Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification
A whole-genome shotgun sequencing (sWGS) approach was applied to chicken clinical tracheal swab samples during metagenomics investigations to identify possible microorganisms among poultry with respiratory diseases. After applying shotgun sequencing, <i>Ornithobacterium rhinotracheale</i>...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-02-01
|
| Series: | Veterinary Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2306-7381/12/2/162 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850229835914280960 |
|---|---|
| author | Klaudia Chrzastek Bruce S. Seal Arun Kulkarni Darrell R. Kapczynski |
| author_facet | Klaudia Chrzastek Bruce S. Seal Arun Kulkarni Darrell R. Kapczynski |
| author_sort | Klaudia Chrzastek |
| collection | DOAJ |
| description | A whole-genome shotgun sequencing (sWGS) approach was applied to chicken clinical tracheal swab samples during metagenomics investigations to identify possible microorganisms among poultry with respiratory diseases. After applying shotgun sequencing, <i>Ornithobacterium rhinotracheale</i> (ORT) and a putative prophage candidate were found in one of the swab samples. A multi-locus sequence typing (MLST) scheme of the ORT genome involved the adk, aroE, fumC, gdhA, pgi, and pmi genes. Antibiotic resistant analysis demonstrated tetracycline-resistan t ribosomal protection protein, tetQ, the aminoglycoside-(3)-acetyltransferase IV gene, aminoglycoside antibiotic inactivation and macrolide resistance, and the ermX gene in the ORT genome. A putative prophage candidate was predicted using Prophage Hunter and PHAST, while BLAST analyses were utilized to identify genes encoding bacteriophage proteins. Interestingly, genes encoding endolysins were detected in bacteriophage genomes. The gene products encoded in the prophage sequence were most closely related to bacteriophages in the N4-like family among the Authographiviridae in the Caudovirales. This study demonstrates the potential of sWGS for the rapid detection and characterization of etiologic agents found in clinical samples. |
| format | Article |
| id | doaj-art-75f876c8f1d240ecaf2086bf14e71c35 |
| institution | OA Journals |
| issn | 2306-7381 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Veterinary Sciences |
| spelling | doaj-art-75f876c8f1d240ecaf2086bf14e71c352025-08-20T02:04:05ZengMDPI AGVeterinary Sciences2306-73812025-02-0112216210.3390/vetsci12020162Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage IdentificationKlaudia Chrzastek0Bruce S. Seal1Arun Kulkarni2Darrell R. Kapczynski3Exotic and Emerging Avian Diseases Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture (USDA), 934 College Station Road, Athens, GA 30605, USABiology Program, Oregon State University—Cascades, 1500 SW Chandler Avenue, Bend, OR 97702, USAGeorgia Poultry Laboratory Network, 3235 Abit Massey Way, Gainesville, GA 30507, USAExotic and Emerging Avian Diseases Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture (USDA), 934 College Station Road, Athens, GA 30605, USAA whole-genome shotgun sequencing (sWGS) approach was applied to chicken clinical tracheal swab samples during metagenomics investigations to identify possible microorganisms among poultry with respiratory diseases. After applying shotgun sequencing, <i>Ornithobacterium rhinotracheale</i> (ORT) and a putative prophage candidate were found in one of the swab samples. A multi-locus sequence typing (MLST) scheme of the ORT genome involved the adk, aroE, fumC, gdhA, pgi, and pmi genes. Antibiotic resistant analysis demonstrated tetracycline-resistan t ribosomal protection protein, tetQ, the aminoglycoside-(3)-acetyltransferase IV gene, aminoglycoside antibiotic inactivation and macrolide resistance, and the ermX gene in the ORT genome. A putative prophage candidate was predicted using Prophage Hunter and PHAST, while BLAST analyses were utilized to identify genes encoding bacteriophage proteins. Interestingly, genes encoding endolysins were detected in bacteriophage genomes. The gene products encoded in the prophage sequence were most closely related to bacteriophages in the N4-like family among the Authographiviridae in the Caudovirales. This study demonstrates the potential of sWGS for the rapid detection and characterization of etiologic agents found in clinical samples.https://www.mdpi.com/2306-7381/12/2/162shotgunmetagenomics<i>Ornitobacterium rhinotracheale</i>prophagegenome annotationDNA sequencing |
| spellingShingle | Klaudia Chrzastek Bruce S. Seal Arun Kulkarni Darrell R. Kapczynski Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification Veterinary Sciences shotgun metagenomics <i>Ornitobacterium rhinotracheale</i> prophage genome annotation DNA sequencing |
| title | Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification |
| title_full | Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification |
| title_fullStr | Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification |
| title_full_unstemmed | Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification |
| title_short | Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification |
| title_sort | whole genome shotgun sequencing from chicken clinical tracheal samples for bacterial and novel bacteriophage identification |
| topic | shotgun metagenomics <i>Ornitobacterium rhinotracheale</i> prophage genome annotation DNA sequencing |
| url | https://www.mdpi.com/2306-7381/12/2/162 |
| work_keys_str_mv | AT klaudiachrzastek wholegenomeshotgunsequencingfromchickenclinicaltrachealsamplesforbacterialandnovelbacteriophageidentification AT brucesseal wholegenomeshotgunsequencingfromchickenclinicaltrachealsamplesforbacterialandnovelbacteriophageidentification AT arunkulkarni wholegenomeshotgunsequencingfromchickenclinicaltrachealsamplesforbacterialandnovelbacteriophageidentification AT darrellrkapczynski wholegenomeshotgunsequencingfromchickenclinicaltrachealsamplesforbacterialandnovelbacteriophageidentification |