Outbreaks: defi nition and classifi cationOutbreaks of infection can be devastating for individuals and societies. In medieval times, the Black Death led to the death of up to a third of the inhabitants of Europe [1]. More recently, an outbreak of Shiga-toxin-producing Escherichia coli (STEC) struck Germany in May-June 2011, resulting in over 3,000 cases and over 50 deaths, and provided ample evidence of the harrowing eff ects of bacterial infection on a modern, industrialized society [2,3].In its loosest sense, the term ‘outbreak’ can be used to refer to any increase in the incidence of a given infection, which can occur in response to local, societal or environ-mental changes: for example, one might see an increase in the prevalence of staphylococcal wound infections when hospital ward or operating theatre cleaning proce-dures change, or when there are changes in the use of antibiotics. However, in the strictest sense (which we adopt here), the term implies a series of infections caused by indistinguishable or closely linked isolates, which are suffi ciently similar to justify talking about ‘an outbreak strain’. Such outbreaks can range in size from a few individuals, for instance in a family outbreak or an outbreak on a hospital ward, to epidemics that rage across countries or continents.Investigation of a suspected outbreak has two aims: termination of the cluster of disease and prevention of similar occurrences by understanding how such out-breaks originate. A key question surfaces at the start of any such investigation: is one really seeing an outbreak in the strictest sense, caused by a single strain, or is one merely seeing an increased incidence of infection, involving multiple unrelated strains? Th e answer to this question is of more than academic interest, as it dictates how the fi nite resources available for infection control are best deployed. For example, evidence of cross infection with a single methicillin-resistant Staphylococcus aureus (MRSA) strain on a ward might prompt an aggressive strategy of patient isolation and decolonization, whereas an increase in infections caused by diverse staphylococcal strains (presumably each derived from the patient’s own microbiota) might prompt a look at policies for wound care or antibiotic usage. Similarly, identifi cation and charac terization of an outbreak strain or the discovery of its source or mode of transmission infl uences the behavior of the infection control team - potential responses include removal of the source, interruption of transmission or strengthening of host defenses.In the past decade, many diff erent kinds of outbreaks have hit the headlines (Table 1), with concern focused on the spread of multi-drug-resistant strains in hospitals (such as MRSA) [4] or in the community (such as multi-drug-resistant tuberculosis [5]); the threat of bioterrorism [6]; and ‘emerging infections’, caused by newly discovered pathogens, such as severe acute respiratory syndrome AbstractOutbreaks of infection can be devastating for individuals and societies. In this review, we examine the applications of new high-throughput sequencing approaches to the identifi cation and characterization of outbreaks, focusing on the application of whole-genome sequencing (WGS) to outbreaks of bacterial infection. We describe traditional epidemiological analysis and show how WGS can be informative at multiple steps in outbreak investigation, as evidenced by many recent studies. We conclude that high-throughput sequencing approaches can make a signifi cant contribution to the investigation of outbreaks of bacterial infection and that the integration of WGS with epidemiological investigation, diagnostic assays and antimicrobial susceptibility testing will precipitate radical changes in clinical microbiology and infectious disease epidemiology in the near future. However, several challenges remain before WGS can be routinely used in outbreak investigation and clinical practice.© 2010 BioMed Central LtdGenomics and outbreak investigation: from sequence to consequenceEsther R Robinson1, Timothy M Walker2 and Mark J Pallen3*REVIEW*Correspondence: m.pallen@warwick.ac.uk3Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UKFull list of author information is available at the end of the articleRobinson et al. Genome Medicine 2013, 5:36 http://genomemedicine.com/content/5/4/36© 2013 BioMed Central Ltd
