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Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection.

Charalampous T, Kay GL, Richardson H, Aydin A, Baldan R, Jeanes C, Rae D, Grundy S, Turner DJ, Wain J, Leggett RM, Livermore DM, O'Grady J.

Nat Biotechnol. 2019 Jul;37(7):783-792. doi: 10.1038/s41587-019-0156-5. Epub 2019 Jun 24.


Evaluation of multiplex tandem PCR (MT-PCR) assays for the detection of bacterial resistance genes among Enterobacteriaceae in clinical urines.

Schmidt K, Stanley KK, Hale R, Smith L, Wain J, O'Grady J, Livermore DM.

J Antimicrob Chemother. 2019 Feb 1;74(2):349-356. doi: 10.1093/jac/dky419.


Ceftriaxone-resistant Salmonella Typhi carries an IncI1-ST31 plasmid encoding CTX-M-15.

Djeghout B, Saha S, Sajib MSI, Tanmoy AM, Islam M, Kay GL, Langridge GC, Endtz HP, Wain J, Saha SK.

J Med Microbiol. 2018 May;67(5):620-627. doi: 10.1099/jmm.0.000727. Epub 2018 Apr 4.


Reply to Wijmans et al.: Optical Coherence Tomography: A Valuable Novel Tool for Assessing the Alveolar Compartment in Interstitial Lung Disease?

Hariri LP, Adams DC, Wain JC, Lanuti M, Muniappan A, Sharma A, Colby TV, Mino-Kenudson M, Mark EJ, Kradin RL, Goulart H, Suter MJ.

Am J Respir Crit Care Med. 2018 May 1;197(9):1232-1233. doi: 10.1164/rccm.201711-2347LE. No abstract available.


Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants.

Alcon-Giner C, Caim S, Mitra S, Ketskemety J, Wegmann U, Wain J, Belteki G, Clarke P, Hall LJ.

BMC Genomics. 2017 Nov 2;18(1):841. doi: 10.1186/s12864-017-4229-x.


Clonality, virulence and antimicrobial resistance of enteroaggregative Escherichia coli from Mirzapur, Bangladesh.

Chattaway MA, Day M, Mtwale J, White E, Rogers J, Day M, Powell D, Ahmad M, Harris R, Talukder KA, Wain J, Jenkins C, Cravioto A.

J Med Microbiol. 2017 Oct;66(10):1429-1435. doi: 10.1099/jmm.0.000594. Epub 2017 Sep 25.


Detection of mutations in gyrB using denaturing high performance liquid chromatography (DHPLC) among Salmonella enterica serovar Typhi and Paratyphi A.

Gupta R, Gaind R, Singh LC, Paglietti B, Deb M, Rubino S, Wain J, Basir SF.

Trans R Soc Trop Med Hyg. 2016 Dec 1;110(12):684-689. doi: 10.1093/trstmh/trx002.


Endobronchial Optical Coherence Tomography for Low-Risk Microscopic Assessment and Diagnosis of Idiopathic Pulmonary Fibrosis In Vivo.

Hariri LP, Adams DC, Wain JC, Lanuti M, Muniappan A, Sharma A, Colby TV, Mino-Kenudson M, Mark EJ, Kradin RL, Goulart H, Tager AM, Suter MJ.

Am J Respir Crit Care Med. 2018 Apr 1;197(7):949-952. doi: 10.1164/rccm.201707-1446LE. No abstract available.


Modified En Bloc Spondylectomy for Tumors of the Thoracic and Lumbar Spine: Surgical Technique and Outcomes.

Shah AA, Paulino Pereira NR, Pedlow FX, Wain JC, Yoon SS, Hornicek FJ, Schwab JH.

J Bone Joint Surg Am. 2017 Sep 6;99(17):1476-1484. doi: 10.2106/JBJS.17.00141.


Development and evaluation of a multiple-locus variable-number tandem-repeats analysis assay for subtyping Salmonella Typhi strains from sub-Saharan Africa.

Tau NP, Smith AM, Wain JR, Tarupiwa A, Coulibaly KJ, Keddy KH, Germs-Sa.

J Med Microbiol. 2017 Jul;66(7):937-945. doi: 10.1099/jmm.0.000526. Epub 2017 Jul 19.


Quality of life after resection of a chordoma of the mobile spine.

Schwab JH, Janssen SJ, Paulino Pereira NR, Chen YLE, Wain JC, DeLaney TF, Hornicek FJ.

Bone Joint J. 2017 Jul;99-B(7):979-986. doi: 10.1302/0301-620X.99B7.BJJ-2016-1126.R1.


Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing.

Schmidt K, Mwaigwisya S, Crossman LC, Doumith M, Munroe D, Pires C, Khan AM, Woodford N, Saunders NJ, Wain J, O'Grady J, Livermore DM.

J Antimicrob Chemother. 2017 Jan;72(1):104-114. Epub 2016 Sep 25.


What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B.

Connor TR, Owen SV, Langridge G, Connell S, Nair S, Reuter S, Dallman TJ, Corander J, Tabing KC, Le Hello S, Fookes M, Doublet B, Zhou Z, Feltwell T, Ellington MJ, Herrera S, Gilmour M, Cloeckaert A, Achtman M, Parkhill J, Wain J, De Pinna E, Weill FX, Peters T, Thomson N.

mBio. 2016 Aug 23;7(4). pii: e00527-16. doi: 10.1128/mBio.00527-16.


Neoadjuvant irinotecan, cisplatin, and concurrent radiation therapy with celecoxib for patients with locally advanced esophageal cancer.

Cleary JM, Mamon HJ, Szymonifka J, Bueno R, Choi N, Donahue DM, Fidias PM, Gaissert HA, Jaklitsch MT, Kulke MH, Lynch TP, Mentzer SJ, Meyerhardt JA, Swanson RS, Wain J, Fuchs CS, Enzinger PC.

BMC Cancer. 2016 Jul 13;16:468. doi: 10.1186/s12885-016-2485-9.


A novel broadly applicable PCR-RFLP method for rapid identification and subtyping of H58 Salmonella Typhi.

Murgia M, Rubino S, Wain J, Gaind R, Paglietti B.

J Microbiol Methods. 2016 Aug;127:219-223. doi: 10.1016/j.mimet.2016.06.018. Epub 2016 Jun 16.


Population structure of Escherichia coli causing bacteraemia in the UK and Ireland between 2001 and 2010.

Day MJ, Doumith M, Abernethy J, Hope R, Reynolds R, Wain J, Livermore DM, Woodford N.

J Antimicrob Chemother. 2016 Aug;71(8):2139-42. doi: 10.1093/jac/dkw145. Epub 2016 May 5.


Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010.

Petrovska L, Mather AE, AbuOun M, Branchu P, Harris SR, Connor T, Hopkins KL, Underwood A, Lettini AA, Page A, Bagnall M, Wain J, Parkhill J, Dougan G, Davies R, Kingsley RA.

Emerg Infect Dis. 2016 Apr;22(4):617-24. doi: 10.3201/eid2204.150531. Erratum in: Emerg Infect Dis. 2016 Oct;22(10):1862.


Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK.

Day MJ, Rodríguez I, van Essen-Zandbergen A, Dierikx C, Kadlec K, Schink AK, Wu G, Chattaway MA, DoNascimento V, Wain J, Helmuth R, Guerra B, Schwarz S, Threlfall J, Woodward MJ, Coldham N, Mevius D, Woodford N.

J Antimicrob Chemother. 2016 May;71(5):1178-82. doi: 10.1093/jac/dkv485. Epub 2016 Jan 23.


Outcomes With Open and Minimally Invasive Ivor Lewis Esophagectomy After Neoadjuvant Therapy.

Tapias LF, Mathisen DJ, Wright CD, Wain JC, Gaissert HA, Muniappan A, Lanuti M, Donahue DM, Morse CR.

Ann Thorac Surg. 2016 Mar;101(3):1097-103. doi: 10.1016/j.athoracsur.2015.09.062. Epub 2015 Dec 1.


Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK.

Dallman TJ, Ashton PM, Byrne L, Perry NT, Petrovska L, Ellis R, Allison L, Hanson M, Holmes A, Gunn GJ, Chase-Topping ME, Woolhouse MEJ, Grant KA, Gally DL, Wain J, Jenkins C.

Microb Genom. 2015 Sep 14;1(3):e000029. doi: 10.1099/mgen.0.000029. eCollection 2015 Sep.


Idiopathic Subglottic Stenosis: Factors Affecting Outcome After Single-Stage Repair.

Wang H, Wright CD, Wain JC, Ott HC, Mathisen DJ.

Ann Thorac Surg. 2015 Nov;100(5):1804-11. doi: 10.1016/j.athoracsur.2015.05.079. Epub 2015 Aug 18.


Lymph Node Assessment and Impact on Survival in Video-Assisted Thoracoscopic Lobectomy or Segmentectomy.

Zhou H, Tapias LF, Gaissert HA, Muniappan A, Wright CD, Wain JC, Donahue DM, Morse CR, Mathisen DJ, Lanuti M.

Ann Thorac Surg. 2015 Sep;100(3):910-6. doi: 10.1016/j.athoracsur.2015.04.034. Epub 2015 Jul 10.


Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157.

Dallman TJ, Byrne L, Ashton PM, Cowley LA, Perry NT, Adak G, Petrovska L, Ellis RJ, Elson R, Underwood A, Green J, Hanage WP, Jenkins C, Grant K, Wain J.

Clin Infect Dis. 2015 Aug 1;61(3):305-12. doi: 10.1093/cid/civ318. Epub 2015 Apr 17.


Long-term lung transplantation in nonhuman primates.

Aoyama A, Tonsho M, Ng CY, Lee S, Millington T, Nadazdin O, Wain JC, Cosimi AB, Sachs DH, Smith RN, Colvin RB, Kawai T, Madsen JC, Benichou G, Allan JS.

Am J Transplant. 2015 May;15(5):1415-20. doi: 10.1111/ajt.13130. Epub 2015 Mar 13.


Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing.

Ashton PM, Perry N, Ellis R, Petrovska L, Wain J, Grant KA, Jenkins C, Dallman TJ.

PeerJ. 2015 Feb 17;3:e739. doi: 10.7717/peerj.739. eCollection 2015.


Characterization of non-classical quinolone resistance in Salmonella enterica serovar Typhi: Report of a novel mutation in gyrB gene and diagnostic challenges.

Gupta R, Gaind R, Wain J, Deb M, Singh LC, Basir SF.

Biomol Detect Quantif. 2015 Jan 20;2:30-34. eCollection 2014 Dec.


MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island.

Ashton PM, Nair S, Dallman T, Rubino S, Rabsch W, Mwaigwisya S, Wain J, O'Grady J.

Nat Biotechnol. 2015 Mar;33(3):296-300. doi: 10.1038/nbt.3103. Epub 2014 Dec 8.


Typhoid fever.

Wain J, Hendriksen RS, Mikoleit ML, Keddy KH, Ochiai RL.

Lancet. 2015 Mar 21;385(9973):1136-45. doi: 10.1016/S0140-6736(13)62708-7. Epub 2014 Oct 21. Review.


Enteroaggregative Escherichia coli have evolved independently as distinct complexes within the E. coli population with varying ability to cause disease.

Chattaway MA, Jenkins C, Rajendram D, Cravioto A, Talukder KA, Dallman T, Underwood A, Platt S, Okeke IN, Wain J.

PLoS One. 2014 Nov 21;9(11):e112967. doi: 10.1371/journal.pone.0112967. eCollection 2014.


Whole-miRNome profiling identifies prognostic serum miRNAs in esophageal adenocarcinoma: the influence of Helicobacter pylori infection status.

Zhai R, Wei Y, Su L, Liu G, Kulke MH, Wain JC, Christiani DC.

Carcinogenesis. 2015 Jan;36(1):87-93. doi: 10.1093/carcin/bgu228. Epub 2014 Nov 8.


Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections.

Doumith M, Day M, Ciesielczuk H, Hope R, Underwood A, Reynolds R, Wain J, Livermore DM, Woodford N.

J Clin Microbiol. 2015 Jan;53(1):160-6. doi: 10.1128/JCM.02562-14. Epub 2014 Oct 29.


Evidence of evolving extraintestinal enteroaggregative Escherichia coli ST38 clone.

Chattaway MA, Jenkins C, Ciesielczuk H, Day M, DoNascimento V, Day M, Rodríguez I, van Essen-Zandbergen A, Schink AK, Wu G, Threlfall J, Woodward MJ, Coldham N, Kadlec K, Schwarz S, Dierikx C, Guerra B, Helmuth R, Mevius D, Woodford N, Wain J.

Emerg Infect Dis. 2014 Nov;20(11):1935-7. doi: 10.3201/eid2011.131845. No abstract available.


Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.

Zhou Z, McCann A, Weill FX, Blin C, Nair S, Wain J, Dougan G, Achtman M.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12199-204. doi: 10.1073/pnas.1411012111. Epub 2014 Aug 4.


Quantification of IgM molecular response by droplet digital PCR as a potential tool for the early diagnosis of sepsis.

Tamayo E, Almansa R, Carrasco E, Ávila-Alonso A, Rodríguez-Fernández A, Wain J, Heredia M, Gomez-Sanchez E, Soria S, Rico L, Iglesias V, Martínez-Martínez A, Andaluz-Ojeda D, Herreras JI, Eiros JM, Bermejo-Martin JF.

Crit Care. 2014 Jun 6;18(3):433. doi: 10.1186/cc13910. No abstract available.


Invasive staging and aggressive surgical resection: essential to management of central NSCLC.

Wain JC.

Oncology (Williston Park). 2014 Mar;28(3):228, 230. No abstract available.


An investigation of the diversity of strains of enteroaggregative Escherichia coli isolated from cases associated with a large multi-pathogen foodborne outbreak in the UK.

Dallman TJ, Chattaway MA, Cowley LA, Doumith M, Tewolde R, Wooldridge DJ, Underwood A, Ready D, Wain J, Foster K, Grant KA, Jenkins C.

PLoS One. 2014 May 20;9(5):e98103. doi: 10.1371/journal.pone.0098103. eCollection 2014.


Salmonella enterica subspecies II infections in England and Wales--the use of multilocus sequence typing to assist serovar identification.

Nair S, Wain J, Connell S, de Pinna E, Peters T.

J Med Microbiol. 2014 Jun;63(Pt 6):831-4. doi: 10.1099/jmm.0.072702-0. Epub 2014 Apr 2.


In vitro activity of rifaximin against clinical isolates of Escherichia coli and other enteropathogenic bacteria isolated from travellers returning to the UK.

Hopkins KL, Mushtaq S, Richardson JF, Doumith M, de Pinna E, Cheasty T, Wain J, Livermore DM, Woodford N.

Int J Antimicrob Agents. 2014 May;43(5):431-7. doi: 10.1016/j.ijantimicag.2014.01.026. Epub 2014 Mar 1.


Invasive adenocarcinoma of the lung is associated with the upper lung regions.

Kinsey CM, Estepar RS, Zhao Y, Yu X, Diao N, Heist RS, Wain JC, Mark EJ, Washko G, Christiani DC.

Lung Cancer. 2014 May;84(2):145-50. doi: 10.1016/j.lungcan.2014.02.002. Epub 2014 Feb 11.


Epidemiological evidence that garden birds are a source of human salmonellosis in England and Wales.

Lawson B, de Pinna E, Horton RA, Macgregor SK, John SK, Chantrey J, Duff JP, Kirkwood JK, Simpson VR, Robinson RA, Wain J, Cunningham AA.

PLoS One. 2014 Feb 26;9(2):e88968. doi: 10.1371/journal.pone.0088968. eCollection 2014.


Risk factors for the development of severe typhoid fever in Vietnam.

Parry CM, Thompson C, Vinh H, Chinh NT, Phuong le T, Ho VA, Hien TT, Wain J, Farrar JJ, Baker S.

BMC Infect Dis. 2014 Feb 10;14:73. doi: 10.1186/1471-2334-14-73.


Evaluating the use of multilocus variable number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 as a routine public health tool in England.

Byrne L, Elson R, Dallman TJ, Perry N, Ashton P, Wain J, Adak GK, Grant KA, Jenkins C.

PLoS One. 2014 Jan 17;9(1):e85901. doi: 10.1371/journal.pone.0085901. eCollection 2014.


Surgical therapy of pulmonary aspergillomas: a 30-year North American experience.

Muniappan A, Tapias LF, Butala P, Wain JC, Wright CD, Donahue DM, Gaissert HA, Lanuti M, Mathisen DJ.

Ann Thorac Surg. 2014 Feb;97(2):432-8. doi: 10.1016/j.athoracsur.2013.10.050. Epub 2013 Dec 21.


Complete Genome Sequence of the Campylobacter coli Clinical Isolate 15-537360.

Pearson BM, Rokney A, Crossman LC, Miller WG, Wain J, van Vliet AH.

Genome Announc. 2013 Dec 12;1(6). pii: e01056-13. doi: 10.1128/genomeA.01056-13.


Revolutionising bacteriology to improve treatment outcomes and antibiotic stewardship.

Livermore DM, Wain J.

Infect Chemother. 2013 Mar;45(1):1-10. doi: 10.3947/ic.2013.45.1.1. Epub 2013 Mar 29. Review.


Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi.

Bronowski C, Fookes MC, Gilderthorp R, Ashelford KE, Harris SR, Phiri A, Hall N, Gordon MA, Wain J, Hart CA, Wigley P, Thomson NR, Winstanley C.

PLoS Negl Trop Dis. 2013 Nov 14;7(11):e2557. doi: 10.1371/journal.pntd.0002557. eCollection 2013 Nov.


Comparative analysis of ESBL-positive Escherichia coli isolates from animals and humans from the UK, The Netherlands and Germany.

Wu G, Day MJ, Mafura MT, Nunez-Garcia J, Fenner JJ, Sharma M, van Essen-Zandbergen A, Rodríguez I, Dierikx C, Kadlec K, Schink AK, Chattaway M, Wain J, Helmuth R, Guerra B, Schwarz S, Threlfall J, Woodward MJ, Woodford N, Coldham N, Mevius D.

PLoS One. 2013 Sep 26;8(9):e75392. doi: 10.1371/journal.pone.0075392. eCollection 2013. Erratum in: PLoS One. 2014;9(9):e108834. Chattaway, Marie [added].


Investigating the link between the presence of enteroaggregative Escherichia coli and infectious intestinal disease in the United Kingdom, 1993 to 1996 and 2008 to 2009.

Chattaway MA, Harris R, Jenkins C, Tam C, Coia JE, Gray J, Iturriza-Gomara M, Wain J.

Euro Surveill. 2013 Sep 12;18(37). pii: 20582.


The impact of coexisting COPD on survival of patients with early-stage non-small cell lung cancer undergoing surgical resection.

Zhai R, Yu X, Shafer A, Wain JC, Christiani DC.

Chest. 2014 Feb;145(2):346-353. doi: 10.1378/chest.13-1176.

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