Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Population Health & Reproduction
Non Technical Summary
p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Calibri; color: #000000}Antibiotic resistance in bacteria is a significant concern for agriculture and human medicine that has resulted in US and global agencies issuing reports and guidelines on their use. Use of antibiotics has been restricted in California so that it can no longer be included in animal feed without a prescription. The genetic features that provide bacteria resistance are growing and can be found using advanced genetics with whole-genome sequencing. Use of this approach provides a framework for traceability and estimation of therapeutic potential to resolve the infection without guessing or using broad-spectrum drugs. As antibiotic use is restricted in agriculture, one would conclude that the genes needed to resist the antibiotic would decline over time. This work will conduct a longitudinal study of historical isolates as well as current isolates with genome sequencing to determine the genetic signature of antibiotic resistance genes in isolates associated with dairy cattle, clinical cases, and food outbreaks. We will sequence at least 100 representatives from four bacterial types to make this estimate. Examination of the genome to find the antibiotic resistance genes combined with the genome diversity determination will provide a solid foundation to conclude if the resistance genes are declining or if the bacteria are just changing in response to the antibiotic use, as has been documented in the literature. Once completed, this framework can be replicated to any isolate source and can be used for surveillance programs that will provide actionable information about how to use antibiotics more prudently.
Animal Health Component
25%
Research Effort Categories
Basic
75%
Applied
25%
Developmental
(N/A)
Goals / Objectives
Antimicrobial resistance (AMR) is an ever-present problem that has reached a crisis level due to overuse. CDC claims that 1 in 5 human infections are a result of food or animal sources leading to pressure on agriculture(www.cdc.gov/drugresistance/protecting_food-supply.html) to reduce the use of antibiotics.Due to the implementationofSB27 in California that limits the use of antibiotics as growth promoters, we hypothesize that antibiotic resistance genes will decline in the food chain. We willexamine this trendusing whole genome sequencing with individual isolatesfrom collections of isolates in California that contain historical and recent isolates from the farm,clinic, and food. If the genes for antimicrobial resistance have changed over time we will observe the differences and characterize them by isolation source and bacteria type. The hypothesis is directly testable using a longitudinal approach which will be done by selecting >100 isolates from each of at least four different pathogens associated with the food chain, including but not limited to Staphylococcus aureus, Escherichia coli, Listeria monocytogenes, Enterococcus, Salmonella enterica, and Campylobacter.the aims are:Select a specific set of isolates for WGS that represent a longitudinal representation of bacteria from California (all investigators)Assemble metadata for each isolate (Aly, Clothier, Kurth)Sequence each isolate and examine the AMR genes for each genome (Weimer)Determine the AMR resistance gene content over time and isolate group with the source (all investigators)Conclude if the hypothesis is true or false
Project Methods
p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica} span.s1 {font: 8.0px Helvetica}Experimental design: This work is a longitudinal evaluation of the genomic AMR genes among historicalthrough recent bacterial pathogen isolates. Three different sources (farm, clinic, food sources) of at least fourpathogens with ~100-200 representatives for each group over ~35 years will be obtained from existing culturecollections. Kaufman and Weimer17-18 demonstrated that population genomics can be used with pathogens with~500 isolates. Weis et al. demonstrated that use of ~700 Campylobacter genomes provide enough informationto follow bacterial populations and determine AMR gene segregation with virulence in livestock abortion.Data analysis: We will follow the approach of Weis et al.16 and Richter et al.24 to determine the genome distance(genome variation) and the CARD database (Resfinder) to obtain the AMR genes for each isolate. Specific allelicvariants will be cataloged for analysis over time. We will use the genome distance (the entire genome) to followgenome scale changes along with the AMR alleles. The phylogenomic distances will be related to antibiotic usewith multivariate statistics, including PMA and random forests to define which genes are declining over time.