Ceftiofur-resistant Salmonella strains isolated from dairy farms represent multiple widely distributed subtypes that evolved by independent horizontal gene transfer

Abstract

Salmonella is the leading cause of known food-borne bacterial infections in the United States, with an incidence rate of approximately 15 cases per 100,000 people. The rise of antimicrobial-resistant Salmonella subtypes, including the appearance of subtypes resistant to ceftriaxone, represents a particular concern. Ceftriaxone is used to treat invasive cases of Salmonella in children and is closely related to ceftiofur, an antibiotic commonly used to treat diseases of cattle. In order to develop a better understanding of the evolution and transmission of ceftiofur resistance in Salmonella, we characterized ceftiofur-resistant and -sensitive Salmonella isolates from seven New York dairy farms. A total of 39 isolates from these seven farms were analyzed for evolutionary relatedness (by DNA sequencing of the Salmonella genes fimA, manB, and mdh), antibiotic resistance profiles, and the presence of bla(CMY-2), a beta-lactamase gene associated with resistance to cephalosporins. Our data indicate that (i) resistance to ceftriaxone and ceftiofur was highly correlated with the presence of bla(CMY-2); (ii) ceftiofur-resistant Salmonella strains were geographically widespread, as shown by their isolation from farms located throughout New York State; (iii) ceftiofur-resistant Salmonella strains isolated from farms represent multiple distinct subtypes and evolutionary lineages, as determined by serotyping, DNA sequence typing, and antimicrobial-resistance profiles; and (iv) ceftiofur-resistant Salmonella strains evolved by multiple independent acquisitions of an identical bla(CMY-2) allele and by clonal spread of ceftiofur-resistant subtypes.

FIG. 1.

Distribution of MLST types across New York dairy farms. Numbers in parenthesis indicate farm number, and boldface numbers indicate MLST types isolated on the respective farms.

FIG. 2.

Phylogenetic tree of Salmonella isolates based on the concatenated manB, mdh, and fimA sequences. The phylogenetic tree was built using the maximum-likelihood method and the TrN+G model, which was selected by MODELTEST as the best model. The outgroup branch length was collapsed for easier viewing. Bootstrap values >50.0 are indicated at the node of the branch. Numbers in parentheses indicate farm numbers, C indicates the presence of bla_CMY-2, and F indicates the presence of floR. The scale bar indicates relative sequence distance.