Genetic Markers for Rapid PCR-Based Identification of Gull, Canada Goose, Duck, and Chicken Fecal Contamination in Water
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 ge...
Published in: | Applied and Environmental Microbiology |
---|---|
Main Authors: | , , , , |
Format: | Text |
Language: | English |
Published: |
American Society for Microbiology
2012
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255751 http://www.ncbi.nlm.nih.gov/pubmed/22081573 https://doi.org/10.1128/AEM.05734-11 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:3255751 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:3255751 2023-05-15T15:48:57+02:00 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. 2012-01 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255751 http://www.ncbi.nlm.nih.gov/pubmed/22081573 https://doi.org/10.1128/AEM.05734-11 en eng American Society for Microbiology http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255751 http://www.ncbi.nlm.nih.gov/pubmed/22081573 http://dx.doi.org/10.1128/AEM.05734-11 Copyright © 2012, American Society for Microbiology. All Rights Reserved. Microbial Ecology Text 2012 ftpubmed https://doi.org/10.1128/AEM.05734-11 2013-09-04T01:05:17Z 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. Text Canada Goose PubMed Central (PMC) Canada New Zealand Applied and Environmental Microbiology 78 2 503 510 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Microbial Ecology |
spellingShingle |
Microbial Ecology 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 |
topic_facet |
Microbial Ecology |
description |
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 |
Text |
author |
Green, Hyatt C. Dick, Linda K. Gilpin, Brent Samadpour, Mansour Field, Katharine G. |
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://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255751 http://www.ncbi.nlm.nih.gov/pubmed/22081573 https://doi.org/10.1128/AEM.05734-11 |
geographic |
Canada New Zealand |
geographic_facet |
Canada New Zealand |
genre |
Canada Goose |
genre_facet |
Canada Goose |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255751 http://www.ncbi.nlm.nih.gov/pubmed/22081573 http://dx.doi.org/10.1128/AEM.05734-11 |
op_rights |
Copyright © 2012, American Society for Microbiology. All Rights Reserved. |
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_ |
1766384040970027008 |