Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance

• DOI: 10.1073/pnas.0409920102
• Publication Date: 2005-05-24T00:26:03Z
• Authors: David J. Ecker; Rangarajan Sampath; Lawrence B. Blyn; Mark W. Eshoo; Cristina Ivy; Joseph A. Ecker; Brian Libby; Vivek Samant; Kristin A. Sannes...; Rachael E. Melton; Kevin Russell; Nikki Freed; Chris Barrozo; Jianguo Wu; Karl Rudnick; Anjali Desai; Emily Moradi; Duane J. Knize; David W. Robbins; James C. Hannis; Patina M. Harrell; Christian Massire; Thomas A. Hall; Yun Jiang; Raymond Ranken; Jared J. Drader; Neill White; John A. McNeil; Stanley T. Crooke; Steven A. Hofstadler
• Keywords: 0301 basic medicine; Base Composition; Spectrometry, Mass, Electrospray Ionization; Bacteria; Genotype; Virulence Factors; California; 3. Good health; 03 medical and health sciences; Military Personnel; Genetic Techniques; Species Specificity; Humans; Respiratory Tract Infections; Sentinel Surveillance; Conserved Sequence; DNA Primers

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.