New paper: SCOTTI Efficient reconstruction of transmission within outbreaks with the structured coalescent

New paper published today in PLoS Computational Biology: Understanding how infectious disease spreads and where it originates is essential for devising policies to prevent and limit outbreaks. Whole genome sequencing of pathogens has proved an extremely promising tool for identifying transmission, particularly when combined with classical epidemiological data. Several statistical and computational approaches are available for exploiting genomics for epidemiological investigation. These methods have seen applications to dozens of outbreak studies. However, they have a number of serious drawbacks.

In this new paper Nicola De Maio, Jessie Wu and I introduce SCOTTI, a method for quickly and accurately inferring who-infected- whom from genomic and epidemiological data. SCOTTI addresses very widespread, but generally neglected problems in joint epidemiological and genomic inference, notably the presence of non-sampled and undetected intermediate cases and within-host pathogen variation caused by microevolution. Using real examples and simulations, we show that these problems cause strong misleading effects on existing popular inference methods. SCOTTI is based on BASTA, our recent breakthrough method for phylogeographic inference, and offers new standards of accuracy, calibration, and computational efficiency. SCOTTI is distributed as an open source package within BEAST2.

Prize PhD Studentships available

I am offering two PhD projects as part of the annual Nuffield Department of Medicine Prize Studentship competition:

• Real-time detection of multidrug resistant tuberculosis and transmission in England
  Joint with David Wyllie, molecular microbiologist, this project is focused on developing statistical methods for recognizing transmission clusters, integrating genomics approaches with molecular typing schemes and developing future-proof taxonomy for strain identification.
  
  
• Tracking future infection threats using genomic data and electronic health records
  Joint with David Clifton, biomedical engineer, this project aims to develop new machine learning and statistical methods to identify genomic markers of antibiotic resistance and susceptibility within various pathogens, to help track future infection threats.

These are fully-funded, four-year awards open to outstanding students of any nationality. Applicants nominate three projects, in order of preference, from the available pool. For how to apply, click here. Only applications submitted through the online system will be considered, but interested applicants are welcome to contact me informally. The deadline for applications is noon, 6th January 2017.

In addition to my projects, the Modernising Medical Microbiology project has announced the following PhD projects as part of the competition:

• Antimicrobial resistance gene/vector transmission across human, animal and environmental reservoirs
  Supervised by Nicole Stoesser, Nicola De Maio and Derrick Crook
  
  
• Healthcare big data and genomics for infectious disease threat detection
  Supervised by David Clifton, David Eyre and Tim Peto
  
  
• Prediction of Mycobacterium tuberculosis drug resistance through genome sequencing clinical samples
  Supervised by Tim Walker and Tim Peto
  
  
• Antibiotic resistance in Tuberculosis: Predicting de novo the effect of individual genetic mutations
  Supervised by Phil Fowler and Sarah Walker

The Rsp virulence regulator: new review in Trends in Microbiology

In the September issue of Trends in Microbiology, Mark Smeltzer casts the spotlight on the story of rsp, a virulence regulator in Staphylococcus aureus that evolves within infected patients and may play a role in disease.

The new review covers recent work on the rsp gene including a series papers that my collaborators and my group have contributed: 
Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation.
Das, S., Lindemann, C., Young, B. C., Muller, J., Österreich, B., Ternette, N., Winkler, A.-C., Paprotka, K., Reinhardt, R., Förstner, K. U., Allen, E., Flaxman, A., Yamaguchi, Y., Rollier, C. S., Van Diemen, P., Blättner, S., Remmele, C. W., Selle, M., Dittrich, M., Müller, T., Vogel, J., Ohlsen, K., Crook, D., Massey, R., Wilson, D. J., Rudel, T., Wyllie, D. H., and M. J. Fraunholz (2016)
Proceedings of the National Academy of Sciences USA 113: E3101–E3110. (abstract pdf)

Evolutionary trade-offs underlie the multi-faceted virulence of Staphylococcus aureus.
Laabei, M., Uhlemann, A.-C., Lowy, F. D., Austin, E. D., Yokoyama, M., Ouadi, K., Feil, E., Thorpe, H. A., Williams, B., Perkins, M., Peacock, S. J., Clarke, S. R., Dordel, J., Holden, M., Votintseva, A. A., Bowden, R., Crook, D. W., Young, B. C., Wilson, D. J., Recker, M. and R. C. Massey (2015)
PLoS Biology 13: e1002229. (abstract pdf)

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease.
Young, B. C., Golubchik, T., Batty, E. M., Fung, R., Larner-Svennson, H., Votintseva, A., Miller, R. R., Godwin, H., Knox, K., Everitt, R. G., Iqbal, Z., Rimmer, A. J., Cule, M., Ip C. L. C., Didelot, X., Harding, R. M., Donnelly, P. J., Peto, T. E., Crook, D. W., Bowden, R. and D. J. Wilson (2012)
Proceedings of the National Academy of Sciences USA 109: 4550-4555. (abstract pdf F1000)

Lyre bird song

Healesville Sanctuary, Yarra Valley, Victoria, Australia

Tackling and tracking TB through DNA analysis

Collaborative PhD and postdoc positions available

Dr Nicole Stoesser, Prof. Derrick Crook, myself and colleagues in Oxford are seeking a postdoc in Microbial Genomics with statistics skills to join a new three-year project investigating antimicrobial resistance in environmental, human and animal reservoirs of E. coli and related organisms. The application deadline is noon Monday 11th July. For more details click here.

Dr Pierre Mahe of bioMérieux in Grenoble, France, is seeking to appoint an industry-linked PhD position developing statistical methods for genome-based characterization of antimicrobial resistance and virulence genes, with a focus on the opportunistic pathogen Pseudomonas aeruginosa. The position involves a secondment here in Oxford. For more details click here or contact Pierre Mahe.

New paper: How low-toxic Staph. aureus mutants cause severe infections

Published today in PNAS Early Edition, our new paper that reveals naturally occurring mutations in the poorly-described rsp gene of Staph. aureus
reduce toxicity while maintaining the ability to survive, proliferate and cause infection within the human body.

In previous work, we have found that Staph. aureus evolves by mutation within the body quickly enough to influence the progression of disease, and that diversity generated by evolution in the body is a widespread phenomenon. In the case of one patient who we followed longitudinally for over a year, we identified that bacteria in the bloodstream differed from those in the nose by several mutations, of which a loss-of-function mutation in the rsp regulatory gene represented the most likely candidate for playing a possible role in causing severe infection.

We collaborated with Ruth Massey at Bath who discovered to our surprise that while rsp loss-of-function mutants do indeed show differences in toxicity - one of several traditional correlates of virulence readily measured in the laboratory - they showed reduced toxicity. Going further, Ruth and her collaborators showed that bloodstream infections in general show reduced toxicity compared to milder skin infections and asymptomatically carried nose populations, overturning previous views on the relationship between Staph. aureus toxicity and virulence.

Today's new paper offers a detailed dissection of rsp. Working with Claudia Lindemann and David Wyllie at the University of Oxford and Martin Fraunholz and collaborators at the University of Würzburg, we found that although rsp mutants show reduced toxicity, crucially they retain their capacity to survive, grow, spread through the body and cause abscesses. In other words, rsp uncouples toxicity from pathogenicity. This decoupling could be important for evading the immune system and establishing severe infections. To find out more, see the full paper.

Postdoctoral Scientist in Statistical Genomics

We are recruiting for a Postdoctoral Scientist in Statistical Genomics working on Antimicrobial Resistance (AMR) gene discovery and focused on Tuberculosis. This will be a joint position at the University of Oxford between Derrick Crook's group and mine, and part of the large international CRyPTIC consortium.

The role is for a population geneticist or statistical geneticist to develop and apply statistical methods, including genome-wide association studies, for discovering rare and common genetic variants underlying antimicrobial resistance in Mycobacterium tuberculosis.

One third of the world's population - 2.5 billion people - are thought to be infected with tuberculosis (TB). This post offers an opportunity to work with global TB experts from five continents, statistical geneticists, clinicians, medical statisticians and software engineers; integrating statistical genetics, bioinformatics and machine learning methods with the aim of uncovering all genomic variants causing at least 1% resistance to first line anti-TB drugs.

We're looking for candidates with a PhD in genomics, evolutionary biology, statistics or a related subject. The post is full-time and fixed-term for up to 3 years initially.

The deadline for applications is noon on Friday 6th May 2016.

Making the most of bacterial GWAS: new paper in Nature Microbiology

In a new paper published this week in Nature Microbiology, we report the performance of genome wide association studies (GWAS) in bacteria to identify causal mechanisms of antibiotic resistance in four major pathogens, and introduce a new method, bugwas,  to make the most of bacterial GWAS for traits under less strong selection.

As explained by Sarah Earle, joint first author with Jessie Wu and Jane Charlesworth, the problem with GWAS in bacteria is strong population structure and the consequent strong coinheritance of genetic variants throughout the genome. This phenomenon - known as genome-wide linkage disequilibrium (LD) - comes about because exchange of genes is relatively infrequent in bacteria, which reproduce clonally, compared to organisms that exchange genes every generation through sexual reproduction.

Genome-wide LD makes it difficult for GWAS to distinguish variants that causally influence a trait from other, coinherited variants that have no direct effect on the trait.

In the case of antibiotic resistance - a trait of high importance to human health - bacteria are under extraordinary selection pressures because resistance is a matter of life and death, to them as well as their human host. This helps overcome coinheritance and pinpoint causal variants because antibiotic usage selects for the independent evolution of the same resistance-causing variants in different genetic backgrounds.

Consequently, bacterial GWAS works very efficiently for antibiotic resistance: the variants most significantly associated with antibiotic resistance in 26 out of the 27 GWAS we performed were genuine resistance-conferring mutations. In the 27th we uncovered a putative novel mechanism of resistance to cefazolin in E. coli. These results for 17 antibiotics (ampicillin, cefazolin, cefuroxime, ceftriaxone, ciprofloxacin, erythromycin, ethambutol, fusidic acid, gentamicin, isoniazid, penicillin, pyrazinamide, methicillin, rifampicin, tetracycline, tobramycin and trimethoprim) across four species (E. coli, K. pneumoniae, M. tuberculosis and S. aureus) build on earlier work investigating beta-lactam resistance in S. pneumoniae, and convincingly demonstrate the potential for bacterial GWAS to discover new genes underlying important traits under strong selection.

What about traits under less strong selection, which probably includes pretty much every other bacterial trait? We show in this context that coinheritance poses a major challenge, based on detailed simulations. Often it may not be possible to use GWAS to pinpoint individual variants responsible for different traits because they are coinherited with - possibly many - other uninvolved variants.

But all is not lost. We show that even when individual locus-level effects cannot be pinpointed, there is often excellent power to characterize lineage-level differences in phenotype between strains. This is helpful for multiple reasons: (1) we often conceptualize trait variability in bacteria at the level of strain-to-strain differences (2) these differences can be highly predictive (3) we can prioritize variants for functional follow-up based on their contribution to strain-level differences.

These concepts represent a substantial departure from regular GWAS. In the human setting for instance, lineage-level differences are usually discarded as uninteresting or artefactual, and variants are almost always prioritized based on statistical evidence for involvement over-and-above any contribution to lineage-level differences. In the bacterial setting, we are forced to depart from these conventions because a large proportion of all genetic variation is strongly strain-stratified. To find out more, see the paper and try our methods.

CRyPTIC: rapid diagnosis of drug resistance in TB

The Modernising Medical Microbiology consortium has announced a new worldwide collaboration called CRyPTIC to speed up diagnosis of antibiotic resistant tuberculosis (TB).

TB infects nearly 10 million people each year and kills 1.5 million, making it one of the leading causes of death worldwide. Almost half a million people each year develop multidrug-resistant (MDR) TB, which defies common TB treatments. Time consuming tests must be run to identify MDR-TB and which drugs will work or fail. This delays diagnosis and creates uncertainty about the best drugs to prescribe to individual patients.

CRyPTIC aims to hasten the identification of MDR-TB using whole genome sequencing to identify genetic variants that give resistance to particular drugs. The project is funded by a $2.2m grant from the Bill & Melinda Gates Foundation and a £4m grant from the Wellcome Trust and MRC Newton Fund.

CRyPTIC aims to collect and analyse 100,000 TB cases from across the world, providing a database of MDR-TB that will underpin diagnosis using WGS. Samples from across Africa, Asia, Europe and the Americas will be collected by teams at more than a dozen centres They will conduct drug resistance testing and much of the genome sequencing. Read more information here.

Snow Monkeys in Japan

Recently got back from the SMBE Satellite meeting on Pathogen Genomics in Japan. The organizers did a fantastic job and the talks were great. There was also time to visit the Japanese macaques at Snow Monkey Park, where one of the little guys climbed on to my shoulders

Thanks Ashlee Earl for the video and Koji Yahara, Alan McNally and Nick Croucher for additional commentary!

Nature Reviews Microbiology: Within-host evolution of bacterial pathogens

Our new review of what genomics has taught us about Within-host evolution of bacterial pathogens has been published in Nature Reviews Microbiology.