In this study, we developed two novel qPCR-assays for the detection of bacteria in house dust; one that determines the total bacterial amount and another that detects Gram-positive and Gram-negative bacteria separately. The methods were tested in silico and in vitro with microbial strains and vacuum cleaner dust samples, and validated in relation to culture and chemical marker analysis. We also compared the results of these three types of methods (qPCR, culture and chemical marker analysis) in 211 house dust samples from farming and non-farming environments. Microbial concentrations determined by the new qPCR assays (median 7.2 × 10⁵ cell equivalents mg⁻¹) were about two orders of magnitude higher than concentrations obtained by culture (median 6.7 × 10³ cfu mg⁻¹). The median concentration of muramic acid was 25.67 ng mg⁻¹ and that of 3-hydroxy fatty acids, expressed as LPS_10–16 was 26.14 pg mg⁻¹. Correlations between qPCR and chemical markers were moderate, while correlations between culture and qPCR and chemical markers were low to moderate. All the methods used in this study showed that the microbial concentrations are statistically significantly higher (p < 0.001, Mann–Whitney) in farming than non-farming environments.

As a conclusion, all tested methods can be used for determining the bacterial load in dust samples, but none of the methods was superior to the others. The results obtained with these methods represent different aspects of bacterial exposure and therefore the results are not expected to be identical with each other.