Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification

被引：0
作者：
Chrzastek, Klaudia [1 ,2 ]
Seal, Bruce S. [3 ]
Kulkarni, Arun [4 ]
Kapczynski, Darrell R. [1 ]
机构：
[1] ARS, Exot & Emerging Avian Viral Dis Res Unit, US Natl Poultry Res Ctr, USDA, 934 Coll Stn Rd, Athens, GA 30605 USA
[2] Georgia State Univ, Inst Biomed Sci, Ctr Translat Antiviral Res, Atlanta, GA 30303 USA
[3] Oregon State Univ Cascades, Biol Program, 1500 SW Chandler Ave, Bend, OR 97702 USA
[4] Georgia Poultry Lab Network, 3235 Abit Massey Way, Gainesville, GA 30507 USA
来源：
VETERINARY SCIENCES | 2025年 / 12卷 / 02期
关键词：
shotgun; metagenomics; <italic>Ornitobacterium rhinotracheale</italic>; prophage; genome annotation; DNA sequencing; bacteria sequencing; ORT; ORNITHOBACTERIUM-RHINOTRACHEALE; CHLAMYDIA-PSITTACI; SINGLE-CELL; POULTRY; INFECTION; TURKEYS; IMPLEMENTATION; SURVEILLANCE; RESISTANCE; OUTBREAK;
D O I：
10.3390/vetsci12020162
中图分类号：
S85 [动物医学（兽医学）];
学科分类号：
0906 ;
摘要：
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, Ornithobacterium rhinotracheale (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.
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页数：19
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