Genomics and outbreak investigation: from sequence to consequence

Esther R Robinson,Mark J Pallen,Timothy M Walker

doi:10.1186/gm440

Abstract

Outbreaks of infection can be devastating for individuals and societies. In this review, we examine the applications of new high-throughput sequencing approaches to the identification 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 significant 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.

Highlights

Outbreaks of infection can be devastating for individuals and societies
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 might prompt a look at policies for wound care or antibiotic usage
Conclusions and future perspectives As we have seen, there is ample evidence that wholegenome sequencing (WGS) can make a significant contribution to the investigation of outbreaks of bacterial infection

Summary

Introduction

Outbreaks of infection can be devastating for individuals and societies. In this review, we examine the applications of new high-throughput sequencing approaches to the identification and characterization of outbreaks, focusing on the application of wholegenome sequencing (WGS) to outbreaks of bacterial infection. We recognize that virologists pioneered the use of WGS for pathogen typing, targeting genomes small enough for WGS with traditional Sanger sequencing [21], here we will concen trate on the application of WGS to outbreaks of bacterial infection, catalyzed by the recent arrival in the market place of a range of technologies that fall under the umbrella term ‘high-throughput sequencing’ (sometimes called ‘next-generation sequencing’) [22,23].

Results

Conclusion