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In recent years， diarrhea in cattle has been spreading in cattle farms with a high mortality rate， causing economic losses. This experiment aims to isolate and identify Shigella flexneri， which causes diarrhea in a Beijing cattle farm， and to clarify the biological characteristics and genomic features of the pathogen’s serotype， drug resistance， and pathogenicity. In this study， fecal samples from diarrheal cattle were collected for bacterial isolation and purification， 16S rRNA amplicon sequencing analysis， virulence gene detection， and whole-genome sequencing of isolated strains. The results showed that one strain of Shigella flexneri Fc was identified through bacterial isolation and purification， and PCR identification. Whole-genome sequencing revealed that the Shigella flexneri Fc strain has a genome size of 4.98 Mb and a GC content of 50.76%. It contains 91 tRNA genes， 7 23S rRNA， 7 16S rRNA， 8 5S rRNA， 283 misc_RNA， and 97 carbohydrate-active enzyme genes. TVBD annotation analysis identified 1 363 transporter genes； CARD annotation analysis identified 80 resistance genes； VFDB and PHI-base annotation analysis identified 1 410 potential virulence factor-related genes and 2 052 phenotypic mutation genes. Phylogenetic tree analysis revealed that Shigella flexneri is closely related to Shigella flexneri 29903， belonging to the same branch. This study completed the isolation and identification of a bovine-origin Shigella flexneri strain and whole-genome sequencing analysis， providing a theoretical basis for the prevention and control research of shigellosis.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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