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Items: 1 to 50 of 69

1.

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data.

Sheppard AE, Stoesser N, German-Mesner I, Vegesana K, Sarah Walker A, Crook DW, Mathers AJ.

Microb Genom. 2018 Nov 22. doi: 10.1099/mgen.0.000232. [Epub ahead of print]

2.

A Large, Refractory Nosocomial Outbreak of Klebsiella pneumoniae Carbapenemase-Producing Escherichia coli Demonstrates Carbapenemase Gene Outbreaks Involving Sink Sites Require Novel Approaches to Infection Control.

Decraene V, Phan HTT, George R, Wyllie DH, Akinremi O, Aiken Z, Cleary P, Dodgson A, Pankhurst L, Crook DW, Lenney C, Walker AS, Woodford N, Sebra R, Fath-Ordoubadi F, Mathers AJ, Seale AC, Guiver M, McEwan A, Watts V, Welfare W, Stoesser N, Cawthorne J; TRACE Investigators’ Group .

Antimicrob Agents Chemother. 2018 Nov 26;62(12). pii: e01689-18. doi: 10.1128/AAC.01689-18. Print 2018 Dec.

PMID:
30249685
3.

Trends over time in Escherichia coli bloodstream infections, urinary tract infections, and antibiotic susceptibilities in Oxfordshire, UK, 1998-2016: a study of electronic health records.

Vihta KD, Stoesser N, Llewelyn MJ, Quan TP, Davies T, Fawcett NJ, Dunn L, Jeffery K, Butler CC, Hayward G, Andersson M, Morgan M, Oakley S, Mason A, Hopkins S, Wyllie DH, Crook DW, Wilcox MH, Johnson AP, Peto TEA, Walker AS.

Lancet Infect Dis. 2018 Oct;18(10):1138-1149. doi: 10.1016/S1473-3099(18)30353-0. Epub 2018 Aug 17.

PMID:
30126643
4.

Transmission Dynamics of Hyper-Endemic Multi-Drug Resistant Klebsiella pneumoniae in a Southeast Asian Neonatal Unit: A Longitudinal Study With Whole Genome Sequencing.

Smit PW, Stoesser N, Pol S, van Kleef E, Oonsivilai M, Tan P, Neou L, Turner C, Turner P, Cooper BS.

Front Microbiol. 2018 Jun 5;9:1197. doi: 10.3389/fmicb.2018.01197. eCollection 2018.

5.

Identification of Biomarkers for Differentiation of Hypervirulent Klebsiella pneumoniae from Classical K. pneumoniae.

Russo TA, Olson R, Fang CT, Stoesser N, Miller M, MacDonald U, Hutson A, Barker JH, La Hoz RM, Johnson JR.

J Clin Microbiol. 2018 Aug 27;56(9). pii: e00776-18. doi: 10.1128/JCM.00776-18. Print 2018 Sep.

PMID:
29925642
6.

Bayesian reconstruction of transmission within outbreaks using genomic variants.

De Maio N, Worby CJ, Wilson DJ, Stoesser N.

PLoS Comput Biol. 2018 Apr 18;14(4):e1006117. doi: 10.1371/journal.pcbi.1006117. eCollection 2018 Apr.

7.

Antimicrobial Resistance in Invasive Bacterial Infections in Hospitalized Children, Cambodia, 2007-2016.

Fox-Lewis A, Takata J, Miliya T, Lubell Y, Soeng S, Sar P, Rith K, McKellar G, Wuthiekanun V, McGonagle E, Stoesser N, Moore CE, Parry CM, Turner C, Day NPJ, Cooper BS, Turner P.

Emerg Infect Dis. 2018 May;24(5):841-851. doi: 10.3201/eid2405.171830.

8.

Intensive Care Unit Wastewater Interventions to Prevent Transmission of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Organisms.

Mathers AJ, Vegesana K, German Mesner I, Barry KE, Pannone A, Baumann J, Crook DW, Stoesser N, Kotay S, Carroll J, Sifri CD.

Clin Infect Dis. 2018 Jul 2;67(2):171-178. doi: 10.1093/cid/ciy052.

PMID:
29409044
9.

Illumina short-read and MinION long-read WGS to characterize the molecular epidemiology of an NDM-1 Serratia marcescens outbreak in Romania.

Phan HTT, Stoesser N, Maciuca IE, Toma F, Szekely E, Flonta M, Hubbard ATM, Pankhurst L, Do T, Peto TEA, Walker AS, Crook DW, Timofte D.

J Antimicrob Chemother. 2017 Dec 8. doi: 10.1093/jac/dkx456. [Epub ahead of print]

10.

Supporting surveillance capacity for antimicrobial resistance: Laboratory capacity strengthening for drug resistant infections in low and middle income countries.

Seale AC, Hutchison C, Fernandes S, Stoesser N, Kelly H, Lowe B, Turner P, Hanson K, Chandler CIR, Goodman C, Stabler RA, Scott JAG.

Wellcome Open Res. 2017 Sep 26;2:91. doi: 10.12688/wellcomeopenres.12523.1. eCollection 2017.

11.

Severity of illness and the weekend effect - Authors' reply.

Walker AS, Watkinson P, Llewelyn M, Stoesser N, Peto T.

Lancet. 2017 Oct 14;390(10104):1735. doi: 10.1016/S0140-6736(17)32425-X. Epub 2017 Oct 12. No abstract available.

PMID:
29047441
12.

High Rates of Human Fecal Carriage of mcr-1-Positive Multidrug-Resistant Enterobacteriaceae Emerge in China in Association With Successful Plasmid Families.

Zhong LL, Phan HTT, Shen C, Vihta KD, Sheppard AE, Huang X, Zeng KJ, Li HY, Zhang XF, Patil S, Crook DW, Walker AS, Xing Y, Lin JL, Feng LQ, Doi Y, Xia Y, Stoesser N, Tian GB.

Clin Infect Dis. 2018 Feb 10;66(5):676-685. doi: 10.1093/cid/cix885.

PMID:
29040419
13.

Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches.

George S, Pankhurst L, Hubbard A, Votintseva A, Stoesser N, Sheppard AE, Mathers A, Norris R, Navickaite I, Eaton C, Iqbal Z, Crook DW, Phan HTT.

Microb Genom. 2017 Jun 9;3(8):e000118. doi: 10.1099/mgen.0.000118. eCollection 2017 Aug.

14.

Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome sequencing demonstrate multiple genetic modes of transmission.

Martin J, Phan HTT, Findlay J, Stoesser N, Pankhurst L, Navickaite I, De Maio N, Eyre DW, Toogood G, Orsi NM, Kirby A, Young N, Turton JF, Hill RLR, Hopkins KL, Woodford N, Peto TEA, Walker AS, Crook DW, Wilcox MH.

J Antimicrob Chemother. 2017 Nov 1;72(11):3025-3034. doi: 10.1093/jac/dkx264.

15.

Epidemiology of Clostridium difficile in infants in Oxfordshire, UK: Risk factors for colonization and carriage, and genetic overlap with regional C. difficile infection strains.

Stoesser N, Eyre DW, Quan TP, Godwin H, Pill G, Mbuvi E, Vaughan A, Griffiths D, Martin J, Fawley W, Dingle KE, Oakley S, Wanelik K, Finney JM, Kachrimanidou M, Moore CE, Gorbach S, Riley TV, Crook DW, Peto TEA, Wilcox MH, Walker AS; Modernising Medical Microbiology Informatics Group (MMMIG).

PLoS One. 2017 Aug 16;12(8):e0182307. doi: 10.1371/journal.pone.0182307. eCollection 2017.

16.

Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli.

Stoesser N, Sheppard AE, Peirano G, Anson LW, Pankhurst L, Sebra R, Phan HTT, Kasarskis A, Mathers AJ, Peto TEA, Bradford P, Motyl MR, Walker AS, Crook DW, Pitout JD.

Sci Rep. 2017 Jul 19;7(1):5917. doi: 10.1038/s41598-017-06256-2.

17.

A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database.

Orlek A, Phan H, Sheppard AE, Doumith M, Ellington M, Peto T, Crook D, Walker AS, Woodford N, Anjum MF, Stoesser N.

Data Brief. 2017 Apr 23;12:423-426. doi: 10.1016/j.dib.2017.04.024. eCollection 2017 Jun.

18.

Mortality risks associated with emergency admissions during weekends and public holidays: an analysis of electronic health records.

Walker AS, Mason A, Quan TP, Fawcett NJ, Watkinson P, Llewelyn M, Stoesser N, Finney J, Davies J, Wyllie DH, Crook DW, Peto TEA.

Lancet. 2017 Jul 1;390(10089):62-72. doi: 10.1016/S0140-6736(17)30782-1. Epub 2017 May 9.

19.

IncX2 and IncX1-X2 Hybrid Plasmids Coexisting in a FosA6-Producing Escherichia coli Strain.

Guo Q, Su J, McElheny CL, Stoesser N, Doi Y, Wang M.

Antimicrob Agents Chemother. 2017 Jun 27;61(7). pii: e00536-17. doi: 10.1128/AAC.00536-17. Print 2017 Jul.

20.

Enhanced Klebsiella pneumoniae Carbapenemase Expression from a Novel Tn4401 Deletion.

Cheruvanky A, Stoesser N, Sheppard AE, Crook DW, Hoffman PS, Weddle E, Carroll J, Sifri CD, Chai W, Barry K, Ramakrishnan G, Mathers AJ.

Antimicrob Agents Chemother. 2017 May 24;61(6). pii: e00025-17. doi: 10.1128/AAC.00025-17. Print 2017 Jun.

21.

Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids.

Orlek A, Phan H, Sheppard AE, Doumith M, Ellington M, Peto T, Crook D, Walker AS, Woodford N, Anjum MF, Stoesser N.

Plasmid. 2017 May;91:42-52. doi: 10.1016/j.plasmid.2017.03.002. Epub 2017 Mar 9.

22.

Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology.

Orlek A, Stoesser N, Anjum MF, Doumith M, Ellington MJ, Peto T, Crook D, Woodford N, Walker AS, Phan H, Sheppard AE.

Front Microbiol. 2017 Feb 9;8:182. doi: 10.3389/fmicb.2017.00182. eCollection 2017.

23.

The Hospital Water Environment as a Reservoir for Carbapenem-Resistant Organisms Causing Hospital-Acquired Infections-A Systematic Review of the Literature.

Kizny Gordon AE, Mathers AJ, Cheong EYL, Gottlieb T, Kotay S, Walker AS, Peto TEA, Crook DW, Stoesser N.

Clin Infect Dis. 2017 May 15;64(10):1435-1444. doi: 10.1093/cid/cix132. Review.

PMID:
28200000
24.

Carriage of β-lactamase-producing Enterobacteriaceae by Chinese travellers.

Zhong LL, Stoesser N, Doi Y, Shen C, Huang X, Tian GB.

Lancet Infect Dis. 2017 Feb;17(2):138-139. doi: 10.1016/S1473-3099(17)30002-6. No abstract available.

PMID:
28134109
25.

Effects of control interventions on Clostridium difficile infection in England: an observational study.

Dingle KE, Didelot X, Quan TP, Eyre DW, Stoesser N, Golubchik T, Harding RM, Wilson DJ, Griffiths D, Vaughan A, Finney JM, Wyllie DH, Oakley SJ, Fawley WN, Freeman J, Morris K, Martin J, Howard P, Gorbach S, Goldstein EJC, Citron DM, Hopkins S, Hope R, Johnson AP, Wilcox MH, Peto TEA, Walker AS, Crook DW; Modernising Medical Microbiology Informatics Group.

Lancet Infect Dis. 2017 Apr;17(4):411-421. doi: 10.1016/S1473-3099(16)30514-X. Epub 2017 Jan 25.

26.

Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, blaKPC, in Klebsiella Species Is Elusive but Not Rare.

Mathers AJ, Stoesser N, Chai W, Carroll J, Barry K, Cherunvanky A, Sebra R, Kasarskis A, Peto TE, Walker AS, Sifri CD, Crook DW, Sheppard AE.

Antimicrob Agents Chemother. 2017 Feb 23;61(3). pii: e01823-16. doi: 10.1128/AAC.01823-16. Print 2017 Mar.

27.

Oral fosfomycin for treatment of urinary tract infection: a retrospective cohort study.

Matthews PC, Barrett LK, Warren S, Stoesser N, Snelling M, Scarborough M, Jones N.

BMC Infect Dis. 2016 Oct 11;16(1):556.

28.

Complete Sequencing of Plasmids Containing blaOXA-163 and blaOXA-48 in Escherichia coli Sequence Type 131.

Stoesser N, Sheppard AE, Peirano G, Sebra R, Lynch T, Anson L, Kasarskis A, Motyl MR, Crook DW, Pitout JD.

Antimicrob Agents Chemother. 2016 Oct 21;60(11):6948-6951. doi: 10.1128/AAC.01130-16. Print 2016 Nov.

29.

Identifying lineage effects when controlling for population structure improves power in bacterial association studies.

Earle SG, Wu CH, Charlesworth J, Stoesser N, Gordon NC, Walker TM, Spencer CCA, Iqbal Z, Clifton DA, Hopkins KL, Woodford N, Smith EG, Ismail N, Llewelyn MJ, Peto TE, Crook DW, McVean G, Walker AS, Wilson DJ.

Nat Microbiol. 2016 Apr 4;1:16041. doi: 10.1038/nmicrobiol.2016.41.

30.

Characterization of a Novel IncHI2 Plasmid Carrying Tandem Copies of blaCTX-M-2 in a fosA6-Harboring Escherichia coli Sequence Type 410 Strain.

Guo Q, Ding B, Jové T, Stoesser N, Cooper VS, Wang M, Doi Y.

Antimicrob Agents Chemother. 2016 Oct 21;60(11):6742-6747. doi: 10.1128/AAC.01173-16. Print 2016 Nov.

31.

Characterisation of Invasive Streptococcus pneumoniae Isolated from Cambodian Children between 2007 - 2012.

Moore CE, Giess A, Soeng S, Sar P, Kumar V, Nhoung P, Bousfield R, Turner P, Stoesser N, Day NP, Parry CM.

PLoS One. 2016 Jul 22;11(7):e0159358. doi: 10.1371/journal.pone.0159358. eCollection 2016.

32.

Separate F-Type Plasmids Have Shaped the Evolution of the H30 Subclone of Escherichia coli Sequence Type 131.

Johnson TJ, Danzeisen JL, Youmans B, Case K, Llop K, Munoz-Aguayo J, Flores-Figueroa C, Aziz M, Stoesser N, Sokurenko E, Price LB, Johnson JR.

mSphere. 2016 Jun 29;1(4). pii: e00121-16. doi: 10.1128/mSphere.00121-16. eCollection 2016 Jul-Aug.

33.

Glutathione-S-transferase FosA6 of Klebsiella pneumoniae origin conferring fosfomycin resistance in ESBL-producing Escherichia coli.

Guo Q, Tomich AD, McElheny CL, Cooper VS, Stoesser N, Wang M, Sluis-Cremer N, Doi Y.

J Antimicrob Chemother. 2016 Sep;71(9):2460-5. doi: 10.1093/jac/dkw177. Epub 2016 Jun 3.

34.

First Report of blaIMP-14 on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131.

Stoesser N, Sheppard AE, Peirano G, Sebra RP, Lynch T, Anson LW, Kasarskis A, Motyl MR, Crook DW, Pitout JD.

Antimicrob Agents Chemother. 2016 Jul 22;60(8):5068-71. doi: 10.1128/AAC.00840-16. Print 2016 Aug.

35.

Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC.

Sheppard AE, Stoesser N, Wilson DJ, Sebra R, Kasarskis A, Anson LW, Giess A, Pankhurst LJ, Vaughan A, Grim CJ, Cox HL, Yeh AJ; Modernising Medical Microbiology (MMM) Informatics Group, Sifri CD, Walker AS, Peto TE, Crook DW, Mathers AJ.

Antimicrob Agents Chemother. 2016 May 23;60(6):3767-78. doi: 10.1128/AAC.00464-16. Print 2016 Jun.

36.

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131.

Stoesser N, Sheppard AE, Pankhurst L, De Maio N, Moore CE, Sebra R, Turner P, Anson LW, Kasarskis A, Batty EM, Kos V, Wilson DJ, Phetsouvanh R, Wyllie D, Sokurenko E, Manges AR, Johnson TJ, Price LB, Peto TE, Johnson JR, Didelot X, Walker AS, Crook DW; Modernizing Medical Microbiology Informatics Group (MMMIG).

MBio. 2016 Mar 22;7(2):e02162. doi: 10.1128/mBio.02162-15.

37.

Correction: Rapid Diagnostic Tests for Dengue Virus Infection in Febrile Cambodian Children: Diagnostic Accuracy and Incorporation into Diagnostic Algorithms.

Carter MJ, Emary KR, Moore CE, Parry CM, Sona S, Putchhat H, Reaksmey S, Chanpheaktra N, Stoesser N, Dobson AD, Day NP, Kumar V, Blacksell SD.

PLoS Negl Trop Dis. 2016 Feb 5;10(2):e0004453. doi: 10.1371/journal.pntd.0004453. eCollection 2016 Feb. No abstract available.

38.

Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193.

Sheppard AE, Stoesser N, Sebra R, Kasarskis A, Deikus G, Anson L, Walker AS, Peto TE, Crook DW, Mathers AJ.

Genome Announc. 2016 Jan 28;4(1). pii: e01649-15. doi: 10.1128/genomeA.01649-15.

39.

Colistin resistance gene mcr-1 and pHNSHP45 plasmid in human isolates of Escherichia coli and Klebsiella pneumoniae.

Stoesser N, Mathers AJ, Moore CE, Day NP, Crook DW.

Lancet Infect Dis. 2016 Mar;16(3):285-6. doi: 10.1016/S1473-3099(16)00010-4. Epub 2016 Jan 8. No abstract available.

PMID:
26774239
40.

Extensive Within-Host Diversity in Fecally Carried Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolates: Implications for Transmission Analyses.

Stoesser N, Sheppard AE, Moore CE, Golubchik T, Parry CM, Nget P, Saroeun M, Day NP, Giess A, Johnson JR, Peto TE, Crook DW, Walker AS; Modernizing Medical Microbiology Informatics Group.

J Clin Microbiol. 2015 Jul;53(7):2122-31. doi: 10.1128/JCM.00378-15. Epub 2015 Apr 22.

41.

Rapid diagnostic tests for dengue virus infection in febrile Cambodian children: diagnostic accuracy and incorporation into diagnostic algorithms.

Carter MJ, Emary KR, Moore CE, Parry CM, Sona S, Putchhat H, Reaksmey S, Chanpheaktra N, Stoesser N, Dobson AD, Day NP, Kumar V, Blacksell SD.

PLoS Negl Trop Dis. 2015 Feb 24;9(2):e0003424. doi: 10.1371/journal.pntd.0003424. eCollection 2015 Feb. Erratum in: PLoS Negl Trop Dis. 2015 Mar;9(3):e0003654. PLoS Negl Trop Dis. 2016 Feb;10(2):e0004453. Moore, Catherine E [corrected to Moore, Catrin E].

42.

Antimicrobial susceptibility of uropathogens isolated from Cambodian children.

Moore CE, Sona S, Poda S, Putchhat H, Kumar V, Sopheary S, Stoesser N, Bousfield R, Day N, Parry CM.

Paediatr Int Child Health. 2016 May;36(2):113-7. doi: 10.1179/2046905515Y.0000000008.

43.

Colonization with Enterobacteriaceae producing ESBLs in children attending pre-school childcare facilities in the Lao People's Democratic Republic.

Stoesser N, Xayaheuang S, Vongsouvath M, Phommasone K, Elliott I, Del Ojo Elias C, Crook DW, Newton PN, Buisson Y, Lee SJ, Dance DA.

J Antimicrob Chemother. 2015;70(6):1893-7. doi: 10.1093/jac/dkv021. Epub 2015 Feb 12.

44.

Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing.

Mathers AJ, Stoesser N, Sheppard AE, Pankhurst L, Giess A, Yeh AJ, Didelot X, Turner SD, Sebra R, Kasarskis A, Peto T, Crook D, Sifri CD.

Antimicrob Agents Chemother. 2015 Mar;59(3):1656-63. doi: 10.1128/AAC.04292-14. Epub 2015 Jan 5.

45.

Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: insights using wider sampling frames and next-generation sequencing.

Stoesser N, Sheppard AE, Shakya M, Sthapit B, Thorson S, Giess A, Kelly D, Pollard AJ, Peto TE, Walker AS, Crook DW.

J Antimicrob Chemother. 2015 Apr;70(4):1008-15. doi: 10.1093/jac/dku521. Epub 2015 Jan 3.

46.

Ophthalmic infections in children presenting to Angkor Hospital for Children, Siem Reap, Cambodia.

Khauv P, Turner P, Soeng C, Soeng S, Moore CE, Bousfield R, Stoesser N, Emary K, Thanh DP, Baker S, Hang VT, van Doorn HR, Day NP, Parry CM.

BMC Res Notes. 2014 Nov 5;7:784. doi: 10.1186/1756-0500-7-784.

47.

Multidrug-resistant Escherichia coli soft tissue infection investigated with bacterial whole genome sequencing.

Buchanan R, Stoesser N, Crook D, Bowler IC.

BMJ Case Rep. 2014 Oct 19;2014. pii: bcr2014207200. doi: 10.1136/bcr-2014-207200.

48.

Genome sequencing of an extended series of NDM-producing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- versus hospital-associated transmission in an endemic setting.

Stoesser N, Giess A, Batty EM, Sheppard AE, Walker AS, Wilson DJ, Didelot X, Bashir A, Sebra R, Kasarskis A, Sthapit B, Shakya M, Kelly D, Pollard AJ, Peto TE, Crook DW, Donnelly P, Thorson S, Amatya P, Joshi S.

Antimicrob Agents Chemother. 2014 Dec;58(12):7347-57. doi: 10.1128/AAC.03900-14. Epub 2014 Sep 29.

49.

Septic arthritis of the hip in a Cambodian child caused by multidrug-resistant Salmonella enterica serovar Typhi with intermediate susceptibility to ciprofloxacin treated with ceftriaxone and azithromycin.

Pocock JM, Khun PA, Moore CE, Vuthy S, Stoesser N, Parry CM.

Paediatr Int Child Health. 2014 Aug;34(3):227-9. doi: 10.1179/2046905514Y.0000000123. Epub 2014 Apr 21.

PMID:
24749773
50.

Treatment of suspected hyper-reactive malarial splenomegaly (HMS) in pregnancy with mefloquine.

Jaroensuk J, Stoesser N, Leimanis ML, Jittamala P, White NJ, Nosten FH, McGready R.

Am J Trop Med Hyg. 2014 Apr;90(4):609-11. doi: 10.4269/ajtmh.13-0706. Epub 2014 Mar 3.

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