Items where Author is "Wain, John"

Article

Djeghout, Bilal, Le-Viet, Thanh, Martins, Leonardo de Oliveira, Savva, George M., Evans, Rhiannon, Baker, David, Page, Andrew, Elumogo, Ngozi, Wain, John and Janecko, Nicol (2024) Capturing clinically relevant Campylobacter attributes through direct whole genome sequencing of stool. Microbial Genomics, 10 (8). ISSN 2057-5858

Crossman, Lisa, Sims, Leanne, Dean, Rachael, Felgate, Heather, Diaz Calvo, Teresa, Hill, Claire, McNamara, Iain, Webber, Mark A. and Wain, John (2024) Sticking together: Independent evolution of biofilm formation in different species of staphylococci has occurred multiple times via different pathways. BMC Genomics, 25. ISSN 1471-2164

Dziegiel, Agata H., Bloomfield, Samuel J., Savva, George M., Palau, Raphaëlle, Janecko, Nicol, Wain, John and Mather, Alison E. (2024) High Campylobacter diversity in retail chicken: Epidemiologically important strains may be missed with current sampling methods. Epidemiology and Infection, 152. ISSN 0950-2688

Mattock, Jennifer, Chattaway, Marie Anne, Hartman, Hassan, Dallman, Timothy J., Smith, Anthony M., Keddy, Karen, Petrovska, Liljana, Manners, Emma J., Duze, Sanelisiwe T., Smouse, Shannon, Tau, Nomsa, Timme, Ruth, Baker, Dave J., Mather, Alison E., Wain, John and Langridge, Gemma C. (2024) A one health perspective on Salmonella enterica serovar Infantis, an emerging human multidrug-resistant pathogen. Emerging Infectious Diseases, 30 (4). pp. 701-710. ISSN 1080-6040

Hurst, Rachel, Brewer, Daniel S. ORCID: https://orcid.org/0000-0003-4753-9794, Gihawi, Abraham ORCID: https://orcid.org/0000-0002-3676-5561, Wain, John and Cooper, Colin S. ORCID: https://orcid.org/0000-0003-2013-8042 (2024) Cancer invasion and anaerobic bacteria: New insights into mechanisms. Journal of Medical Microbiology, 73 (3). ISSN 0022-2615

Graham, Alice, Hawkins, Lois, Balasegaram, Sooria, Narasimhan, Subha, Wain, John, Clarke, John and Manuel, Rohini (2024) A decade of Campylobacter and Campylobacter bacteraemias in a district general hospital and the surrounding London and South East region, England. Journal of Infection, 88 (1). pp. 15-20. ISSN 0163-4453

Felgate, Heather, Sethi, Dheeraj, Faust, Kirsten, Kiy, Cemsid, Härtel, Christoph, Rupp, Jan, Clifford, Rebecca, Dean, Rachael, Tremlett, Catherine, Wain, John, Langridge, Gemma, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Page, Andrew J. and Webber, Mark A. (2023) Characterisation of neonatal Staphylococcus capitis NRCS-A isolates compared with non NRCS-A Staphylococcus capitis from neonates and adults. Microbial Genomics, 9 (10). ISSN 2057-5858

Cuypers, Wim L., Meysman, Pieter, Weill, François-Xavier, Hendriksen, Rene S., Beyene, Getenet, Wain, John, Nair, Satheesh, Chattaway, Marie A., Perez-Sepulveda, Blanca M., Ceyssens, Pieter-Jan, de Block, Tessa, Lee, Winnie W. Y., Pardos de la Gandara, Maria, Kornschober, Christian, Moran-Gilad, Jacob, Veldman, Kees T., Cormican, Martin, Torpdahl, Mia, Fields, Patricia I., Černý, Tomáš, Hardy, Liselotte, Tack, Bieke, Mellor, Kate C., Thomson, Nicholas, Dougan, Gordon, Deborggraeve, Stijn, Jacobs, Jan, Laukens, Kris and Van Puyvelde, Sandra (2023) A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia. Nature Communications, 14. ISSN 2041-1723

Bloomfield, Samuel J., Zomer, Aldert L., O'Grady, Justin, Kay, Gemma L., Wain, John, Janecko, Nicol, Palau, Raphaëlle and Mather, Alison E. (2023) Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics. Food Microbiology, 110. ISSN 0740-0020

Holden, Emma R., Yasir, Muhammad, Turner, A. Keith, Wain, John, Charles, Ian G. and Webber, Mark A. (2023) Genome-wide analysis of genes involved in efflux function and regulation within Escherichia coli and Salmonella enterica serovar Typhimurium. Microbiology (United Kingdom), 169 (2). ISSN 1350-0872

Djeghout, Bilal, Bloomfield, Samuel J., Rudder, Steven, Elumogo, Ngozi, Mather, Alison E., Wain, John and Janecko, Nicol (2022) Comparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens. Gut Pathogens, 14. ISSN 2076-0817

Waters, Emma V., Tucker, Liam A., Ahmed, Jana K., Wain, John and Langridge, Gemma C. (2022) Impact of Salmonella genome rearrangement on gene expression. Evolution Letters, 6 (6). pp. 426-437. ISSN 2056-3744

Noel, Dawang, Wain, John and Lar, Patricia (2022) Use of Vitex doniana (black plum) and Abutilon hirtum (Florida keys) extracts as an integral part of phytomedicine in tackling multidrug-resistant Salmonella. Journal of Infection in Developing Countries, 16 (08). pp. 1323-1328. ISSN 2036-6590

Van Be Bay, Pham, Wain, John, Phuong, Le Thi, Ho, Vo Anh, Hien, Tran Tinh and Parry, Christopher M. (2022) Quantitative bacterial counts in the bone marrow of Vietnamese patients with typhoid fever. Transactions of the Royal Society of Tropical Medicine and Hygiene, 116 (8). pp. 736-744. ISSN 0035-9203

Hurst, Rachel, Meader, Emma, Gihawi, Abraham ORCID: https://orcid.org/0000-0002-3676-5561, Rallapalli, Ghanasyam, Clark, Jeremy, Kay, Gemma L., Webb, Martyn, Manley, Kate, Curley, Helen, Walker, Helen, Kumar, Ravi, Schmidt, Katarzyna, Crossman, Lisa, Eeles, Rosalind A., Wedge, David C., Lynch, Andy G., Massie, Charlie E., Yazbek-Hanna, Marcelino, Rochester, Mark, Mills, Robert D., Mithen, Richard F., Traka, Maria H., Ball, Richard Y., O'Grady, Justin, Brewer, Daniel S. ORCID: https://orcid.org/0000-0003-4753-9794, Wain, John and Cooper, Colin S. ORCID: https://orcid.org/0000-0003-2013-8042 (2022) Microbiomes of urine and the prostate are linked to human prostate cancer risk groups. European Urology Oncology, 5 (4). pp. 412-419. ISSN 2588-9311

Mattock, Jennifer, Smith, Anthony M., Keddy, Karen H., Manners, Emma J., Duze, Sanelisiwe T., Smouse, Shannon, Tau, Nomsa, Baker, David, Chattaway, Marie Anne, Mather, Alison E., Wain, John and Langridge, Gemma C. (2022) Genetic characterization of Salmonella Infantis from South Africa, 2004–2016. Access Microbiology, 4 (7). ISSN 2516-8290

Stoakes, Emily, Savva, George M., Coates, Ruby, Tejera, Noemi, Poolman, Mark G., Grant, Andrew J., Wain, John and Singh, Dipali (2022) Substrate utilisation and energy metabolism in non-growing Campylobacter jejuni M1cam. Microorganisms, 10 (7). ISSN 2076-2607

Díaz Calvo, Teresa, Tejera, Noemi, Mcnamara, Iain, Langridge, Gemma C., Wain, John, Poolman, Mark and Singh, Dipali (2022) Genome-scale metabolic modelling approach to understand the metabolism of the opportunistic human pathogen Staphylococcus epidermidis RP62A. Metabolites, 12 (2). ISSN 2218-1989

Holden, Emma R., Yasir, Muhammad, Turner, A. Keith, Wain, John, Charles, Ian G. and Webber, Mark A. (2021) Massively parallel transposon mutagenesis identifies temporally essential genes for biofilm formation in Escherichia coli. Microbial Genomics, 7 (11). ISSN 2057-5858

Lee, Winnie W. Y., Mattock, Jennifer, Greig, David R., Langridge, Gemma C., Baker, David, Bloomfield, Samuel, Mather, Alison E., Wain, John R., Edwards, Andrew M., Hartman, Hassan, Dallman, Timothy J., Chattaway, Marie A. and Nair, Satheesh (2021) Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica infantis isolates in England and Wales. Microbial Genomics, 7 (10). ISSN 2057-5858

Wain, John, Simpson, Julie A., Thi Diem Nga, Luong, Song Diep, To, Thanh Duy, Pham, Baker, Stephen, Day, Nicholas P.J., White, Nicholas J. and Parry, Christopher M. (2021) Bactericidal activities and post-antibiotic effects of ofloxacin and ceftriaxone against drug-resistant Salmonella enterica serovar Typhi. Journal of Antimicrobial Chemotherapy, 76 (10). pp. 2606-2609. ISSN 0305-7453

Page, Andrew J., Mather, Alison E., Le-Viet, Thanh, Meader, Emma J., Alikhan, Nabil-Fareed, Kay, Gemma L., De Oliveira Martins, Leonardo, Aydin, Alp, Baker, David J., Trotter, Alexander J., Rudder, Steven, Tedim, Ana P., Kolyva, Anastasia, Stanley, Rachael, Yasir, Muhammad, Diaz, Maria, Potter, Will, Stuart, Claire, Meadows, Lizzie, Bell, Andrew, Gutierrez, Ana Victoria, Thomson, Nicholas M., Adriaenssens, Evelien M., Swingler, Tracey, Gilroy, Rachel A. J., Griffith, Luke, Sethi, Dheeraj K., Aggarwal, Dinesh, Brown, Colin S., Davidson, Rose K. ORCID: https://orcid.org/0000-0002-6624-4011, Kingsley, Robert A., Bedford, Luke, Coupland, Lindsay J., Charles, Ian G., Elumogo, Ngozi, Wain, John, Prakash, Reenesh, Webber, Mark A., Smith, S. J. Louise, Chand, Meera, Dervisevic, Samir and O’Grady, Justin (2021) Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Microbial Genomics, 7 (6). ISSN 2057-5858

Chattaway, Marie A., Langridge, Gemma C. and Wain, John (2021) Salmonella nomenclature in the genomic era: a time for change. Scientific Reports, 11. ISSN 2045-2322

Baker, Dave J., Aydin, Alp, Le Viet, Thanh, Kay, Gemma L., Rudder, Steven, de Oliveira Martins, Leonardo, Tedim, Ana P., Kolyva, Anastasia, Diaz, Maria, Alikhan, Nabil-Fareed, Meadows, Lizzie, Bell, Andrew, Gutierrez, Ana Victoria, Trotter, Alexander J., Thomson, Nicholas M., Gilroy, Rachel, Griffith, Luke, Adriaenssens, Evelien M., Stanley, Rachael, Charles, Ian, Franslem-Elumogo, Ngozi, Wain, John, Prakash, Reenesh, Meader, Emma, Mather, Alison, Webber, Mark, Dervisevic, Samir, Page, Andrew J. and O'Grady, Justin (2021) CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes. Genome Medicine, 13. ISSN 1756-994X

Rasheed, Farhan, Saeed, Muhammad, Alikhan, Nabil-Fareed, Baker, David, Khurshid, Mohsin, Ainsworth, Emma V., Turner, A. Keith, Imran, Ambereen Anwar, Rasool, Muhammad Hidayat, Saqalein, Muhammad, Nisar, Muhammad Atif, Fayyaz Ur Rehman, Muhammad, Wain, John, Yasir, Muhammad, Langridge, Gemma C. and Ikram, Aamer (2020) Emergence of resistance to fluoroquinolones and third-generation cephalosporins in Salmonella Typhi in Lahore, Pakistan. Microorganisms, 8 (9). ISSN 2076-2607

Turner, A Keith, Eckert, Sabine E, Turner, Daniel J, Yasir, Muhammud, Webber, Mark A, Charles, Ian G, Parkhill, Julian and Wain, John (2020) A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility. Journal of Antimicrobial Chemotherapy, 75 (9). 2516–2525. ISSN 0305-7453

Chessa, Daniela, Murgia, Manuela, Sias, Emanuela, Deligios, Massimo, Mazzarello, Vittorio, Fiamma, Maura, Rovina, Daniela, Carenti, Gabriele, Ganau, Giulia, Pintore, Elisabetta, Fiori, Mauro, Kay, Gemma L., Ponzeletti, Alessandro, Cappuccinelli, Piero, Kelvin, David J., Wain, John and Rubino, Salvatore (2020) Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace. Scientific Reports, 10. ISSN 2045-2322

Baker, Dave J., Kay, Gemma L., Aydin, Alp, Le-Viet, Thanh, Rudder, Steven, Tedim, Ana P., Kolyva, Anastasia, Diaz, Maria, de Oliveira Martins, Leonardo, Alikhan, Nabil-Fareed, Meadows, Lizzie, Bell, Andrew, Gurierrez, Ana Victoria, Trotter, Alexander J., Thomson, Nicholas M., Gilroy, Rachel, Griffith, Luke, Adriaenssens, Evelien M., Stanley, Rachael, Charles, Ian G., Elumogo, Nzogi, Wain, John, Prakash, Reenesh, Meader, Emma, Mather, Alison E., Webber, Mark A., Dervisevic, Samir, Page, Andrew J. and O'Grady, Justin (2020) CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes.

Tejera, Noemi, Crossman, Lisa, Pearson, Bruce, Stoakes, Emily, Nasher, Fauzy, Djeghout, Bilal, Poolman, Mark, Wain, John and Singh, Dipali (2020) Genome-scale metabolic model driven design of a defined medium for Campylobacter jejuni M1cam. Frontiers in Microbiology, 11. ISSN 1664-302X

Trotter, Alexander J., Dean, Rachael, Whitehouse, Celia E., Mikalsen, Jarle, Hill, Claire, Brunton-Sim, Roxanne, Kay, Gemma L., Shakokani, Majeed, Durst, Alexander Z. E., Wain, John, Mcnamara, Iain and O’Grady, Justin (2020) Preliminary evaluation of a rapid lateral flow calprotectin test for the diagnosis of prosthetic joint infection. Bone and Joint Research, 9 (5). pp. 202-210. ISSN 2046-3758

Ellis, Samuel J., Crossman, Lisa C., McGrath, Conor J., Chattaway, Marie A., Hölken, Johanna M., Brett, Bernard, Bundy, Leah, Kay, Gemma L., Wain, John and Schüller, Stephanie ORCID: https://orcid.org/0000-0003-3260-9112 (2020) Identification and characterisation of enteroaggregative Escherichia coli subtypes associated with human disease. Scientific Reports, 10. ISSN 2045-2322

Nair, Satheesh, Fookes, Maria, Corton, Craig, Thomson, Nicholas R., Wain, John and Langridge, Gemma C. (2020) Genetic markers in s. Paratyphi c reveal primary adaptation to pigs. Microorganisms, 8 (5). ISSN 2076-2607

Charalampous, Themoula, Kay, Gemma, Richardson, Hollian, Aydin, Alp, Baldan, Rossella, Jeanes, Christopher, Rae, Duncan, Grundy, Sara, Turner, Daniel J., Wain, John, Leggett, Richard M., Livermore, David ORCID: https://orcid.org/0000-0002-9856-3703 and O'Grady, Justin (2019) Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nature Biotechnology, 37. 783–792. ISSN 1087-0156

Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632, Craig, Jean V., Wain, John, Tremlett, Catherine, Linsell, Louise, Bowler, Ursula, Juszczak, Ed and Heath, Paul T. (2019) Safety and efficacy of 2% chlorhexidine gluconate aqueous versus 2% chlorhexidine gluconate in 70% isopropyl alcohol for skin disinfection prior to percutaneous central venous catheter insertion in preterm neonates:The ARCTIC randomised-controlled feasibility trial protocol. BMJ Open, 9 (2). ISSN 2044-6055

Schmidt, K., Stanley, K. K., Hale, R., Smith, L., Wain, J., O'Grady, J. and Livermore, D. M. ORCID: https://orcid.org/0000-0002-9856-3703 (2019) Evaluation of multiplex tandem PCR (MT-PCR) assays for the detection of bacterial resistance genes among Enterobacteriaceae in clinical urines. Journal of Antimicrobial Chemotherapy, 74 (2). 349–356. ISSN 0305-7453

Djeghout, Bilal, Saha, Senjuti, Islam Sajib, Mohammad Saiful, Islam, Maksuda, Kay, Gemma L., Langridge, Gemma C., Wain, John and Saha, Samir K. (2018) Ceftriaxone resistant Salmonella Typhi carries an IncI1-ST31 plasmid encoding CTXM-15. Journal of Medical Microbiology, 67 (5). pp. 620-627. ISSN 0022-2615

Charalampous, Themoula, Richardson, Hollian, Kay, Gemma, Baldan, Rossella, Jeanes, Christopher, Turner, Daniel, Wain, John, Livermore, David ORCID: https://orcid.org/0000-0002-9856-3703, Leggett, Richard and O'Grady, Justin (2018) Diagnosis of lower respiratory tract infections using nanopore sequencing. European Respiratory Journal, 52 (Suppl.). ISSN 0903-1936

Alcon-Giner, Cristina, Caim, Shabhonam, Mitra, Suparna, Ketskemety, Jennifer, Wegmann, Udo, Wain, John, Belteki, Gusztav, Clarke, Paul ORCID: https://orcid.org/0000-0001-6203-7632 and Hall, Lindsay J. ORCID: https://orcid.org/0000-0001-8938-5709 (2017) Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants. BMC Genomics, 18. ISSN 1471-2164

Chattaway, Marie Anne, Day, Michaela, Mtwale, Julia, White, Emma, Rogers, James, Day, Martin, Powell, David, Ahmad, Marwa, Harris, Ross, Ali Talukder, Kaisar, Wain, John, Jenkins, Claire and Cravioto, Alejandro (2017) Clonality, virulence and antimicrobial resistance of enteroaggregative Escherichia coli from Bangladesh. Journal of Medical Microbiology, 66. pp. 1429-1435. ISSN 0022-2615

Tau, Nomsa P., Smith, Anthony M., Wain, John R., Tarupiwa, Andrew, Coulibaly, Kalpy J. and Keddy, Karen H. and GERMS-SA (2017) Development and evaluation of a multiple-locus variable-number tandem-repeats analysis assay for subtyping Salmonella Typhi strains from sub-Saharan Africa. Journal of Medical Microbiology, 66 (7). pp. 937-945. ISSN 0022-2615

Gupta, Ruchi, Gaind, Rajni, Chandreshwor Singh, Laishram, Paglietti, Bianca, Deb, Monorama, Rubino, Salvatore, Wain, John and Farhat Basir, Seemi (2017) Detection of mutations in gyrB using denaturing high performance liquid chromatography (DHPLC) among Salmonella enterica serovar Typhi and Paratyphi A. Transactions of the Royal Society of Tropical Medicine and Hygiene, 110 (12). pp. 684-689. ISSN 0035-9203

Schmidt, K., Mwaigwisya, S., Crossman, L. C., Doumith, M., Munroe, D., Pires, C., Khan, A. M., Woodford, N., Saunders, N. J., Wain, J., O'Grady, J. and Livermore, D. M. ORCID: https://orcid.org/0000-0002-9856-3703 (2017) Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. Journal of Antimicrobial Chemotherapy, 72 (1). pp. 104-114. ISSN 0305-7453

Connor, Thomas R., Owen, Sian V., Langridge, Gemma, Connell, Steve, Nair, Satheesh, Reuter, Sandra, Dallman, Timothy J., Corander, Jukka, Tabing, Kristine C., Le Hello, Simon, Fookes, Maria, Doublet, Benoît, Zhou, Zhemin, Feltwell, Theresa, Ellington, Matthew J., Herrera, Silvia, Gilmour, Matthew, Cloeckaert, Axel, Achtman, Mark, Parkhill, Julian, Wain, John, De Pinna, Elizabeth, Weill, François-Xavier, Peters, Tansy and Thomson, Nick (2016) What’s in a name? Species-wide whole-genome sequencing resolves invasive and noninvasive lineages of Salmonella enterica Serotype Paratyphi B. mBIO, 7 (4). ISSN 2150-7511

Murgia, Manuela, Rubino, Salvatore, Wain, John, Gaind, Rajni and Paglietti, Bianca (2016) A novel broadly applicable PCR-RFLP method for rapid identification and subtyping of H58 Salmonella Typhi. Journal of Microbiological Methods, 127. pp. 219-223. ISSN 0167-7012

Day, M. J., Doumith, M., Abernethy, J., Hope, R., Reynolds, R., Wain, J., Livermore, D. M. ORCID: https://orcid.org/0000-0002-9856-3703 and Woodford, N. (2016) The population structure of Escherichia coli causing bacteraemia in the UK and Ireland between 2001 and 2010. Journal of Antimicrobial Chemotherapy, 71 (8). pp. 2139-2142. ISSN 0305-7453

Day, Michaela J., Rodríguez, Irene, Van Essen-zandbergen, Alieda, Dierikx, Cindy, Kadlec, Kristina, Schink, Anne-Kathrin, Wu, Guanghui, Chattaway, Marie A., Donascimento, Vivienne, Wain, John, Helmuth, Reiner, Guerra, Beatriz, Schwarz, Stefan, Threlfall, John, Woodward, Martin J., Coldham, Nick, Mevius, Dik and Woodford, Neil (2016) Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK. Journal of Antimicrobial Chemotherapy, 71 (5). pp. 1178-1182. ISSN 0305-7453

Petrovska, Liljana, Mather, Alison E., AbuOun, Manal, Branchu, Priscilla, Harris, Simon R., Connor, Thomas, Hopkins, K. L., Underwood, A., Lettini, Antonia A., Page, Andrew J., Bagnall, Mary, Wain, John, Parkhill, Julian, Dougan, Gordon, Davies, Robert and Kingsley, Robert A. ORCID: https://orcid.org/0000-0002-0194-6485 (2016) Microevolution during the emergence of a monophasic Salmonella Typhimurium epidemic in the United Kingdom. Emerging Infectious Diseases, 22 (4). pp. 617-624. ISSN 1080-6040

Dallman, Timothy J., Ashton, Philip M., Byrne, Lisa, Perry, Neil T., Petrovska, Liljana, Ellis, Richard, Allison, Lesley, Hanson, Mary, Holmes, Anne, Gunn, George G., Chase-Topping, Margo E., Woolhouse, Mark E.J., Grant, Kathie A., Gally, David L., Wain, John and Jenkins, Claire (2015) Applying phylogenomics to understand the emergence of Shiga Toxin producing Escherichia coli O157:H7 strains causing severe human disease in the United Kingdom. Microbial Genomics, 1 (3). ISSN 2057-5858

Dallman, Timothy J., Byrne, Lisa, Ashton, Philip M., Cowley, Lauren A., Perry, Neil T., Adak, Goutam, Petrovska, Liljana, Ellis, Richard J., Elson, Richard, Underwood, Anthony, Green, Jonathan, Hanage, William P., Jenkins, Claire, Grant, Kathie and Wain, John (2015) Whole-genome sequencing for national surveillance of Shiga toxin–producing Escherichia coli O157. Clinical Infectious Diseases, 61 (3). pp. 305-312. ISSN 1058-4838

Ashton, Philip, Nair, Satheesh, Dallman, Tim, Rubino, Salvatore, Rabsch, Wolfgang, Mwaigwisya, Solomon, Wain, John and O'Grady, Justin (2015) MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nature Biotechnology, 33 (3). 296–300. ISSN 1546-1696

Ashton, Philip M., Perry, Neil, Ellis, Richard, Petrovska, Liljana, Wain, John, Grant, Kathie A., Jenkins, Claire and Dallman, Tim J. (2015) Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing. PeerJ, 3. ISSN 2167-8359

Doumith, M, Day, M, Ciesielczuk, H, Hope, R, Underwood, A, Reynolds, R, Wain, J, Livermore, D M ORCID: https://orcid.org/0000-0002-9856-3703 and Woodford, N (2015) Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections. Journal of Clinical Microbiology, 53 (1). pp. 160-166. ISSN 0095-1137

Gupta, Ruchi, Gaind, Rajni, Wain, John, Deb, Monorama, Singh, Laishram Chandreshwor and Basir, Seemi Farhat (2014) Characterization of non-classical quinolone resistance in Salmonella enterica serovar Typhi:Report of a novel mutation in gyrB gene and diagnostic challenges. Biomolecular Detection and Quantification, 2 (C). pp. 30-34. ISSN 2214-7535

Chattaway, Marie Anne, Jenkins, Claire, Rajendram, Dunstan, Cravioto, Alejandro, Talukder, Kaisar Ali, Dallman, Tim, Underwood, Anthony, Platt, Steve, Okeke, Iruka N. and Wain, John (2014) Enteroaggregative escherichia coli have evolved independently as distinct complexes within the E. Coli population with varying ability to cause disease. PLoS One, 9 (11). ISSN 1932-6203

Chattaway, Marie Anne, Jenkins, Claire, Ciesielczuk, Holly, Day, Martin, DoNascimento, Vivienne, Day, Michaela, Rodríguez, Irene, van Essen-Zandbergen, Alieda, Schink, Anne-Kathrin, Wu, Guanghui, Threlfall, John, Woodward, Martin J., Coldham, Nick, Kadlec, Kristina, Schwarz, Stefan, Dierikx, Cindy M., Guerra, Beatriz, Helmuth, Reiner, Mevius, Dik J., Woodford, Neil and Wain, John and SAFEFOODERA (2014) Evidence of evolving extraintestinal enteroaggregative Escherichia coli ST38 clone. Emerging Infectious Diseases, 20 (11). pp. 1935-1937. ISSN 1080-6040

Zhou, Zhemin, McCann, Angela, Weill, François-Xavier, Blin, Camille, Nair, Satheesh, Wain, John, Dougan, Gordon and Achtman, Mark (2014) Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 111 (33). pp. 12199-204. ISSN 1091-6490

Nair, Satheesh, Wain, John, Connell, Steve, de Pinna, Elizabeth and Peters, Tansy (2014) Salmonella enterica subspecies II infections in England and Wales--the use of multilocus sequence typing to assist serovar identification. Journal of Medical Microbiology, 63 (Pt 6). pp. 831-4. ISSN 0022-2615

Dallman, Timothy J, Chattaway, Marie A, Cowley, Lauren A, Doumith, Michel, Tewolde, Rediat, Wooldridge, David J, Underwood, Anthony, Ready, Derren, Wain, John, Foster, Kirsty, Grant, Kathie A and Jenkins, Claire (2014) 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. PLoS One, 9 (5). e98103. ISSN 1932-6203

Hopkins, Katie L, Mushtaq, Shazad, Richardson, Judith F, Doumith, Michel, de Pinna, Elizabeth, Cheasty, Tom, Wain, John, Livermore, David M ORCID: https://orcid.org/0000-0002-9856-3703 and Woodford, Neil (2014) In vitro activity of rifaximin against clinical isolates of Escherichia coli and other enteropathogenic bacteria isolated from travellers returning to the UK. International Journal of Antimicrobial Agents, 43 (5). pp. 431-437. ISSN 0924-8579

Threlfall, E. J., Wain, J., Peters, T., Lane, C., De Pinna, E., Little, C. L., Wales, A. D. and Davies, R. A. (2014) Egg-borne infections of humans with salmonella:Not only an S. enteritidis problem. World's Poultry Science Journal, 70 (1). pp. 15-26. ISSN 0043-9339

Lawson, Becki, de Pinna, Elizabeth, Horton, Robert A, Macgregor, Shaheed K, John, Shinto K, Chantrey, Julian, Duff, J Paul, Kirkwood, James K, Simpson, Victor R, Robinson, Robert A, Wain, John and Cunningham, Andrew A (2014) Epidemiological evidence that garden birds are a source of human salmonellosis in England and Wales. PLoS One, 9 (2). ISSN 1932-6203

Parry, Christopher M, Thompson, Corinne, Vinh, Ha, Chinh, Nguyen Tran, Phuong, Le Thi, Ho, Vo Anh, Hien, Tran Tinh, Wain, John, Farrar, Jeremy J and Baker, Stephen (2014) Risk factors for the development of severe typhoid fever in Vietnam. BMC Infectious Diseases, 14. ISSN 1471-2334

Byrne, Lisa, Elson, Richard, Dallman, Timothy J, Perry, Neil, Ashton, Philip, Wain, John, Adak, Goutam K, Grant, Kathie A and Jenkins, Claire (2014) 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. PLoS One, 9 (1). ISSN 1932-6203

Tamayo, Eduardo, Almansa, Raquel, Carrasco, Elena, Avila-Alonso, Ana, Rodríguez-Fernández, Ana, Wain, John, Heredia, María, Gomez-Sanchez, Esther, Soria, Susana, Rico, Lucia, Iglesias, Verónica, Martínez-Martínez, Angel, Andaluz-Ojeda, David, Herreras, Jose Ignacio Gómez, Eiros, Jose Maria and Bermejo-Martin, Jesús F (2014) Quantification of IgM molecular response by droplet digital PCR as a potential tool for the early diagnosis of sepsis. Critical Care, 18 (3). p. 433. ISSN 1466-609X

Pearson, Bruce M., Rokney, Assaf, Crossman, Lisa C., Miller, William G., Wain, John and van Vliet, Arnoud H. M. (2013) Complete genome sequence of the Campylobacter coli clinical isolate 15-537360. Genome Announcements, 1 (6).

Bronowski, Christina, Fookes, Maria C., Gilderthorp, Ruth, Ashelford, Kevin E., Harris, Simon R., Phiri, Amos, Hall, Neil, Gordon, Melita A., Wain, John, Hart, Charles A., Wigley, Paul, Thomson, Nicholas R. and Winstanley, Craig (2013) Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi. PLoS Neglected Tropical Diseases, 7 (11). ISSN 1935-2727

Halstead, Fenella D, Lee, Adele V, Couto-Parada, Xose, Polley, Spencer D, Ling, Clare, Jenkins, Claire, Chalmers, Rachel M, Elwin, Kristin, Gray, Jim J, Iturriza-Gómara, Miren, Wain, John, Clark, Duncan A, Bolton, Frederick J and Manuel, Rohini J and Olympics GI Group (2013) Universal extraction method for gastrointestinal pathogens. Journal of Medical Microbiology, 62 (Pt 10). pp. 1535-9. ISSN 0022-2615

Wu, Guanghui, Day, Michaela J., Mafura, Muriel T., Nunez-Garcia, Javier, Fenner, Jackie J., Sharma, Meenaxi, van Essen-Zandbergen, Alieda, Rodríguez, Irene, Dierikx, Cindy, Kadlec, Kristina, Schink, Anne-Kathrin, Wain, John, Helmuth, Reiner, Guerra, Beatriz, Schwarz, Stefan, Threlfall, John, Woodward, Martin J., Woodford, Neil, Coldham, Nick and Mevius, Dik (2013) Comparative analysis of ESBL-positive Escherichia coli isolates from animals and humans from the UK, The Netherlands and Germany. PLoS One, 8 (9). ISSN 1932-6203

Paglietti, Bianca, Falchi, Giovanni, Mason, Peter, Chitsatso, Owen, Nair, Satheesh, Gwanzura, Lovemore, Uzzau, Sergio, Cappuccinelli, Piero, Wain, John and Rubino, Salvatore (2013) Diversity among human non-typhoidal salmonellae isolates from Zimbabwe. Transactions of the Royal Society of Tropical Medicine and Hygiene, 107 (8). pp. 487-92. ISSN 0035-9203

Barquist, Lars, Langridge, Gemma C., Turner, Daniel J., Phan, Minh-Duy, Turner, A. Keith, Bateman, Alex, Parkhill, Julian, Wain, John and Gardner, Paul P. (2013) A comparison of dense transposon insertion libraries in the Salmonella serovars Thypi and Typhimurium. Nucleic Acids Research, 41 (8). pp. 4549-4564. ISSN 0305-1048

Wain, John and Mavrogiorgou, Eleni (2013) Next-generation sequencing in clinical microbiology. Expert Review of Molecular Diagnostics, 13 (3). pp. 225-227. ISSN 1744-8352

Livermore, David M. ORCID: https://orcid.org/0000-0002-9856-3703 and Wain, John (2013) Revolutionising bacteriology to improve treatment outcomes and antibiotic stewardship. Infection & Chemotherapy, 45 (1). pp. 1-10. ISSN 2093-2340

Underwood, Anthony P., Dallman, Tim, Thomson, Nicholas R., Williams, Michaela, Harker, Katy, Perry, Neil, Adak, Bob, Willshaw, Geraldine, Cheasty, Tom, Green, Jonathan, Dougan, Gordon, Parkhill, Julian and Wain, John (2013) Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak. Journal of Clinical Microbiology, 51 (1). pp. 232-237. ISSN 0095-1137

Wain, John, Keddy, Karen H, Hendriksen, Rene S and Rubino, Salvatore (2013) Using next generation sequencing to tackle non-typhoidal Salmonella infections. Journal of Infection in Developing Countries, 7 (01). pp. 1-5. ISSN 1972-2680

Almansa, Raquel, Wain, John, Tamayo, Eduardo, Andaluz-Ojeda, David, Martin-Loeches, Ignacio, Ramirez, Paula and Bermejo-Martin, Jesús F. (2013) Immunological monitoring to prevent and treat sepsis. Critical Care, 17 (1). ISSN 1364-8535

Chattaway, M A, Harris, R, Jenkins, C, Tam, C, Coia, J E, Gray, J, Iturriza-Gomara, M and Wain, J (2013) 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. Eurosurveillance, 18 (37). ISSN 1560-7917

Nadon, C A, Trees, E, Ng, L K, Møller Nielsen, E, Reimer, A, Maxwell, N, Kubota, K A, Gerner-Smidt, P and Wain, John and MLVA Harmonization Working Group (2013) Development and application of MLVA methods as a tool for inter-laboratory surveillance. Eurosurveillance, 18 (35). ISSN 1560-7917

Stone, Madeline J., Wain, John, Ivens, Alasdair, Feltwell, Theresa, Kearns, Angela M. and Bamford, Kathleen B. (2013) Harnessing the genome: development of a hierarchical typing scheme for meticillin-resistant Staphylococcus aureus. Journal of Medical Microbiology, 62 (Pt_1). pp. 36-45. ISSN 0022-2615

Tam, Clarence C., O'Brien, Sarah J., Tompkins, David S., Bolton, Frederick J., Berry, Lisa, Dodds, Julie, Choudhury, Dalia, Halstead, Fenella, Iturriza-Gomara, Miren, Mather, Katherine, Rait, Greta, Ridge, Alan, Rodrigues, Laura C., Wain, John, Wood, Bernard and Gray, James (2012) Changes in causes of acute gastroenteritis in the United Kingdom over 15 years: Microbiologic findings from 2 prospective, population-based studies of infectious intestinal disease. Clinical Infectious Diseases, 54 (9). pp. 1275-1286. ISSN 1058-4838

Nga, Tran Vu Thieu, Parry, Christopher M., Le, Thuy, Lan, Nguyen Phu Huong, Diep, To Song, Campbell, James I., Hoang, Nguyen Van Minh, Dung, Le Thi, Wain, John, Dolecek, Christiane, Farrar, Jeremy J., Chau, Nguyen Van Vinh, Hien, Tran Tinh, Day, Jeremy N. and Baker, Stephen (2012) The decline of typhoid and the rise of non-typhoid salmonellae and fungal infections in a changing HIV landscape: bloodstream infection trends over 15 years in southern Vietnam. Transactions of the Royal Society of Tropical Medicine and Hygiene, 106 (1). pp. 26-34. ISSN 1878-3503

Okoro, Chinyere K., Kingsley, Robert A., Connor, Thomas R., Harris, Simon R., Parry, Christopher M., Al-Mashhadani, Manar N., Kariuki, Samuel, Msefula, Chisomo L., Gordon, Melita A., de Pinna, Elizabeth, Wain, John, Heyderman, Robert S., Obaro, Stephen, Alonso, Pedro L., Mandomando, Inacio, MacLennan, Calman A., Tapia, Milagritos D., Levine, Myron M., Tennant, Sharon M., Parkhill, Julian and Dougan, Gordon (2012) Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nature Genetics, 44 (11). pp. 1215-1221. ISSN 1061-4036

Ricci, Vito, Loman, Nick, Pallen, Mark, Ivens, Alasdair, Fookes, Maria, Langridge, Gemma C., Wain, John and Piddock, Laura J. V. (2012) The TCA cycle is not required for selection or survival of multidrug-resistant Salmonella. Journal of Antimicrobial Chemotherapy, 67 (3). pp. 589-599. ISSN 0305-7453

Lamikanra, Adebayo, Crowe, Jennifer L., Lijek, Rebeccah S., Odetoyin, Babatunde W., Wain, John, Aboderin, A. Oladipo and Okeke, Iruka N. (2011) Rapid evolution of fluoroquinolone-resistant Escherichia coli in Nigeria is temporally associated with fluoroquinolone use. BMC Infectious Diseases, 11. ISSN 1471-2334

Le Hello, Simon, Hendriksen, Rene S., Doublet, Benoît, Fisher, Ian, Møller Nielsen, Eva, Whichard, Jean M., Bouchrif, Brahim, Fashae, Kayode, Granier, Sophie A., Jourdan-Da Silva, Nathalie, Cloeckaert, Axel, Threlfall, E. John, Angulo, Frederick J., Aarestrup, Frank M., Wain, John and Weill, François-Xavier (2011) International spread of an epidemic population of Salmonella enterica serotype Kentucky ST198 resistant to ciprofloxacin. Journal of Infectious Diseases, 204 (5). pp. 675-684. ISSN 0022-1899

Holt, Kathryn E., Phan, Minh Duy, Baker, Stephen, Duy, Pham Thanh, Nga, Tran Vu Thieu, Nair, Satheesh, Turner, A. Keith, Walsh, Ciara, Fanning, Séamus, Farrell-Ward, Sinéad, Dutta, Shanta, Kariuki, Sam, Weill, François-Xavier, Parkhill, Julian, Dougan, Gordon and Wain, John (2011) Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid. PLoS Neglected Tropical Diseases, 5 (7). ISSN 1935-2727

Parry, Christopher M., Vinh, Ha, Chinh, Nguyen Tran, Wain, John, Campbell, James I., Hien, Tran Tinh, Farrar, Jeremy J. and Baker, Stephen (2011) The influence of reduced susceptibility to fluoroquinolones in Salmonella enterica serovar Typhi on the clinical response to ofloxacin therapy. PLoS Neglected Tropical Diseases, 5 (6). ISSN 1935-2727

Janmohamed, K, Zenner, D, Little, C, Lane, C, Wain, J, Charlett, A, Adak, B and Morgan, D (2011) National outbreak of Salmonella Enteritidis phage type 14b in England, September to December 2009: case-control study. Eurosurveillance, 16 (15). ISSN 1560-7917

Beyene, Getenet, Nair, Satheesh, Asrat, Daniel, Mengistu, Yohannes, Engers, Howard and Wain, John (2011) Multidrug resistant Salmonella Concord is a major cause of salmonellosis in children in Ethiopia. Journal of Infection in Developing Countries, 5 (1). pp. 23-33. ISSN 1972-2680

Al-Mashhadani, Manar, Hewson, Robert, Vivancos, Roberto, Keenan, Alex, Beeching, Nick J., Wain, John and Parry, Christopher M. (2011) Foreign travel and decreased ciprofloxacin susceptibility in Salmonella enterica infections. Emerging Infectious Diseases, 17 (1). pp. 123-125. ISSN 1080-6059

Zafar, A., Stone, M., Ibrahim, S., Parveen, Z., Hasan, Z., Khan, E., Hasan, R., Wain, J. and Bamford, K. (2011) Prevalent genotypes of meticillin-resistant Staphylococcus aureus: report from Pakistan. Journal of Medical Microbiology, 60 (1). pp. 56-62. ISSN 0022-2615

Molloy, Aoife, Nair, Satheesh, Cooke, Fiona J., Wain, John, Farrington, Mark, Lehner, Paul J. and Torok, M. Estee (2010) First report of Salmonella enterica serotype Paratyphi A azithromycin resistance leading to treatment failure. Journal of Clinical Microbiology, 48 (12). pp. 4655-4657. ISSN 0095-1137

Parry, Christopher M., Thuy, Chau Tran, Dongol, Sabina, Karkey, Abhilasha, Vinh, Ha, Chinh, Nguyen Tran, Duy, Pham Thanh, Thieu Nga, Tran Vu, Campbell, James I., Van Minh Hoang, Nguyen, Arjyal, Amit, Bhutta, Zulfiqar A., Bhattacharya, Sujit K., Agtini, Magdarina D., Dong, Baiqing, Canh, Do Gia, Naheed, Aliya, Wain, John, Tinh Hien, Tran, Basnyat, Buddha, Ochiai, Leon, Clemens, John, Farrar, Jeremy J., Dolecek, Christiane and Baker, Stephen (2010) Suitable disk antimicrobial susceptibility breakpoints defining Salmonella enterica serovar Typhi isolates with reduced susceptibility to fluoroquinolones. Antimicrobial Agents and Chemotherapy, 54 (12). pp. 5201-5208. ISSN 0066-4804

Pickard, Derek, Toribio, Ana Luisa, Petty, Nicola K., van Tonder, Andries, Yu, Lu, Goulding, David, Barrell, Bart, Rance, Richard, Harris, David, Wetter, Michael, Wain, John, Choudhary, Jyoti, Thomson, Nicholas and Dougan, Gordon (2010) A conserved acetyl esterase domain targets diverse bacteriophages to the Vi capsular receptor of Salmonella enterica serovar Typhi. Journal of Bacteriology, 192 (21). pp. 5746-5754. ISSN 0021-9193

Okeke, Iruka N., Wallace-Gadsden, Faith, Simons, Hannah R., Matthews, Nicholas, Labar, Amy S., Hwang, Jennifer and Wain, John (2010) Multi-locus sequence typing of enteroaggregative Escherichia coli isolates from Nigerian children uncovers multiple lineages. PLoS One, 5 (11). ISSN 1932-6203

Peters, Tansy, Hopkins, Katie L., Lane, Chris, Nair, Satheesh, Wain, John and de Pinna, Elizabeth (2010) Emergence and characterization of Salmonella enterica serovar Typhimurium phage type DT191a. Journal of Clinical Microbiology, 48 (9). pp. 3375-3377. ISSN 0095-1137

Song, Yajun, Roumagnac, Philippe, Weill, François-Xavier, Wain, John, Dolecek, Christiane, Mazzoni, Camila J., Holt, Kathryn E. and Achtman, Mark (2010) A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A. Journal of Antimicrobial Chemotherapy, 65 (8). pp. 1631-1641. ISSN 0305-7453

Walsh, Fiona, Cooke, Niamh M., Smith, Stephen G., Moran, Gary P., Cooke, Fiona J., Ivens, Alasdair, Wain, John and Rogers, Thomas R. (2010) Comparison of two DNA microarrays for detection of plasmid-mediated antimicrobial resistance and virulence factor genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae. International Journal of Antimicrobial Agents, 35 (6). pp. 593-598. ISSN 1872-7913

Bailey, Andrew M., Ivens, Al, Kingsley, Rob, Cottell, Jennifer L., Wain, John and Piddock, Laura J. V. (2010) RamA, a member of the AraC/XylS family, influences both virulence and efflux in Salmonella enterica Serovar Typhimurium. Journal of Bacteriology, 192 (6). pp. 1607-1616. ISSN 0021-9193

Matheson, Nicholas, Kingsley, Robert A., Sturgess, Katherine, Aliyu, Sani H., Wain, John, Dougan, Gordon and Cooke, Fiona J. (2010) Ten years experience of Salmonella infections in Cambridge, UK. Journal of Infection, 60 (1). pp. 21-25. ISSN 1532-2742

Langridge, Gemma C., Phan, Minh-Duy, Turner, Daniel J., Perkins, Timothy T., Parts, Leopold, Haase, Jana, Charles, Ian, Maskell, Duncan J., Peters, Sarah E., Dougan, Gordon, Wain, John, Parkhill, Julian and Turner, A. Keith (2009) Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Research, 19 (12). pp. 2308-2316. ISSN 1088-9051

Bailey, Andrew M., Constantinidou, Chrystala, Ivens, Al, Garvey, Mark I., Webber, Mark A., Coldham, Nick, Hobman, Jon L., Wain, John, Woodward, Martin J. and Piddock, Laura J. V. (2009) Exposure of Escherichia coli and Salmonella enterica serovar Typhimurium to triclosan induces a species-specific response, including drug detoxification. Journal of Antimicrobial Chemotherapy, 64 (5). pp. 973-985. ISSN 0305-7453

Cooke, Fiona J., Ginwalla, Sara, Hampton, Michael D., Wain, John, Ross-Russell, Robert, Lever, Andrew and Farrington, Mark (2009) Report of neonatal meningitis due to Salmonella enterica serotype Agona and review of breast milk-associated neonatal Salmonella infections. Journal of Clinical Microbiology, 47 (9). pp. 3045-3049. ISSN 0095-1137

Holt, Kathryn E., Teo, Yik Y., Li, Heng, Nair, Satheesh, Dougan, Gordon, Wain, John and Parkhill, Julian (2009) Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. Bioinformatics, 25 (16). pp. 2074-2075. ISSN 1367-4803

Webber, Mark A., Bailey, Andrew M., Blair, Jessica M. A., Morgan, Eirwen, Stevens, Mark P., Hinton, Jay C. D., Ivens, Al, Wain, John and Piddock, Laura J. V. (2009) The global consequence of disruption of the AcrAB-TolC efflux pump in Salmonella enterica includes reduced expression of SPI-1 and other attributes required to infect the host. Journal of Bacteriology, 191 (13). pp. 4276-4285. ISSN 0021-9193

Phan, Minh-Duy, Kidgell, Claire, Nair, Satheesh, Holt, Kathryn E., Turner, Arthur K., Hinds, Jason, Butcher, Philip, Cooke, Fiona J., Thomson, Nicholas R., Titball, Richard, Bhutta, Zulfiqar A., Hasan, Rumina, Dougan, Gordon and Wain, John (2009) Variation in Salmonella enterica serovar Typhi IncHI1 plasmids during the global spread of resistant typhoid fever. Antimicrobial Agents and Chemotherapy, 53 (2). pp. 716-727. ISSN 0066-4804

Holt, Kathryn E., Thomson, Nicholas R., Wain, John, Langridge, Gemma C., Hasan, Rumina, Bhutta, Zulfiqar A., Quail, Michael A., Norbertczak, Halina, Walker, Danielle, Simmonds, Mark, White, Brian, Bason, Nathalie, Mungall, Karen, Dougan, Gordon and Parkhill, Julian (2009) Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi. BMC Genomics, 10. ISSN 1471-2164

Cooke, Fiona J., Brown, Derek J., Fookes, Maria, Pickard, Derek, Ivens, Alasdair, Wain, John, Roberts, Mark, Kingsley, Robert A., Thomson, Nicholas R. and Dougan, Gordon (2008) Characterization of the genomes of a diverse collection of Salmonella enterica Serovar Typhimurium definitive phage type 104. Journal of Bacteriology, 190 (24). pp. 8155-8162. ISSN 0021-9193

Tse, Darren, Zhai, Rihong, Zhou, Wei, Heist, Rebecca S., Asomaning, Kofi, Su, Li, Lynch, Thomas J., Wain, John C., Christiani, David C. and Liu, Geoffrey (2008) Polymorphisms of the NER pathway genes, ERCC1 and XPD are associated with esophageal adenocarcinoma risk. Cancer Causes & Control, 19 (10). pp. 1077-1083. ISSN 0957-5243

Okeke, Iruka N. and Wain, John (2008) Post-genomic challenges for collaborative research in infectious diseases. Nature Reviews Microbiology, 6 (11). pp. 854-864. ISSN 1740-1526

Pickard, Derek, Thomson, Nicholas R., Baker, Stephen, Wain, John, Pardo, Mercedes, Goulding, David, Hamlin, Nancy, Choudhary, Jyoti, Threfall, John and Dougan, Gordon (2008) Molecular Characterization of the Salmonella enterica Serovar Typhi Vi-Typing Bacteriophage E1. Journal of Bacteriology, 190 (7). pp. 2580-2587. ISSN 0021-9193

Chau, Tran Thuy, Campbell, James Ian, Galindo, Claudia M., Van Minh Hoang, Nguyen, Diep, To Song, Nga, Tran Thu Thi, Chau, Nguyen Van Vinh, Tuan, Phung Quoc, Page, Anne Laure, Ochiai, R. Leon, Schultsz, Constance, Wain, John, Bhutta, Zulfiqar A., Parry, Christopher M., Bhattacharya, Sujit K., Dutta, Shanta, Agtini, Magdarina, Dong, Baiqing, Honghui, Yang, Anh, Dang Duc, Canh, Do Gia, Naheed, Aliya, Albert, M. John, Phetsouvanh, Rattanaphone, Newton, Paul N., Basnyat, Buddha, Arjyal, Amit, La, Tran Thi Phi, Rang, Nguyen Ngoc, Phuong, Le Thi, Van Be Bay, Phan, von Seidlein, Lorenz, Dougan, Gordon, Clemens, John D., Vinh, Ha, Hien, Tran Tinh, Chinh, Nguyen Tran, Acosta, Camilo J., Farrar, Jeremy and Dolecek, Christiane (2007) Antimicrobial drug resistance of Salmonella enterica Serovar Typhi in Asia and molecular mechanism of reduced susceptibility to the fluoroquinolones. Antimicrobial Agents and Chemotherapy, 51 (12). pp. 4315-4323. ISSN 0066-4804

Choi, Seon Young, Jeon, Yoon-Seong, Lee, Je Hee, Choi, Boram, Moon, Sun Hwa, von Seidlein, Lorenz, Clemens, John D., Dougan, Gordon, Wain, John, Yu, Jun, Lee, Je Chul, Seol, Sung Yong, Lee, Bok Kwon, Song, Jae-Hoon, Song, Manki, Czerkinsky, Cecil, Chun, Jongsik and Kim, Dong Wook (2007) Multilocus sequence typing analysis of Shigella flexneri isolates collected in Asian countries. Journal of Medical Microbiology, 56 (11). pp. 1460-1466. ISSN 0022-2615

Chart, Henrik, Cheasty, Thomas, de Pinna, Elizabeth, Siorvanes, Lisa, Wain, John, Alam, Didar, Nizami, Qamarauddin, Bhutta, Zulfiqar and Threlfall, E. John (2007) Serodiagnosis of Salmonella enterica serovar Typhi and S. enterica serovars Paratyphi A, B and C human infections. Journal of Medical Microbiology, 56 (9). pp. 1161-1166. ISSN 0022-2615

Cooke, Fiona J., Wain, John, Fookes, Maria, Ivens, Alasdair, Thomson, Nicholas, Brown, Derek J., Threlfall, E. John, Gunn, George, Foster, Geoffrey and Dougan, Gordon (2007) Prophage sequences defining hot spots of genome variation in Salmonella enterica serovar Typhimurium can be used to discriminate between field isolates. Journal of Clinical Microbiology, 45 (8). pp. 2590-2598. ISSN 0095-1137

Holt, Kathryn E., Thomson, Nicholas R., Wain, John, Phan, Minh Duy, Nair, Satheesh, Hasan, Rumina, Bhutta, Zulfiqar A., Quail, Michael A., Norbertczak, Halina, Walker, Danielle, Dougan, Gordon and Parkhill, Julian (2007) Multidrug-resistant Salmonella enterica serovar Paratyphi A harbors IncHI1 plasmids similar to those found in serovar Typhi. Journal of Bacteriology, 189 (11). pp. 4257-4264. ISSN 0021-9193

Wallace-Gadsden, Faith, Johnson, James R., Wain, John and Okeke, Iruke N. (2007) Enteroaggregative Escherichia coli related to uropathogenic clonal group A. Emerging Infectious Diseases, 13 (5). pp. 757-760. ISSN 1080-6040

Cooke, Fiona J., Day, Martin, Wain, John, Ward, Linda R. and Threlfall, E. John (2007) Cases of typhoid fever imported into England, Scotland and Wales (2000–2003). Transactions of the Royal Society of Tropical Medicine and Hygiene, 101 (4). pp. 398-404. ISSN 1878-3503

Parry, Christopher M., Ho, Vo Anh, Phuong, Le Thi, Bay, Phan Van Be, Lanh, Mai Ngoc, Tung, Le Thanh, Tham, Nguyen Thi Hong, Wain, John, Hien, Tran Tinh and Farrar, Jeremy J. (2007) Randomized controlled comparison of ofloxacin, azithromycin, and an ofloxacin-azithromycin combination for treatment of multidrug-resistant and nalidixic acid-resistant typhoid fever. Antimicrobial Agents and Chemotherapy, 51 (3). pp. 819-825. ISSN 0066-4804

Doyle, Marie, Fookes, Maria, Ivens, Al, Mangan, Michael W., Wain, John and Dorman, Charles J. (2007) An H-NS-like stealth protein aids horizontal DNA transmission in bacteria. Science, 315 (5809). pp. 251-252. ISSN 0036-8075

Dutta, Shanta, Sur, Dipika, Manna, Byomkesh, Sen, Bhaswati, Deb, Alok Kumar, Deen, Jacqueline L., Wain, John, von Seidlein, Lorenz, Ochiai, Leon, Clemens, John D. and Bhattacharya, Sujit Kumar (2006) Evaluation of new-generation serologic tests for the diagnosis of typhoid fever: data from a community-based surveillance in Calcutta, India. Diagnostic Microbiology and Infectious Disease, 56 (4). pp. 359-365. ISSN 1879-0070

Han, Kyung Ho, Choi, Seon Young, Lee, Je Hee, Lee, Hyejon, Shin, Eun Hee, Agtini, Magdarina D., von Seidlein, Lorenz, Ochiai, R. Leon, Clemens, John D., Wain, John, Hahn, Ji-Sook, Lee, Bok Kwon, Song, Manki, Chun, Jongsik and Kim, Dong Wook (2006) Isolation of Salmonella enterica subspecies enterica serovar Paratyphi B dT+, or Salmonella Java, from Indonesia and alteration of the d-tartrate fermentation phenotype by disrupting the ORF STM 3356. Journal of Medical Microbiology, 55 (12). pp. 1661-1665. ISSN 0022-2615

Turner, Arthur K., Nair, Satheesh and Wain, John (2006) The acquisition of full fluoroquinolone resistance in Salmonella Typhi by accumulation of point mutations in the topoisomerase targets. Journal of Antimicrobial Chemotherapy, 58 (4). pp. 733-740. ISSN 0305-7453

Heist, Rebecca Suk, Marshall, Ariela L., Liu, Geoffrey, Zhou, Wei, Su, Li, Neuberg, Donna, Lynch, Thomas J., Wain, John and Christiani, David C. (2006) Matrix metalloproteinase polymorphisms and survival in stage I non-small cell lung cancer. Clinical Cancer Research, 12 (18). pp. 5448-5453. ISSN 1078-0432

Cooke, Graham S., Cooke, Fiona J., Stone, Madeline, Turner, Keith, Al Nahhas, Adil, Win, Zarni, Wain, John, Rogers, Thomas R., Friedland, Jon S. and Bamford, Kathleen B. (2006) Deep-seated resistance in relapsed paratyphoid fever. Clinical Infectious Diseases, 42 (11). e92-e94. ISSN 1058-4838

Nair, Satheesh, Unnikrishnan, Madhulika, Turner, Keith, Parija, Subash Chandra, Churcher, Carol, Wain, John and Harish, Belgode Narasimha (2006) Molecular analysis of fluoroquinolone-resistant Salmonella Paratyphi A isolate, India. Emerging Infectious Diseases, 12 (3). pp. 489-491. ISSN 1080-6040

Ochiai, R. Leon, Wang, XuanYi, von Seidlein, Lorenz, Yang, Jin, Bhutta, Zulfiqar A., Bhattacharya, Sujit K., Agtini, Magdarina, Deen, Jacqueline L., Wain, John, Kim, Deok Ryun, Ali, Mohammad, Acosta, Camilo J., Jodar, Luis and Clemens, John D. (2005) Salmonella paratyphi A rates, Asia. Emerging Infectious Diseases, 11 (11). pp. 1764-1766. ISSN 1080-6040

Baker, Stephen, Sarwar, Yasra, Aziz, Hafsa, Haque, Asma, Ali, Aamir, Dougan, Gordon, Wain, John and Haque, Abdul (2005) Detection of Vi-negative Salmonella enterica Serovar Typhi in the peripheral blood of patients with typhoid fever in the Faisalabad region of Pakistan. Journal of Clinical Microbiology, 43 (9). pp. 4418-4425. ISSN 0095-1137

House, Deborah, Chinh, Nguyen T., Diep, To S., Parry, Christopher M., Wain, John, Dougan, Gordon, White, Nicholas J., Hien, Tran Tinh and Farrar, Jeremy J. (2005) Use of paired serum samples for serodiagnosis of typhoid fever. Journal of Clinical Microbiology, 43 (9). pp. 4889-4890. ISSN 0095-1137

Dunstan, Sarah J., Hawn, Thomas R., Hue, Nguyen Thi, Parry, Christopher P., Ho, Vo An, Vinh, Ha, Diep, To Song, House, Deborah, Wain, John, Aderem, Alan, Hien, Tran Tinh and Farrar, Jeremy J. (2005) Host susceptibility and clinical outcomes in toll-like receptor 5–deficient patients with typhoid fever in Vietnam. Journal of Infectious Diseases, 191 (7). pp. 1068-1071. ISSN 0022-1899

Wain, John, House, Deborah, Zafar, Afia, Baker, Stephen, Nair, Satheesh, Kidgell, Claire, Bhutta, Zulfiqar, Dougan, Gordon and Hasan, Rumina (2005) Vi Antigen Expression in Salmonella enterica Serovar Typhi Clinical Isolates from Pakistan. Journal of Clinical Microbiology, 43 (3). pp. 1158-1165. ISSN 0095-1137

Vinh, Ha, Duong, Nguyen Minh, Phuong, Le Thi, Truong, Nguyen Thanh, Bay, Phan Van Be, Wain, J, Diep, To Song, Ho, Vo Anh, White, Nicholas J., Day, Nicholas P.J. and Parry, Christopher M. (2005) Comparative trial of short-course ofloxacin for uncomplicated typhoid fever in Vietnamese children. Annals of Tropical Paediatrics: International Child Health, 25 (1). pp. 17-22.

Chanh, Nguyen Quoc, Everest, Paul, Khoa, Tran Tan, House, Deborah, Murch, Simon, Parry, Christopher, Connerton, Phillippa, Van Bay, Phan, Diep, To Song, Mastroeni, Pietro, White, Nicholas J., Hien, Tran T., Van Ho, Vo, Dougan, Gordon, Farrar, Jeremy J. and Wain, John (2004) A clinical, microbiological, and pathological study of intestinal perforation associated with typhoid fever. Clinical Infectious Diseases, 39 (1). pp. 61-67. ISSN 1058-4838

Thomson, Nicholas, Baker, Stephen, Pickard, Derek, Fookes, Maria, Anjum, Muna, Hamlin, Nancy, Wain, John, House, Deborah, Bhutta, Zulfiqar, Chan, Kaman, Falkow, Stanley, Parkhill, Julian, Woodward, Martin, Ivens, Al and Dougan, Gordon (2004) The role of prophage-like elements in the diversity of Salmonella enterica Serovars. Journal of Molecular Biology, 339 (2). pp. 279-300. ISSN 1089-8638

Vinh, Ha, Parry, Christopher M., Hanh, Vo T. N., Chinh, Mai T., House, Deborah, Tham, Cao T., Thao, Nguyen T. T., Diep, To S., Wain, John, Day, Nicholas P. J., White, Nicholas J. and Farrar, Jeremy J. (2004) Double blind comparison of ibuprofen and paracetamol for adjunctive treatment of uncomplicated typhoid fever. Pediatric Infectious Disease Journal, 23 (3). pp. 226-230. ISSN 0891-3668

Pickard, Derek, Wain, John, Baker, Stephen, Line, Alexandra, Chohan, Sonia, Fookes, Maria, Barron, Andrew, O Gaora, Peadar, Chabalgoity, José A., Thanky, Niren, Scholes, Christoph, Thomson, Nicholas, Quail, Michael, Parkhill, Julian and Dougan, Gordon (2003) Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7. Journal of Bacteriology, 185 (17). pp. 5055-5065. ISSN 0021-9193

Wain, John, Diem Nga, L. T., Kidgell, Claire, James, Keith, Fortune, Sarah, Song Diep, To, Ali, Tahir, Ó Gaora, Peadar, Parry, Christopher, Parkhill, Julian, Farrar, Jeremy, White, Nicholas J. and Dougan, Gordon (2003) Molecular analysis of incHI1 antimicrobial resistance plasmids from Salmonella serovar Typhi strains associated with typhoid fever. Antimicrobial Agents and Chemotherapy, 47 (9). pp. 2732-2739. ISSN 0066-4804

Parry, Christopher M., Duong, Nguyen Minh, Zhou, Jiaji, Mai, Nguyen Thi Hoang, Diep, To Song, Thinh, Le Quoc, Wain, John, Chau, Nguyen Van Vinh, Griffiths, David, Day, Nicholas P. J., White, Nicholas J., Hien, Tran Tinh, Spratt, Brian G. and Farrar, Jeremy J. (2002) Emergence in Vietnam of Streptococcus pneumoniae resistant to multiple antimicrobial agents as a result of dissemination of the multiresistant Spain23F-1 clone. Antimicrobial Agents and Chemotherapy, 46 (11). pp. 3512-3517. ISSN 0066-4804

House, Deborah, Chinh, Nguyen T., Hien, Tran T., Parry, Christopher P., Ly, Nguyen T., Diep, To S., Wain, John, Dunstan, Sarah, White, Nicholas J., Dougan, Gordon and Farrar, Jeremy J. (2002) Cytokine release by lipopolysaccharide-stimulated whole blood from patients with typhoid fever. Journal of Infectious Diseases, 186 (2). pp. 240-245. ISSN 0022-1899

Kidgell, Claire, Pickard, Derek, Wain, John, James, Keith, Nga, L. T. Diem, Diep, To Song, Levine, Myron M., O'Gaora, Peadar, Prentice, Michael B., Parkhill, Julian, Day, Nicholas, Farrar, Jeremy and Dougan, Gordon (2002) Characterisation and distribution of a cryptic Salmonella typhi plasmid pHCM2. Plasmid, 47 (3). pp. 159-171. ISSN 1095-9890

Wain, John, House, Deborah, Parkhill, Julian, Parry, Christopher and Dougan, Gordon (2002) Unlocking the genome of the human typhoid bacillus. The Lancet Infectious Diseases, 2 (3). pp. 163-170. ISSN 1473-3099

Book Section

Wain, John and O'Grady, Justin (2017) Genomic Diversity in Salmonella enterica. In: Applied Genomics of Foodborne Pathogens. Food Microbiology and Food Safety . Springer, pp. 91-107. ISBN 978-3-319-43749-1

Crump, John A. and Wain, John (2017) Salmonella. In: International Encyclopedia of Public Health. Elsevier, pp. 425-433. ISBN 9780128037089

Threlfall, E. J., Wain, J. and Lane, C. (2011) Salmonellosis. In: Zoonoses. Oxford University Press.