title: Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations.
abstract: Multidrug-resistant (MDR)Salmonella entericacan be spread from cattle to humans through direct contact with animals sheddingSalmonellaas well as through the food chain, making MDRSalmonellaa serious threat to human health. The objective of this study was to use whole-genome sequencing to compare antimicrobial-resistant (AMR)Salmonella entericaserovars Typhimurium, Newport, and Dublin isolated from dairy cattle and humans in Washington State and New York State at the genotypic and phenotypic levels. A total of 90 isolates were selected for the study (37STyphimurium, 32SNewport, and 21SDublin isolates). All isolates were tested for phenotypic antibiotic resistance to 12 drugs using Kirby-Bauer disk diffusion. AMR genes were detected in the assembled genome of each isolate using nucleotide BLAST and ARG-ANNOT. Genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.2 and specificity of 85.2. Sulfamethoxazole-trimethoprim resistance was observed only in human isolates (P< 0.05), while resistance to quinolones and fluoroquinolones was observed only in 6STyphimurium isolates from humans in Washington State.SNewport isolates showed a high degree of AMR profile similarity, regardless of source.SDublin isolates from New York State differed from those from Washington State based on the presence/absence of plasmid replicons, as well as phenotypic AMR susceptibility/nonsusceptibility (P< 0.05). The results of this study suggest that distinct factors may contribute to the emergence and dispersal of AMRS. entericain humans and farm animals in different regions.IMPORTANCEThe use of antibiotics in food-producing animals has been hypothesized to select for AMRSalmonella entericaand associated AMR determinants, which can be transferred to humans through different routes. Previous studies have sought to assess the degree to which AMR livestock- and human-associatedSalmonellastrains overlap, as well as the spatial distribution ofSalmonella's associated AMR determinants, but have often been limited by the degree of resolution at which isolates can be compared. Here, a comparative genomics study of livestock- and human-associatedSalmonellastrains from different regions of the United States shows that while many AMR genes and phenotypes were confined to human isolates, overlaps between the resistomes of bovine and human-associatedSalmonellaisolates were observed on numerous occasions, particularly forSNewport. We have also shown that whole-genome sequencing can be used to reliably predict phenotypic resistance acrossSalmonellaisolated from bovine sources.
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, USA.
authors.forename: Laura M
authors.initials: LM
authors.lastname: Carroll
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Wiedmann
authors.affiliation: Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA.
authors.forename: Henk
authors.initials: H
authors.lastname: den Bakker
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, USA.
authors.forename: Julie
authors.initials: J
authors.lastname: Siler
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Warchocki
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, USA.
authors.forename: David
authors.initials: D
authors.lastname: Kent
authors.affiliation: J. D. Gladstone Institutes, San Francisco, California, USA.
authors.forename: Svetlana
authors.initials: S
authors.lastname: Lyalina
authors.affiliation: Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, USA.
authors.forename: Margaret
authors.initials: M
authors.lastname: Davis
authors.affiliation: Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, USA.
authors.forename: William
authors.initials: W
authors.lastname: Sischo
authors.affiliation: Paul G. Allen School for Global Animal Health, Washington State University, Pullman, Washington, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Besser
authors.affiliation: Department of Food Science, Cornell University, Ithaca, New York, USA.
authors.forename: Lorin D
authors.initials: LD
authors.lastname: Warnick
authors.affiliation: Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, USA rvpereira@ucdavis.edu.
authors.forename: Richard V
authors.identifier: http://orcid.org/0000-0003-2028-8761
authors.initials: RV
authors.lastname: Pereira
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D002417:Cattle; D002418:Cattle Diseases / Q000382:microbiology*; D024901:Drug Resistance, Multiple, Bacterial; D016680:Genome, Bacterial; D005838:Genotype; D008826:Microbial Sensitivity Tests; D009518:New York; D012480:Salmonella Infections / Q000382:microbiology*; D012481:Salmonella Infections, Animal / Q000382:microbiology*; D019779:Salmonella enterica / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA; D014861:Washington
chemical_list: D000900:Anti-Bacterial Agents
keywords: dairy cattle; drug resistance evolution; genomics; nontyphoidal Salmonella; whole-genome sequencing; zoonosis