**3. Potential human pathogens in organic fertilizers from faecal materials and implications**

Pathogen-free organic fertilizer can be developed and microbiological safety assured for the reuse of sludge and manure. Various factors affecting the survival of pathogens in composting include time, temperature, pH, aerobic/anaerobic, biological activity, UV or irradiation, moisture, combination and chemical effects (e.g. ammonia). These factors are considered with regard to some pathogens discussed in Sections 3.1 and 3.2.

The inherent pathogens in an organic fertilizer depend on the animal source of the faecal materials used. When considering heat-dependent anoxic degradation of product for manure from dairy cattle, studies have shown the rate of kill of *E. coli* O157:H7 at 55°C to be 3 logs per 30 min and 4 logs per 100 min [70]. **Table 5** show the heat-based inactivation of some pathogens with values of decimal reduction time (*D*) at test temperature (*T*) Thermal death times for *Salmonella* to achieve reduction of 9 log has been reported to be 40 min at 55°C. Some pathogens can survive for longer periods of time in compost especially when they are located on the surface part of the compost pile where the heat effects may be inefficient. They also survive better in mesophilic composting (<45°C) than at elevated temperature. Moisture availability in biowaste compost (denoted by water activity, *a*w) is also an important determinant for the survival time of many pathogens.



**Table 5.** Heat inactivation: values of decimal reduction time (*D*) at test temperature (*T*) (Adapted from Romdhana [68]).

#### **3.1. Soil-transmitted helminths**

**Type of treatment Viruses Bacteria Parasite egg**

Mesophilic (30–35°C) Poor Poor Poor Thermophilic (50–55°C) Good Good Good

Mesophilic (up to 20°C) Poor Poor Poor Thermophilic (50–55°C) Good Good Good Compost (50–60°C) – Good Good

**3. Potential human pathogens in organic fertilizers from faecal materials**

Pathogen-free organic fertilizer can be developed and microbiological safety assured for the reuse of sludge and manure. Various factors affecting the survival of pathogens in composting include time, temperature, pH, aerobic/anaerobic, biological activity, UV or irradiation, moisture, combination and chemical effects (e.g. ammonia). These factors are considered with

The inherent pathogens in an organic fertilizer depend on the animal source of the faecal materials used. When considering heat-dependent anoxic degradation of product for manure from dairy cattle, studies have shown the rate of kill of *E. coli* O157:H7 at 55°C to be 3 logs per 30 min and 4 logs per 100 min [70]. **Table 5** show the heat-based inactivation of some pathogens with values of decimal reduction time (*D*) at test temperature (*T*) Thermal death times for *Salmonella* to achieve reduction of 9 log has been reported to be 40 min at 55°C. Some pathogens can survive for longer periods of time in compost especially when they are located on the surface part of the compost pile where the heat effects may be inefficient. They also survive better in mesophilic composting (<45°C) than at elevated temperature. Moisture availability in biowaste compost (denoted by water activity, *a*w) is also an important determinant for the

**Protozoan parasites** Soil-transmitted helminths (STHs) 20–30°C Several [69] **Bacteria** *Campylobacter* sp. 55.4–61.2 89–10.3 [70]

**Pathogens** *T* **(°C)** *DT* **(***s***) References**

*Escherichia coli* 55–70 1281.6–1.86 [71] *Escherichia coli* O157:H7 55 1500 [72] *Listeria* sp. 55–70 3370.14–7.56 [73] *Salmonella* sp. 55–70 3370.14–7.56 [74]

**Table 4.** Pathogen-reduction performance of the different treatments of sludge [28, 63, 64].

regard to some pathogens discussed in Sections 3.1 and 3.2.

**Anaerobic digestion**

350 Organic Fertilizers - From Basic Concepts to Applied Outcomes

**Aerobic digestion**

**and implications**

survival time of many pathogens.

Both human and animal waste and wastewater may contain different soil-transmitted helminths (STHs). These are among the most resistant microorganisms and will develop in soils or poorly treated biosolids from the non-invasive stages that are excreted to an infective one. Thus, when poorly handled, soil and crops get contaminated with eggs or larvae of STHs, which in turn will be transmitted orally through crops or due to accidental ingestion (e.g. *Ascaris* sp.) or penetrate bare skin (hookworms). Due to their resistance to environmental stress, helminth parasite eggs are widely used as hygiene indicators. STHs are resistant to sublethal composting temperatures and they require longer time at alkaline pH (months at pH 9–10, but much more rapid at pH 11–12) to effect appreciable die-off. A report by Jensen and Vrsle [65] showed that it would take a period of 117 days to achieve 99% die-off of an *Ascaris suum* eggs when placed on human excreta with pH levels between 9.4 and 11.6. When temperatures of above 50°C are reached, a rapid die-off occurs. Thus, a properly composted night soil with crop residues can destroy the parasitic infective stages efficiently.

When assessing the effectiveness of composting, *A. suum* eggs from pigs may be utilized as a model for the survival of human parasitic roundworm, *A. lumbricoides* [66,67].

#### **3.2. Zoonotic organisms in waste dung as components of organic fertilizer**

Chicken litters and pig dungs are rich in nutrients and are valuable animal wastes as organic fertilizer. However, chicken litter exemplify one organic fertilizer that may contain important human pathogens like *Salmonella* sp., *Campylobacter jejuni* and *Listeria monocytogenes*. If not properly sanitized these pathogens can easily get deposited on crop/plants, with transmission to consumers with, for example, fruits and vegetables [79,80]. Several human pathogens have been reported in organic fertilizer and may be conveyed to human, while other may function as animal or plant pathogens [81]. *L. monocytogenes* is a typical example of a pathogen easily conveyed via food crop.

**Figure 1.** The cycling of potential pathogens in faecal materials for making organic fertilizer.

**Figure 2.** Prevalence and concentration of zoonotic pathogens observed in British livestock manure (modified based on Ref. [84]).

Boulter et al. [82] reported that *Salmonella* sp. was observed among several other Gram negative bacterial potential pathogens in green compost for organic fertilizer. Even some Gram positive bacteria may occur, for example *Bacillus cereus* which is associated mainly with food poisoning and as a cause of serious and potentially fatal non-gastrointestinal-tract infections [83]. This resembles contamination of the farmland through poorly formulated organic fertilizers that circulates egested pathogens from human or animal back to them or another is pictorial as a cycle (**Figure 1**). Pathogens from wastes like *E. coli, Salmonella* sp., *Listeria* sp., *Cryptosporidi‐ um* sp. and *Campylobacter* sp. among others are usually conveyed to the farmland through poorly composted organic fertilizers or through contaminated irrigation water. **Figure 2** illustrates the occurrence of a number of different zoonotic pathogens found in manure [84].

Treated wastewater effluents contain nutrients (nitrogen, phosphorus and potassium), inorganic matter (dissolved minerals) and other chemicals which can complement the enrichment of the farmland in enhancing plants' growth. Enhanced concentrations of different excreted pathogens may also occur in wastewater being used for irrigation. Most of these pathogens are of known aetiologies of various infection (exemplified in **Table 6**). This is likely more prevalent in developing countries where wastewater for irrigation is not pretreated and disease prevalence may be higher. Intestinal nematodes released with the irrigated water are of special concern. The risk becomes higher in a farmland in which organic fertilizer is already in use, as it enriches the environment for the pathogens to thrive.

**Table 6** gives the summary of potential human pathogens found in wastewater effluent and sewage sludge as components that are used for organic fertilizers. Some of these pathogens have been reported in zoonotic infection as discussed hereafter.

**Figure 1.** The cycling of potential pathogens in faecal materials for making organic fertilizer.

352 Organic Fertilizers - From Basic Concepts to Applied Outcomes

Ref. [84]).

**Figure 2.** Prevalence and concentration of zoonotic pathogens observed in British livestock manure (modified based on

Boulter et al. [82] reported that *Salmonella* sp. was observed among several other Gram negative bacterial potential pathogens in green compost for organic fertilizer. Even some Gram positive bacteria may occur, for example *Bacillus cereus* which is associated mainly with food poisoning and as a cause of serious and potentially fatal non-gastrointestinal-tract infections [83]. This resembles contamination of the farmland through poorly formulated organic fertilizers that circulates egested pathogens from human or animal back to them or another is pictorial as a cycle (**Figure 1**). Pathogens from wastes like *E. coli, Salmonella* sp., *Listeria* sp., *Cryptosporidi‐ um* sp. and *Campylobacter* sp. among others are usually conveyed to the farmland through poorly composted organic fertilizers or through contaminated irrigation water. **Figure 2** illustrates the occurrence of a number of different zoonotic pathogens found in manure [84].

Treated wastewater effluents contain nutrients (nitrogen, phosphorus and potassium), inorganic matter (dissolved minerals) and other chemicals which can complement the enrichment of the farmland in enhancing plants' growth. Enhanced concentrations of different excreted pathogens may also occur in wastewater being used for irrigation. Most of these pathogens are of known aetiologies of various infection (exemplified in **Table 6**). This is likely more prevalent in developing countries where wastewater for irrigation is not pretreated and



**Table 6.** Potential human pathogens identified in municipal wastewater and sewage sludge being used for fertilizing farmland [26].

#### **3.3. Pathogens from organic fertilizers into crops and vegetables**

Pathogen can be passed on to crop plants through direct contact, through deposition on the surface or in splash contamination. Human pathogens may also get internalized in plants from fertilizers in the soil, where the probability for internalization may be increased by mechanical damage. The pathogens may migrate within the plants' tissues. **Figure 3** gives a pictorial illustration of the process of internalization of pathogens from organic fertilizers into crops and vegetables. Pathogens in the organic fertilizers are deposited on the surface of the crops and/or vegetables. The pathogens in subsurface parts of the crops are difficult to be removed or disinfected. The potential for enteric pathogens to be absorbed by roots has been considered [85].

Enteric pathogens may further enter plant tissues through both natural apertures (stomata, lateral junctions of roots) and damaged (wounds, cut surfaces) tissue (**Figure 3**). Researchers [86–88] have demonstrated the internalization of *E. coli* from soil into hypocotyl of spinach, lettuce and cabbage using different bioluminescent labels.

Regrowth contribute to high concentration of pathogens. Either *E. coli* O157:H7 or *Salmonella* may Multiply, get internalized into the tissues of raddish [89–91] and mung bean [87]. Surface

**Figure 3.** Pathogens' deposition (A) and internalization (B) in crop on an organically fertilized farm.

sterilization will then have little effect as the pathogens are already within the tissues. Similar experiment involving *Salmonella* and alfalfa seeds was demonstrated by Gandhi et al. [92] in which the bacterium penetrated into the hypocotyls.

### **3.4. Fate of pathogens in consumers of the plants products**

**Pathogens Potential disease (s) /Symptoms**

**Table 6.** Potential human pathogens identified in municipal wastewater and sewage sludge being used for fertilizing

Pathogen can be passed on to crop plants through direct contact, through deposition on the surface or in splash contamination. Human pathogens may also get internalized in plants from fertilizers in the soil, where the probability for internalization may be increased by mechanical damage. The pathogens may migrate within the plants' tissues. **Figure 3** gives a pictorial illustration of the process of internalization of pathogens from organic fertilizers into crops and vegetables. Pathogens in the organic fertilizers are deposited on the surface of the crops and/or vegetables. The pathogens in subsurface parts of the crops are difficult to be removed or disinfected. The potential for enteric pathogens to be absorbed by roots has been considered

Enteric pathogens may further enter plant tissues through both natural apertures (stomata, lateral junctions of roots) and damaged (wounds, cut surfaces) tissue (**Figure 3**). Researchers [86–88] have demonstrated the internalization of *E. coli* from soil into hypocotyl of spinach,

Regrowth contribute to high concentration of pathogens. Either *E. coli* O157:H7 or *Salmonella* may Multiply, get internalized into the tissues of raddish [89–91] and mung bean [87]. Surface

**Figure 3.** Pathogens' deposition (A) and internalization (B) in crop on an organically fertilized farm.

*Giardia* sp. Giardiasis *Cyclospora* sp. Cyclosporiasis *Cryptosporidium* sp. Cryptosporidiosis

**3.3. Pathogens from organic fertilizers into crops and vegetables**

lettuce and cabbage using different bioluminescent labels.

*lumbricoides*, whipworm and hookworm)

354 Organic Fertilizers - From Basic Concepts to Applied Outcomes

farmland [26].

[85].

Pathogens associated with plant products can be conveyed to consumers through crops mainly eaten raw from contaminated organic fertilizers. Surface washing will reduce surfaceassociated pathogens [48, 93]. Fruit- and vegetable-related outbreaks have been reported globally, affecting from a few infected person to causing major epidemics [94–96]. One recent outbreak was in 2011, affecting several countries in Europe involving ingestion of *E. coli* O157 from fruits and vegetables [94]. About 46 million food-related cases with 400,000 hospitaliza‐ tion and 3000 deaths were summarized by Scallan et al. [95,96]. The increasing numbers of immunocompromised individuals globally will enhance the effects of pathogens from contaminated fruits and vegetables. The risk to public health exists, and it is imperative for each country to remodel the agriculture extension to address this challenge.

The original source before food contamination differs. Some pathogens like norovirus and *Salmonella* sp. serotype *Typhi* are sustained in human reservoirs, but several others are sustained in animal reservoir. Surface contamination and/or internalization of pathogens in fruits and vegetable may not be the major pathway for contamination of food supply. How‐ ever, the outbreaks via this channel may have high public health significance [97, 98]. An estimated, 131 produce-related food-borne outbreaks were reported in the USA between 1996 and 2010. A large *E. coli* O157:H7 outbreak of food-related illness involving vegetable occurred in 1996 in Japan in which >11,000 individuals were reported severely ill. Several deaths occurred among young school children [98].

In England, 60 outbreaks of food-related illnesses from fruit- and vegetable-related infections were reported during 7 years, beginning from 1992. Contamination with human pathogens on farms can be attributed not only to faeces from human, and manure from farm and wild animal but also to poor environmental waste handling [99]. A report of an *E. coli* outbreak confirmed the contributions of water, manure from cattle dung and wild pig faeces, etc. towards con‐ tamination on spinach [100]. The same strains of pathogens found in spinach fields have also been found internalized in the spinach. This informed the initiation of safety plan against *E. coli* O157 infection through pathogens in vegetables [101].

When fruits harbour internalized pathogens, they pose an enhanced risk especially when used for sprouted seeds and unpasteurized fruit juices [102–104]. This is more important for internalized fruits as surface contaminant are usually steam washed away in processing companies.

#### **3.5. Exposure pathway and health risks when reusing contaminated organic materials as agricultural fertilizers**

Consumption of crops, including fodder crops, serves as the most common transmission pathway to chemical and pathogens from biosolids used as fertilizer. Investigations have also been performed related to contamination of crops used for medicinal products and supple‐ ments [105]. The direct exposure of agricultural workers is also significant and relates to different transmission routes, as well as the frequency and duration of exposure. Farmworker exposure has been examined [106, 107], including the impact on family members [108]. Direct exposure relates to the level of manual work and mechanization. The risk further relates to the type of fertilizer, from human and animal urine to untreated or treated wastewater, manure or human excreta. A special situation is when stored organic fractions or mixture thereof function as breeding site for fly/mosquito vectors of parasitic disease or attract vermin's that can act as carriers of pathogens. This is for example considered in the USEPA guidelines [109].

In addition to microbiological contaminants, organic fertilizers may, especially when sludge constitute parts of the input material, contain metals and other chemicals that may affect the receiving soils as well as be of relevance for occupational exposures. To appropriately assess human risk from chemicals found in biosolids, the form of the chemicals, and their fate, transport and bioavailability needs to be known, for example, arsenic, lead, mercury, antibi‐ otics.

Jerkins et al. [110] reported two studies that were suggestive that compost workers were affected by fungi. One cross-sectional study in Germany reported a significant increase in symptoms from lungs and airways as well as dermal effects and related these to increased exposure to fungi and Actinomycetes. The other was a prospective study in multiple US cities where significant increases in eye and skin irritation occurred and fungal colonization was documented but no serological evidence of other infections was reported. Indirect evidences were presented by Harrison and Oakes [111] that reported 39 incidence of illness among neighbours to biosolids application sites. The evidences were however not appropriately backed up.

The infection risks have been estimated using quantitative microbial risk assessment (QMRA) when urine or human faeces are used for garden fertilization [112]. A study in South Africa reported enhanced infection risks of *Salmonella* sp. and *Ascaris* sp. associated with spinach or carrots fertilized with human excreta [113]. An assessment of the health risk associated with daily consumption of vegetables (lettuce, 11.5 g) fertilized with compost was done by Wata‐ nabe et al. [114]. If the concentration of pathogenic virus in compost, for example is 10−1–102 PFU/g of lettuce, the risk would still be higher than the WHO tolerable annual infection risks.
