The same features of the Genpax analysis that mean that all strains of a species can be compared in one location with a common analysis resource (as opposed to others, such as those that must use multiple reference genomes or where resolution reduces with increasing numbers and diversity of strains), and its open scalability means it will generate equally comparable and integratable findings from information generated and submitted from different laboratories. This is enabled

Genpax analysis was created for the real-world problem from the bottom-up with scalability as an essential requirement. Scalability is a constraint for existing solutions, the three main reasons being: • The statistical nature of relationship determinations that are impossible to scale (they are ‘NP-hard’ problems) • The loss of resolution with increasing diversity and number of compared strains with common genome SNP • Data generated with more than one reference genome when

When strains are evolving at 1 to 10 nucleotides per year per genome, it is important to address as much of the genome sequence information as possible within the limits of what can be achieved accurately. This cannot be 100% of the genome with current sequencing technologies. For example, regions that are repeatedly present in the genome either identically or with minor variations (for example the ribosomal RNA sequences) are inherently difficult to address. Exactly how much

With some variation by species and genome size, most bacterial pathogens normally change at a rate of up to 10 SNP changes per genome per year. A clinical outbreak spanning weeks or months will include strains diverging at double this rate but also contain strains that differ by less because 99% of strains replicate without error. Meanwhile, sequencing, assembly, and mapping errors can generate tens of errors per MB, resulting in noise that exceeds the essential signal to ide

While the costs and ease of sequencing have been falling, one common obstacle to adoption is the requirement for local genomics staff and infrastructure. High costs of IT staff, bioinformaticians, and genomic epidemiologists (plus sufficient staff to provide continuity of service) and the initial and ongoing costs of computational infrastructure often provide a barrier to entry. Initial capital and equipment costs that are commonly encountered, particularly in resource-limite

It is repeatedly stated that we face a global challenge of antimicrobial resistance and catastrophic health and economic impacts, and that this is the product of misuse, abuse, and essentially over-use of antibiotics. It is hard to argue, and I would not wish to, that this is at least partly the case, but it is both dangerous and misleading to present this as the whole of the explanation. What we are seeing is an inevitable consequence of many pressures and their inevitable e

At one level, the numbers look good, but if you look again, maybe not. Once upon a time, TB started out as something else, probably some environmental predecessor that lived in watery or other environments, perhaps starting out in another animal, but eventually, it got to humans. There was a ‘patient zero’ for TB, just as there is for all new and emergent pathogens, and for TB, it is guessed that this happened around 5,000 to 10,000 years ago. There is evidence that it has be

As Sun Tzu famously said: ‘know your enemy’, or more correctly: ‘If you know the enemy and know yourself, you need not fear the result of a hundred battles.’ This is true not only for human conflict but in what is probably the greatest and longest running battle the human race has ever engaged in: that between humans and their pathogens. Ultimately, COVID-19, our current enemy of focus, might kill 1%, but hopefully, many fewer now that there is a vaccine and better treatments

COVID-19 is not the pandemic I was predicting. Year after year, for just over 10 years a new class of about 150 young, smart medical students would come to my lectures on medical bacteriology and infection at Oxford. I would explain what things contribute to virulence (what makes pathogens dangerous); most years I would get them to play an online game in which a pandemic was simulated and from which they would learn some key things, with a prize for the person who could take

Life is full of initially hidden and unintended impacts and consequences; for something as huge and pervasive as COVID, no doubt they will be many and varied: some good, some bad, some just resulting in different. The global infrastructural leadership of the UK in the area of genomics, underpinned by the public and charitable contributions of the UK Research Councils and the Wellcome Trust, has been critical in surveillance, variant detection, and now screening. By February 2

Sequence Typing (ST) is a widely established and used methodology. It is most certainly better than its predecessors from the era before affordable and accessible DNA sequencing, and its development and implementation was an enormous step forward for pathogen identification and the study of bacterial population genetics. In its original form, MLST, it was very much a DNA-based version of its protein-based predecessor, only better in every meaningful way. The conceptual predec