LABORATORY INFORMATICS


”You will typically find five million base differences between the maternal and paternal genomes of an individual mosquito. This diversity makes genome assembly in these species one of the most complex current problems in computational genomics”


g


in both institutes, developing computational resources that combine statistical and genomics methods to monitor infectious disease worldwide. 'We cover endemic situations, as well as epidemic outbreaks, and both viral and bacterial diseases', he explains. This is a massive


undertaking, and one that cannot be achieved by one research group – or even two – without a comprehensive, worldwide network of collaborators. The centre and its financial backers, particularly the UK’s National Institute for Health Research, are adding to their number by investing heavily in capacity-building. They have set up a worldwide network of genomics labs in low and middle-income countries including India, the Philippines, Nigeria and Colombia, and are providing bioinformatics support and training. This has clinical, as well


as research applications, as Aanensen explains: ‘Any of the labs in our global network can upload a pathogen genome sequence, and our software will immediately generate two lists of antibiotics: one of those that can be used safely and effectively, and another of those to which resistance has developed or is developing.' All the data generated by the network is


kept on open access and can be downloaded and analysed using smartphones, putting such analysis theoretically in reach of almost any hospital worldwide. 'We need to deliver our tools in such a way they can be used by the people who stand to benefit the most: those with the fewest resources', says Aanensen. Clinicians and researchers


can also use epicollect5, a tool developed by centre researchers that is available as a smartphone app, to upload geo-tagged information about infections that has been collected in the field. Stored data typically includes demographic information about the patients, locations, symptoms, pathogens and resistance phenotypes; this, again, is completely open access and can be mapped or downloaded in different formats for further analysis. This tool was developed


to be completely generic, and it is frequently used by businesses, ecologists, citizen scientists and schools, as well as epidemiologists and clinicians. ‘One of its most popular current applications is in marine biology; boat owners and tourists in the Channel Islands use the app to upload photos of dolphins, seals, sharks and other sea fauna, automatically-generated GPS data is added and the records


22 Scientific Computing World August/September 2019


stored in a free-to-access database', adds Aanensen. Well over a million people still die of tuberculosis (TB) every year, mainly in low- income countries; it is one of the biggest killers of HIV- infected people worldwide. While drug-susceptible TB can be relatively easily treated with affordable antibiotics, the prognosis is much bleaker for the hundreds of thousands diagnosed with drug-resistant disease. The World Health


Organisation categorises tuberculosis that is resistant to the two mainstay drugs, isoniazid and rifampicin, as multi-drug resistant (MDR). Hundreds of thousands of cases of MDR-TB are diagnosed every year, and, more worryingly still, a growing proportion have extensively drug resistant disease (XDR- TB), which is resistant to two further groups of second- line antibiotics. Almost no treatment is available for tuberculosis classified as


totally drug resistant (TDR- TB) which has so far been identified in three countries: India, Iran and Italy. Determining whether a patient has been infected by the eponymous bacterium Mycobacterium tuberculosis, and if so, whether the strain was drug-resistant, used to be a slow and complex process. This has changed largely thanks to GeneXpert, a desktop machine about the size of a microwave oven that can rapidly amplify DNA in bacteria taken from a patient’s sputum and test for mutations in the gene that determines rifampicin resistance. ‘This machine, which is


relatively cheap, will pick up about 95 per cent of all cases of such resistance, enabling healthcare workers to select drugs more likely to be effective in those patients’, says Tim McHugh, professor of medical microbiology at University College London. Whole genome sequencing is also increasingly used in


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