Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a ‘One Health’ framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue ‘The role of soils in delivering Nature's Contributions to People’.

Nontyphoidal Salmonella infections contribute to approximately 1.2 million annual illnesses in the United States. Historical and recent outbreaks have been associated with dairy products, ground beef, and direct contact with cattle. Salmonella antimicrobial resistance (AMR) is a serious concern that can reduce successful treatment of infections, increasing recovery time, medical costs, and mortality rates in humans and animals. This highlights the need to track AMR in Salmonella isolated from cattle to improve treatment plans, manage trends in AMR, and prevent future AMR development. A total of 242 Salmonella isolates were retrieved from 9,162 cattle fecal samples submitted to the University of California, Davis Veterinary Medical Teaching Hospital from 2002 to 2016. These isolates were tested for antimicrobial susceptibility using a standardized broth dilution panel. Multidrug resistance (MDR) to three or more classes of antimicrobials was observed in 50.8% of isolates, and the most common MDR pattern was amoxicillin-ampicillin-cefoxitin-ceftiofur-ceftriaxone-chloramphenicol-streptomycin-tetracycline (23.2%). There were significantly greater odds for antimicrobial resistance to aminoglycosides (OR: 2.03, 95% CI: 1.1–3.7), penicillins (OR: 1.87, 95% CI: 1.007–3.5), and tetracyclines (OR: 1.87, 95% CI: 1.017–3.4) for the 2002–2009 period when compared to the 2010–2016 period. The most prevalent MDR serotypes were Newport (100% MDR, n = 52), Typhimurium (100%, n = 20), and Dublin (71% MDR, n = 46). Risk factors associated with higher odds for isolating MDR Salmonella included isolates from calves when compared to adult cattle (OR: 22.0; 95% C.I.: 3.9–125.7), and isolates obtained from cattle suspect of having salmonellosis versus from the infectious disease control surveillance program (OR:13.7; 95%C.I.: 2.8–66.8). Despite a temporal trend for reduced AMR to most antimicrobial drug classes, a lack of this observed in the 2002–2009 period when compared to the 2010–2016 period for important drug classes such as cephalosporins (OR: 1.6, 95% CI: 0.87–3.1), and a trend for temporal increase in resistant to quinolones drugs (P value 0.004) highlight the relevance of AMR surveillance in cattle with Salmonella infections with the aim of targeting future prophylactic interventions.

The number of small-scale and backyard livestock and poultry owners in urban and peri-urban areas has increased greatly over the last 10 years in the U.S. However, these animal owners may live in areas without access to livestock and/or poultry veterinary care. The purpose of this study was to identify potential veterinary service needs of these animal owners in the western US, assess their use of management and husbandry practices with regards to disease prevention, and assess their attitudes about animal health and food safety. A semi-structured survey was made available to small-scale and backyard livestock and poultry owners in Washington State, California, Colorado and Oregon. The survey instrument included questions about types of animals reared, uses of the animals, veterinary services and information-seeking behaviors of owners, attitudes on animal health and food safety, and management practices. Four hundred thirty-five individuals completed at least some portion of the survey. Most described themselves as living in rural areas (76%). Most (86%) owned chickens, 53% owned small ruminants, and 31% owned cattle. Many individuals owned more than one species and most had fewer than 20 animals of a given species. About 74% of respondents utilized their animals’ products for their own consumption but 48% sold animal products (primarily through internet sales (35%) or farmers’ markets (25%)). Overwhelmingly, respondents gained information about animal health (82%) and animal treatment procedures (71%) from the internet. Respondents reported their veterinarian’s practice type as companion animal (26%) or a mixed animal or food animal predominant (66%). Overall, respondents were very satisfied with the level of care (82%), but 43% had not sought animal health care in last 12 months. However, the veterinarian’s primary practice type and owner’s satisfaction with veterinary care were associated with their location (state), species owned, and urban or peri-urban setting. Livestock species type (cattle, small ruminants and swine), and use (personal or commercial) were associated with implementation of different biosecurity practices. The results of this survey highlight some of the needs of these animal owners for veterinary care and information which are location- and species-specific. Veterinary care for these small-scale and backyard animals is vital to the health and welfare of the animals as well as for identification of zoonoses and assurance of the food safety of animal products.

SUMMARY: A 3-year longitudinal study was conducted on a multi-site farrow-to-finish production system. For each of 18 cohorts at three finishing sites, 50 pigs were randomly selected. Faecal samples were collected every 2 weeks for 16 weeks.Salmonellawas cultured from 453 (6·6%) of 6836 faecal samples. The pig-level incidence ofSalmonellawas 20·8% (187/899 pigs).Salmonellaprevalence varied between cohorts and within pigs. The adjustedSalmonellaprevalence decreased over the finishing period from 6·4% to 0·8%. Intermittent detection ofSalmonellawas found in more than 50% of pigs that were positive at more than one collection. The finding that the majority of pigs shed intermittently has implications for surveillance and research study design when determiningSalmonellastatus. The variability in shedding over time, as well as between and within cohorts and pigs suggests that there may be time-variant risk factors forSalmonellashedding in swine.

Diversified farms are operations that raise a variety of crops and/or multiple species of livestock, with the goal of utilising the products of one for the growth of the other, thus fostering a sustainable cycle. This type of farming reflects consumers' increasing demand for sustainably produced, naturally raised or pasture-raised animal products that are commonly produced on diversified farms. The specific objectives of this study were to characterise diversified small-scale farms (DSSF) in California, estimate the prevalence ofSalmonella entericaandCampylobacterspp. in livestock and poultry, and evaluate the association between farm- and sample-level risk factors and the prevalence ofCampylobacterspp. on DSSF in California using a multilevel logistic model. Most participating farms were organic and raised more than one animal species. OverallSalmonellaprevalence was 1.19% (95% confidence interval (CI₉₅) 0.6–2), and overallCampylobacterspp. prevalence was 10.8% (CI₉₅= 9–12.9). Significant risk factors associated withCampylobacterspp. were farm size (odds ratio (OR)_{10–50 acres: less than 10 acres}= 6, CI₉₅= 2.11–29.8), ownership of swine (OR = 9.3, CI₉₅= 3.4–38.8) and season (OR_{Spring: Coastal summer}= 3.5, CI₉₅= 1.1–10.9; OR_{Winter: Coastal summer}= 3.23, CI₉₅= 1.4–7.4). As the number of DSSF continues to grow, evaluating risk factors and management practices that are unique to these operations will help identify risk mitigation strategies and develop outreach materials to improve the food safety of animal and vegetable products produced on DSSF.

The use of biological soil amendments of animal origin (BSAAOs) to improve soil fertility and quality plays an important role in organic agriculture in the U.S. However, organic practices, such as untreated manure application, may introduce foodborne pathogens and consequently increase the risk of fresh produce contamination. Certified organic farms follow the USDA-National Organic Program (NOP) standards, which stipulate a 90- or 120-day waiting period between incorporating raw manure into the soil and crop harvest, depending on whether the edible portions of the crops come into indirect or direct contact, respectively, with the soil. To determine knowledge, attitudes, behaviors, and practices of organic farmers related to use of biological soil amendments, we employed three evaluation tools: a national workshop held at the University of California-Davis (UC-Davis); multiple in-person focus groups (listening sessions) conducted around the United States, and an online survey. Results reveal that untreated BSAAOs (untreated manure and immature composted manure) are critical tools in organic production for managing soil fertility and improving soil quality. Overall, organic producers surveyed in this study agreed that there is a need for more science-based data to evaluate and establish an appropriately protective time interval between untreated manure application and crop harvest to reduce the risk of surviving foodborne pathogens contaminating organic fresh produce. This study highlights the need for development of outreach and educational tools intended to help organic producers implement mitigation strategies to reduce food safety risks related to BSAAOs in organically grown produce covered by the Produce Safety Rule (PSR) of the U.S. Food and Drug Administration Food Safety Modernization Act (FSMA). This study informs and will aid prioritization of research (e.g., on a time interval protective of fresh produce food safety when soil is amended with animal-biological amendments in organic fresh produce systems) and outreach programs (e.g., GAPs, food safety programs, soil testing, pre-harvest food safety mitigation strategies, and organic rules and regulations) aimed at improving food safety for organic vegetable, fruit, and nut growers who use animal-based soil inputs, including amendments and rotational grazing.