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Use of Whole-Genome Sequencing of Adenovirus in Immunocompromised Pediatric Patients to Identify Nosocomial Transmission and Mixed-Genotype Infection.

Houldcroft CJ, Roy S, Morfopoulou S, Margetts BK, Depledge DP, Cudini J, Shah D, Brown JR, Romero EY, Williams R, Cloutman-Green E, Rao K, Standing JF, Hartley JC, Breuer J.

J Infect Dis. 2018 Sep 8;218(8):1261-1271. doi: 10.1093/infdis/jiy323.


Description of an adenovirus A31 outbreak in a paediatric haematology unit.

Leruez-Ville M, Chardin-Ouachée M, Neven B, Picard C, Le Guinche I, Fischer A, Rouzioux C, Blanche S.

Bone Marrow Transplant. 2006 Jul;38(1):23-8. Epub 2006 May 15.


Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing.

Garcia-Hermoso D, Criscuolo A, Lee SC, Legrand M, Chaouat M, Denis B, Lafaurie M, Rouveau M, Soler C, Schaal JV, Mimoun M, Mebazaa A, Heitman J, Dromer F, Brisse S, Bretagne S, Alanio A.

MBio. 2018 Apr 24;9(2). pii: e00573-18. doi: 10.1128/mBio.00573-18.


Whole-genome sequencing improves discrimination of relapse from reinfection and identifies transmission events among patients with recurrent Clostridium difficile infections.

Mac Aogáin M, Moloney G, Kilkenny S, Kelleher M, Kelleghan M, Boyle B, Rogers TR.

J Hosp Infect. 2015 Jun;90(2):108-16. doi: 10.1016/j.jhin.2015.01.021. Epub 2015 Feb 26.


Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial.

Witney AA, Bateson AL, Jindani A, Phillips PP, Coleman D, Stoker NG, Butcher PD, McHugh TD; RIFAQUIN Study Team.

BMC Med. 2017 Mar 29;15(1):71. doi: 10.1186/s12916-017-0834-4.


Whole-genome Sequencing Provides Data for Stratifying Infection Prevention and Control Management of Nosocomial Influenza A.

Roy S, Hartley J, Dunn H, Williams R, Williams CA, Breuer J.

Clin Infect Dis. 2019 Apr 17. pii: ciz020. doi: 10.1093/cid/ciz020. [Epub ahead of print]


Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients.

Kundu S, Lockwood J, Depledge DP, Chaudhry Y, Aston A, Rao K, Hartley JC, Goodfellow I, Breuer J.

Clin Infect Dis. 2013 Aug;57(3):407-14. doi: 10.1093/cid/cit287. Epub 2013 May 3.


Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis.

Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL.

Clin Microbiol Rev. 2017 Oct;30(4):1015-1063. doi: 10.1128/CMR.00016-17. Review. Erratum in: Clin Microbiol Rev. 2017 Nov 1;31(1):.


Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing.

Stucki D, Ballif M, Bodmer T, Coscolla M, Maurer AM, Droz S, Butz C, Borrell S, Längle C, Feldmann J, Furrer H, Mordasini C, Helbling P, Rieder HL, Egger M, Gagneux S, Fenner L.

J Infect Dis. 2015 Apr 15;211(8):1306-16. doi: 10.1093/infdis/jiu601. Epub 2014 Oct 30.


Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: A systematic review.

Nikolayevskyy V, Kranzer K, Niemann S, Drobniewski F.

Tuberculosis (Edinb). 2016 May;98:77-85. doi: 10.1016/ Epub 2016 Mar 10. Review.


Whole-genome Sequencing for Tracing the Transmission Link between Two ARD Outbreaks Caused by a Novel HAdV Serotype 7 Variant, China.

Qiu S, Li P, Liu H, Wang Y, Liu N, Li C, Li S, Li M, Jiang Z, Sun H, Li Y, Xie J, Yang C, Wang J, Li H, Yi S, Wu Z, Jia L, Wang L, Hao R, Sun Y, Huang L, Ma H, Yuan Z, Song H.

Sci Rep. 2015 Sep 4;5:13617. doi: 10.1038/srep13617.


Metagenomic analysis identifies human adenovirus 31 in children with acute flaccid paralysis in Tunisia.

Haddad-Boubaker S, Joffret ML, Pérot P, Bessaud M, Meddeb Z, Touzi H, Delpeyroux F, Triki H, Eloit M.

Arch Virol. 2019 Mar;164(3):747-755. doi: 10.1007/s00705-018-04141-5. Epub 2019 Jan 10.


Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks.

Fitzpatrick MA, Ozer EA, Hauser AR.

J Clin Microbiol. 2016 Mar;54(3):593-612. doi: 10.1128/JCM.01818-15. Epub 2015 Dec 23.


Molecular characterization of a nosocomial outbreak of influenza B virus in an acute care hospital setting.

Sansone M, Wiman Å, Karlberg ML, Brytting M, Bohlin L, Andersson LM, Westin J, Nordén R.

J Hosp Infect. 2019 Jan;101(1):30-37. doi: 10.1016/j.jhin.2018.06.004. Epub 2018 Aug 23.


Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rüsch-Gerdes S, Supply P, Kalinowski J, Niemann S.

PLoS Med. 2013;10(2):e1001387. doi: 10.1371/journal.pmed.1001387. Epub 2013 Feb 12.


Genome-Based Infection Tracking Reveals Dynamics of Clostridium difficile Transmission and Disease Recurrence.

Kumar N, Miyajima F, He M, Roberts P, Swale A, Ellison L, Pickard D, Smith G, Molyneux R, Dougan G, Parkhill J, Wren BW, Parry CM, Pirmohamed M, Lawley TD.

Clin Infect Dis. 2016 Mar 15;62(6):746-752. doi: 10.1093/cid/civ1031. Epub 2015 Dec 18.


Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information.

Zoll J, Rahamat-Langendoen J, Ahout I, de Jonge MI, Jans J, Huijnen MA, Ferwerda G, Warris A, Melchers WJ.

J Clin Virol. 2015 May;66:6-11. doi: 10.1016/j.jcv.2015.02.010. Epub 2015 Feb 18.


[Future prospects of molecular epidemiology in tuberculosis].

Matsumoto T, Iwamoto T.

Kekkaku. 2009 Dec;84(12):783-4. Japanese.


Norovirus Transmission Dynamics in a Pediatric Hospital Using Full Genome Sequences.

Brown JR, Roy S, Shah D, Williams CA, Williams R, Dunn H, Hartley J, Harris K, Breuer J.

Clin Infect Dis. 2019 Jan 7;68(2):222-228. doi: 10.1093/cid/ciy438.

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