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Using machine learning to guide targeted and locally-tailored empiric antibiotic prescribing in a children's hospital in Cambodia.

Oonsivilai M, Mo Y, Luangasanatip N, Lubell Y, Miliya T, Tan P, Loeuk L, Turner P, Cooper BS.

Wellcome Open Res. 2018 Oct 10;3:131. doi: 10.12688/wellcomeopenres.14847.1. eCollection 2018.


Decontamination Strategies and Bloodstream Infections With Antibiotic-Resistant Microorganisms in Ventilated Patients: A Randomized Clinical Trial.

Wittekamp BH, Plantinga NL, Cooper BS, Lopez-Contreras J, Coll P, Mancebo J, Wise MP, Morgan MPG, Depuydt P, Boelens J, Dugernier T, Verbelen V, Jorens PG, Verbrugghe W, Malhotra-Kumar S, Damas P, Meex C, Leleu K, van den Abeele AM, Gomes Pimenta de Matos AF, Fernández Méndez S, Vergara Gomez A, Tomic V, Sifrer F, Villarreal Tello E, Ruiz Ramos J, Aragao I, Santos C, Sperning RHM, Coppadoro P, Nardi G, Brun-Buisson C, Bonten MJM.

JAMA. 2018 Nov 27;320(20):2087-2098. doi: 10.1001/jama.2018.13765.


Reactive and pre-emptive vaccination strategies to control hepatitis E infection in emergency and refugee settings: A modelling study.

Cooper BS, White LJ, Siddiqui R.

PLoS Negl Trop Dis. 2018 Sep 25;12(9):e0006807. doi: 10.1371/journal.pntd.0006807. eCollection 2018 Sep.


A Maladaptive Combination of Traits Contributes to the Maintenance of a Drosophila Hybrid Zone.

Cooper BS, Sedghifar A, Nash WT, Comeault AA, Matute DR.

Curr Biol. 2018 Sep 24;28(18):2940-2947.e6. doi: 10.1016/j.cub.2018.07.005. Epub 2018 Aug 30.


Path-planning with waiting in spatiotemporally-varying threat fields.

Cooper BS, Cowlagi RV.

PLoS One. 2018 Aug 23;13(8):e0202145. doi: 10.1371/journal.pone.0202145. eCollection 2018.


Enumerating the economic cost of antimicrobial resistance per antibiotic consumed to inform the evaluation of interventions affecting their use.

Shrestha P, Cooper BS, Coast J, Oppong R, Do Thi Thuy N, Phodha T, Celhay O, Guerin PJ, Wertheim H, Lubell Y.

Antimicrob Resist Infect Control. 2018 Aug 9;7:98. doi: 10.1186/s13756-018-0384-3. eCollection 2018.


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.


Cost-effectiveness of interventions to improve hand hygiene in healthcare workers in middle-income hospital settings: a model-based analysis.

Luangasanatip N, Hongsuwan M, Lubell Y, Limmathurotsakul D, Srisamang P, Day NPJ, Graves N, Cooper BS.

J Hosp Infect. 2018 Oct;100(2):165-175. doi: 10.1016/j.jhin.2018.05.007. Epub 2018 Aug 6.


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.


Rapid Global Spread of wRi-like Wolbachia across Multiple Drosophila.

Turelli M, Cooper BS, Richardson KM, Ginsberg PS, Peckenpaugh B, Antelope CX, Kim KJ, May MR, Abrieux A, Wilson DA, Bronski MJ, Moore BR, Gao JJ, Eisen MB, Chiu JC, Conner WR, Hoffmann AA.

Curr Biol. 2018 Mar 19;28(6):963-971.e8. doi: 10.1016/j.cub.2018.02.015. Epub 2018 Mar 8.


Simulations for designing and interpreting intervention trials in infectious diseases.

Halloran ME, Auranen K, Baird S, Basta NE, Bellan SE, Brookmeyer R, Cooper BS, DeGruttola V, Hughes JP, Lessler J, Lofgren ET, Longini IM, Onnela JP, Özler B, Seage GR, Smith TA, Vespignani A, Vynnycky E, Lipsitch M.

BMC Med. 2017 Dec 29;15(1):223. doi: 10.1186/s12916-017-0985-3.


Why sensitive bacteria are resistant to hospital infection control.

van Kleef E, Luangasanatip N, Bonten MJ, Cooper BS.

Wellcome Open Res. 2017 Mar 10;2:16. doi: 10.12688/wellcomeopenres.11033.1. eCollection 2017.


Multiplex PCR point of care testing versus routine, laboratory-based testing in the treatment of adults with respiratory tract infections: a quasi-randomised study assessing impact on length of stay and antimicrobial use.

Andrews D, Chetty Y, Cooper BS, Virk M, Glass SK, Letters A, Kelly PA, Sudhanva M, Jeyaratnam D.

BMC Infect Dis. 2017 Oct 10;17(1):671. doi: 10.1186/s12879-017-2784-z.


Clostridium difficile in England: can we stop washing our hands?

van Kleef E, Kuijper EJ, Bonten MJM, Cooper BS.

Lancet Infect Dis. 2017 May;17(5):478. doi: 10.1016/S1473-3099(17)30186-X. No abstract available.


Impact of a structured ICU training programme in resource-limited settings in Asia.

Haniffa R, Lubell Y, Cooper BS, Mohanty S, Alam S, Karki A, Pattnaik R, Maswood A, Haque R, Pangeni R, Schultz MJ, Dondorp AM; ICU Training in South Asia Group.

PLoS One. 2017 Mar 14;12(3):e0173483. doi: 10.1371/journal.pone.0173483. eCollection 2017.


Wolbachia in the Drosophila yakuba Complex: Pervasive Frequency Variation and Weak Cytoplasmic Incompatibility, but No Apparent Effect on Reproductive Isolation.

Cooper BS, Ginsberg PS, Turelli M, Matute DR.

Genetics. 2017 Jan;205(1):333-351. doi: 10.1534/genetics.116.196238. Epub 2016 Nov 7.


Point-of-care universal screening for meticillin-resistant Staphylococcus aureus: a cluster-randomized cross-over trial.

Wu PJ, Jeyaratnam D, Tosas O, Cooper BS, French GL.

J Hosp Infect. 2017 Mar;95(3):245-252. doi: 10.1016/j.jhin.2016.08.017. Epub 2016 Aug 24.


Multiple time scales in modeling the incidence of infections acquired in intensive care units.

Wolkewitz M, Cooper BS, Palomar-Martinez M, Alvarez-Lerma F, Olaechea-Astigarraga P, Barnett AG, Schumacher M.

BMC Med Res Methodol. 2016 Sep 1;16(1):116. doi: 10.1186/s12874-016-0199-y.


Electrostatically Guided Rydberg Positronium.

Deller A, Alonso AM, Cooper BS, Hogan SD, Cassidy DB.

Phys Rev Lett. 2016 Aug 12;117(7):073202. doi: 10.1103/PhysRevLett.117.073202. Epub 2016 Aug 12.


High Prevalence of Antimicrobial-resistant Gram-negative Colonization in Hospitalized Cambodian Infants.

Turner P, Pol S, Soeng S, Sar P, Neou L, Chea P, Day NP, Cooper BS, Turner C.

Pediatr Infect Dis J. 2016 Aug;35(8):856-61. doi: 10.1097/INF.0000000000001187.


Reconstructing transmission trees for communicable diseases using densely sampled genetic data.

Worby CJ, O'Neill PD, Kypraios T, Robotham JV, De Angelis D, Cartwright EJ, Peacock SJ, Cooper BS.

Ann Appl Stat. 2016 Mar;10(1):395-417. Epub 2016 Mar 25.


Evaluating hospital infection control measures for antimicrobial-resistant pathogens using stochastic transmission models: Application to vancomycin-resistant enterococci in intensive care units.

Wei Y, Kypraios T, O'Neill PD, Huang SS, Rifas-Shiman SL, Cooper BS.

Stat Methods Med Res. 2018 Jan;27(1):269-285. doi: 10.1177/0962280215627299. Epub 2016 Mar 16.


More Research Is Needed to Quantify Risks, Benefits, and Cost-Effectiveness of Universal Mupirocin Usage.

Deeny SR, Worby CJ, Tosas Auguet O, Cooper BS, Edgeworth J, Cookson B, Robotham JV.

Clin Infect Dis. 2016 May 1;62(9):1193-4. doi: 10.1093/cid/ciw077. Epub 2016 Feb 21. No abstract available.


Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data.

Tosas Auguet O, Betley JR, Stabler RA, Patel A, Ioannou A, Marbach H, Hearn P, Aryee A, Goldenberg SD, Otter JA, Desai N, Karadag T, Grundy C, Gaunt MW, Cooper BS, Edgeworth JD, Kypraios T.

PLoS Med. 2016 Jan 26;13(1):e1001944. doi: 10.1371/journal.pmed.1001944. eCollection 2016 Jan.


Cost-effectiveness of Ward Closure to Control Outbreaks of Norovirus Infection in United Kingdom National Health Service Hospitals.

Sadique Z, Lopman B, Cooper BS, Edmunds WJ.

J Infect Dis. 2016 Feb 1;213 Suppl 1:S19-26. doi: 10.1093/infdis/jiv410.


Controlling Positronium Annihilation with Electric Fields.

Alonso AM, Cooper BS, Deller A, Hogan SD, Cassidy DB.

Phys Rev Lett. 2015 Oct 30;115(18):183401. doi: 10.1103/PhysRevLett.115.183401. Epub 2015 Oct 27.


A trap-based pulsed positron beam optimised for positronium laser spectroscopy.

Cooper BS, Alonso AM, Deller A, Wall TE, Cassidy DB.

Rev Sci Instrum. 2015 Oct;86(10):103101. doi: 10.1063/1.4931690.


Impact of mupirocin resistance on the transmission and control of healthcare-associated MRSA.

Deeny SR, Worby CJ, Tosas Auguet O, Cooper BS, Edgeworth J, Cookson B, Robotham JV.

J Antimicrob Chemother. 2015 Dec;70(12):3366-78. doi: 10.1093/jac/dkv249. Epub 2015 Sep 3.


Similar Efficacies of Selection Shape Mitochondrial and Nuclear Genes in Both Drosophila melanogaster and Homo sapiens.

Cooper BS, Burrus CR, Ji C, Hahn MW, Montooth KL.

G3 (Bethesda). 2015 Aug 21;5(10):2165-76. doi: 10.1534/g3.114.016493.


Comparative efficacy of interventions to promote hand hygiene in hospital: systematic review and network meta-analysis.

Luangasanatip N, Hongsuwan M, Limmathurotsakul D, Lubell Y, Lee AS, Harbarth S, Day NP, Graves N, Cooper BS.

BMJ. 2015 Jul 28;351:h3728. doi: 10.1136/bmj.h3728. Review.


Revisiting classic clines in Drosophila melanogaster in the age of genomics.

Adrion JR, Hahn MW, Cooper BS.

Trends Genet. 2015 Aug;31(8):434-44. doi: 10.1016/j.tig.2015.05.006. Epub 2015 Jun 10. Review.


How to Determine the Accuracy of an Alternative Diagnostic Test when It Is Actually Better than the Reference Tests: A Re-Evaluation of Diagnostic Tests for Scrub Typhus Using Bayesian LCMs.

Lim C, Paris DH, Blacksell SD, Laongnualpanich A, Kantipong P, Chierakul W, Wuthiekanun V, Day NP, Cooper BS, Limmathurotsakul D.

PLoS One. 2015 May 29;10(5):e0114930. doi: 10.1371/journal.pone.0114930. eCollection 2015.


Seasonal influenza vaccination for children in Thailand: a cost-effectiveness analysis.

Meeyai A, Praditsitthikorn N, Kotirum S, Kulpeng W, Putthasri W, Cooper BS, Teerawattananon Y.

PLoS Med. 2015 May 26;12(5):e1001829; discussion e1001829. doi: 10.1371/journal.pmed.1001829. eCollection 2015 May.


Selective production of Rydberg-stark states of positronium.

Wall TE, Alonso AM, Cooper BS, Deller A, Hogan SD, Cassidy DB.

Phys Rev Lett. 2015 May 1;114(17):173001. Epub 2015 Apr 28.


Defining the in vivo phenotype of artemisinin-resistant falciparum malaria: a modelling approach.

White LJ, Flegg JA, Phyo AP, Wiladpai-ngern JH, Bethell D, Plowe C, Anderson T, Nkhoma S, Nair S, Tripura R, Stepniewska K, Pan-Ngum W, Silamut K, Cooper BS, Lubell Y, Ashley EA, Nguon C, Nosten F, White NJ, Dondorp AM.

PLoS Med. 2015 Apr 28;12(4):e1001823. doi: 10.1371/journal.pmed.1001823. eCollection 2015 Apr.


Mortality attributable to seasonal influenza A and B infections in Thailand, 2005-2009: a longitudinal study.

Cooper BS, Kotirum S, Kulpeng W, Praditsitthikorn N, Chittaganpitch M, Limmathurotsakul D, Day NP, Coker R, Teerawattananon Y, Meeyai A.

Am J Epidemiol. 2015 Jun 1;181(11):898-907. doi: 10.1093/aje/kwu360. Epub 2015 Apr 20.


Variable performance of models for predicting methicillin-resistant Staphylococcus aureus carriage in European surgical wards.

Lee AS, Pan A, Harbarth S, Patroni A, Chalfine A, Daikos GL, Garilli S, Martínez JA, Cooper BS; MOSAR-04 Study Team.

BMC Infect Dis. 2015 Feb 27;15:105. doi: 10.1186/s12879-015-0834-y.


Evaluating clinical trial designs for investigational treatments of Ebola virus disease.

Cooper BS, Boni MF, Pan-ngum W, Day NP, Horby PW, Olliaro P, Lang T, White NJ, White LJ, Whitehead J.

PLoS Med. 2015 Apr 14;12(4):e1001815. doi: 10.1371/journal.pmed.1001815. eCollection 2015 Apr.


Contact precautions for patients with multidrug-resistant pathogens.

Derde LP, Cooper BS, Brun-Buisson C.

JAMA. 2015 Feb 10;313(6):629-30. doi: 10.1001/jama.2014.17439. No abstract available.


Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting.

Tong SY, Holden MT, Nickerson EK, Cooper BS, Köser CU, Cori A, Jombart T, Cauchemez S, Fraser C, Wuthiekanun V, Thaipadungpanit J, Hongsuwan M, Day NP, Limmathurotsakul D, Parkhill J, Peacock SJ.

Genome Res. 2015 Jan;25(1):111-8. doi: 10.1101/gr.174730.114. Epub 2014 Dec 9.


Thermal adaptation of cellular membranes in natural populations of Drosophila melanogaster.

Cooper BS, Hammad LA, Montooth KL.

Funct Ecol. 2014 Aug 1;28(4):886-894.


Effectiveness of Hand Hygiene Promotion in Relation to Level of Investment: A Systematic Review.

Luangasanatip N, Hongsuwan M, Lubell Y, Cooper BS.

Value Health. 2014 Nov;17(7):A803. doi: 10.1016/j.jval.2014.08.507. Epub 2014 Oct 26. No abstract available.


Increasing incidence of hospital-acquired and healthcare-associated bacteremia in northeast Thailand: a multicenter surveillance study.

Hongsuwan M, Srisamang P, Kanoksil M, Luangasanatip N, Jatapai A, Day NP, Peacock SJ, Cooper BS, Limmathurotsakul D.

PLoS One. 2014 Oct 13;9(10):e109324. doi: 10.1371/journal.pone.0109324. eCollection 2014.


Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids.

San Millan A, Peña-Miller R, Toll-Riera M, Halbert ZV, McLean AR, Cooper BS, MacLean RC.

Nat Commun. 2014 Oct 10;5:5208. doi: 10.1038/ncomms6208.


Interpreting and comparing risks in the presence of competing events.

Wolkewitz M, Cooper BS, Bonten MJ, Barnett AG, Schumacher M.

BMJ. 2014 Aug 21;349:g5060. doi: 10.1136/bmj.g5060. No abstract available.


Care bundles in intensive care units - authors' reply.

Bonten MJ, Brun-Buisson C, Cooper BS, Derde LP; all authors.

Lancet Infect Dis. 2014 May;14(5):372. doi: 10.1016/S1473-3099(14)70740-6. No abstract available.


Multilevel competing risk models to evaluate the risk of nosocomial infection.

Wolkewitz M, Cooper BS, Palomar-Martinez M, Alvarez-Lerma F, Olaechea-Astigarraga P, Barnett AG, Harbarth S, Schumacher M.

Crit Care. 2014 Apr 8;18(2):R64. doi: 10.1186/cc13821.


Using a web-based application to define the accuracy of diagnostic tests when the gold standard is imperfect.

Lim C, Wannapinij P, White L, Day NP, Cooper BS, Peacock SJ, Limmathurotsakul D.

PLoS One. 2013 Nov 12;8(11):e79489. doi: 10.1371/journal.pone.0079489. eCollection 2013.


Nested case-control studies in cohorts with competing events.

Wolkewitz M, Cooper BS, Palomar-Martinez M, Olaechea-Astigarraga P, Alvarez-Lerma F, Schumacher M.

Epidemiology. 2014 Jan;25(1):122-5. doi: 10.1097/EDE.0000000000000029.


Interventions to reduce colonisation and transmission of antimicrobial-resistant bacteria in intensive care units: an interrupted time series study and cluster randomised trial.

Derde LPG, Cooper BS, Goossens H, Malhotra-Kumar S, Willems RJL, Gniadkowski M, Hryniewicz W, Empel J, Dautzenberg MJD, Annane D, Aragão I, Chalfine A, Dumpis U, Esteves F, Giamarellou H, Muzlovic I, Nardi G, Petrikkos GL, Tomic V, Martí AT, Stammet P, Brun-Buisson C, Bonten MJM; MOSAR WP3 Study Team.

Lancet Infect Dis. 2014 Jan;14(1):31-39. doi: 10.1016/S1473-3099(13)70295-0. Epub 2013 Oct 23. Erratum in: Lancet Infect Dis. 2014 Jan;14(1):11.

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