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An Interdisciplinary Research Centre at the University of Cambridge


Postdoctoral Researcher

Pathogen genomics

I graduated with a BSc (Hons) in Biology and a MRes in Bioinformatics from the University of York in 2006 and 2007 respectively.  Following three years working as a genome analyst at the Wellcome Sanger Institute, I moved to the University of Oxford as a research assistant in the Brueggemann lab in the Department of Zoology.  This position transitioned into a DPhil in Clinical Medicine focusing on pneumococcal genomics and evolution.  Following my graduation in 2017, I took up a post as a postdoctoral fellow in the Parkhill group at the Wellcome Sanger Institute working on Mycobacterium bovis transmission dynamics and evolution, and non-tuberculous mycobacteria in cystic fibrosis and bronchiectasis patients.  In June 2019, the Parkhill group moved to the Department of Veterinary Medicine where I’m currently based.


Key publications: 

van Tonder AJ, Bray JE, Quirk SJ, Haraldsson G, Jolley KA, Maiden MCJ, Hoffmann S, Bentley SD, Haraldsson A, Erlendsdóttir H, Kristinsson KG, Brueggemann AB. 2016. Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes.  Microbial Genomics 2(10). doi: 10.1099/mgen.0.000090.


van Tonder AJ, Bray JE, Roalfe L, White R, Zancolli M, Quirk SJ, Haraldsson G, Jolley KA, Maiden MC, Bentley SD, Haraldsson Á, Erlendsdóttir H, Kristinsson KG, Goldblatt D, Brueggemann AB. 2015. Genomics reveals the worldwide distribution of multidrug-resistant serotype 6E pneumococci. J Clin Microbiol. 53(7):2271-85. doi: 10.1128/JCM.00744-15.


van Tonder AJ, Mistry S, Bray JE, Hill DM, Cody AJ, Farmer CL, Klugman KP, von Gottberg A, Bentley SD, Parkhill J, Jolley KA, Maiden MC, Brueggemann AB.  2014. Defining the estimated core genome of bacterial populations using a Bayesian decision model. PLoS Comput Biol10(8):e1003788. doi: 10.1371/journal.pcbi.1003788

Other publications: 

Quirk SJ, Haraldsson G, Erlendsdóttir H, Hjálmarsdóttir MÁ, van Tonder AJ, Hrafnkelsson B, Sigurðsson S, Bentley SD, Haraldsson Á, Brueggemann AB, Kristinsson KG. 2018. Effect of vaccination on pneumococci isolated from the nasopharynx of healthy children and the middle ear of children with otitis media in Iceland. J Clin Microbiol. doi: 10.1128/JCM.01046-18


Tiwari S, van Tonder AJ, Vilchèze C, Mendes V, Thomas SE, Malek A, Chen B, Chen M, Kim J, Blundell TL, Parkhill J, Weinrick B, Berney M, Jacobs WR Jr. 2018. Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis. Proc Natl Acad Sci. doi: 10.1073/pnas.1808874115


Rezaei Javan R, van Tonder AJ, King JP, Harrold CL, Brueggemann AB. 2018. Genome sequencing reveals a large and diverse repertoire of antimicrobial peptides. Front. Microbiol. doi: 10.3389/fmicb.2018.02012


Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD, Page AJ, Keane JA. 2018. SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data. Microbial Genomics. doi: 10.1099/mgen.0.000186


Lo SW, Gladstone RA, van Tonder AJ, Hawkins PA, Kwambama-Adams B, Cornick JE, Madhi SA, Nzenze SA, du Plessis M, Kandasamy R, Carter PE, Koseoglu Eser O, Leungo Ho P, Elmdaghri N, Shakoor S, Clarke SC, Antonio M, Everett DB, von Gottberg A, Klugman KP, McGee L, Breiman RF, Bentley SD, Global Pneumococcal Sequencing Consortium. 2018 Global distribution of invasive serotype 35D Streptococcus pneumoniae post-PCV13 introduction. J Clin Microbiol. 00228-18.


Kurioka A, van Wilgenburg B, Rezaei Javan R, Hoyle R, van Tonder AJ, Harrold CL, Leng T, Howson LJ, Shepherd D, Cerundolo V, Brueggemann AB, Klenerman P. 2017. Diverse Streptococcus pneumoniae strains drive a MAIT cell response through MR1-dependent and cytokine-driven pathways.  The Journal of Infectious Diseases, jix647.


Brueggemann AB, Harrold CL, Rezaei Javan R, van Tonder AJ, McDonnell AJ, Edwards BA. 2017. Pneumococcal prophages are diverse, but not without structure or history. Scientific Reports 7. doi: 10.1038/srep42976


Bogaardt C, van Tonder AJ, Brueggemann AB. 2015. Genomic analyses of pneumococci reveal a wide diversity of bacteriocins - including pneumocyclicin, a novel circular bacteriocin.  BMC Genomics 16(1):554. doi: 10.1186/s12864-015-1729-4.


Olasz F, Nagy T, Szabó M, Kiss J, Szmolka A, Barta E, van Tonder A, Thomson N, Barrow P, Nagy B. 2015. Genome sequences of three Salmonella enterica subsp. enterica serovar Infantis strains from healthy broiler chicks in Hungary and in the United Kingdom. Genome Announc. 3(1). pii: e01468-14. doi: 10.1128/genomeA.01468-14.


Wyres KL, van Tonder A, Lambertsen LM, Hakenbeck R, Parkhill J, Bentley SD, Brueggemann, AB. 2013. Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974.  BMC Genomics 14(500).  doi: 10.1186/1471-2164-14-500.



Kos VN, Desjardins CA, Griggs A, Cerqueira G, van Tonder A, Holden MT, Godfrey P, Palmer KL, Bodi K, Mongodin EF, Wortman J, Feldgarden M, Lawley T, Gill SR, Haas BJ, Birren B, Gilmore MS.  2012 Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with methicillin-resistant S. aureus hospital-acquired infection in the United States.  MBio3(3). pii: e00112-12. doi: 10.1128/mBio.00112-12.


Hauser H, Richter D, van Tonder A, Clark, L, Preston A. 2012.  Comparative genomic analyses of the TaylorellaeVeterinary Microbiology 159(1-2): 195-203.


Strouts FR, Power P, Croucher NJ, Corton N, van Tonder A, Quail MA, Langford PR, Hudson MJ, Parkhill J, Kroll JS, Bentley SD. 2012. Lineage-specific virulence determinants of Haemophilus influenzae biogroup aegyptiusEmerging Infectious Diseases 18(3): 449-457.


Jackson AP, Berry A, Aslett M, Allison HC, Burton P, Vavrova-Anderson J, Brown R, Browne H, Corton N, Hauser H, Gamble J, Gilderthorp R, Marcello L, McQuillan J, Otto TD, Quail MA, Sanders MJ, van Tonder A, Ginger ML, Field MC, Barry JD, Hertz-Fowler C, Berriman M. 2012. Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species.  Proc. Natl Acad. Sci. 109(9):3416-21.


Heilbronner S, Holden MT, van Tonder A, Geoghegan JA, Foster TJ, Parkhill J, Bentley SD. 2011. Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors. FEMS Microbiol. Lett. 322(1):60-7.


Pickard D, Toribio AL, Petty NK, van Tonder A, Yu L, Goulding D, Barrell B, Rance R, Harris D, Wetter M, Wain J, Choudhary J, Thomson N, Dougan G. 2010  A conserved acetyl esterase domain targets diverse bacteriophages to the Vi capsular receptor of Salmonella enterica serovar Typhi. J Bacteriol. 192(21):5746-54.


He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, Martin MJ, Holt KE, Seth-Smith HM, Quail MA, Rance R, Brooks K, Churcher C, Harris D, Bentley SD, Burrows C, Clark L, Corton C, Murray V, Rose G, Thurston S, van Tonder A, Walker D, Wren BW, Dougan G, Parkhill J. 2010.  Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc. Natl Acad. Sci. 107(16):7527-32.

Postdoctoral fellow, Department of Veterinary Medicine
Pathogen genomics; Streptococcus pneumoniae (pneumococcus) and various Mycobacterium species.
Dr Andries J Van Tonder
Not available for consultancy


Departments and institutes: 
Person keywords: 
Pathogen Evolution
Host-Pathogen Interaction
Molecular epidemiology
Antimicrobial resistance
Cross-species transmission