Friday, 9 October 2015

PLoS Biology: Staphylococcus aureus invading the blood are less toxic

Toxicity in nose, blood and skin bacteria.
Collaborative work with Ruth Massey's group at the University of Bath taking forward a study of within-host evolution of Staphylococcus aureus during infection has been published in PLoS Biology. Previously we reported in PNAS that in one patient, bacteria causing a serious bloodstream infection differed by just eight mutations from a persistently carried nose population. We identified one of those mutations as playing a potentially causative role in transforming the nose bacteria into a form capable of bloodstream infection - a regulatory protein called rsp. To investigate further, Ruth applied a number of tests to characterize bacteria taken prior to and during infection. In this new paper, we report the surprising result that the bloodstream isolates show reduced toxicity and that rsp is the responsible for this change.

The notion that isolates responsible for serious human infection are less toxic challenges some long-held beliefs about the mechanism of disease in Staphylococcus aureus infections. Most models of disease assume a straightforward relationship between increased toxicity and greater virulence - the propensity to cause, or severity of, disease.

To test her observation, Ruth collaborated with groups from New York and Cambridge to investigate whether the pattern observed in one patient held more generally across 134 Staphylococcus aureus belonging to the notorious USA300 strain. It did.

Curiously, bacteria isolated from the skin and from superficial infections were equally toxic to nose bacteria. These findings raise new questions about the role of toxicity in colonization, transmission and serious infections of Staphylococcus aureus. One possibility that we wish to investigate further is whether toxicity might be required for the usual transmission of Staphylococcus aureus populations in the nose, skin or superficial infections (such as impetigo), whereas loss of toxicity may promote transition to deep tissue and bloodstream infections by evading immune defences.

Tuesday, 8 September 2015

New paper: Rapid host switching in Campylobacter

Our new open access paper Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections was published last week in the ISME Journal.

Figure from paper 
With Bethany Dearlove, Sam Sheppard and colleagues, we investigated common strains of campylobacter, the most frequent cause of bacterial gastroenteritis worldwide. Campylobacter infection is associated with food poisoning, particularly contaminated chicken. But in previous work, we found that certain strains (the ST-21, ST-45 and ST-828 complexes) are often found contaminating a range of meat and poultry, making it difficult to trace the source of human infection.

That previous work was based on partial genome sequencing known as MLST. In MLST, less than 1% of the information in the genome is captured. Now that whole genome sequencing is available, the expectation was that we should be able to distinguish easily between between ST-21, 45 and 828 strains contaminating poultry versus beef versus lamb, and so on.

What we found was surprising. Instead of these strains harbouring previously unobserved sub-structure that allowed them to be associated with different animal sources, we found rapidly mixing populations undergoing extremely fast transmission between animal species, with campylobacter strains ricocheting among animal species on a timescale of just a few years. This is faster than they can accumulate enough mutations to differentiate populations colonizing different animal species.

Our results present an unforeseen roadblock to tracing transmission with whole genome sequencing, and suggests these strains are adapted to a generalist lifestyle, shedding new light on the ecology of this pathogen. These findings push back against the tide of opinion that whole genome sequencing is necessarily a panacea for detecting transmission, and demonstrate that going forwards, a detailed understanding of the biology of zoonotic bacteria (those transmitting between multiple species) and intensive sampling of potential sources are essential for effectively tracing the source of human infection.

Monday, 17 August 2015

BASTA: Improved method for phylogeography

This week sees publication of our paper New Routes to Phylogeography: a Bayesian Structured Coalescent Approximation in PLoS Genetics.

Phylogeography is the recovery of migration history from genome sequences, and has exploded as a field in recent years. Over a thousand papers have used contemporary sequences and ancient DNA to reconstruct migratory trends, locate the origin of outbreaks and track the spread of infectious diseases. In many high profile examples phylogeography has informed our understanding of how major human pathogens spread.

In our new paper we solve a severe and apparently widely unappreciated problem: that the most popular approaches to phylogeography are heavily biased, extremely sensitive to sampling structure and substantially underestimate statistical uncertainty. The problems stem from the treatment of migration as equivalent to mutation (discrete trait analysis; DTA), and the assumption that sampling locations are phylogeographically informative.

To solve these problems we introduce and demonstrate a new method BASTA, implemented in the phylogenetic software package BEAST2, that employs a novel approximation to enable inference under the structured coalescent – the bottom-up population genetics model of migration. Previously, methods for exact inference under the structured coalescent have proven too slow for many practical purposes, hence the need for a fast and accurate approximation.

The biases we highlight with popular phylogeography methods are much more important than might appear from what is at one level a question of model choice. To underline this, we present an analysis of around 100 Ebola virus genome sequences to investigate the emergence of human outbreaks. Epidemiological studies have found that animals act as a reservoir, maintaining the virus between the sporadic human outbreaks that have unfolded over the past four decades, a scenario that our structured coalescent-based model correctly identifies.

Remarkably, DTA, the de facto standard method for phylogeography, wrongly concluded with high confidence that Ebola has been maintained since 1976 by undetected human-to-human transmission between outbreaks. Although such a conclusion would never be believed in the case of Ebola, it makes clear the potential for highly misleading inference about transmission that could, for much less well understood diseases, have serious implications for public health policy.

BASTA is the result of a lot of hard work by Nicola De Maio, who is a James Martin Fellow at the Oxford Martin School Institute for Emerging Infections, with help from Jessie Wu and Kathleen O'Reilly. You can read the paper here and download BASTA here.

Friday, 24 July 2015

New Journal: Microbial Genomics

This week sees the launch of Microbial Genomics, a new open access journal from the Society for General Microbiology. Here's an excerpt from the journal's mission statement:

"Microbial Genomics (MGen) publishes high quality, original research on archaea, bacteria, microbial eukaryotes and viruses. MGen welcomes papers that use genomic approaches to understand microbial evolution, population genomics and phylogeography, outbreaks and epidemiological investigations, impact of climate or changing niche, metagenomic and whole transcriptome studies, and bioinformatic analysis covering the breadth of microbiology, from clinically important pathogens to microbial life in diverse ecosystems."

The journal, whose tag line is Bases to Biology, will publish microbiological discoveries and innovations in research methods and bioinformatics. The journal is headed by renowned Wellcome Trust Sanger Institute scientists Stephen Bentley and Nicholas Thompson with an impressive editorial board that I joined earlier this year. Article processing charges have been waived during the journal's launch year - so get in there fast!

Tuesday, 21 July 2015

Resistance is Futile: Science Museum Lates and Cheltenham Science Festival

Some photos from this summer's Science Museum Lates event with the Royal Society and the Cheltenham Science Festival. Thanks to everyone who helped: Liz Batty, Phelim Bradley, Jane Charlesworth, Dilly De Silva, Sarah Earle, Nicki Fawcett, Jess Hedge, Brian Mackenwells, Amy Mason, Charvy Narain, Anna Sheppard and Jessie Wu!

Science Museum Lates: The next big thing Science Museum Lates: The next big thing Science Museum Lates: The next big thing

We had two activities. Dance Dance Evolution is a computer game which uses an adapted dance-dance mat with four squares representing bases in the DNA (A, C, G and T). Participants act as the DNA replicator, and mistakes cause mutations in the DNA sequence. The next dancer copies the sequence left by the previous dancer, demonstrating evolution by mutation over time. The game shows the percentage similarity of the current sequence to the original sequence, showing the amount of 'evolution' over the time period of the game. We discussed with visitors the relevance of this to the development of antibiotic resistance.

Wednesday, 8 April 2015

World Health Day: Food-borne disease theme

For World Health Day 2015, the group's research into food-borne campylobacter infection was featured on the Nuffield Department of Medicine's home page. The piece features recent work Bethany Dearlove and I have conducted into zoonotic (animal-human) transmission with Sam Sheppard. The paper is currently under review, and a preprint can be downloaded from the website.

Tuesday, 31 March 2015

ClonalFrameML: accounting for recombination in bacterial phylogenies

Horizontal gene transfer in bacteria, mediated by transformation, transduction or conjugation, can result in gain, loss and replacement of genes. The replacement of horizontally transferred genes or gene fragments in a process known as homologous recombination has far-reaching effects on bacterial phylogenetics - the study of relatedness between bacteria. A new method published by Xavier Didelot and me last month in PLoS Computational Biology corrects for these distorting effects of homologous recombination on bacterial phylogenies.

Two forms of phylogenetic distortion are caused by recombination. The first affects the shape of the tree topology. Although this is a potentially serious difficulty, Jessica Hedge and I recently showed that phylogenies estimated from whole bacterial genomes are surprisingly robust to this problem. The second affects the lengths of the branches. When genetic material is replaced by a homologous but distantly related sequence, it gives the appearance of a cluster of substitutions in the genome, and this can exaggerate branch lengths. ClonalFrameML detects these clusters of substitutions, identifies them as recombination events, and corrects the branch lengths of the tree.

Correcting for recombination is important in a variety of settings. In transmission studies, recent transmission between patients can be detected by comparing the genomes of the infecting bacteria. As we show in the paper, ClonalFrameML improves detection of transmission events by accounting for the tendency of recombination to elevate the evolutionary distance between genomes. We also report the discovery of a remarkably large chromosomal replacement event spanning 310 kilobases that may have led to the evolution of the ST582 strain of Staphylococcus aureus, underlining the importance of recombination over short and long timescales.

ClonalFrameML is a much faster implementation of the popular ClonalFrame method by Xavier and Daniel Falush. It is based on the same underlying assumptions and the same explicit evolutionary model, so it provides interpretable estimates of rates of recombination, the length of DNA imported by recombination, and the relative impact of recombination versus mutation. However, it can now analyse thousands of whole bacterial genomes in a matter of hours, representing a substantial improvement over the earlier method.