Improving Exploitation of Whole Genome Sequencing Data for Public Health, Forensic Microbiology and Biosafety

Bacillus anthracis, a Gram-positive spore forming rod-shaped bacteIn this issue of EBioMedicine, Keim and colleagues (Keim et al., rium, is the causative agent of anthrax. This zoonotic disease principally affects herbivores but B. anthracis can also infect other livestock and wildlife species (WHO, 1998). Human cases mainly occur sporadically and infectionsmostly follow direct or indirect contact with contaminated animal products. Three major forms of human anthrax are described in the literature: cutaneous, gastrointestinal and pulmonary. All these forms can successively lead to septicemia and meningitis. The development of a specific clinical manifestation is dependent upon the route of infection (WHO, 1998). Recently, growing concern was raised by reports describing a new form of anthrax found in heroin users resulting from the injection of the drug contaminated with spores of B. anthracis (Hanczaruk et al., 2014). Symptoms of injectional anthrax (IA) aremore severe than those observed in classical cutaneous anthrax and clinical outcome is poor (Berger et al., 2014). Two outbreaks of IA occurred in 2009–2010 (UK, Germany) and in 2012–2013 (Denmark, France, Germany, UK), respectively (Berger et al., 2014). The subsequent investigations performed to determine the source of infection involved multi-disciplinary teams and turned out to be a complicated task as a consequence of the illegal aspects related to heroin production, distribution and use (Team NAOC, 2011). Among the large amount of data collected during these investigations, genotyping of strains of B. anthracis was fundamental (Price et al., 2012). The recent improvements in the field of whole genome sequencing (WGS) opened up a large panel of applications for bacterial research and diagnostics. However, WGS generates an enormous quantity of data and it is essential to maximize exploitation of the produced information for epidemiological and evolutionary studies. Public health authorities need typing of pathogenic bacterial isolates to plan and implement disease surveillance and rapid outbreak response (Sabat et al., 2013). This facilitates a better understanding of the dynamics of epidemic events and improves traceability of sources of infection. From this point of view, WGS allows a higher resolution for typing bacteria than the previously available methods based onmolecular biology techniques (Bertelli and Greub, 2013). Moreover, the comparison of genomes and consequent assessment of variation among related and unrelated isolates enables the selection of adequate genetic markers for rapid screening of isolates.