Professor Alan McNally BSc PhD

Alan McNally

Institute of Microbiology and Infection
Professor in Microbial Evolutionary Genomics
Director of Institute of Microbiology and Infection within the College of Medical and Dental Sciences

Contact details

Institute of Microbiology and Infection
College of Medical and Dental Sciences
University of Birmingham
B15 2TT

Alan McNally is a Professor in Microbial Genomics and works on the evolutionary genomics of pathogenesis and antimicrobial resistance in bacterial pathogens.  Alan has also been funded by the European Union, Medical Research Council and Royal Society.

Alan has a strong belief in the collaborative nature of genomics research with active collaborations in the UK, China, Germany, France, Vietnam, and the US.

During the COVID-19 outbreak, Alan was seconded to the Milton Keynes Lighthouse Lab as Infectious Disease lead at the Government’s first flagship COVID-19 testing facility. Launched on 9 April 2020, the Milton Keynes Lighthouse Lab was the first of three Government ‘mega-labs’ to be set-up across the UK, vastly increasing testing capacity and allowing tens of thousands more patient samples to be processed each day.


  • PhD Molecular Microbiology, University of Edinburgh Royal (Dick) Vet Shool, 1999-2003
  • BSc Hons 2.i Molecular Microbiology with work placement, University of Glasgow, 1994-1999


Alan McNally began his scientific career studying molecular microbiology at University of Glasgow, including a year’s placement at SmithKline Beecham in Hertfordshire. He then went on to do a PhD studying gene regulation in E. coli O157 with Prof David Gally at University of Edinburgh. A short post-doc in microbial biochemistry at Bristol was followed by two post-doctoral projects at the Veterinary Laboratories Agency in Surrey. It was here whilst working on H5N1 avian influenza that Alan developed an interest in phylogenetics and evolution, which he developed in his first academic PI position at Nottingham Trent University. During 10 succesful years Alan established his group as an internationally renowned group studying microbial genomics and evolution, leading to him joining the IMI in September 2016.


Teaching Programmes

Postgraduate supervision

Alan has successfully supervised 9 PhD students. He is interested to hear from students interested in undertaking a PhD in the fields of:

  • Population genomics of multi-drug resistant E. coli
  • Evolution of antimicrobial resistance in gram negative pathogens
  • Evolution of pathogenesis in the Yersinia genus
  • Experimental evolution of MDR plasmid carriage in gram negative pathogens

If you are interested in studying any of these subject areas please contact Prof Alan McNally directly, or
for any general doctoral research enquiries, please email

For a full list of available Doctoral Research opportunities, please visit our Doctoral Research programme listings  


E. coli

We work on extra-intestinal pathogenic E. coli, or ExPEC. These are now the most common cause of drug-resistant infections worldwide, and the most common cause of hospital associated infections. 

ExPEC Genomics

We study population genomics of the predominant sequence types associated with extra-intestinal infections in humans, in particular ST131, ST73 and ST95. By doing this we hope to determine how these STs have become the dominant causative agents of human disease from the enormous population of E. coli. We also hope to be able to use this data to inform phylogenetic based epidemiology of these bacteria, better informing us how multi-drug resistant bacteria transmit in the hospital and community setting.

Classical bacterial pathogenesis

We also translate our genomic data into biological relevance, by attributing observations in our genome data to particular phenotypes. In particular we are interested in metabolic differences between ExPEC clades, and also differences in their transmission and environmental survival strategies.


We also work on the enteropathogenic members of the Yersinia genus. Again we use genomics data to investigate the evolution of pathogenesis in this model bacterial genus. We also have a keen interest in studying localised short term evolution in subsets of the enteropathogenic species.

As with ExPEC our goal is to marry the genomic data with differential phenotype data across population sets. To do this we heavily employ classical bacterial genetics techniques with surrogate infection models, in particular Galleria mellonella.

Other activities

  • Elected member of the Microbiology Society Prokaryotic Division since 2012
    Alan is now in his second elected term having organised several key symposia for the society annual conference
  • Editor for the society journal Microbial Genomics


Recent publications


The COVID-19 Genomics UK (COG-UK) Consortium & McNally, A 2021, 'Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England', Nature, vol. 593, no. 7858, pp. 266–269.

Zong, Z, Feng, Y & McNally, A 2021, 'Carbapenem and colistin resistance in Enterobacter: determinants and clones', Trends in Microbiology, vol. 29, no. 6, pp. 473-476.

COVID-19 Genomics UK (COG-UK) Consortium 2021, 'Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study', The Lancet. Public health, vol. 6, no. 5, pp. e335-e345.

Kantele, A, Kuenzli, E, Dunn, SJ, Dance, DAB, Newton, PN, Davong, V, Mero, S, Pakkanen, SH, Neumayr, A, Hatz, C, Snaith, A, Kallonen, T, Corander, J & McNally, A 2021, 'Dynamics of intestinal multidrug-resistant bacteria colonisation contracted by visitors to a high-endemic setting: a prospective, daily, real-time sampling study', The Lancet. Microbe, vol. 2, no. 4, pp. e151-e158.

Gladstone, RA, McNally, A, Pöntinen, AK, Tonkin-Hill, G, Lees, JA, Skytén, K, Cléon, F, Christensen, MOK, Haldorsen, BC, Bye, KK, Gammelsrud, KW, Hjetland, R, Kümmel, A, Larsen, HE, Lindemann, PC, Löhr, IH, Marvik, Å, Nilsen, E, Noer, MT, Simonsen, GS, Steinbakk, M, Tofteland, S, Vattøy, M, Bentley, SD, Croucher, NJ, Parkhill, J, Johnsen, PJ, Samuelsen, Ø & Corander, J 2021, 'Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study', The Lancet Microbe, vol. 2, no. 7, pp. e331-e341.

Hall, RJ, Whelan, FJ, Cummins, EA, Connor, C, McNally, A & McInerney, JO 2021, 'Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility', Microbial Genomics, vol. 7, no. 9, 000650.

Dunn, S, Carrilero, L, Brockhurst, M & McNally, A 2021, 'Limited and strain-specific transcriptional and growth responses to acquisition of a multidrug resistance plasmid in genetically diverse Escherichia coli lineages', mSystems, vol. 6, no. 2, e00083-21.

Papakonstantinou, D, Dunn, SJ, Draper, SJ, Cunningham, AF, O’Shea, MK, McNally, A & Achkar, JM (ed.) 2021, 'Mapping gene-by-gene single-nucleotide variation in 8,535 Mycobacterium tuberculosis genomes: a resource to support potential vaccine and drug development', mSphere, vol. 6, no. 2, e01224-20.

The COVID-19 Genomics UK (COG-UK) Consortium, Meng, B, Kemp, SA, Papa, G, Datir, R, Ferreira, IATM, Marelli, S, Harvey, WT, Lytras, S, Mohamed, A, Gallo, G, Thakur, N, Collier, DA, Mlcochova, P, Duncan, LM, Carabelli, AM, Kenyon, JC, Lever, AM, De Marco, A, Saliba, C, Culap, K, Cameroni, E, Matheson, NJ, Piccoli, L, Corti, D, James, LC, Robertson, DL, Bailey, D & Gupta, RK 2021, 'Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7', Cell Reports, vol. 35, no. 13, 109292.

Kidd, M, Richter, A, Best, A, Cumley, N, Mirza, J, Percival, B, Mayhew, M, Megram, O, Ashford, F, White, T, Moles-Garcia, E, Crawford, L, Bosworth, A, Atabani, SF, Plant, T & McNally, A 2021, 'S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR', The Journal of Infectious Diseases.

Wei, L, Wu, L, Wen, H, Feng, Y, Zhu, S, Liu, Y, Tang, L, Doughty, E, van Schaik, W, McNally, A & Zong, Z 2021, 'Spread of carbapenem-resistant Klebsiella pneumoniae in an intensive care unit: a whole-genome sequence-based prospective observational study', Microbiology spectrum, vol. 9, no. 1, e00058-21.

Liu, H, Moran, RA, Chen, Y, Doughty, EL, Hua, X, Jiang, Y, Xu, Q, Zhang, L, Blair, JMA, McNally, A, Schaik, WV & Yu, Y 2021, 'Transferable Acinetobacter baumannii plasmid pDETAB2 encodes OXA-58 and NDM-1 and represents a new class of antibiotic resistance plasmids', Journal of Antimicrobial Chemotherapy, vol. 76, no. 5, pp. 1130-1134.

Ferguson, J, Dunn, S, Best, A, Mirza, J, Percival, B, Mayhew, M, Megram, O, Ashford, F, White, T, Moles-Garcia, E, Crawford, L, Plant, T, Bosworth, A, Kidd, M, Richter, A, Deeks, J & McNally, A 2021, 'Validation testing to determine the sensitivity of lateral flow testing for asymptomatic SARS-CoV-2 detection in low prevalence settings: testing frequency and public health messaging is key', PLoS Biology, vol. 19, no. 4, e3001216.

Azimi, S, Roberts, AEL, Peng, S, Weitz, JS, McNally, A, Brown, SP & Diggle, SP 2020, 'Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations', The ISME Journal.


McNally, A 2021, 'What makes new variants of SARS-CoV-2 concerning is not where they come from, but the mutations they contain', BMJ, vol. 372, n504.

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