Methods Mol Biol. 2020;2075:285-294. doi: 10.1007/978-1-4939-9877-7_20.


2CS-CHXT Operon Signature of Chlorhexidine Tolerance among Enterococcus faecium Isolates.

Duarte B, Pereira AP, Freitas AR, Coque TM, Hammerum AM, Hasman H, Antunes P, Peixe L, Novais C.

Appl Environ Microbiol. 2019 Nov 14;85(23). pii: e01589-19. doi: 10.1128/AEM.01589-19. Print 2019 Dec 1.


Surveillance of vancomycin-resistant enterococci reveals shift in dominating clones and national spread of a vancomycin-variable vanA Enterococcus faecium ST1421-CT1134 clone, Denmark, 2015 to March 2019.

Hammerum AM, Justesen US, Pinholt M, Roer L, Kaya H, Worning P, Nygaard S, Kemp M, Clausen ME, Nielsen KL, Samulioniené J, Kjærsgaard M, Østergaard C, Coia J, Søndergaard TS, Gaini S, Schønning K, Westh H, Hasman H, Holzknecht BJ.

Euro Surveill. 2019 Aug;24(34). doi: 10.2807/1560-7917.ES.2019.24.34.1900503.


Complete Genome Sequence of Escherichia coli MT102, a Plasmid-Free Recipient Resistant to Rifampin, Azide, and Streptomycin, Used in Conjugation Experiments.

Valcek A, Overballe-Petersen S, Hansen F, Dolejska M, Hasman H.

Microbiol Resour Announc. 2019 May 16;8(20). pii: e00383-19. doi: 10.1128/MRA.00383-19.


IncI1 ST3 and IncI1 ST7 plasmids from CTX-M-1-producing Escherichia coli obtained from patients with bloodstream infections are closely related to plasmids from E. coli of animal origin.

Valcek A, Roer L, Overballe-Petersen S, Hansen F, Bortolaia V, Leekitcharoenphon P, Korsgaard HB, Seyfarth AM, Hendriksen RS, Hasman H, Hammerum AM.

J Antimicrob Chemother. 2019 Aug 1;74(8):2171-2175. doi: 10.1093/jac/dkz199.


Appearance of vanD-positive Enterococcus faecium in a tertiary hospital in the Netherlands: prevalence of vanC and vanD in hospitalized patients.

Flipse J, von Wintersdorff CJH, van Niekerk JM, Jamin C, van Tiel FH, Hasman H, van Alphen LB.

Sci Rep. 2019 May 6;9(1):6949. doi: 10.1038/s41598-019-42824-4.


LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences.

Hasman H, Clausen PTLC, Kaya H, Hansen F, Knudsen JD, Wang M, Holzknecht BJ, Samulioniené J, Røder BL, Frimodt-Møller N, Lund O, Hammerum AM.

J Antimicrob Chemother. 2019 Jun 1;74(6):1473-1476. doi: 10.1093/jac/dkz092.


Fecal Carriage and Whole-Genome Sequencing-Assisted Characterization of CMY-2 Beta-Lactamase-Producing Escherichia coli in Calves at Czech Dairy Cow Farm.

Manga I, Hasman H, Smidkova J, Medvecky M, Dolejska M, Cizek A.

Foodborne Pathog Dis. 2019 Jan;16(1):42-53. doi: 10.1089/fpd.2018.2531.


Infection with multiple carbapenemase-producing bacteria following cosmetic surgery in Iran detected after the introduction of systematic screening of repatriates.

Andrews V, Hansen F, Hammerum AM, Hasman H, Roer L, Hansen DS, Olesen B, Krogstrup NV, Dohrn N, Holzknecht BJ.

J Glob Antimicrob Resist. 2019 Mar;16:144-146. doi: 10.1016/j.jgar.2018.12.005. Epub 2019 Jan 10. No abstract available.


Evaluation of temocillin for phenotypic carbapenemase screening of Escherichia coli and Salmonella enterica isolates in relation to the presence of genes encoding ESBLs and carbapenemase production.

Cavaco LM, Hansen F, Mushtaq S, Hill RLR, Woodford N, Le Hello S, Hendriksen RS, Hammerum AM, Hasman H.

J Antimicrob Chemother. 2019 Mar 1;74(3):639-644. doi: 10.1093/jac/dky493.


Complete Genome Sequence of a Vancomycin-Resistant Sequence Type 203 Enterococcus faecium Strain with vanA Belonging to Complex Type 859.

Hoffmann M, Yao K, Allard M, Sanchez M, Andersen LP, Hasman H, Hammerum AM.

Microbiol Resour Announc. 2018 Jul 19;7(2). pii: e00815-18. doi: 10.1128/MRA.00815-18. eCollection 2018 Jul.


ST131 fimH22 Escherichia coli isolate with a blaCMY-2/IncI1/ST12 plasmid obtained from a patient with bloodstream infection: highly similar to E. coli isolates of broiler origin.

Roer L, Overballe-Petersen S, Hansen F, Johannesen TB, Stegger M, Bortolaia V, Leekitcharoenphon P, Korsgaard HB, Seyfarth AM, Mossong J, Wattiau P, Boland C, Hansen DS, Hasman H, Hammerum AM, Hendriksen RS.

J Antimicrob Chemother. 2019 Mar 1;74(3):557-560. doi: 10.1093/jac/dky484.


Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones.

Roer L, Overballe-Petersen S, Hansen F, Schønning K, Wang M, Røder BL, Hansen DS, Justesen US, Andersen LP, Fulgsang-Damgaard D, Hopkins KL, Woodford N, Falgenhauer L, Chakraborty T, Samuelsen Ø, Sjöström K, Johannesen TB, Ng K, Nielsen J, Ethelberg S, Stegger M, Hammerum AM, Hasman H.

mSphere. 2018 Jul 18;3(4). pii: e00337-18. doi: 10.1128/mSphere.00337-18.


Recommendations To Address the Difficulties Encountered When Determining Linezolid Resistance from Whole-Genome Sequencing Data.

Beukers AG, Hasman H, Hegstad K, van Hal SJ.

Antimicrob Agents Chemother. 2018 Jul 27;62(8). pii: e00613-18. doi: 10.1128/AAC.00613-18. Print 2018 Aug.


Vancomycin resistance in Enterococcus faecium isolated from Danish chicken meat is located on a pVEF4-like plasmid persisting in poultry for 18 years.

Leinweber H, Alotaibi SMI, Overballe-Petersen S, Hansen F, Hasman H, Bortolaia V, Hammerum AM, Ingmer H.

Int J Antimicrob Agents. 2018 Aug;52(2):283-286. doi: 10.1016/j.ijantimicag.2018.03.019. Epub 2018 Apr 3.


SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data.

Kaya H, Hasman H, Larsen J, Stegger M, Johannesen TB, Allesøe RL, Lemvigh CK, Aarestrup FM, Lund O, Larsen AR.

mSphere. 2018 Feb 14;3(1). pii: e00612-17. doi: 10.1128/mSphere.00612-17. eCollection 2018 Jan-Feb.


Complete Nucleotide Sequence of an Escherichia coli Sequence Type 410 Strain Carrying blaNDM-5 on an IncF Multidrug Resistance Plasmid and blaOXA-181 on an IncX3 Plasmid.

Overballe-Petersen S, Roer L, Ng K, Hansen F, Justesen US, Andersen LP, Stegger M, Hammerum AM, Hasman H.

Genome Announc. 2018 Feb 1;6(5). pii: e01542-17. doi: 10.1128/genomeA.01542-17.


CHTyper, a Web Tool for Subtyping of Extraintestinal Pathogenic Escherichia coli Based on the fumC and fimH Alleles.

Roer L, Johannesen TB, Hansen F, Stegger M, Tchesnokova V, Sokurenko E, Garibay N, Allesøe R, Thomsen MCF, Lund O, Hasman H, Hammerum AM.

J Clin Microbiol. 2018 Mar 26;56(4). pii: e00063-18. doi: 10.1128/JCM.00063-18. Print 2018 Apr. No abstract available.


Use of a Regression Model to Study Host-Genomic Determinants of Phage Susceptibility in MRSA.

Zschach H, Larsen MV, Hasman H, Westh H, Nielsen M, Międzybrodzki R, Jończyk-Matysiak E, Weber-Dąbrowska B, Górski A.

Antibiotics (Basel). 2018 Jan 29;7(1). pii: E9. doi: 10.3390/antibiotics7010009.


Molecular Methods for Detection of Antimicrobial Resistance.

Anjum MF, Zankari E, Hasman H.

Microbiol Spectr. 2017 Dec;5(6). doi: 10.1128/microbiolspec.ARBA-0011-2017. Review.


Dissemination and Characteristics of a Novel Plasmid-Encoded Carbapenem-Hydrolyzing Class D β-Lactamase, OXA-436, Found in Isolates from Four Patients at Six Different Hospitals in Denmark.

Samuelsen Ø, Hansen F, Aasnæs B, Hasman H, Lund BA, Leiros HS, Lilje B, Janice J, Jakobsen L, Littauer P, Søes LM, Holzknecht BJ, Andersen LP, Stegger M, Andersen PS, Hammerum AM.

Antimicrob Agents Chemother. 2017 Dec 21;62(1). pii: e01260-17. doi: 10.1128/AAC.01260-17. Print 2018 Jan.


RUCS: rapid identification of PCR primers for unique core sequences.

Thomsen MCF, Hasman H, Westh H, Kaya H, Lund O.

Bioinformatics. 2017 Dec 15;33(24):3917-3921. doi: 10.1093/bioinformatics/btx526.


Novel mcr-3 variant, encoding mobile colistin resistance, in an ST131 Escherichia coli isolate from bloodstream infection, Denmark, 2014.

Roer L, Hansen F, Stegger M, Sönksen UW, Hasman H, Hammerum AM.

Euro Surveill. 2017 Aug 3;22(31). doi: 22846.


Development of a Web Tool for Escherichia coli Subtyping Based on fimH Alleles.

Roer L, Tchesnokova V, Allesøe R, Muradova M, Chattopadhyay S, Ahrenfeldt J, Thomsen MCF, Lund O, Hansen F, Hammerum AM, Sokurenko E, Hasman H.

J Clin Microbiol. 2017 Aug;55(8):2538-2543. doi: 10.1128/JCM.00737-17. Epub 2017 Jun 7.


Detection of the optrA gene in a clinical ST16 Enterococcus faecalis isolate in Denmark.

Vorobieva V, Roer L, Justesen US, Hansen F, Frimodt-Møller N, Hasman H, Hammerum AM.

J Glob Antimicrob Resist. 2017 Sep;10:12-13. doi: 10.1016/j.jgar.2017.05.002. Epub 2017 May 30. No abstract available.


Emergence of vanA Enterococcus faecium in Denmark, 2005-15.

Hammerum AM, Baig S, Kamel Y, Roer L, Pinholt M, Gumpert H, Holzknecht B, Røder B, Justesen US, Samulioniené J, Kjærsgaard M, Østergaard C, Holm A, Dzajic E, Søndergaard TS, Gaini S, Edquist P, Alm E, Lilje B, Westh H, Stegger M, Hasman H.

J Antimicrob Chemother. 2017 Aug 1;72(8):2184-2190. doi: 10.1093/jac/dkx138.


Turn Up the Heat-Food and Clinical Escherichia coli Isolates Feature Two Transferrable Loci of Heat Resistance.

Boll EJ, Marti R, Hasman H, Overballe-Petersen S, Stegger M, Ng K, Knøchel S, Krogfelt KA, Hummerjohann J, Struve C.

Front Microbiol. 2017 Apr 7;8:579. doi: 10.3389/fmicb.2017.00579. eCollection 2017.


WGS-based surveillance of third-generation cephalosporin-resistant Escherichia coli from bloodstream infections in Denmark.

Roer L, Hansen F, Thomsen MCF, Knudsen JD, Hansen DS, Wang M, Samulioniené J, Justesen US, Røder BL, Schumacher H, Østergaard C, Andersen LP, Dzajic E, Søndergaard TS, Stegger M, Hammerum AM, Hasman H.

J Antimicrob Chemother. 2017 Jul 1;72(7):1922-1929. doi: 10.1093/jac/dkx092.


Detection of mcr-1-encoding plasmid-mediated colistin-resistant Salmonella isolates from human infection in Denmark.

Torpdahl M, Hasman H, Litrup E, Skov RL, Nielsen EM, Hammerum AM.

Int J Antimicrob Agents. 2017 Feb;49(2):261-262. doi: 10.1016/j.ijantimicag.2016.11.010. Epub 2017 Jan 3. No abstract available.


Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods.

Ahrenfeldt J, Skaarup C, Hasman H, Pedersen AG, Aarestrup FM, Lund O.

BMC Genomics. 2017 Jan 5;18(1):19. doi: 10.1186/s12864-016-3407-6.


First report of metronidazole resistant, nimD-positive, Bacteroides stercoris isolated from an abdominal abscess in a 70-year-old woman.

Otte E, Nielsen HL, Hasman H, Fuglsang-Damgaard D.

Anaerobe. 2017 Feb;43:91-93. doi: 10.1016/j.anaerobe.2016.12.010. Epub 2016 Dec 21.


The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.

Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MTG, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM, Samuelsen Ø, Woodford N.

Clin Microbiol Infect. 2017 Jan;23(1):2-22. doi: 10.1016/j.cmi.2016.11.012. Epub 2016 Nov 23. Review.


[Epidemic increase in the incidence of carbapenemase-producing Enterobacteriaceae in Denmark].

Wang M, Ellermann-Eriksen S, Hansen DS, Kjerulf A, Fuglsang-Damgaard D, Holm A, Østergaard C, Røder B, Sönksen UW, Detlefsen M, Hansen F, Hasman H, Hammerum A, Skov RL.

Ugeskr Laeger. 2016 Nov 7;178(45). pii: V06160422. Review. Danish.


Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems?

Roer L, Hendriksen RS, Leekitcharoenphon P, Lukjancenko O, Kaas RS, Hasman H, Aarestrup FM.

mSystems. 2016 Jun 21;1(3). pii: e00009-16. eCollection 2016 May-Jun.


Characterization of a novel blaIMP gene, blaIMP-58, using whole genome sequencing in a Pseudomonas putida isolate detected in Denmark.

Holmgaard DB, Hansen F, Hasman H, Justesen US, Hammerum AM.

Diagn Microbiol Infect Dis. 2017 Jan;87(1):68-70. doi: 10.1016/j.diagmicrobio.2016.10.002. Epub 2016 Oct 7.


Polyclonal spread of vanA Enterococcus faecium in Central Denmark Region, 2009-2013, investigated using PFGE, MLST and WGS.

Landerslev KG, Jakobsen L, Olsen SS, Pedersen MB, Kristensen B, Lemming LE, Wang M, Kjærsgaard M, Stegger M, Hasman H, Hammerum AM.

Int J Antimicrob Agents. 2016 Dec;48(6):767-768. doi: 10.1016/j.ijantimicag.2016.09.001. Epub 2016 Sep 28. No abstract available.


Use of WGS data for investigation of a long-term NDM-1-producing Citrobacter freundii outbreak and secondary in vivo spread of blaNDM-1 to Escherichia coli, Klebsiella pneumoniae and Klebsiella oxytoca.

Hammerum AM, Hansen F, Nielsen HL, Jakobsen L, Stegger M, Andersen PS, Jensen P, Nielsen TK, Hansen LH, Hasman H, Fuglsang-Damgaard D.

J Antimicrob Chemother. 2016 Nov;71(11):3117-3124. Epub 2016 Aug 1.


A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance.

Thomsen MC, Ahrenfeldt J, Cisneros JL, Jurtz V, Larsen MV, Hasman H, Aarestrup FM, Lund O.

PLoS One. 2016 Jun 21;11(6):e0157718. doi: 10.1371/journal.pone.0157718. eCollection 2016.


Sequence-Based Characterization of Tn5801-Like Genomic Islands in Tetracycline-Resistant Staphylococcus pseudintermedius and Other Gram-positive Bacteria from Humans and Animals.

de Vries LE, Hasman H, Jurado Rabadán S, Agersø Y.

Front Microbiol. 2016 Apr 26;7:576. doi: 10.3389/fmicb.2016.00576. eCollection 2016.


Fatal Septicemia Linked to Transmission of MRSA Clonal Complex 398 in Hospital and Nursing Home, Denmark.

Nielsen RT, Kemp M, Holm A, Skov MN, Detlefsen M, Hasman H, Aarestrup FM, Kaas RS, Nielsen JB, Westh H, Kolmos HJ.

Emerg Infect Dis. 2016 May;22(5):900-2. doi: 10.3201/eid2205.151835.


What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?

Zschach H, Joensen KG, Lindhard B, Lund O, Goderdzishvili M, Chkonia I, Jgenti G, Kvatadze N, Alavidze Z, Kutter EM, Hasman H, Larsen MV.

Viruses. 2015 Dec 12;7(12):6570-89. doi: 10.3390/v7122958.


Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015.

Hasman H, Hammerum AM, Hansen F, Hendriksen RS, Olesen B, Agersø Y, Zankari E, Leekitcharoenphon P, Stegger M, Kaas RS, Cavaco LM, Hansen DS, Aarestrup FM, Skov RL.

Euro Surveill. 2015;20(49). doi: 10.2807/1560-7917.ES.2015.20.49.30085. Erratum in: Euro Surveill. 2015;20(50). doi: 10.2807/1560-7917.ES.2015.20.50.30091.


Genome sequences of copper resistant and sensitive Enterococcus faecalis strains isolated from copper-fed pigs in Denmark.

Zhang S, Wang D, Wang Y, Hasman H, Aarestrup FM, Alwathnani HA, Zhu YG, Rensing C.

Stand Genomic Sci. 2015 Jul 8;10:35. doi: 10.1186/s40793-015-0021-1. eCollection 2015.


Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance.

Nordahl Petersen T, Rasmussen S, Hasman H, Carøe C, Bælum J, Schultz AC, Bergmark L, Svendsen CA, Lund O, Sicheritz-Pontén T, Aarestrup FM.

Sci Rep. 2015 Jul 10;5:11444. doi: 10.1038/srep11444.


Limited similarity between plasmids encoding CTX-M-1 β-lactamase in Escherichia coli from humans, pigs, cattle, organic poultry layers and horses in Denmark.

Jakobsen L, Bortolaia V, Bielak E, Moodley A, Olsen SS, Hansen DS, Frimodt-Møller N, Guardabassi L, Hasman H.

J Glob Antimicrob Resist. 2015 Jun;3(2):132-136. doi: 10.1016/j.jgar.2015.03.009. Epub 2015 May 7.


An OXA-48-producing Escherichia coli isolated from a Danish patient with no hospitalization abroad.

Gedebjerg A, Hasman H, Sørensen CM, Wang M.

Infect Dis (Lond). 2015 Aug;47(8):593-5. doi: 10.3109/23744235.2015.1019920. Epub 2015 Mar 9.


Identification of a Pseudomonas aeruginosa co-producing NDM-1, VIM-5 and VIM-6 metallo-β-lactamases in Denmark using whole-genome sequencing.

Wang M, Borris L, Aarestrup FM, Hasman H.

Int J Antimicrob Agents. 2015 Mar;45(3):324-5. doi: 10.1016/j.ijantimicag.2014.11.004. Epub 2014 Dec 5. No abstract available.


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