The applicability of hns and fimA primers for detecting Salmonella in bioaerosols associated with animal and municipal wastes

The ability to rapidly screen environmental samples for specific pathogens such as Salmonella spp., is of particular importance in molecular epidemiol ogy. Although gene amplification reactions allow the rapid detection of mic roorganisms, the use of appropriate oligonucleotide primers targeted agains t specific microbial genes is critical for accurate detection specificity a nd sensitivity. Primers such as fimA and hns have been previously shown to be specific for pure cultures of Salmonella. However, the analysis of envir onmental samples requires post-amplification hybridizations to detect ampli cons, since the presence of inhibitory environmental components reduces amp lification efficiency of the target organism. These sensitive post-amplific ation approaches also enable the detection of spurious amplification from n on-target sequences. Bioaerosols associated with animal facilities and muni cipal wastes contain a diverse array of pathogens including Clostridium spp . In our studies, hybridization sensor data revealed spurious amplification of clostridial species with Salmonella hns primers. Specificity checks usi ng type cultures of Clostridium spp. revealed non-specific amplification by hns primers. These results suggest that fimA primers may be better suited to screen Salmonella-specific sequences in environmental samples, especiall y those obtained from animal and municipal waste facilities.