Avian feces contaminate waterways but contribute fewer human pathogens than human sources. Rapid identification and quantification of avian contamination would therefore be useful to prevent overestimation of human health risk. We used subtractive hybridization of PCR-amplified gull fecal 16S RNA genes to identify avian-specific fecal rRNA gene sequences. The subtracters were rRNA genes amplified from human, dog, cat, cow, and pig feces. Recovered sequences were related to Enterobacteriaceae (47%), Helicobacter (26%), Catellicoccus (11%), Fusobacterium (11%), and Campylobacter (5%). Three PCR assays, designated GFB, GFC, and GFD, were based on recovered sequence fragments. Quantitative PCR assays for GFC and GFD were developed using SYBR green. GFC detected down to 0.1 mg gull feces/100 ml (corresponding to 2 gull enterococci most probable number [MPN]/100 ml). GFD detected down to 0.1 mg chicken feces/100 ml (corresponding to 13 Escherichia coli MPN/100 ml). GFB and GFC were 97% and 94% specific to gulls, respectively. GFC cross-reacted with 35% of sheep samples but occurred at about 100,000 times lower concentrations in sheep. GFD was 100% avian specific and occurred in gulls, geese, chickens, and ducks. In the United States, Canada, and New Zealand, the three markers differed in their geographic distributions but were found across the range tested. These assays detected four important bird groups contributing to fecal contamination of waterways: gulls, geese, ducks, and chickens. Marker distributions across North America and in New Zealand suggest that they will have broad applicability in other parts of the world as well.
Contamination from gulls, Canada geese, ducks, and other birds negatively impacts water quality (5, 16, 24, 33a, 49, 56). Their feces are sources of fecal coliforms, enterococci, and Escherichia coli, and their presence is correlated with elevated fecal indicator bacteria (FIB) and beach closures (2,22,23,38). Pathogenic E. coli and Campylobacter, Salmonella, Giardia, and Cryptosporidium spp. occur in bird feces (11,18,19,42) and can infect domestic poultry and humans (27, 41) and contaminate shellfish (1). Bird feces are also a source of antibiotic resistance genes (34,39,50). Recently, because of avian influenza, concerns have risen about pathogen movement due to bird migration (8,10,17,28,30).Although pathogens occur in bird feces, exposure to bird feces is considered less harmful to humans than exposure to other sources of fecal contaminants, especially that of humans (43, 51). For example, molecular evidence indicates that genotypes of certain parasites in birds, such as Giardia and Cryptosporidium, are host adapted and cannot cross-infect among different hosts (20, 57). The relative human health risks of bird and human fecal contamination will be more amenable to measurement once reliable methods are developed to distinguish them quantitatively. The ability to rapidly identify and quantify fecal contamination from birds will improve our ability to estimate human health risk from conta...