Journal Article

Rapid Identification and Strain-Typing of Respiratory Pathogens for Epidemic Surveillance

Robbins, David W., Freed, Nikki, Rudnick, Karl, Massire, Christian, Jiang, Yun, Ivy, Cristina, Sampath, Rangarajan, Barrozo, Chris, Blyn, Lawrence B., Crooke, Stanley T., Moradi, Emily, Ecker, David J., Harrell, Patina M., Falkow, Stanley, Hall, Thomas A., Hannis, James C., Melton, Rachael E., Russell, Kevin, Ecker, Joseph A., Samant, Vivek, Desai, Anjali, McNeil, John A., Ranken, Raymond, Eshoo, Mark W., Knize, Duane J., Wu, Jianguo, Libby, Brian, Drader, Jared J., White, Neill, Hofstadler, Steven A., Sannes-Lowery, Kristin A.

2005

Overview

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.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: Bacteria / Bacteria - genetics / Base Composition / Biological Sciences / California - epidemiology / Conserved Sequence - genetics / Disease outbreaks / DNA Primers / Epidemics / Genetic Techniques / Genotype / Humans / Infections / Ionization / Mass spectrometry / Military / Military Personnel / Military recruitment / Military training / Pathogens / Polymerase chain reaction / Respiratory diseases / Respiratory system / Respiratory Tract Infections - epidemiology / Respiratory Tract Infections - microbiology / Sentinel Surveillance / Sequencing / Species Specificity / Spectrometry, Mass, Electrospray Ionization / Surveillance / Throat / Virulence Factors - genetics