Comparative Genomics Approaches for Tracking the Emergence and Spread of Disease-associated Bacteria
Tracy H. Hazen and David A. Rasko
from: Advanced Vaccine Research Methods for the Decade of Vaccines (Edited by: Fabio Bagnoli and Rino Rappuoli). Caister Academic Press, U.K. (2015) Pages: 65-74.
The development of effective vaccines hinges on an understanding of the underlying genetic diversity of the disease-causing bacteria targeted by the vaccine. The decreasing cost of genome sequencing has lead to the use of comparative genomics of collections of bacteria associated with recent outbreaks. Large-scale comparative genomics studies have also been used to track the emergence and spread of antibiotic resistant Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus (MRSA), and Clostridium difficile. Also, comparative genomics has been used to understand the occurrence of the Haiti cholera outbreak and identify factors that may contribute to increase virulence in O157:H7 E. coli associated with outbreaks, and the O104:H4 E. coli responsible for the deadly German outbreak in 2011. Approaches used in comparative genomics studies range from gene-based comparisons of diverse groups of isolates, to SNP-based analyses of often clonally-related isolates associated with outbreaks. Both the gene-based and SNP-based analyses have lead to the development of assays for detection and classification of disease-associated bacteria and their virulence-associated genes as indicators of their pathogenic potential. In the following, we provide an overview of the utility of different comparative genomics approaches for investigating the emergence and dissemination of disease-associated bacteria and discuss specific studies that have resulted in the development of assays for rapid identification of clinical bacteria based on insights from comparative genomics studies. The use of whole-genome sequencing and comparative genomics for identifying outbreak-associated bacteria can aid public health decisions regarding the treatment of patients and the appropriate vaccines to distribute in order to prevent further spread of the outbreak read more ...