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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Environmental Microbial & Food Safety Laboratory » Research » Publications at this Location » Publication #355060

Research Project: Antimicrobial Resistance and Ecology of Zoonotic Foodborne Pathogens in Dairy Cattle

Location: Environmental Microbial & Food Safety Laboratory

Title: Whole genome sequencing and comparative genome analysis of human and bovine Salmonella Dublin isolates

item KIM, SEON-WOO - US Department Of Agriculture (USDA)
item Harhay, Dayna
item SALAHEEN, SERAJUS - US Department Of Agriculture (USDA)
item Van Kessel, Jo Ann
item Haley, Bradd

Submitted to: American Society for Microbiology
Publication Type: Abstract Only
Publication Acceptance Date: 7/16/2018
Publication Date: 9/24/2018
Citation: Kim, S., Harhay, D.M., Salaheen, S., Van Kessel, J.S., Haley, B.J. 2018. Whole genome sequencing and comparative genome analysis of human and bovine Salmonella Dublin isolates. American Society for Microbiology.

Interpretive Summary:

Technical Abstract: Background: Salmonella Dublin is a bovine-adapted serovar and, although infrequent, S. Dublin infections in humans can result in serious complications with relatively high hospitalization and mortality rates. Human clinical and bovine isolates are often resistant to multiple antimicrobials. Methods: To investigate the temporal, geographic, and host-specific diversity of S. Dublin isolates a total of 115 isolates recovered in the US between 2002 and 2014 were sequenced on an Illumina NextSeq 500. Reads were trimmed using Trimmomatic and assembled using SPAdes. In addition, 782 publicly available S. Dublin genomes were included in this analysis. Single nucleotide polymorphisms were identified among all the genomes using Parsnp with default parameters and a recombination filter. A Maximum Likelihood phylogenetic tree was inferred using RAxML. Antimicrobial resistance (AMR) genes were identified using DIAMOND (sequence identity = 90%, AMR/VF gene coverage > 60%). Results: S. Dublin genomes clustered into five major clades, and isolates from the US clustered in one clade. Four subclades were further identified among the US isolates. Two clades comprised only a few isolates from two states. The third clade comprised isolates from seven states and the remaining clade included isolates from 26 states. Multiple clusters of isolates originating from the same geographic location were observed, indicating that multiple sub-lineages of S. Dublin are circulating within some states. Most of the genomes were sequence type (ST)10; only one isolate was ST3208, two were ST2829, three were ST2037 and four were ST73. All the non-ST10 S. Dublin had similar multilocus sequence typing alleles as ST10 with one or two differences and were all members of eBurstGroup 53. Aminoglycoside resistance genes were identified in most isolates. Genes conferring resistance to ß-lactams, tetracycline, phenicol, and sulfonamides were observed in 48, 31, 23, and 11% of isolates, respectively. More than 33% of genomes encoded genes associated with resistance to four or more classes of antimicrobials and were thus considered multidrug resistant (MDR). Greater odds were observed for MDR isolates from bovine (OR:7.87, 95% CI: 3.51-17.69), in the US (OR:26.60 95% CI: 15.16- 46.67), between 2010 and 2017 (OR:1.42 95% CI: 1.05- 1.92) compared to isolates from humans, as well as those isolated outside of the US, and before 2010, respectively. Conclusions: Results of this study indicate that there is a high level of diversity among globally isolated S. Dublin with a high percentage of publicly available and study genomes encoding resistance to multiple antibiotics. This study also demonstrated that there are phylogenetic and resistance gene content differences between isolates from different regions as well as between those isolated in different years and from different sources.