disclosed are methods of diagnosis of a pathogen - associated disease . these methods comprise : providing a biological sample from a human subject ; determining presence , absence and / or quantity of a bacterial pathogen , a viral pathogen , or a combination thereof , by a pathogen culture , a serum antibody detection test , a pathogen antigen detection test , a pathogen dna and / or rna detection test , or a combination thereof ; determining in the sample , expression levels of at least one endogenous gene in which aberrant expression levels are associated with infection with a pathogen , by a microarray hybridization assay , rna - seq assay , polymerase chain reaction assay , a lamp assay , a ligase chain reaction assay , a southern , northern , or western blot assay , an elisa or a combination thereof . the subject can be diagnosed with the disease if the subject comprises the pathogen and an aberrant level of expression of an endogenous gene .