Approaches to Assess the Effects and Risks of Veterinary Antibiotics Applied with Manure to Soil

In veterinary medicine, large quantities of antibiotic substances are administered each year for therapeutic and prophylactic purposes or to promote growth. As a consequence, the antibiotics and bacteria carrying transferable antibiotic resistance genes are excreted by the animals and reach the environment through run-off, leaching, and/or following manure application to agricultural fields, where they have been found to affect the structure and function of soil bacterial communities. However, we are only beginning to understand the global effects of environmental pollution with antibiotics and resistance determinants and the resulting risks for human health. For regulatory purposes, there is urgent need for criteria and methods that allow reliable and reproducible assessment of risks associated with release of realistic concentrations of antibiotics and resistance determinants into the environment following manure application. In this chapter, we will summarize recent advances, limitations, and research needed to optimize the methods to quantify and evaluate the effects and risks associated with these compounds. Approaches that are discussed focus on antibiotic resistance genes and include classical tools such as cultivation and PCR detection as well as quantitative real-time PCR and next-generation sequencing technologies used in combination with functional screening

Interaction between Salmonella and Plants: Potential Hosts and Vectors for Human Infection

Fruits and vegetables are important for a healthy diet. However, when eaten raw and contaminated with human pathogens (HPs) they may cause a disease outbreak. Contamination with HPs can occur along the entire farm-to-fork production chain and Salmonella enterica is one of the most common foodborne pathogens. A range of biotic and abiotic environmental factors can influence the complex interactions between Salmonella and plants. Moreover, the outcome of experiments largely depends on the experimental design and parameters or methods employed, and on top, on the accompanying plant microbiome and the genetic equipment of the plant and the Salmonella strain. Particularly mobile genetic elements contribute to the diversification and adaptation of Salmonella to the plant environment. So far, little is known about the key processes and factors influencing the attachment and potential internalization of Salmonella in plants and the plant specific responses. It is therefore important to better understand the ecology of Salmonella in the soil and plant environment, in order to propose practicable recommendations for prevention of foodborne diseases. This also requires improved sensitivity and specificity of detection methods. In this chapter, we present the current knowledge, research needs, and methodology regarding the complex interactions between Salmonella and plants

Composted sewage sludge influences the microbiome and persistence of human pathogens in soil

Composted sewage sludge (CSS) gained attention as a potential fertilizer in agriculture. Application of CSS increases soil microbial activity and microbial biomass, however, it can also lead to increased chemical and microbiological risks. In this study, we performed microcosm experiments to assess how CSS reshapes the microbial community of diluvial sand (DS) soil. Further, we assessed the potential of CSS to increase the persistence of human pathogens in DS soil and the colonization of Chinese cabbage (Brassica rapa L. subsp. pekinensis (Lour.) Hanelt). The results revealed that CSS substantially altered the prokaryotic community composition. Moreover, addition of CSS increased the persistence of Salmonella enterica serovar Typhimurium strain 14028s and S. enterica serovar Senftenberg in DS soil. However, the enhanced persistence in soil had no impact on the colonization rate of B. rapa grown on soil inoculated with Salmonella. We detected Salmonella in leaves of 1.9% to 3.6% of plants. Addition of CSS had no impact on the plant colonization rate. The use of sewage sludge composts is an interesting option. However, safety measures should be applied in order to avoid contamination of crop plants by human pathogens

Salmonella Establishment in Agricultural Soil and Colonization of Crop Plants Depend on Soil Type and Plant Species

Human pathogenic bacteria, such as Salmonella enterica, are able to colonize crop plants. So far, not much is known about biotic and abiotic factors influencing this colonization in field soil. This understanding, however, is imperative for the provision of safe fresh produce to the consumer. In this study, we investigated the effects of soil type, organic fertilization, plant species and the way of Salmonella entry into the plant production system, on the survival of S. enterica in soil as well as the colonization of plants. The selected S. enterica serovar Typhimurium strain 14028s, S. Typhimurium strain LT2 and S. Senftenberg were able to persist in soil for several weeks. Salmonella’s persistence in soil was prolonged in loamy, if compared to sandy soil, and when applied together with organic fertilizer. The leaves of lettuce and corn salad were colonized by S. enterica providing evidence for internalization from the soil via the root. Colonization rates were affected by soil type, plant species and S. enterica strain. Overall, S. enterica was detected in leaves of 0.5–0.9% of the plants, while lettuce was more frequently colonized than corn salad. Plants grown in sandy soil were more often colonized than plants grown in loamy soil. After spray inoculation, S. enterica could be detected on and in leaves for several weeks by cultivation-depending methods, confirmed by confocal microscopy using GFP-labeled S. Typhimurium 14028s. On the one hand, transcriptome data from S. Typhimurium 14028s assessed in response to lettuce medium or lettuce root exudates showed an upregulation of genes associated with biofilm formation and virulence. On the other hand, lettuce inoculated with S. Typhimurium 14028s showed a strong upregulation of genes associated with plant immune response and genes related to stress response. In summary, these results showed that organic fertilizers can increase the persistence of Salmonella in soil and that soil type and plant species play a crucial role in the interactions between human pathogens and crop plants. This understanding is therefore a starting point for new strategies to provide safe food for the consumer