Andries van Tonder, DPhil

Edao B, Ameni G, Berg S, Tekle M, Whatmore AM, Wood JLN, van Tonder AJ, Ashford RT. 2023. Whole genome sequencing of Ethiopian Brucella abortus isolates expands the known diversity of an early branching sub-Saharan African lineage. Front. Microbiol. doi: 10.3389/fmicb.2023.1128966.

van Tonder AJ, McCullagh F, McKeand H, Thaw S, Bellis K, Raisen C, Lay E, Aggarwal D, Holmes M, Parkhill J, Harrison EM, Kucharski A, Conlan A.  2023. Colonization and transmission of Staphylococcus aureus in schools: a citizen science project. Microb Genom. doi: 10.1099/mgen.0.000993

Ganaie FA, Saad JS, Lo SW, McGee L, Bentley SD, van Tonder AJ, Hawkins P, Keenan JD, Calix JJ, Nahm MH. 2023. Discovery and Characterization of Pneumococcal Serogroup 36 Capsule Subtypes, Serotypes 36A and 36B. J Clin Microbiol. doi: 10.1128/jcm.00024-23.

Hadjirin NF, van Tonder AJ, Blane B, Lees JA, Kumar N, Delappe N, Brennan W, McGrath E, Parkhill J, Cormican M, Peacock SJ, Ludden C. 2023. Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study. Microb Genom. doi: 10.1099/mgen.0.000924.

Farzana R, Jones LS, Rahman MA, Sands K, van Tonder AJ, Portal E, Criollo JM, Parkhill J, Guest MF, John Watkins W, Pervin M, Boostrom I, Hassan B, Mathias J, Kalam MA, Walsh TR. 2023. Genomic insights into the mechanism of carbapenem resistance dissemination in Enterobacterales from a tertiary public heath setting in South Asia. Clin Infect Dis. doi: 10.1093/cid/ciac287

van Tonder AJ, Ellis HC, Churchward CP, Kumar K, Ramadan N, Benson S, Parkhill J, Moffatt MF, Loebinger MR, Cookson WO. 2022. Mycobacterium avium complex (MAC) genomics and transmission in a London hospital. Eur Respir J. doi: 10.1183/13993003.01237-2022

Gladstone RA, Siira L, Brynildsrud OB, Vestrheim DF, Turner P, Clarke SC, Srifuengfung S, Ford R, Lehmann D, Egorova E, Voropaeva E, Haraldsson G, Kristinsson KG, McGee L, Breiman RF, Bentley SD, Sheppard CL, Fry NK, Corander J, Toropainen M, Steens A, Global Pneumococcal Sequencing Consortium. 2022. International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease. Vaccine doi: 10.1016/j.vaccine.2021.10.046

van Tonder AJ, Thornton MJ, Conlan AJK, Jolley KA, Goolding L, Mitchell AP, Dale J, Palkopoulou E, Hogarth PJ, Hewinson RG, Wood JLN, Parkhill J. 2021. Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial. PLoS Pathog. doi: 10.1371/journal.ppat.1010075

Beaudoin CA, Jamasb AR, Alsulami AF, Copoiu L, van Tonder AJ, Hala S, Bannerman BP, Thomas SE, Vedithi SC, Torres PHM, Blundell TL. 2021. Predicted structural mimicry of spike receptor-binding motifs from highly pathogenic human coronaviruses. Comput Struct Biotechnol J doi: 10.1016/j.csbj.2021.06.041

Rodrigues R, Araujo F, Dávila A, Etges R, Parkhill J, van Tonder AJ. 2021.  Genomic and temporal analyses of Mycobacterium bovis in Southern Brazil. Microb Genom. doi: 10.1099/mgen.0.000569

Almaw G, Mekonnen GA, Mihret A, Aseffa A, Taye H, Conlan AJK, Gumi B, Zewude A, Aliy A, Tamiru M, Olani A, Sombo M, Gebre S, Lakew M, Diguimbaye C, Hilty M, Fané A, Müller B, Hewinson RG, Ellis RJ, Nunez-Garcia J, Palkopoulou E, Abebe T, Ameni G, Parkhill J, Wood JLN, Berg S, van Tonder AJ. 2021. Population structure and transmission of Mycobacterium bovis in Ethiopia. Microb Genom. doi: 10.1099/mgen.0.000539

Ganaie F, Saad JS, McGee L, van Tonder AJ, Bentley SD, Lo SW, Gladstone RA, Turner P, Keenan JD, Breiman RF, Nahm MH. 2020. A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large cps Fragment from an Oral Streptococcus. MBio. doi: 10.1128/mBio.00937-20.

Sadowy E, Bojarska A, Kuch A, Skoczyńska A, Jolley KA, Maiden MCJ, van Tonder AJ, Hammerschmidt S, Hryniewicz W. 2020. Relationships Among Streptococci From the Mitis Group, Misidentified as Streptococcus Pneumoniae. Eur J Clin Microbiol Infect Dis. doi: 10.1007/s10096-020-03916-6.

Gladstone RA​, Lo SW, Goater R​, Yeats C​, Taylor B, Hadfield J​, Lees JA​, Croucher NJ, van Tonder AJ, Bentley​ LJ, Quah FX​, Blaschke​ AJ, Pershing​ NL, Byington CL, Balaji​ V, Hryniewicz​ W, Sigauque B, Ravikumar​ KL, Grassi Almeida SC​, Ochoa TJ​, Ho PL, Plessis M, Ndlangisa​ KM, Cornick JE​, Kwambana-Adams​ B, Benisty​ R, Nzenze SA, Madhi SA​, Hawkins​ PA, Pollard​ AJ, Everett DB​, Antonio M​, Dagan R, Klugman KP​, von Gottberg​ A, Metcalf​ BJ, Li​ Y, Beall​ BW, McGee L, Breiman RF, Aanensen DM, Bentley SD​, The Global Pneumococcal Sequencing Consortium. 2020. Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates. Microb Genom. doi: 10.1099/mgen.0.000357.

Lo SW, Gladstone RA, van Tonder AJ, Du Plessis M, Cornick JE, Hawkins PA, Madhi S, Nzenze SA, Kandasamy R, Ravikumar KL, Elmdaghri N, Kwambana-Adams B, Almeida SCG, Skoczynska A, Egorova E, Titov L, Saha SK, Paragi M, Everett DB, Antonio M, Klugman KP, Li Y, Metcalf BJ, Beall B, McGee L, Breiman RF, Bentley SD, von Gottberg A, The Global Pneumococcal Sequencing Consortium. 2019. A mosaic tetracycline resistance gene tet (S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa.  Journal of Antimicrobial Chemotherapy. doi: 10.1093/jac/dkz477.

van Tonder AJ, Gladstone RA, Lo SW, Nahm MH, du Plessis M, Cornick J, Kwambana-Adams B, Madhi SA, Hawkins PA, Benisty R, Dagan R, Everett D, Antonio M, Klugman KP, von Gottberg A, Breiman RF, McGee L, Bentley SD, The Global Pneumococcal Sequencing Consortium. 2019. Putative novel cps loci in a large global collection of pneumococci. Microb Genom. doi: 10.1099/mgen.0.000274.

Lo SW, Gladstone RA, van Tonder AJ, Lees JA, du Plessis M, Benisty R, Givon-Lavi N, Hawkins PA, Cornick J, Kwambana-Adams B, Law PY, Ho PL, Antonio M, Everett D, Dagan R, von Gottberg A, Klugman KP, McGee L, Breiman RF, Bentley SD, The Global Pneumococcal Sequencing Consortium. 2019. Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study. Lancet Infect Dis doi:10.1016/S1473-3099(19)30297-X.

Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, Page AJ, Marttinen P, Bentley LJ, Ochoa TJ, Ho PL, du Plessis M, Cornick JE, Kwambana-Adams B, Benisty R, Nzenze SA, Madhi SA, Hawkins PA, Everett DB, Antonio M, Dagan R, Klugman KP, von Gottberg A, McGee L, Breiman RF, Bentley SD, Global Pneumococcal Sequencing Consortium. 2019. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine. doi: 10.1016/j.ebiom.2019.04.021.

Otchere ID, van Tonder AJ, Asante-Poku A, Sánchez-Busó L, Coscollá M, Osei-Wusu S, Asare P, Aboagye SY, Ekuban SA, Yahayah AI, Forson A, Baddoo A, Laryea C, Parkhill J, Harris SR, Gagneux S, Yeboah-Manu D. 2019. Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana. PLoS One. doi: 10.1371/journal.pone.0209395

van Tonder AJ, Bray JE, Jolley KA, Jansen van Rensburg M, Quirk SJ, Haraldsson G, Maiden MCJ, Bentley SD, Haraldsson Á, Erlendsdóttir H, Kristinsson KG, Brueggemann AB. 2019. Genomic analyses of >3,100 nasopharyngeal pneumococci revealed significant differences between pneumococci recovered in four different geographical regions. Front. Microbiol. doi: 10.3389/fmicb.2019.00317

Quirk SJ, Haraldsson G, Hjálmarsdóttir MÁ, van Tonder AJ, Hrafnkelsson B, Bentley SD, Haraldsson Á, Erlendsdóttir H, Brueggemann AB, Kristinsson KG. 2019.  Vaccination of Icelandic children with the 10-valent pneumococcal vaccine leads to significant herd effect among adults in Iceland.  J Clin Microbiol. doi: 10.1128/JCM.01766-18

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

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. doi: 10.1128/JCM.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. doi: 10.1093/infdis/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

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. doi: 10.1099/mgen.0.000090.

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. doi: 10.1186/s12864-015-1729-4.

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 Biol. doi: 10.1371/journal.pcbi.1003788

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. doi: 10.1186/1471-2164-14-500.

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 aegyptius.  Emerging Infectious Diseases. doi: 10.3201/eid1803.110728.

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. doi: 10.1073/pnas.1117313109.

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. doi: 10.1111/j.1574-6968.2011.02339.x.

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. doi: 10.1128/JB.00659-10.

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. doi: 10.1073/pnas.0914322107.