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Items: 26

1.

Worldwide human mitochondrial haplogroup distribution from urban sewage.

Pipek OA, Medgyes-Horváth A, Dobos L, Stéger J, Szalai-Gindl J, Visontai D, Kaas RS, Koopmans M, Hendriksen RS, Aarestrup FM, Csabai I.

Sci Rep. 2019 Aug 12;9(1):11624. doi: 10.1038/s41598-019-48093-5.

2.

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage.

Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Röder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, Vogt JK, Leekitcharoenphon P, van de Schans MGM, Zuidema T, de Roda Husman AM, Rasmussen S, Petersen B; Global Sewage Surveillance project consortium, Amid C, Cochrane G, Sicheritz-Ponten T, Schmitt H, Alvarez JRM, Aidara-Kane A, Pamp SJ, Lund O, Hald T, Woolhouse M, Koopmans MP, Vigre H, Petersen TN, Aarestrup FM.

Nat Commun. 2019 Mar 8;10(1):1124. doi: 10.1038/s41467-019-08853-3.

3.

An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes.

Henri C, Leekitcharoenphon P, Carleton HA, Radomski N, Kaas RS, Mariet JF, Felten A, Aarestrup FM, Gerner Smidt P, Roussel S, Guillier L, Mistou MY, Hendriksen RS.

Front Microbiol. 2017 Nov 29;8:2351. doi: 10.3389/fmicb.2017.02351. eCollection 2017.

4.

First detection of linezolid resistance due to the optrA gene in enterococci isolated from food products in Denmark.

Cavaco LM, Korsgaard H, Kaas RS, Seyfarth AM, Leekitcharoenphon P, Hendriksen RS.

J Glob Antimicrob Resist. 2017 Jun;9:128-129. doi: 10.1016/j.jgar.2017.04.001. Epub 2017 May 20. No abstract available.

PMID:
28535965
5.

Erratum to: Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease.

Joensen KG, Engsbro ALØ, Lukjancenko O, Kaas RS, Lund O, Westh H, Aarestrup FM.

Eur J Clin Microbiol Infect Dis. 2017 Jul;36(7):1339-1342. doi: 10.1007/s10096-017-2993-9. No abstract available.

PMID:
28488022
6.

Draft Genome Sequence of Acinetobacter johnsonii C6, an Environmental Isolate Engaging in Interspecific Metabolic Interactions.

Kaas RS, Mordhorst H, Leekitcharoenphon P, Dyring Jensen J, Haagensen JAJ, Molin S, Pamp SJ.

Genome Announc. 2017 Apr 20;5(16). pii: e00155-17. doi: 10.1128/genomeA.00155-17.

7.

Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease.

Joensen KG, Engsbro ALØ, Lukjancenko O, Kaas RS, Lund O, Westh H, Aarestrup FM.

Eur J Clin Microbiol Infect Dis. 2017 Jul;36(7):1325-1338. doi: 10.1007/s10096-017-2947-2. Epub 2017 Mar 11. Erratum in: Eur J Clin Microbiol Infect Dis. 2017 May 9;:.

8.

Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand.

Siriphap A, Leekitcharoenphon P, Kaas RS, Theethakaew C, Aarestrup FM, Sutheinkul O, Hendriksen RS.

PLoS One. 2017 Jan 19;12(1):e0169324. doi: 10.1371/journal.pone.0169324. eCollection 2017.

9.

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.

10.

The Lake Chad Basin, an Isolated and Persistent Reservoir of Vibrio cholerae O1: A Genomic Insight into the Outbreak in Cameroon, 2010.

Kaas RS, Ngandjio A, Nzouankeu A, Siriphap A, Fonkoua MC, Aarestrup FM, Hendriksen RS.

PLoS One. 2016 May 18;11(5):e0155691. doi: 10.1371/journal.pone.0155691. eCollection 2016.

11.

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.

12.

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.

13.

Genomic dissection of travel-associated extended-spectrum-beta-lactamase-producing Salmonella enterica serovar typhi isolates originating from the Philippines: a one-off occurrence or a threat to effective treatment of typhoid fever?

Hendriksen RS, Leekitcharoenphon P, Mikoleit M, Jensen JD, Kaas RS, Roer L, Joshi HB, Pornruangmong S, Pulsrikarn C, Gonzalez-Aviles GD, Reuland EA, Al Naiemi N, Wester AL, Aarestrup FM, Hasman H.

J Clin Microbiol. 2015 Feb;53(2):677-80. doi: 10.1128/JCM.03104-14. Epub 2014 Nov 26.

14.

Genomic signature of multidrug-resistant Salmonella enterica serovar typhi isolates related to a massive outbreak in Zambia between 2010 and 2012.

Hendriksen RS, Leekitcharoenphon P, Lukjancenko O, Lukwesa-Musyani C, Tambatamba B, Mwaba J, Kalonda A, Nakazwe R, Kwenda G, Jensen JD, Svendsen CA, Dittmann KK, Kaas RS, Cavaco LM, Aarestrup FM, Hasman H, Mwansa JC.

J Clin Microbiol. 2015 Jan;53(1):262-72. doi: 10.1128/JCM.02026-14. Epub 2014 Nov 12.

15.

Solving the problem of comparing whole bacterial genomes across different sequencing platforms.

Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O.

PLoS One. 2014 Aug 11;9(8):e104984. doi: 10.1371/journal.pone.0104984. eCollection 2014.

16.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.

Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; MetaHIT Consortium.

Nat Biotechnol. 2014 Aug;32(8):822-8. doi: 10.1038/nbt.2939. Epub 2014 Jul 6.

PMID:
24997787
17.

Veillonella, Firmicutes: Microbes disguised as Gram negatives.

Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW.

Stand Genomic Sci. 2013 Dec 15;9(2):431-48. doi: 10.4056/sigs.2981345. eCollection 2013 Dec 20.

18.

Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.

Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM.

J Clin Microbiol. 2014 May;52(5):1501-10. doi: 10.1128/JCM.03617-13. Epub 2014 Feb 26.

19.

Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus Sequence Type 398 survival.

Christiansen MT, Kaas RS, Chaudhuri RR, Holmes MA, Hasman H, Aarestrup FM.

PLoS One. 2014 Feb 12;9(2):e89018. doi: 10.1371/journal.pone.0089018. eCollection 2014.

20.

Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica.

Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM.

PLoS One. 2014 Feb 4;9(2):e87991. doi: 10.1371/journal.pone.0087991. eCollection 2014.

21.

snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.

Leekitcharoenphon P, Kaas RS, Thomsen MC, Friis C, Rasmussen S, Aarestrup FM.

BMC Genomics. 2012;13 Suppl 7:S6. doi: 10.1186/1471-2164-13-S7-S6. Epub 2012 Dec 13.

22.

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing.

Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agersø Y, Lund O, Larsen MV, Aarestrup FM.

J Antimicrob Chemother. 2013 Apr;68(4):771-7. doi: 10.1093/jac/dks496. Epub 2012 Dec 11.

PMID:
23233485
23.

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes.

Kaas RS, Friis C, Ussery DW, Aarestrup FM.

BMC Genomics. 2012 Oct 31;13:577. doi: 10.1186/1471-2164-13-577.

24.

Draft genome sequence of the yeast Pachysolen tannophilus CBS 4044/NRRL Y-2460.

Liu X, Kaas RS, Jensen PR, Workman M.

Eukaryot Cell. 2012 Jun;11(6):827. doi: 10.1128/EC.00114-12.

25.

European freshwater VHSV genotype Ia isolates divide into two distinct subpopulations.

Kahns S, Skall HF, Kaas RS, Korsholm H, Bang Jensen B, Jonstrup SP, Dodge MJ, Einer-Jensen K, Stone D, Olesen NJ.

Dis Aquat Organ. 2012 May 15;99(1):23-35. doi: 10.3354/dao02444.

26.

Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak.

Hendriksen RS, Price LB, Schupp JM, Gillece JD, Kaas RS, Engelthaler DM, Bortolaia V, Pearson T, Waters AE, Upadhyay BP, Shrestha SD, Adhikari S, Shakya G, Keim PS, Aarestrup FM.

MBio. 2011 Sep 1;2(4):e00157-11. doi: 10.1128/mBio.00157-11. Print 2011.

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