Isolation, Identification, Antimicrobial Resistance Testing, and Whole-Genome Sequencing Analysis of Pathogenic Bacteria Causing Yak Calves Diarrhea in Qinghai Province

Backgroud Pathogenic Escherichia coli ( E. coli ) causes calf diarrhea, which is a serious threat to animal husbandry and health development in the Qinghai-Tibet Plateau. Here, we aimed to characterize the pathogenicity and explore the key pathogens which cause diarrhea in calves. Anal swabs were isolated and identified pathogenic bacteria from diarrheal yak calves in Qinghai Province. The strains were identified by Gram staining, 16S rDNA amplification, and 16S rRNA sequencing. The Kirby-Bauer (K-B) disk diffusion was utilized to confirm the antibiotic resistance. Furthermore, the whole-genome sequencing was revealed to genome characterization、virulent genes and resistance genes by the Nanopore sequencing system, while H&E and survival curve assays were performed to evaluate the pathogenicity of HYCQ01 strain. Results A total of 8 E . coli strains (8/8, 100 %) were obtained from the sample and confirmed to be E. coli . The antibiotic sensitivity test revealed that all E. coli strains from the diarrheic yak calves exhibited multidrug resistance (MDR) phenotypes. E. coli isolates were found 100 % resistant to Penicillin G (PEN) and Clindamycin (LIN), whereas 87.5% and 75.0 % isolates were resistant to Sulfafurazole (SUL) and Erythromycin (ERY), respectively. Whole Genome Sequence Analysis showed that the complete genome of HYCQ01 strain was 5,448,231 bp in length, with 50.8% G+C content, and a gene coverage of 100%; A total of 337 and 635 items, in VFDB Set A (the core dataset of VFDB) and Set B (the full dataset of VFDB) of HYCQ01 strain, respectively; HYCQ01 strain harbored 32 types of antibiotic resistance and 152 antibiotic resistance genes. Phylogenetic analysis suggested that the HYCQ01 strain shared the closest homology with Escherichia coli O139:H28(E24377A, ETEC). Meanwhile, 1×10 ⁸ CFU suspension could cause all mice dead after being injected with HYCQ01 for 16 h, with tissues damage in different levels. Conclusion In this study, eight strains were isolated from a 12-point sample from Huangyuan area of Qinghai-Tibet, and 16S rRNA sequencing showed that all of them were E. coli . Clinical samples were highly multidrug resistant which included SIZ, ERY, PEN and LIN, and sensitive to ceftazidime, FOX, GEN and cotrimoxazole. β-lactam. HYCQ01 is a multidrug-resistant strain and confirms the presence of resistance genes. The drug resistance genes and virulence genes carried by HYCQ01 revealed the pathogenicity and resistance mechanisms to a certain degree which demonstrated the horizontal transfer of these genes among different species. These findings provide a theoretical basis for the rational use of antibiotic drugs for the prevention and treatment of yak calf diarrhea in the Tibetan Plateau region.