title: Navigating the future of bacterial molecular epidemiology.
abstract: Technological advances in high-throughput genome sequencing have led to an enhanced appreciation of the genetic diversity found within populations of pathogenic bacteria. Methods based on single nucleotide polymorphisms (SNPs) and insertions or deletions (indels) build upon the framework established by multi-locus sequence typing (MLST) and permit a detailed, targeted analysis of variation within related organisms. Robust phylogenetics, when combined with epidemiologically informative data, can be applied to study ongoing temporal and geographical fluctuations in bacterial pathogens. As genome sequencing, SNP detection and geospatial information become more accessible these methods will continue to transform the way molecular epidemiology is used to study populations of bacterial pathogens.
authors.affiliation: Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hospital for Tropical Diseases, 190 Ben Ham Tu, Quan 5, Ho Chi Minh City, Viet Nam. sbaker@oucru.org
authors.forename: Stephen
authors.initials: S
authors.lastname: Baker
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Holt
mesh_terms: D014644:Genetic Variation; D054643:INDEL Mutation; D017720:Molecular Epidemiology / Q000639:trends*; D058885:Multilocus Sequence Typing; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D012485:Salmonella typhi / Q000235:genetics; D017422:Sequence Analysis, DNA; D013203:Staphylococcal Infections / Q000453:epidemiology* / Q000635:transmission; D014435:Typhoid Fever / Q000453:epidemiology* / Q000382:microbiology