Identification of a Brevibacterium marker gene specific to poultry litter and development of a quantitative PCR assay

To identify a DNA sequence specific to a bacterium found in poultry litter that was indicative of faecal contamination by poultry sources.

Faecally contaminated poultry litter and soils were used as source material for the development of a quantitative polymerase chain reaction (qPCR) method targeting the 16S rRNA gene of a Brevibacterium sp. The identified sequence had 98% nucleotide identity to the 16S rRNA gene of Brevibacterium avium. The qPCR method was tested on 17 soiled litter samples; 40 chicken faecal samples; and 116 nontarget faecal samples from cattle, swine, ducks, geese, and human sewage collected across the United States. The 571-bp product was detected in 76% of poultry-associated samples, but not in 93% of faecal samples from other sources. Marker concentrations were 10(7) -10(9) gene copies per gram in soiled litter, up to 10(5) gene copies per gram in spread-site soils, and 10(7) gene copies per litre in field run-off water. Results were corroborated by a blinded study conducted by a second laboratory.

The poultry-specific PCR product is a useful marker gene for assessing the impact of faecal contamination as a result of land-applied poultry litter.

This study describes the first quantitative, sensitive and specific microbial source tracking method for the detection of poultry litter contamination.