Dr Alan McNally BSc PhD

Image of Alan McNally

Institute of Microbiology and Infection
Senior Lecturer in Microbial Genomics

Contact details

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

Alan McNally is Senior Lecturer in Microbial Genomics, a position he took up in September 2016. Alan works on the evolutionary genomics of pathogenesis and antimicrobial resistance in bacterial pathogens and has 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.


  • PhD Molecular Microbiology, University of Edinburgh Royal (Dick) Vert 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.

For further information visit: www.alanmcnally.com


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 Alan on the contact details above, or for any general doctoral research enquiries, please email: dr@contacts.bham.ac.uk or call +44 (0)121 414 5005.

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


McNally A, Oren Y, Kelly D, Pascoe B, Dunn S, Sreecharan T, Vehkala M, Välimäki N, Prentice MB, Ashour A, Avram O, Pupko T, Dobrindt U, Literak I, Guenther S, Schaufler K, Wieler LH, Zhiyong Z, Sheppard SK, McInerney JO and Corander J (2016) Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations. PLoS Genet 12(9):e1006280

Alenizi D, Ringwood T, Redhwan A, Bouraha B, Wren BW, Prentice M and McNally A (2016) All Yersinia enterocolitica are pathogenic: Virulence of phylogroup 1 Y. enterocolitica in a Galleria mellonella infection modelMicrobiology 162(8):1379-87

McNally A, Thomson NR, Reuter S and Wren BW (2016) 'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution. Nat Rev Microbiol 14(3):177-90

Alhashash F, Wang X, Paszkiewicz K, Diggle M, Zong Z and McNally A (2016) Increase in bacteraemia cases in the East Midlands region of the UK due to MDR Escherichia coli ST73: high levels of genomic and plasmid diversity in causative isolates. J Antimicrob Chemother 71(2):339-43

Baig A, McNally A, Dunn S, Paszkiewicz KH, Corander J and Manning G7 (2015) Genetic import and phenotype specific alleles associated with hyper-invasion in Campylobacter jejuni. BMC Genomics 16(1):852

Feng Y, Yang P, Xie Y, Wang X, McNally A and Zong Z (2015) Escherichia coli of sequence type 3835 carrying blaNDM-1, blaCTX-M-15, blaCMY-42 and blaSHV-12. Sci Rep 5:12275

Morley L, McNally A, Paszkiewicz K, Corander J, Méric G, Sheppard SK, Blom J and Manning G (2015) Gene loss and lineage-specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni sequence type 403 clonal complex. Appl Environ Microbiol 81(11):3641-7

Darch SE, McNally A, Harrison F, Corander J, Barr HL, Paszkiewicz K, Holden S, Fogarty A, Crusz SA and Diggle SP (2015) Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection. Sci Rep 5:7649

Reuter S, Corander J, de Been M, Harris S, Cheng L, Hall M, Thomson NR and McNally A (2015) Directional gene flow and ecological separation in Yersinia enterocolitica. Microbial Genomics 1

Hall M, Chattaway MA, Reuter S, Savin C, Strauch E, Carniel E, Connor T, Van Damme I, Rajakaruna L, Rajendram D, Jenkins C, Thomson NR and McNally A (2015) Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels. J Clin Microbiol 53(1):35-42

Alqasim A, Scheutz F, Zong Z and McNally A (2014) Comparative genome analysis identifies few traits unique to the Escherichia coli ST131 H30Rx clade and extensive mosaicism at the capsule locus. BMC Genomics 15(1):830

Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, Corander J, Dufour M, Ringwood T, Savin C, Bouchier C, Martin L, Miettinen M, Shubin M, Riehm JM, Laukkanen-Ninios R, Sihvonen LM, Siitonen A, Skurnik M, Falcão JP, Fukushima H, Scholz HC, Prentice MB, Wren BW, Parkhill J, Carniel E, Achtman M, McNally A and Thomson NR (2014) Parallel independent evolution of pathogenicity within the genus Yersinia. Proc Natl Acad Sci U S A 111(18):6768-73

Alqasim A, Emes R, Clark G, Newcombe J, La Ragione R and McNally A (2014) Phenotypic microarrays suggest Escherichia coli ST131 is not a metabolically distinct lineage of extra-intestinal pathogenic E. coli. PloS One 9(2):e88374