title: Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance.
abstract: Epidemic respiratory infections are responsible for extensive morbidity and mortality within both military and civilian populations. We describe a high-throughput method to simultaneously identify and genotype species of bacteria from complex mixtures in respiratory samples. The process uses electrospray ionization mass spectrometry and base composition analysis of PCR amplification products from highly conserved genomic regions to identify and determine the relative quantity of pathogenic bacteria present in the sample. High-resolution genotyping of specific species is achieved by using additional primers targeted to highly variable regions of specific bacterial genomes. This method was used to examine samples taken from military recruits during respiratory disease outbreaks and for follow up surveillance at several military training facilities. Analysis of respiratory samples revealed high concentrations of pathogenic respiratory species, including Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pyogenes. When S. pyogenes was identified in samples from the epidemic site, the identical genotype was found in almost all recruits. This analysis method will provide information fundamental to understanding the polymicrobial nature of explosive epidemics of respiratory disease.
authors.affiliation: Ibis Division of Isis Pharmaceuticals, 1891 Rutherford Road, Carlsbad, CA 92008, USA. decker@isisph.com
authors.forename: David J
authors.initials: DJ
authors.lastname: Ecker
authors.forename: Rangarajan
authors.initials: R
authors.lastname: Sampath
authors.forename: Lawrence B
authors.initials: LB
authors.lastname: Blyn
authors.forename: Mark W
authors.initials: MW
authors.lastname: Eshoo
authors.forename: Cristina
authors.initials: C
authors.lastname: Ivy
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Ecker
authors.forename: Brian
authors.initials: B
authors.lastname: Libby
authors.forename: Vivek
authors.initials: V
authors.lastname: Samant
authors.forename: Kristin A
authors.initials: KA
authors.lastname: Sannes-Lowery
authors.forename: Rachael E
authors.initials: RE
authors.lastname: Melton
authors.forename: Kevin
authors.initials: K
authors.lastname: Russell
authors.forename: Nikki
authors.initials: N
authors.lastname: Freed
authors.forename: Chris
authors.initials: C
authors.lastname: Barrozo
authors.forename: Jianguo
authors.initials: J
authors.lastname: Wu
authors.forename: Karl
authors.initials: K
authors.lastname: Rudnick
authors.forename: Anjali
authors.initials: A
authors.lastname: Desai
authors.forename: Emily
authors.initials: E
authors.lastname: Moradi
authors.forename: Duane J
authors.initials: DJ
authors.lastname: Knize
authors.forename: David W
authors.initials: DW
authors.lastname: Robbins
authors.forename: James C
authors.initials: JC
authors.lastname: Hannis
authors.forename: Patina M
authors.initials: PM
authors.lastname: Harrell
authors.forename: Christian
authors.initials: C
authors.lastname: Massire
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Hall
authors.forename: Yun
authors.initials: Y
authors.lastname: Jiang
authors.forename: Raymond
authors.initials: R
authors.lastname: Ranken
authors.forename: Jared J
authors.initials: JJ
authors.lastname: Drader
authors.forename: Neill
authors.initials: N
authors.lastname: White
authors.forename: John A
authors.initials: JA
authors.lastname: McNeil
authors.forename: Stanley T
authors.initials: ST
authors.lastname: Crooke
authors.forename: Steven A
authors.initials: SA
authors.lastname: Hofstadler
mesh_terms: D001419:Bacteria / Q000235:genetics*; D001482:Base Composition; D002140:California / Q000453:epidemiology; D017124:Conserved Sequence / Q000235:genetics; D017931:DNA Primers; D005821:Genetic Techniques; D005838:Genotype; D006801:Humans; D008889:Military Personnel; D012141:Respiratory Tract Infections / Q000453:epidemiology* / Q000382:microbiology*; D018571:Sentinel Surveillance; D013045:Species Specificity; D021241:Spectrometry, Mass, Electrospray Ionization; D037521:Virulence Factors / Q000235:genetics*
chemical_list: D017931:DNA Primers; D037521:Virulence Factors