Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing
According to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also carry antibiotic resistance gene...
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MDPI AG
2025-01-01
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| author | Smriti Shringi Devendra H. Shah Kimberly Carney Ashutosh Verma |
| author_facet | Smriti Shringi Devendra H. Shah Kimberly Carney Ashutosh Verma |
| author_sort | Smriti Shringi |
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| description | According to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also carry antibiotic resistance genes (ARGs), serving as a reservoir for antimicrobial resistance (AMR) transmission. This study aimed to utilize whole metagenome sequencing (WMS) to screen for microbial pathogens and assess the resistome in healthy shelter dogs. Fecal samples from 58 healthy shelter dogs across 10 shelters in Kentucky, Tennessee, and Virginia were analyzed using WMS. Genomic DNA was extracted, and bioinformatics analyses were performed to identify pathogens and ARGs. The WMS detected 53 potentially zoonotic or known pathogens including thirty-eight bacterial species, two protozoa, five yeast species, one nematode, four molds, and three viruses. A total of 4560 ARGs signatures representing 182 unique genes across 14 antibiotic classes were detected. Tetracycline resistance genes were most abundant (49%), while β-lactam resistance genes showed the highest diversity with 75 unique ARGs. ARGs were predominantly detected in commensal bacteria; however, nearly half (18/38, 47.4%) of known bacterial pathogens detected in this study carried ARGs for resistance to one or more antibiotic classes. This study provides evidence that healthy shelter dogs carry a diverse range of zoonotic and antibiotic-resistant pathogens, posing a transmission risk through fecal shedding. These findings highlight the value of WMS for pathogen detection and AMR surveillance, informing therapeutic and prophylactic strategies to mitigate the transmission of pathogens among shelter dog populations and the risk associated with zoonoses. |
| format | Article |
| id | doaj-art-5c1439212b6b426d96bf879c4207606c |
| institution | Kabale University |
| issn | 2076-0817 |
| language | English |
| publishDate | 2025-01-01 |
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| series | Pathogens |
| spelling | doaj-art-5c1439212b6b426d96bf879c4207606c2025-01-24T13:44:40ZengMDPI AGPathogens2076-08172025-01-011413310.3390/pathogens14010033Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome SequencingSmriti Shringi0Devendra H. Shah1Kimberly Carney2Ashutosh Verma3School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USASchool of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USACollege of Veterinary Medicine, Lincoln Memorial University, Orange Park, FL 32073, USACenter for Infectious, Zoonotic and Vector-Borne Diseases, Lincoln Memorial University, Harrogate, TN 37752, USAAccording to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also carry antibiotic resistance genes (ARGs), serving as a reservoir for antimicrobial resistance (AMR) transmission. This study aimed to utilize whole metagenome sequencing (WMS) to screen for microbial pathogens and assess the resistome in healthy shelter dogs. Fecal samples from 58 healthy shelter dogs across 10 shelters in Kentucky, Tennessee, and Virginia were analyzed using WMS. Genomic DNA was extracted, and bioinformatics analyses were performed to identify pathogens and ARGs. The WMS detected 53 potentially zoonotic or known pathogens including thirty-eight bacterial species, two protozoa, five yeast species, one nematode, four molds, and three viruses. A total of 4560 ARGs signatures representing 182 unique genes across 14 antibiotic classes were detected. Tetracycline resistance genes were most abundant (49%), while β-lactam resistance genes showed the highest diversity with 75 unique ARGs. ARGs were predominantly detected in commensal bacteria; however, nearly half (18/38, 47.4%) of known bacterial pathogens detected in this study carried ARGs for resistance to one or more antibiotic classes. This study provides evidence that healthy shelter dogs carry a diverse range of zoonotic and antibiotic-resistant pathogens, posing a transmission risk through fecal shedding. These findings highlight the value of WMS for pathogen detection and AMR surveillance, informing therapeutic and prophylactic strategies to mitigate the transmission of pathogens among shelter dog populations and the risk associated with zoonoses.https://www.mdpi.com/2076-0817/14/1/33metagenomicsshelter dogsantimicrobial resistancepathogen |
| spellingShingle | Smriti Shringi Devendra H. Shah Kimberly Carney Ashutosh Verma Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing Pathogens metagenomics shelter dogs antimicrobial resistance pathogen |
| title | Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing |
| title_full | Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing |
| title_fullStr | Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing |
| title_full_unstemmed | Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing |
| title_short | Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing |
| title_sort | pathogen detection and resistome analysis in healthy shelter dogs using whole metagenome sequencing |
| topic | metagenomics shelter dogs antimicrobial resistance pathogen |
| url | https://www.mdpi.com/2076-0817/14/1/33 |
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