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Sequencing

Oxford University Lead: Derrick Crook

PHE co-lead: Saheer Garbia

We aim to determine how to analyse and compare the genetic code of millions of microbes causing infections from across the world. Our vision is to find better ways to manage and prevent threats from antimicrobial resistance and healthcare associated infections by detecting them faster, working out who needs protecting most and how we can do this.  We will develop automated software to read, interpret and report results from genetic code identifying the type of microbe, whether it is resistant to certain antimicrobials and whether there is an. We will also improve our workflow to obtain the pathogen DNA/RNA (and thus genetic code) directly from clinical samples and our understanding of how the genetic changes leads to antimicrobial resistance.

 

 Sequencing Theme Populations

 

  • Evaluation of methods for detecting human reads in microbial sequencing datasets

Bush S, Connor T, Peto T, Crook D, Walker A

 https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000393

 

  • Read trimming has minimal effect on bacterial SNP-calling accuracy

Bush SJ

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000434

 

  • The importance of using whole genome sequencing and extended spectrum beta-lactamase selective media when monitoring antimicrobial resistance

Duggett N, AbuOun M, Randall L, Horton R, Lemma F, Rogers J, Crook D, Teale C, Anjum M

https://www.nature.com/articles/s41598-020-76877-7

 

 

  • Utility of whole genome sequencing in assessing and enhancing partner notification of Neisseria gonorrhoeae infection

Kong L, Wilson J, Moura I, Fawley W, Kelly L, Walker, Eyre D, Wilcox M

Please contact rosalind.hathway@ndm.ox.ac.uk to receive a copy of this publication

 

  • Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing

Peto L, Rodger G, Carter D, Osman K, Yavuz M, Johnson K, Raza M, Parker M, Wyles M, Andersson M, Justice A, Vaughan A, Hoosdally S, Stoesser N, Matthews P, Eyre D, Peto T, Carroll M, De Silva T, Crook D, Evans C, Pullan S

https://journals.asm.org/doi/10.1128/JCM.03271-20