Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance.
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.
Ecker
David J
DJ
Ibis Division of Isis Pharmaceuticals, 1891 Rutherford Road, Carlsbad, CA 92008, USA. decker@isisph.com
Sampath
Rangarajan
R
Blyn
Lawrence B
LB
Eshoo
Mark W
MW
Ivy
Cristina
C
Ecker
Joseph A
JA
Libby
Brian
B
Samant
Vivek
V
Sannes-Lowery
Kristin A
KA
Melton
Rachael E
RE
Russell
Kevin
K
Freed
Nikki
N
Barrozo
Chris
C
Wu
Jianguo
J
Rudnick
Karl
K
Desai
Anjali
A
Moradi
Emily
E
Knize
Duane J
DJ
Robbins
David W
DW
Hannis
James C
JC
Harrell
Patina M
PM
Massire
Christian
C
Hall
Thomas A
TA
Jiang
Yun
Y
Ranken
Raymond
R
Drader
Jared J
JJ
White
Neill
N
McNeil
John A
JA
Crooke
Stanley T
ST
Hofstadler
Steven A
SA
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*
D017931:DNA Primers; D037521:Virulence Factors