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

摘要

Epidemic respiratory infections are responsible for extensive morbidity and mortality within both military and civilian populations. We describe a methodology to examine respiratory samples that simultaneously identifies broad groups of bacteria. The process uses electrospray ionization mass spectrometry and base composition analysis of broad-range PCK amplification products. The base composition analyses from a small set of broad- range primer pairs are used to 'triangulate' the identity of pathogenic organisms present in the sample. Once a species has been identified, the rapid recursive use of species-specific primers to housekeeping genes allows strain- typing. This strategy was used to examine samples from military recruits sickened in a recent Group A streptococcal (GAS) pneumonia outbreak (MMWK 52, 6, p106-109, 2003). The strain-typing results were essentially identical to those obtained using classic emm typing and Multi Locus Sequence Typing. This method allows real-time evaluation of patient samples and will make possible more rapid and appropriate treatment of patients in an ongoing epidemic, regardless of the etiology, in a time frame not previously achievable.