The invention provides methods useful for identifying polynucleotides expressed in vivo by a microbe during infection of a host. Antibodies against antigens that are expressed by the microbe in vivo and in vitro are adsorbed with cells or cellular extracts of the microbe that have been grown in vitro. Unadsorbed antibodies are isolated and are probed against a phage display library of the microbe's DNA or RNA. A polynucleotide of the microbe that is expressed in vivo is isolated and identified.

 
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