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Items: 36

1.

Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium.

Arredondo-Alonso S, Top J, McNally A, Puranen S, Pesonen M, Pensar J, Marttinen P, Braat JC, Rogers MRC, van Schaik W, Kaski S, Willems RJL, Corander J, Schürch AC.

mBio. 2020 Feb 11;11(1). pii: e03284-19. doi: 10.1128/mBio.03284-19.

2.

Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content.

van Hout D, Verschuuren TD, Bruijning-Verhagen PCJ, Bosch T, Schürch AC, Willems RJL, Bonten MJM, Kluytmans JAJW.

PLoS One. 2020 Jan 14;15(1):e0227604. doi: 10.1371/journal.pone.0227604. eCollection 2020.

3.

Prevalence, risk factors and genetic characterisation of extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE): a community-based cross-sectional study, the Netherlands, 2014 to 2016.

van den Bunt G, van Pelt W, Hidalgo L, Scharringa J, de Greeff SC, Schürch AC, Mughini-Gras L, Bonten MJM, Fluit AC.

Euro Surveill. 2019 Oct;24(41). doi: 10.2807/1560-7917.ES.2019.24.41.1800594.

4.

Sequence-based epidemiology of an OXA-48 plasmid during a hospital outbreak.

Hidalgo L, de Been M, Rogers MRC, Schürch AC, Scharringa J, van der Zee A, Bonten MJM, Fluit AC.

Antimicrob Agents Chemother. 2019 Oct 7. pii: AAC.01204-19. doi: 10.1128/AAC.01204-19. [Epub ahead of print]

PMID:
31591122
5.

Draft Genome Sequence of Haemophilus haemolyticus Strain 16/010 O, Isolated from a Sputum Sample from a Cystic Fibrosis Patient.

Fluit AC, Bayjanov JR, Tunney M, Elborn JS, Rogers MRC, Schürch AC, Ekkelenkamp MB.

Microbiol Resour Announc. 2019 Jun 6;8(23). pii: e00243-19. doi: 10.1128/MRA.00243-19.

6.

Corrigendum: mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species.

Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL, Schürch AC.

Microb Genom. 2019 Jan;5(1). doi: 10.1099/mgen.0.000249. No abstract available.

7.

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species.

Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL, Schürch AC.

Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000224. Epub 2018 Nov 1. Erratum in: Microb Genom. 2019 Jan;5(1):.

8.

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.

Schürch AC, Arredondo-Alonso S, Willems RJL, Goering RV.

Clin Microbiol Infect. 2018 Apr;24(4):350-354. doi: 10.1016/j.cmi.2017.12.016. Epub 2018 Jan 5. Review.

9.

On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data.

Arredondo-Alonso S, Willems RJ, van Schaik W, Schürch AC.

Microb Genom. 2017 Aug 18;3(10):e000128. doi: 10.1099/mgen.0.000128. eCollection 2017 Oct.

10.

Identification of HCV Resistant Variants against Direct Acting Antivirals in Plasma and Liver of Treatment Naïve Patients.

Raj VS, Hundie GB, Schürch AC, Smits SL, Pas SD, Le Pogam S, Janssen HLA, de Knegt RJ, Osterhaus ADME, Najera I, Boucher CA, Haagmans BL.

Sci Rep. 2017 Jul 5;7(1):4688. doi: 10.1038/s41598-017-04931-y.

11.

Challenges and opportunities for whole-genome sequencing-based surveillance of antibiotic resistance.

Schürch AC, van Schaik W.

Ann N Y Acad Sci. 2017 Jan;1388(1):108-120. doi: 10.1111/nyas.13310. Review.

PMID:
28134443
12.

CRISPR/Cas9-Mediated Genome Editing of Herpesviruses Limits Productive and Latent Infections.

van Diemen FR, Kruse EM, Hooykaas MJ, Bruggeling CE, Schürch AC, van Ham PM, Imhof SM, Nijhuis M, Wiertz EJ, Lebbink RJ.

PLoS Pathog. 2016 Jun 30;12(6):e1005701. doi: 10.1371/journal.ppat.1005701. eCollection 2016 Jun.

13.

Recovering full-length viral genomes from metagenomes.

Smits SL, Bodewes R, Ruiz-González A, Baumgärtner W, Koopmans MP, Osterhaus AD, Schürch AC.

Front Microbiol. 2015 Oct 1;6:1069. doi: 10.3389/fmicb.2015.01069. eCollection 2015. Review.

14.

Virus characterization and discovery in formalin-fixed paraffin-embedded tissues.

Bodewes R, van Run PR, Schürch AC, Koopmans MP, Osterhaus AD, Baumgärtner W, Kuiken T, Smits SL.

J Virol Methods. 2015 Mar;214:54-9. doi: 10.1016/j.jviromet.2015.02.002. Epub 2015 Feb 12.

PMID:
25681526
15.

Assembly of viral genomes from metagenomes.

Smits SL, Bodewes R, Ruiz-Gonzalez A, Baumgärtner W, Koopmans MP, Osterhaus AD, Schürch AC.

Front Microbiol. 2014 Dec 18;5:714. doi: 10.3389/fmicb.2014.00714. eCollection 2014.

16.

Novel divergent rhabdovirus in feces of red fox, Spain.

Bodewes R, Ruiz-Gonzalez A, Schürch AC, Osterhaus AD, Smits SL.

Emerg Infect Dis. 2014 Dec;20(12):2172-4. doi: 10.3201/eid2012.140236. No abstract available.

17.

Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.

Schürch AC, Schipper D, Bijl MA, Dau J, Beckmen KB, Schapendonk CM, Raj VS, Osterhaus AD, Haagmans BL, Tryland M, Smits SL.

PLoS One. 2014 Aug 20;9(8):e105227. doi: 10.1371/journal.pone.0105227. eCollection 2014.

18.

Exploring the potential of next-generation sequencing in detection of respiratory viruses.

Prachayangprecha S, Schapendonk CM, Koopmans MP, Osterhaus AD, Schürch AC, Pas SD, van der Eijk AA, Poovorawan Y, Haagmans BL, Smits SL.

J Clin Microbiol. 2014 Oct;52(10):3722-30. doi: 10.1128/JCM.01641-14. Epub 2014 Aug 6.

19.

Novel divergent nidovirus in a python with pneumonia.

Bodewes R, Lempp C, Schürch AC, Habierski A, Hahn K, Lamers M, von Dörnberg K, Wohlsein P, Drexler JF, Haagmans BL, Smits SL, Baumgärtner W, Osterhaus ADME.

J Gen Virol. 2014 Nov;95(Pt 11):2480-2485. doi: 10.1099/vir.0.068700-0. Epub 2014 Jul 25.

PMID:
25063552
20.

New viruses in idiopathic human diarrhea cases, the Netherlands.

Smits SL, Schapendonk CM, van Beek J, Vennema H, Schürch AC, Schipper D, Bodewes R, Haagmans BL, Osterhaus AD, Koopmans MP.

Emerg Infect Dis. 2014 Jul;20(7):1218-22. doi: 10.3201/eid2007.140190.

21.

Genetic relatedness of dolphin rhabdovirus with fish rhabdoviruses.

Siegers JY, van de Bildt MW, van Elk CE, Schürch AC, Tordo N, Kuiken T, Bodewes R, Osterhaus AD.

Emerg Infect Dis. 2014 Jun;20(6):1081-2. doi: 10.3201/eid2006.131880. No abstract available.

22.

Optimization of standard in-house 24-locus variable-number tandem-repeat typing for Mycobacterium tuberculosis and its direct application to clinical material.

de Beer JL, Akkerman OW, Schürch AC, Mulder A, van der Werf TS, van der Zanden AG, van Ingen J, van Soolingen D.

J Clin Microbiol. 2014 May;52(5):1338-42. doi: 10.1128/JCM.03436-13. Epub 2014 Feb 5.

23.

Novel cyclovirus in human cerebrospinal fluid, Malawi, 2010-2011.

Smits SL, Zijlstra EE, van Hellemond JJ, Schapendonk CM, Bodewes R, Schürch AC, Haagmans BL, Osterhaus AD.

Emerg Infect Dis. 2013;19(9). doi: 10.3201/eid1909.130404.

24.

Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data.

Bryant JM, Schürch AC, van Deutekom H, Harris SR, de Beer JL, de Jager V, Kremer K, van Hijum SA, Siezen RJ, Borgdorff M, Bentley SD, Parkhill J, van Soolingen D.

BMC Infect Dis. 2013 Feb 27;13:110. doi: 10.1186/1471-2334-13-110.

25.

Picobirnaviruses in the human respiratory tract.

Smits SL, van Leeuwen M, Schapendonk CM, Schürch AC, Bodewes R, Haagmans BL, Osterhaus AD.

Emerg Infect Dis. 2012 Sep;18(9):1539-40. doi: 10.3201/eid1809.120507. No abstract available.

26.

Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints.

McEvoy CR, Cloete R, Müller B, Schürch AC, van Helden PD, Gagneux S, Warren RM, Gey van Pittius NC.

PLoS One. 2012;7(4):e30593. doi: 10.1371/journal.pone.0030593. Epub 2012 Apr 4.

27.

SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes.

Schürch AC, Kremer K, Hendriks AC, Freyee B, McEvoy CR, van Crevel R, Boeree MJ, van Helden P, Warren RM, Siezen RJ, van Soolingen D.

PLoS One. 2011;6(12):e28365. doi: 10.1371/journal.pone.0028365. Epub 2011 Dec 5.

28.

DNA fingerprinting of Mycobacterium tuberculosis: from phage typing to whole-genome sequencing.

Schürch AC, van Soolingen D.

Infect Genet Evol. 2012 Jun;12(4):602-9. doi: 10.1016/j.meegid.2011.08.032. Epub 2011 Nov 3.

PMID:
22067515
29.

European 2--a clonal complex of Mycobacterium bovis dominant in the Iberian Peninsula.

Rodriguez-Campos S, Schürch AC, Dale J, Lohan AJ, Cunha MV, Botelho A, De Cruz K, Boschiroli ML, Boniotti MB, Pacciarini M, Garcia-Pelayo MC, Romero B, de Juan L, Domínguez L, Gordon SV, van Soolingen D, Loftus B, Berg S, Hewinson RG, Aranaz A, Smith NH.

Infect Genet Evol. 2012 Jun;12(4):866-72. doi: 10.1016/j.meegid.2011.09.004. Epub 2011 Sep 14.

PMID:
21945286
30.

Preferential deletion events in the direct repeat locus of Mycobacterium tuberculosis.

Schürch AC, Kremer K, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D.

J Clin Microbiol. 2011 Apr;49(4):1318-22. doi: 10.1128/JCM.01848-10. Epub 2011 Feb 16.

31.

Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype.

Schürch AC, Kremer K, Warren RM, Hung NV, Zhao Y, Wan K, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D.

Infect Genet Evol. 2011 Apr;11(3):587-97. doi: 10.1016/j.meegid.2011.01.009. Epub 2011 Jan 28.

PMID:
21277396
32.

Genomic tracing of epidemics and disease outbreaks.

Schürch AC, Siezen RJ.

Microb Biotechnol. 2010 Nov;3(6):628-33. doi: 10.1111/j.1751-7915.2010.00224.x. No abstract available.

33.

Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database.

de Souza GA, Arntzen MØ, Fortuin S, Schürch AC, Målen H, McEvoy CR, van Soolingen D, Thiede B, Warren RM, Wiker HG.

Mol Cell Proteomics. 2011 Jan;10(1):M110.002527. doi: 10.1074/mcp.M110.002527. Epub 2010 Oct 28.

34.

High-resolution typing by integration of genome sequencing data in a large tuberculosis cluster.

Schürch AC, Kremer K, Daviena O, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D.

J Clin Microbiol. 2010 Sep;48(9):3403-6. doi: 10.1128/JCM.00370-10. Epub 2010 Jun 30.

35.

The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale.

Schürch AC, Kremer K, Kiers A, Daviena O, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D.

Infect Genet Evol. 2010 Jan;10(1):108-14. doi: 10.1016/j.meegid.2009.10.002. Epub 2009 Oct 14. Erratum in: Infect Genet Evol. 2010 Aug;10(6):805.

PMID:
19835997
36.

Physical mapping and identification of a candidate for the leaf rust resistance gene Lr1 of wheat.

Qiu JW, Schürch AC, Yahiaoui N, Dong LL, Fan HJ, Zhang ZJ, Keller B, Ling HQ.

Theor Appl Genet. 2007 Jul;115(2):159-68. Epub 2007 May 4.

PMID:
17479240

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