Quantitative detection of fecal contamination with domestic poultry feces in environments in China

Abstract

Poultry are an important source of fecal contamination in environments. However, tools for detecting and tracking this fecal contamination are in the early stages of development. In practice, we have found that source tracking methods targeting the 16S rRNA genes of poultry-specific microbiota are not sufficiently sensitive. We therefore developed two quantitative PCR assays for detection of poultry fecal contamination, by targeting chicken and duck mitochondrial genes: NADH dehydrogenase subunit 5 (ND5) and cytochrome b (cytb). The sensitivity of both assays was 100% when tested on 50 chicken and duck fecal samples from 10 provinces of China. These assays were also tested in field samples, including soil and water collected adjacent to duck farms, and soils fertilized with chicken manure. Poultry mitochondrial DNA was detected in most of these samples, indicating that the assays are a robust method for monitoring environmental contamination with poultry feces. Complemented with existing indicators of fecal contamination, these markers should improve the efficiency and accuracy of microbial source tracking.

Quantification of Microbial Source Tracking and Pathogenic Bacterial Markers in Water and Sediments of Tiaoxi River (Taihu Watershed)

“…The only possible explanation for the consistent detection of swine associated markers at location 12 is the transport of bacteria from location 13, as the distance between two locations is ∼1 km. In China, both backyard and commercial based poultry farming are common and the existence of such farms nearby leads to the release of poultry feces into the watershed (Zhuang et al, 2017). The provincial government of Zhejiang had concerns over the illegal discharge of poultry wastes into the watershed and has recently initiated monitoring control measures (Zheijiang, 2016).…”

Validation of microbial source tracking markers for the attribution of fecal contamination in indoor-household environments of the Peruvian Amazon

“…Four avian markers were tested: two ( ND5 and cytb ) targeting avian mitochondrial gene segments of chickens and ducks, one targeting a gene segment of Lactobacillus sp. associated with domestic and waterfowl birds ( Av4143 ) and one targeting a gene segment of Brevibacterium avium associated with chickens only ( LA35 ) ( Ohad et al, 2016 ; Zhuang et al, 2017 ; Weidhaas and Lipscomb, 2013 ). Of all four markers, Av4143 and cytB presented the highest sensitivity (72.7% and 87.0%) and specificity (87.5% and 82.4%) combination.…”

“…Eight MST markers were selected for validation. Four markers targeted avian species ( LA35 , Av4143 , ND5 and CytB ) and the other four targeted mammalian species including humans ( HF183-Taq and BacHum ), dogs ( BacCan ) and pigs ( Pig2Bac )( Kildare et al, 2007 ; Weidhaas et al, 2010 ; Ohad et al, 2016 ; Zhuang et al, 2017 ; Pisanic et al, 2015 ). Two markers ( cytB and ND5 ) targeted avian mitochondrial DNA segments, and the remaining six targeted host-specific gastrointestinal bacteria, including Brevibacterium avium (LA35) , a species of Lactobacillus spp.…”

“…These bacteria have been extensively used as a MST tool given the bacterium's ability to adapt to the intestinal environment of specific animal hosts ( Dick et al, 2005 ). Other markers targeting host-specific enteric bacterial flora, as well as mitochondrial DNA segments, have also been developed ( Kildare et al, 2007 ; Bernhard and Field, 2000 ; Boehm et al, 2013 ; Weidhaas et al, 2010 ; Ohad et al, 2016 ; Zhuang et al, 2017 ). Validation of MST markers has proven that their discriminatory power is site specific, and as a result, requires a performance evaluation to determine the sensitivity, specificity and accuracy of each marker ( Gawler et al, 2007 ).…”

Associations among Household Animal Ownership, Infrastructure, and Hygiene Characteristics with Source Attribution of Household Fecal Contamination in Peri-Urban Communities of Iquitos, Peru

“…29 Specifically, two avian fecal markers (Av4143 and LA35), two avian mitochondrial fecal markers (cytb and ND5), two human fecal markers (BachHum and HF83-Taqman), one dog fecal marker (BactCan), and one pig fecal marker (Pig2Bac) were used. [33][34][35][36][37] Details regarding the target species, gene, and internal validity parameters of all eight MST markers are presented in Supplemental Table 1.…”