Comparative Analysis of Drug Resistance Phenotype and Genotype of 157 Strains of Riemerella anatipestifer

Riemerella anatipestifer is one of the important bacterial infectious diseases that threaten the waterfowl farming industry. In this study, 157 suspected R. anatipestifer strains was isolated from diseased ducks and geese from seven regions of China during 2019-2020, then identified using multiple PCR. Furthermore, drug susceptibility tests and whole-genome sequencing analysis were performed for comparative analysis of drug resistance phenotype and genotype. The results showed that these strains were sensitive to florfenicol, ceftriaxone, cefradine, spectinomycin, sulfafurazole and cefepime, but resistant to kanamycin, amikacin, gentamicin, streptomycin and neomycin, exhibiting multiple drug resistance. Whole-genome sequencing analysis revealed a wide distribution of genotypes among the 157 strains with no apparent regional pattern. Through next-generation sequencing analysis of drug resistance genes, a total of 105 resistant genes were identified. Of them, 19 tetracycline resistance genes were most commonly found, followed by 11 glycopeptide and efflux pump encoding genes, and 7 macrolide resistance genes. The 157 R. anatipestifer strains contained 56-72 resistant genes each, with the strains carrying 63 different resistant genes being the most abundant. By comparing the drug resistance genotypes and phenotypes, it was observed that, except for a significant difference in aminoglycoside resistance genotypes and phenotypes, there was a high correlation between the genotypes and phenotypes of the other drug resistance detected. In conclusion, 157 R. anatipestifer strains exhibited severe multidrug resistance, emphasizing the need for improved antibiotic usage guidelines. The wide distribution and diverse types of resistant genes among these strains provide a foundation for studying novel mechanisms of drug resistance.