Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water
ABSTRACT 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 1...
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Online Access: | http://dx.doi.org/10.1128/aem.05734-11 https://journals.asm.org/doi/pdf/10.1128/AEM.05734-11 |
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crasmicro:10.1128/aem.05734-11 2024-09-30T14:33:25+00:00 Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water Green, Hyatt C. Dick, Linda K. Gilpin, Brent Samadpour, Mansour Field, Katharine G. 2012 http://dx.doi.org/10.1128/aem.05734-11 https://journals.asm.org/doi/pdf/10.1128/AEM.05734-11 en eng American Society for Microbiology https://journals.asm.org/non-commercial-tdm-license Applied and Environmental Microbiology volume 78, issue 2, page 503-510 ISSN 0099-2240 1098-5336 journal-article 2012 crasmicro https://doi.org/10.1128/aem.05734-11 2024-09-17T04:08:04Z ABSTRACT 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. Article in Journal/Newspaper Canada Goose ASM Journals (American Society for Microbiology) Canada New Zealand Applied and Environmental Microbiology 78 2 503 510 |
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ASM Journals (American Society for Microbiology) |
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crasmicro |
language |
English |
description |
ABSTRACT 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. |
format |
Article in Journal/Newspaper |
author |
Green, Hyatt C. Dick, Linda K. Gilpin, Brent Samadpour, Mansour Field, Katharine G. |
spellingShingle |
Green, Hyatt C. Dick, Linda K. Gilpin, Brent Samadpour, Mansour Field, Katharine G. Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water |
author_facet |
Green, Hyatt C. Dick, Linda K. Gilpin, Brent Samadpour, Mansour Field, Katharine G. |
author_sort |
Green, Hyatt C. |
title |
Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water |
title_short |
Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water |
title_full |
Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water |
title_fullStr |
Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water |
title_full_unstemmed |
Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water |
title_sort |
genetic markers for rapid pcr-based identification of gull, canada goose, duck, and chicken fecal contamination in water |
publisher |
American Society for Microbiology |
publishDate |
2012 |
url |
http://dx.doi.org/10.1128/aem.05734-11 https://journals.asm.org/doi/pdf/10.1128/AEM.05734-11 |
geographic |
Canada New Zealand |
geographic_facet |
Canada New Zealand |
genre |
Canada Goose |
genre_facet |
Canada Goose |
op_source |
Applied and Environmental Microbiology volume 78, issue 2, page 503-510 ISSN 0099-2240 1098-5336 |
op_rights |
https://journals.asm.org/non-commercial-tdm-license |
op_doi |
https://doi.org/10.1128/aem.05734-11 |
container_title |
Applied and Environmental Microbiology |
container_volume |
78 |
container_issue |
2 |
container_start_page |
503 |
op_container_end_page |
510 |
_version_ |
1811637317081759744 |