title: Pyroprinting: a rapid and flexible genotypic fingerprinting method for typing bacterial strains.
abstract: Bacterial strain typing is commonly employed in studies involving epidemiology, population ecology, and microbial source tracking to identify sources of fecal contamination. Methods for differentiating strains generally use either a collection of phenotypic traits or rely on some interrogation of the bacterial genotype. This report introduces pyroprinting, a novel genotypic strain typing method that is rapid, inexpensive, and discriminating compared to the most sensitive methods already in use. Pyroprinting relies on the simultaneous pyrosequencing of polymorphic multicopy loci, such as the intergenic transcribed spacer regions of rRNA operons in bacterial genomes. Data generated by sequencing combinations of variable templates are reproducible and intrinsically digitized. The theory and development of pyroprinting in Escherichia coli, including the selection of similarity thresholds to define matches between isolates, are presented. The pyroprint-based strain differentiation limits and phylogenetic relevance compared to other typing methods are also explored. Pyroprinting is unique in its simplicity and, paradoxically, in its intrinsic complexity. This new approach serves as an excellent alternative to more cumbersome or less phylogenetically relevant strain typing methods.
authors.affiliation: Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, USA. Electronic address: mblack@calpoly.edu.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Black
authors.affiliation: Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: VanderKelen
authors.affiliation: Computer Science Department, California Polytechnic State University, San Luis Obispo, CA, USA.
authors.forename: Aldrin
authors.initials: A
authors.lastname: Montana
authors.affiliation: Computer Science Department, California Polytechnic State University, San Luis Obispo, CA, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Dekhtyar
authors.affiliation: Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Neal
authors.affiliation: Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA.
authors.forename: Anya
authors.initials: A
authors.lastname: Goodman
authors.affiliation: Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA, USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Kitts
mesh_terms: D016172:DNA Fingerprinting / Q000379:methods*; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics*; D017720:Molecular Epidemiology; D058889:Molecular Typing / Q000379:methods*
keywords: DNA fingerprinting; Escherichia coli; Microbial source tracking (MST); Pyrosequencing; Strain typing; rRNA