Performing Department
Population Health & Reproduction
Non Technical Summary
Integrated mixed crop-livestock farms (i.e. bio-diversified farms) are farms where animals and produce crops are raised with the goal of utilizing the products of one for the growth of the other, to foster a sustainable cycle. Integrated produce growers in California have diversified their production system to include a rotation of livestock, re-integrating animals back into cropland, which provides financial benefits and environmental sustainability such as, reducing pests/weeds, improving soil fertility, strengthening farm economies, and increasing regional food security. However, these systems face challenges, including potential food safety risks and compliance with the new FSMA produce safety rule. Specifically, raw manure from grazing animals may introduce foodborne pathogens into fields, and these pathogens can persist in the soil for extended periods of time. There is limited data defining the microbial risk or an adequate waiting period after animals graze a produce field prior to planting. Moreover little scientific data exist regarding the genetic similarity of Campylobacter strains isolated from livestock sharing the same farm environment and the resulting risk to microbial contamination of fresh produce crops. The overall goal of this project is to gain a better understanding of the ecological dynamics of Campylobacter spp. and demonstrate the genetic relatedness of Campylobacter isolates from different ecological niches in the farm environment (i.e., livestock species, water, untreated manure, and produce) and assess the risk of cross-contamination of produce.
Animal Health Component
100%
Research Effort Categories
Basic
0%
Applied
100%
Developmental
0%
Goals / Objectives
The overall goal of this project is to gain a better understanding of the ecological dynamics of Campylobacter spp. and demonstrate the genetic relatedness of Campylobacter isolates from different ecological niches in the farm environment. The objectives include: 1) To determine the prevalence of Campylobacter spp. in livestock on integrated crop-livestock farms raising two or more different animal species (poultry, cattle, small ruminants and swine); 2) To assess the genetic relatedness of Campylobacter genotype isolates from different ecological niches in the farm environment (livestock sharing grazing/pasture areas, untreated manure, water, and produce).
Project Methods
A cross-sectional study will be conducted in two phases. Phase 1: Characterization and genotyping of Campylobacter isolates from our on-going small farm study, data collected in 2015-2016. 85 isolates from 14 integrated crop-livestock farms located in 4 CA regions (38 C. jejuni; 24 C. coli; 23 C. spp isolates) from cattle, small ruminants, swine and poultry will be characterized. Isolates will be re-grown and subtyped by sequencing the porA gene that encodes the major outer membrane protein ("MOMP typing"). Farm information (e.g., demographics, agricultural and management practices, animal health, biosecurity, etc.) and environmental parameters (e.g., temperature, humidity) will be retrieved from the previous small farm study surveys. Phase 2: Ten additional farms (with comparable management practices as Phase 1 from two regions of California (Northern California and Central Valley), will be enrolled in this study. Farms will be visited twice (summer/fall and winter/spring) to account for seasonal variations. A total of 260 samples will be collected during Phase 2 (13 samples/visit X 10 farms X 2 visits). A stratified proportional sampling will be conducted per farm, depending on the total animals and egg mobiles . Individual fecal samples of ruminants/swine (5g) and chicken composite fecal samples (1gram x 5 individual fecal) will be collected from the ground and drag swabs from the chicken tractors. During each visit, farm samples [water (1), untreated manure (1, 100 g) and produce samples (2) will be collected. Fecal samples will be collected from the ground (no animal interaction or restrain). A questionnaire will include the following: 1) demographics, 2) management practices (e.g., integrated grazing, crops, grazing density, total grazing days) 3) animal health (e.g., abortion history, disease morbidity, vaccinations, etc.) and disease prevention, and 4) biosecurity. The outcome of interest is the prevalence of Campylobacter spp. in ruminants, swine and poultry. The association between potential risk factors and Campylobacter spp. prevalence will be calculated using generalized linear mixed models. Multiple sequence alignment will be used to compare genetic relationships between Campylobacter strains from livestock and other environmental farm samples. All sequences will be submitted to the international database of porA subtypes (http://pubmlst.org/).