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 School, 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

  • BMedSc - years 2 and 3

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


Ba, X, Guo, Y, Moran, RA, Doughty, EL, Liu, B, Yao, L, Li, J, He, N, Shen, S, Li, Y, van Schaik, W, Mcnally, A, Holmes, MA & Zhuo, C 2024, 'Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone', Nature Communications, vol. 15, no. 1, 494.

Pöntinen, AK, Gladstone, RA, Pesonen, H, Pesonen, M, Cléon, F, Parcell, BJ, Kallonen, T, Simonsen, GS, Croucher, NJ, McNally, A, Parkhill, J, Johnsen, PJ, Samuelsen, Ø & Corander, J 2024, 'Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study', The Lancet. Microbe.

Hall, RJ, Snaith, AE, Thomas, MJN, Brockhurst, MA & McNally, A 2024, 'Multidrug resistance plasmids commonly reprogram the expression of metabolic genes in Escherichia coli', mSystems, vol. 9, no. 3, e0119323.

Hall, RJ, Snaith, AE, Element, SJ, Moran, RA, Smith, H, Cummins, EA, Bottery, MJ, Chowdhury, KF, Sareen, D, Ahmad, I, Blair, JMA, Carter, LJ & McNally, A 2024, 'Non-antibiotic pharmaceuticals are toxic against Escherichia coli with no evolution of cross-resistance to antibiotics', npj Antimicrobials and Resistance, vol. 2, no. 1, 11 .

Quarton, S, McGee, K, Cumley, N, Behruznia, M, Jeff, C, Belchamber, K, Cox, M, Thickett, D, Scott, A, Parekh, D, McNally, A & Sapey, E 2024, 'Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol', PLoS ONE, vol. 19, no. 3, e0298425.

Pugh, HL, Connor, C, Siasat, P, McNally, A & Blair, JMA 2023, 'E. coli ST11 (O157:H7) does not encode a functional AcrF efflux pump', Microbiology, vol. 169, no. 4, 001324.

Doughty, EL, Liu, H, Moran, RA, Hua, X, Ba, X, Guo, F, Chen, X, Zhang, L, Holmes, M, van Schaik, W, McNally, A & Yu, Y 2023, 'Endemicity and diversification of carbapenem-resistant Acinetobacter baumannii in an intensive care unit', The Lancet regional health. Western Pacific, vol. 37, 100780.

Arredondo-Alonso, S, Blundell-Hunter, G, Fu, Z, Gladstone, RA, Fillol-Salom, A, Loraine, J, Cloutman-Green, E, Johnsen, PJ, Samuelsen, Ø, Pöntinen, AK, Cléon, F, Chavez-Bueno, S, De la Cruz, MA, Ares, MA, Vongsouvath, M, Chmielarczyk, A, Horner, C, Klein, N, McNally, A, Reis, JN, Penadés, JR, Thomson, NR, Corander, J, Taylor, PW & McCarthy, AJ 2023, 'Evolutionary and functional history of the Escherichia coli K1 capsule', Nature Communications, vol. 14, no. 1, 3294 .

Carrilero, L, Dunn, SJ, Moran, RA, McNally, A & Brockhurst, MA 2023, 'Evolutionary responses to acquiring a multidrug resistance plasmid are dominated by metabolic functions across diverse Escherichia coli lineages', mSystems.

Moran, RA, Baomo, L, Doughty, EL, Guo, Y, Ba, X, van Schaik, W, Zhuo, C & McNally, A 2023, 'Extended-Spectrum β-Lactamase Genes Traverse the Escherichia coli Populations of Intensive Care Unit Patients, Staff, and Environment', Microbiology spectrum, vol. 11, no. 2, e0507422.

Ma, K, Feng, Y, McNally, A & Zong, Z 2023, 'Hijacking a small plasmid to confer high-level resistance to aztreonam-avibactam and ceftazidime-avibactam', International Journal of Antimicrobial Agents.

Connor, CH, Zucoloto, AZ, Munnoch, JT, Yu, I, Corander, J, Hoskisson, PA, Mcdonald, B & Mcnally, A 2023, 'Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract', PLoS Biology, vol. 21, no. 10, e3002329.

Cummins, EA, Moran, RA, Snaith, AE, Hall, RJ, Connor, CH, Dunn, SJ & McNally, A 2023, 'Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages', Microbial Genomics, vol. 9, no. 11, 001133.

Review article

Fang, Q, Ying, X, He, Y, Feng, Y, Zhang, L, Luo, H, Yin, G, McNally, A & Zong, Z 2024, 'Safety and efficacy of phage application in bacterial decolonisation: a systematic review', The Lancet. Microbe.

Yang, Y, Yan, Y-H, Schofield, CJ, McNally, A, Zong, Z & Li, G-B 2023, 'Metallo-β-lactamase-mediated antimicrobial resistance and progress in inhibitor discovery', Trends in Microbiology.

View all publications in research portal