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An Interdisciplinary Research Centre at the University of Cambridge


Development of assays for genotypic and phenotypic antimicrobial susceptibility testing for the Mycobacterium tuberculosis complex


Key publications: 

J Clin Microbiol. 2021 Feb 10;JCM.02328-20.
On the consequences of poorly defined breakpoints for rifampin susceptibility testing of Mycobacterium tuberculosis complex.
Köser CU, Georghiou SB, Schön T, Salfinger M.

Senior scientific analyst. Technical Report on critical concentrations for drug susceptibility testing of isoniazid and the rifamycins (rifampicin, rifabutin and rifapentine). World Health Organization. Available from:

Int J Tuberc Lung Dis. 2020 Dec 1;24(12):1307-1311.
Systematic rifampicin resistance errors with Xpert® MTB/RIF Ultra: implications for regulation of genotypic assays.
Omar SV, Hillemann D, Pandey S, Merker M, Witt AK, Nadarajan D, Barilar I, Bainomugisa A, Kelly EC, Diel R, Vidanagama DS, Samarasinghe AIP, Cader MR, Götsch U, Lavu E, Alabi A, Schön T, Coulter C, Niemann S, Maurer FP, Ismail NA, Köser CU, Ismail F.

Clin Microbiol Infect. 2020 Nov;26(11):1453-1455. doi: 10.1016/j.cmi.2020.07.037.
What is the role of the EUCAST reference method for MIC testing of the Mycobacterium tuberculosis complex?
Schön T, Köser CU, Werngren J, Viveiros M, Georghiou S, Kahlmeter G, Giske C, Maurer F, Lina G, Turnidge J, van Ingen J, Jankovic M, Goletti D, Cirillo DM, Santin M, Cambau E; ESGMYC.

Antimicrob Agents Chemother. 2020 Aug 20;64(9):e01003-20.
How to optimally combine genotypic and phenotypic drug susceptibility testing methods for pyrazinamide.
Köser CU, Cirillo DM, Miotto P.

Int J Infect Dis. 2019 Mar;80S:S32-S35.
'Those who cannot remember the past are condemned to repeat it': Drug-susceptibility testing for bedaquiline and delamanid.
Köser CU, Maurer FP, Kranzer K.

Lead scientific analyst. Technical report on critical concentrations for drug susceptibility testing of medicines used in the treatment of drug-resistant tuberculosis. World Health Organization. Available from:

Eur Respir J. 2017 Dec 28;50(6). pii: 1701354.
A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis.
Miotto P, Tessema B, Tagliani E, Chindelevitch L, Starks AM, Emerson C, Hanna D, Kim PS, Liwski R, Zignol M, Gilpin C, Niemann S, Denkinger CM, Fleming J, Warren RM, Crook D, Posey J, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Murray M, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, Ranganathan UDK, McNerney R, Ezewudo M, Cirillo DM, Schito M, Köser CU, Rodwell TC.

Antimicrob Agents Chemother. 2017 Mar 24;61(4). pii: e02169-16.
Some synonymous and nonsynonymous gyrA mutations in Mycobacterium tuberculosis lead to systematic false-positive fluoroquinolone resistance results with the Hain GenoType MTBDRsl assays.
Ajileye A, Alvarez N, Merker M, Walker TM, Akter S, Brown K, Moradigaravand D, Schön T, Andres S, Schleusener V, Omar SV, Coll F, Huang H, Diel R, Ismail N, Parkhill J, de Jong BC, Peto TE, Crook DW, Niemann S, Robledo J, Smith EG, Peacock SJ, Köser CU.

Lancet. 2015 Jan 24;385(9965):305-7.
Drug-resistance mechanisms and tuberculosis drugs.
Köser CU, Javid B, Liddell K, Ellington MJ, Feuerriegel S, Niemann S, Brown NM, Burman WJ, Abubakar I, Ismail NA, Moore D, Peacock SJ, Török ME.

Trends Genet. 2014 Sep;30(9):401-7.
Whole-genome sequencing to control antimicrobial resistance.
Köser CU, Ellington MJ, Peacock SJ.

N Engl J Med. 2013 Jul 18;369(3):290-2.
Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis.
Köser CU, Bryant JM, Becq J, Török ME, Ellington MJ, Marti-Renom MA, Carmichael AJ, Parkhill J, Smith GP, Peacock SJ 

Antimicrob Agents Chemother. 2012 Dec;56(12):6080-7.
Importance of the genetic diversity within the Mycobacterium tuberculosis complex for the development of novel antibiotics and diagnostic tests of drug resistance.
Köser CU, Feuerriegel S, Summers DK, Archer JA, Niemann S.

PLoS Pathog. 2012 Aug;8(8):e1002824.
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology.
Köser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, Holden MT, Dougan G, Bentley SD, Parkhill J, Peacock SJ.

N Engl J Med. 2012 Jun 14;366(24):2267-75.
Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.
Köser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM, Ogilvy-Stuart AL, Hsu LY, Chewapreecha C, Croucher NJ, Harris SR, Sanders M, Enright MC, Dougan G, Bentley SD, Parkhill J, Fraser LJ, Betley JR, Schulz-Trieglaff OB, Smith GP, Peacock SJ.

Visiting scientist at Department of Genetics. Consultant for Becton Dickinson, the Foundation for Innovative New Diagnostics (FIND), the TB Alliance, and the World Health Organization.
Dr Claudio  Köser
Available for consultancy


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