Biography

John Wain is Professor of Medical Microbiology at the University of East Anglia, the CSO and director for Discuva and Bactevo Ltd. and founding editor of the Journal of Infection in Developing Countries.

He is a bacteriologist and international authority on Salmonella and other gastrointestinal pathogens with over 30 years' experience in the identification of bacterial pathogens and antibiotic resistance. Having started work as a graduate biologist in the public health laboratory service in the UK in 1981, and continued into the NHS from 1989-1992, John Wain pursued a research career in medical microbiology with a Ph.D at Birmingham University a decade at the Wellcome Trust oversees Unit in Vietnam and three years postdoctoral research at Imperial College. This was followed by a faculty position in Cambridge at the Welcome Trust Sanger Institute and a senior lectureship at the University of Liverpool. In 2008 Dr Wain became the head of the largest bacteriology reference laboratory in the UK at Colindale: The laboratory for Gastrointestinal Pathogens, before moving into his current role of leading research in GI infections and developing translational research in diagnostic microbiology at the UEA.

Summary of research achievements in translational microbiology

1999 - Initiated as part of his PhD studies the sequencing of first Salmonella genome, published in Nature in 2001, and was awarded the young microbiologist of the year by the American Society for Microbiology (the first non-American to receive this prestigious award) for work on outcome prediction for chemotherapy in typhoid fever.

 2003 - Established lab at Sanger to exploit Salmonella genome data and developed transposon mutagenesis for describing globally essential gene sets and small non-coding RNAs for Salmonella.

 2007 - Described involvement of H-NS global regulation of newly acquired horizontal DNA 

 2008 - As director of the HPA’s reference lab for GI infection established evidence base for the use of next generation sequencing (NGS) as the routine method for outbreak investigation - and drove the effort to be the first public health service laboratory to sequence, in house, an outbreak strain - from the German E. coli outbreak.

 2011 - Founded Discuva and established translation microbiology laboratory at UEA

 2013 - Founded Bactevo

Career History

1980

   Biomedical Scientist, Public Health, Laboratory, Dorchester.

   Granted two years leave of absence for volunteer work in West Africa with the VSO.

1988

   Adult education - Teacher of Microbiology, College of Health Technology, Sokoto, Nigeria.

1990

   Senior Biomedical Scientist, Weston General Hospital, Somerset, UK.
   At this time I moved out of a career in clinical laboratories to start my academic career and registered part time for a PhD.

1992

   Head of Microbiology Labs. Wellcome Trust Research Unit, Vietnam.

1999

   Academic Visitor, Dept Biochemistry, Imperial College, London.

2000

   Senior Research Fellow, Centre for Molecular Microbiology and Infection, Imperial College, London.

2001

   Consultant Microbiologist for the International Vaccine Institute, Soule, Korea. This position ran concurrently with jobs in the UK.

2004

   Junior Fellow, the Wellcome Trust Sanger Institute, UK.

2007

   Senior Lecturer in Medical Microbiology, University of Liverpool, and

2008

   Director of the Laboratory for Gastrointestinal Infections Health Protection Agency, Colindale, London.

Academic Background

1976-79            B.Sc. Biological Sciences, honours class III, Portsmouth Polytechnic

1991-92            M.Sc. in Medical Microbiology (Parasitology) with distinction, London School of Hygiene and Tropical Medicine

1996-2000        Ph.D. “Antimicrobial resistance in S. typhi” Birmingham University, Dept, Infection

Highlighted Publications

See All

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

(2015)

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

in Nature Biotechnology

Full Text UEA Repository

(Article)


Livermore, D. M., Wain, J.

(2013)

Revolutionising bacteriology to improve treatment outcomes and antibiotic stewardship

in Infection & Chemotherapy

45.

pp. 1-10

Full Text UEA Repository

(Article)


Wain, J., Keddy, K., Hendriksen, R., Rubino, S.

(2013)

Using next-generation sequencing to tackle non-typhoidal Salmonella infections

in Journal of infection in developing countries

7.

pp. 1-5

Full Text UEA Repository

(Article)


Wain, J., Mavrogiorgou, E., Sequence Analysis, DNA

(2013)

Next-generation sequencing in clinical microbiology

in Expert Review of Molecular DIagnostics

13.

pp. 225-227

Full Text UEA Repository

(Article)


Underwood, A., Dallman, T., Thomson, N., Williams, M., Harker, K., Perry, N., Adak, B., Willshaw, G., Cheasty, T., Green, J., Dougan, G., Parkhill, J., Wain, J.

(2013)

Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak

in Journal of Clinical Microbiology

51.

pp. 232-237

Full Text UEA Repository

(Article)


All Publications

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

(2015)

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

in Nature Biotechnology

Full Text UEA Repository

(Article)


Hopkins, K. L., Mushtaq, S., Richardson, J. F., Doumith, M., de Pinna, E., Cheasty, T., Wain, J., Livermore, D. M., Woodford, N.

(2014)

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

in International Journal of Antimicrobial Agents

43.

pp. 431-437

Full Text UEA Repository

(Article)


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

(2014)

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

in Journal of Clinical Microbiology

Full Text UEA Repository

(Article)


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

(2014)

Evidence of Evolving Extraintestinal Enteroaggregative Escherichia coli ST38 Clone

in Emerging Infectious Diseases

20.

pp. 1935-7

Full Text UEA Repository

(Article)


Zhou, Z., McCann, A., Weill, F., Blin, C., Nair, S., Wain, J., Dougan, G., Achtman, M., Genes, Bacterial, Polymorphism, Single Nucleotide, Selection, Genetic

(2014)

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

in Proceedings of the National Academy of Sciences of the United States of America (PNAS)

111.

pp. 12199-204

Full Text UEA Repository

(Article)


Tamayo, E., Almansa, R., Carrasco, E., Avila-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, J. I. G., Eiros, J. M., Bermejo-Martin, J. F.

(2014)

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

in Critical care (London, England)

18.

pp. 433

Full Text UEA Repository

(Article)


Nair, S., Wain, J., Connell, S., de Pinna, E., Peters, T., Child, Preschool, Drug Resistance, Bacterial

(2014)

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

in Journal of Medical Microbiology

63.

pp. 831-4

Full Text UEA Repository

(Article)


Dallman, T. J., Chattaway, M. A., Cowley, L. A., Doumith, M., Tewolde, R., Wooldridge, D. J., Underwood, A., Ready, D., Wain, J., Foster, K., Grant, K. A., Jenkins, C.

(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

in PLoS ONE

9.

pp. e98103

Full Text UEA Repository

(Article)


Lawson, B., de Pinna, E., Horton, R. A., Macgregor, S. K., John, S. K., Chantrey, J., Duff, J. P., Kirkwood, J. K., Simpson, V. R., Robinson, R. A., Wain, J., Cunningham, A. A.

(2014)

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

in PLoS ONE

9.

pp. e88968

Full Text UEA Repository

(Article)


Parry, C. M., Thompson, C., Vinh, H., Chinh, N. T., Phuong, L. T., Ho, V. A., Hien, T. T., Wain, J., Farrar, J. J., Baker, S., Drug Resistance, Multiple

(2014)

Risk factors for the development of severe typhoid fever in Vietnam

in BMC Infectious Diseases

14.

pp. 73

Full Text UEA Repository

(Article)


Byrne, L., Elson, R., Dallman, T. J., Perry, N., Ashton, P., Wain, J., Adak, G. K., Grant, K. A., Jenkins, C.

(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

in PLoS ONE

9.

pp. e85901

Full Text UEA Repository

(Article)


Almansa, R., Wain, J., Tamayo, E., Andaluz-Ojeda, D., Martin-Loeches, I., Ramirez, P., Bermejo-Martin, J.

(2013)

Immunological monitoring to prevent and treat sepsis

in Critical Care

17.

pp. 109

Full Text UEA Repository

(Article)


Stone, M., Wain, J., Ivens, A., Feltwell, T., Kearns, A., Bamford, K.

(2013)

Harnessing the genome: development of a hierarchical typing scheme for meticillin-resistant Staphylococcus aureus

in Journal of Medical Microbiology

62.

pp. 36-45

Full Text UEA Repository

(Article)


Underwood, A., Dallman, T., Thomson, N., Williams, M., Harker, K., Perry, N., Adak, B., Willshaw, G., Cheasty, T., Green, J., Dougan, G., Parkhill, J., Wain, J.

(2013)

Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak

in Journal of Clinical Microbiology

51.

pp. 232-237

Full Text UEA Repository

(Article)


Wain, J., Mavrogiorgou, E., Sequence Analysis, DNA

(2013)

Next-generation sequencing in clinical microbiology

in Expert Review of Molecular DIagnostics

13.

pp. 225-227

Full Text UEA Repository

(Article)


Wain, J., Keddy, K., Hendriksen, R., Rubino, S.

(2013)

Using next-generation sequencing to tackle non-typhoidal Salmonella infections

in Journal of infection in developing countries

7.

pp. 1-5

Full Text UEA Repository

(Article)


Livermore, D. M., Wain, J.

(2013)

Revolutionising bacteriology to improve treatment outcomes and antibiotic stewardship

in Infection & Chemotherapy

45.

pp. 1-10

Full Text UEA Repository

(Article)


Barquist, L., Langridge, G., Turner, D. J., Phan, M., Turner, A., Wain, J., Bateman, A., Parkhill, J., Gardner, P.

(2013)

A comparison of dense transposon insertion libraries in the Salmonella serovarsThypi and Typhimurium

in Nucleic Acids Research

41.

pp. 4549-4564

Full Text UEA Repository

(Article)


Pearson, B. M., Rokney, A., Crossman, L. C., Miller, W. G., Wain, J., van Vliet, A. H. M.

(2013)

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

in Genome announcements

1.

Full Text UEA Repository

(Article)


Bronowski, C., Fookes, M. C., Gilderthorp, R., Ashelford, K. E., Harris, S. R., Phiri, A., Hall, N., Gordon, M. A., Wain, J., Hart, C. A., Wigley, P., Thomson, N. R., Winstanley, C.

(2013)

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

in PLoS Neglected Tropical Diseases

7.

pp. e2557

Full Text UEA Repository

(Article)


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Key Research Interests

My research is centred on the use of new technologies in clinical and public health microbiology; in particular the development of sequence based tools for molecular epidemiology and bacterial identification. I have a long standing interest in Salmonella particularly Salmonella Typhi and in the biological impact of acquired antibiotic resistance. I work within the translational microbiology group at UEA which has an overarching program to improve clinical diagnosis of infectious disease through the development of new techniques for nucleic acid extraction and sequencing. In collaboration with TGAC we are also pioneering bioinformatic analyses to identify and type pathogens. A major challenge is to predict the antibiotic susceptibility of bacteria and to understand the “normal flora” of sterile sites. I also maintain a keen interest in the use of new technology in countries with developing economies and have research collaborations in India, China, South Africa and Ethiopia.

In the past: My research has described the influence of reduced ciprofloxacin resistance on the clinical outcome of typhoid fever patients; linked resistance plasmids and virulence; defined the role of global regulators in the acquisition of resistance plasmids; I initiated the first genome sequencing project for Salmonella; and I pioneered next generation sequencing as a routine method for the molecular epidemiology of gastrointestinal pathogens.

My first PhD student developed the Multi Locus Sequence Typing scheme for Salmonella and my most recent developed the transposon insertion method known as TraDIS.

Research Keywords: Next generation sequencing, The acquisition of antibiotic resistance, The microbiology of Salmonella, Molecular epidemiology of IncH plasmids

Research Topics for PGR SupervisionSalmonella 

Selected Publications

1.     L Barquist, GC Langridge, DJ Turner, MD Phan, AK Turner, A Bateman, J Wain… (2013) A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic acids research 41 (8), 4549-456

 2.     Achtman M, Wain J, Weill FX, Nair S, Zhou Z, Sangal V, Krauland MG, Hale JL, Harbottle H, Uesbeck A, Dougan G, Harrison LH, Brisse S (2012) Multilocus sequence typing as a replacement for serotyping in Salmonella enterica. PLoS Pathog 8: e1002776 (joint first author - no senior author) 

3.     Holt KE, Phan MD, Baker S, Duy PT, Nga TV, Nair S, Turner AK, Walsh C, Fanning S, Farrell-Ward S, Dutta S, Kariuki S, Weill FX, Parkhill J, Dougan G, Wain J (2011) Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid. PLoS Negl Trop Dis 5: e1245. 

4.     Beyene G, Nair S, Asrat D, Mengistu Y, Engers H, Wain J (2011) Multidrug resistant Salmonella Concord is a major cause of salmonellosis in children in Ethiopia. J Infect Dev Ctries 5: 23-33. (highly cited for developing country work) 

5.     Phan MD, Kidgell C, Nair S, Holt KE, Turner AK, Hinds J, Butcher P, Cooke FJ, Thomson NR, Titball R, Bhutta ZA, Hasan R, Dougan G, Wain J (2009) Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever. Antimicrob Agents Chemother 53: 716-727. (one of the two top antibiotic resistance journals)

6.     Okeke IN, Wain J (2008) Post-genomic challenges for collaborative research in infectious diseases. Nat Rev Microbiol 6: 858-864. 

7.     Turner AK, Nair S, Wain J (2006) The acquisition of full fluoroquinolone resistance in Salmonella Typhi by accumulation of point mutations in the topoisomerase targets. J Antimicrob Chemother 58: 733-740. (one of the two top antibiotic resistance journals) 

8.     Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30: 434-439. 

9.     Langridge GC, Phan MD, Turner DJ, Perkins TT, Parts L, Haase J, Charles I, Maskell DJ, Peters SE, Dougan G, Wain J, Parkhill J, Turner AK (2009) Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res 19: 2308-2316. (very highly cited paper) 

10.  Doyle M, Fookes M, Ivens A, Mangan MW, Wain J, Dorman CJ (2007) An H-NS-like stealth protein aids horizontal DNA transmission in bacteria. Science 315: 251-252
 

Teaching Interests

I have an active interest in teaching both under and post graduate students. I currently supervise three PhD students, two MSc students and there are usually two or three undergraduate students working it the laboratory. I am a keen supporter of problem based learning.

External Activities and Indicators of Esteem

  • Key note speaker at the annual Health Protection Agency Conference “Microbial diversity and infectious disease epidemiology”, September 2012 - one of many invited speaker engagements at international conferences
  • Organiser “One Bug, One Drug” Conference, Cambridge, September 2012 and September 2013, http://www.discuva.com/newsevents/events/
  • Steering committee member for the NIHR, UK funded project: 'The clinical diagnostic accuracy of rapid detection of healthcare associated bloodstream infection in intensive care using multipathogen real-time PCR technology', 2013
  • Member of the directorate of the Institute for Food Research, 2013
  • Honorary contracts with Public Health England and Norfolk and Norwich University Teaching Hospitals, 2013
  • Visiting professor at the University of Sassari and Honorary academic at University College, London, 2011
  • Founding Editor of the Journal of Infection in Developing Countries2008, www.jidc.org

Professional Activities

  • Co-founder of the community interest company JIDCuk, 2010
  • Co-founder, CSO and director of Discuva Ltd, 2011, www.discuva.com
  • Co-founder, CSO and director of Bactevo Ltd, 2013, www.bactevo.com
  • Advisor to the Chief Medical Officer on new research call for public health, 2012
  • Advisor to the Chief Medical Officer on the CMOs annual report on infectious diseases, 2013
  • Devised and delivered “build-a-bug” activity for sixth form students, 2006, http://www.nationalstemcentre.org.uk/elibrary/resource/5287/build-a-bug-activity

Key Responsibilities

Advisor to three MBBS degree students.