Evaluation of the occurrence of sporulating and nonsporulating pathogenic bacteria in manure and in digestate of five agricultural biogas plants

Enterobacteriaceae in Sewage Sludge and Digestate Intended for Soil Fertilization

Substances of organic origin are seeing increasing use in agriculture as rich sources of nutrients for plants. The aim of this study was to determine the microbiological contamination of sewage sludge and digestate to assess their safe use as fertilizers in Poland. The assessment of microbial soil, sewage sludge and digestate contamination was based on the total number of mesophilic bacteria and Gram-negative bacteria from the Enterobacteriaceae family. The presence of Escherichia coli and Salmonella spp. was identified via culture and the presence of Enterobacteriaceae species was determined via biochemical and molecular methods. In laboratory conditions, the survival of E. coli in soil fertilized with sewage sludge or digestate inoculated with a reference strain was determined. The average concentration of Enterobacteriaceae in soil, sewage sludge and digestate samples was 1.1 × 104 CFU/g, 9.4 × 105 CFU/g and 5.6 × 106 CFU/g, respectively. Escherichia coli was detected in all sample types. From the soil samples, Serratia, Enterobacter, Pantoea, Citrobacter and Pseudomonas genera were identified the most frequently, while in sewage sludge and digestate, E. coli was predominant. Based on the results of our laboratory experiment, it can be concluded that after three weeks, fertilization with organic waste in acceptable doses does not significantly increase soil contamination with Enterobacteriaceae.

Listeria monocytogenes prevalence and genomic diversity along the pig and pork production chain

The facultative intracellular bacterium Listeria monocytogenes (L. monocytogenes) is the causative agent of listeriosis, a severe invasive illness. This ubiquitous species is widely distributed in the environment, but infection occurs almost exclusively through ingestion of contaminated food. The pork production sector has been heavily affected by a series of L. monocytogenes-related foodborne outbreaks in the past around the world. Ready-to-eat (RTE) pork products represent one of the main food sources for strong-evidence listeriosis outbreaks. This pathogen is known to be present throughout the entire pig and pork production chain. Some studies hypothesized that the main source of contamination in final pork products was either living pigs or the food-processing environment. A detailed genomic picture of L. monocytogenes can provide a renewed understanding of the routes of contamination from pig farms to the final products. This review provides an overview of the prevalence, the genomic diversity and the genetic background linked to virulence of L. monocytogenes along the entire pig and pork production chain, from farm to fork.

Evaluation of the additive effects of volatile fatty acids and moderate heat treatment for enhancing the inactivation of vegetative cells and spores of Clostridium perfringens by flow cytometry

OBJECTIVES

Clostridium perfringens is a well-known spore-forming bacterium that can resist the environment. A mixture of volatile fatty acids or thermal treatments can interact with these bacteria. The aim of this study was to evaluate the effects of different volatile fatty acid concentrations and moderate heat treatment on Clostridium perfringens sporulation.

METHODS

A pure culture of Clostridium perfringens type A in Duncan Strong medium was treated with a mixture of volatile fatty acids at several concentrations. A thermal treatment was also tested. To evaluate the effects, a double staining method was employed, and treatments on Clostridium perfringens were analysed by flow cytometry.

RESULTS

Moderate heat treatment destroyed vegetative forms but had no effect on sporulating forms. Volatile fatty acids combined with moderate heat treatment inhibited Clostridium perfringens sporulation.

CONCLUSIONS

The use of flow cytometry as an original method for evaluating the treatment of Clostridium perfringens is of interest because of its simplicity, short time to obtain results, and the level of information provided on the microbial population (impact on metabolism). A combination of mild treatments (moderate heat treatment + volatile fatty acids) to decrease the Clostridium perfringens concentration when these bacteria sporulate is a very promising finding for inhibiting Clostridium perfringens propagation.

Quantification of indicator and pathogenic bacteria in manures and digestates from three agricultural biogas plants over a one-year period

Interest in the conversion of manure in biogas via anaerobic digestion (AD) is growing, but questions remain about the biosafety of digestates. For a period of one year, we monitored the impact of three mesophilic agricultural biogas plants (BPs) mainly fed with pig manure (BP1, BP3) or bovine manure (BP2) on the physicochemical parameters, the composition of the microbial community and the concentration of bacteria (E. coli, enterococci, Salmonella, Campylobacter, Listeria monocytogenes, Clostridium perfringens, Clostridium botulinum and Clostridioides difficile). The BP2 digestate differed from those of the two other BPs with a higher nitrogen content, more total solids and greater abundance of Clostridia MBA03 and Disgonomonadacea. Persistence during digestion ranked from least to most, was: Campylobacter (1.6 to >2.9 log10 reduction, according to the BP) < E. coli (1.8 to 2.2 log10) < Salmonella (1.1 to 1.4 log10) < enterococci (0.2 to 1.2 log10) and C. perfringens (0.2 to 1 log10) < L. monocytogenes (-1.2 to 1.6 log10) < C. difficile and C. botulinum (≤0.5 log10). No statistical link was found between the reduction in the concentration of the targeted bacteria and the physicochemical and operational parameters likely to have an effect (NH3, volatile fatty acids and total solids contents, hydraulic retention time, presence of co-substrates), underlining the fact that the fate of the bacteria during mesophilic digestion depends on many interacting factors. The reduction in concentrations varied significantly over the sampling period, underlining the need for longitudinal studies to estimate the impact of AD on pathogenic microorganisms.

A Small Study on Clostridioides difficile in Spinach Field Soil and the Chemical and Microbial Factors that may Influence Prevalence

Clostridioides difficile is a human pathogen that is ubiquitous in soil. Despite increasing infection rates and evidence of foodborne transmission, there is limited data on prevalence in soil or which factors influence persistence. The aim of this study was to investigate the prevalence of these bacteria in soil from three different spinach fields and to examine the chemical composition (carbon, organic carbon, nitrogen, organic matter, minerals and pH) and microbiota to gain insight into the factors that may promote/inhibit C. difficile. The overall C. difficile prevalence (10%) was lower than expected (based on international studies) and a significantly (P < 0.05) higher prevalence was obtained in Field 3 (20%) as compared to Fields 1 and 2 (5% each). Analysis of the soil suggested that the pH as well as organic matter, calcium and phosphorus content directly and indirectly (via the microbiota) influenced the prevalence of C. difficile in adjacent fields, where other factors (eg. climate) are similar. Although further studies are required to validate our findings, the data provides the first step in developing potential soil based control strategies.

Detection and Genomic Characterisation of Clostridioides difficile from Spinach Fields

Despite an increased incidence of Clostridioides difficile infections, data on the reservoirs and dissemination routes of this bacterium are limited. This study examined the prevalence and characteristics of C. difficile isolates in spinach fields. C. difficile was detected in 2/60 (3.3%) of spinach and 6/60 (10%) of soil samples using culture-based techniques. Whole genome sequencing (WGS) analysis identified the spinach isolates as belonging to the hypervirulent clade 5, sequence type (ST) 11, ribotypes (RT) 078 and 126 and carried the genes encoding toxins A, B and CDT. The soil isolates belonged to clade 1 with different toxigenic ST/RT (ST19/RT614, ST12/RT003, ST46/RT087, ST16/RT050, ST49/RT014/0) strains and one non-toxigenic ST79/RT511 strain. Antimicrobial resistance to erythromycin (one spinach isolate), rifampicin (two soil isolates), clindamycin (one soil isolate), both moxifloxacin and rifampicin (one soil isolate), and multi-drug resistance to erythromycin, vancomycin and rifampicin (two soil isolates) were observed using the E test, although a broader range of resistance genes were detected using WGS. Although the sample size was limited, our results demonstrate the presence of C. difficile in horticulture and provide further evidence that there are multiple sources and dissemination routes for these bacteria.

Impact of mesophilic anaerobic digestion and post-treatment of digestates on the transfer of conjugative antimicrobial resistance plasmids

Manure is a major source of antimicrobial-resistant bacteria and resistance genes carried by mobile genetic elements such as plasmids. In France, the number of on-farm biogas plants has increased significantly in recent years. Our study investigated the impact of mesophilic anaerobic digestion (AD) and the post-treatment of digestates on the fate of conjugative plasmids, along with their potential transfer of antimicrobial resistance. Samples of raw manure, digestates and post-treated digestates were collected from three on-farm biogas plants. Conjugative plasmids were captured using the Escherichia coli CV601 recipient strain and media supplemented with rifampicin and kanamycin - to which the recipient strain is resistant - and tetracycline, sulfamethoxazole, gentamicin, trimethoprim, amoxicillin, cefotaxime, ciprofloxacin or colistin. Putative transconjugants were identified and characterised by disc diffusion and whole genome sequencing. The results showed that the antimicrobial resistance genes transferred from the different matrices conferred resistance to tetracyclines, sulphonamides, trimethoprim, and/or streptomycin. Transconjugants were obtained from raw manure samples but not from digestates or post-digestates, suggesting that mesophilic AD processes may produce fewer conjugative plasmids potentially able to be transferred to Enterobacterales.

Fate of Clostridia and other spore-forming Firmicute bacteria during feedstock anaerobic digestion and aerobic composting

Pathogenic spore-forming Firmicutes are commonly present in animal and human wastes that are used as fertilizers in crop production. Pre-treatments of organic waste prior to land application offer the potential to abate enteric microorganisms, and therefore reduce the risk of contamination of crops or adjacent water resources with pathogens carried in these materials. The inactivation and reduction of gram-positive spore formers such as Clostridium spp., Clostridioides spp. and Bacillus spp. from animal and human waste can be challenging given the recalcitrance of the spores these bacteria produce. Given the significance of these organisms to human and animal health, information concerning spore-forming bacteria inactivation during anaerobic digestion (AD) and aerobic composting (AC) is required as the basis for recommending safe organic waste management practices. In this review, an assessment of the inactivation of spore-forming Firmicutes during AD and AC was conducted to provide guidance for practical management of organic matrices of animal or human origin. Temperature and pH may be the main factors contributing to the inactivation of spore-forming Firmicutes during batch lab-scale AD (log reduction <0.5-5 log). In continuous digesters, wet AD systems do not effectively inactivate spore-forming Firmicutes even under thermopholic conditions (log reduction -1.09 - 0.98), but dry AD systems could be a feasible management practice to inactivate spore-forming Firmicutes from organic materials with high solid content (log reduction 1.77-3.1). In contrast, composting is an effective treatment to abate spore-forming Firmicutes (log reduction 1.7-6.5) when thermophilic conditions last at least six consecutive days. Temperature, moisture content and composting scale are the key operating conditions influencing the inactivation of spore-forming Firmicutes during composting. Where possible, undertaking AD with subsequent composting to ensure the biosafety of digestate before its downstream processing and recycling is recommended to abate recalcitrant bacteria in digestate.

Occurrence and Diversity of Listeria monocytogenes Isolated from Two Pig Manure Treatment Plants in France

The presence of Listeria monocytogenes in piggery effluents intended for irrigation crops may be a source of bacterial dissemination in agriculture. The occurrence and diversity of L. monocytogenes in the farm environment were examined in two pig manure treatment systems (S1 and S2). Samples collected over the course of one year consisted of manure, the liquid fraction of treated manure (lagoon effluent), and soil surrounding the lagoon. L. monocytogenes was enumerated using the Most Probable Number (MPN) method, serotyped by PCR, genotyped by pulsed-field gel electrophoresis (PFGE), and sequenced for multilocus sequence typing (MLST). L. monocytogenes was detected in 92% of manure samples and in approximately 50% of lagoon effluent and soil samples. Concentrations ranged between 5 and 10³ MPN 100‍ ‍mL^-1. Serogroups IIa, IIb, and IVb were identified. Diversity was high with 44 PFGE profiles (252 isolates) and 17 clonal complexes (CCs) (96 isolates) with higher diversity in manure at site S1 supplied by four farms. Some PFGE profiles and CCs identified in manure or in pig feces from a previous study were also detected in lagoons and/or soil, reflecting pig L. monocytogenes circulation throughout the manure treatment and in the vicinity of the sampling sites. However, some PFGE profiles and CCs were only found in the lagoon and/or in soil, suggesting an origin other than pigs. The present study highlights the limited ability of biological treatments to eliminate L. monocytogenes from pig manure. The persistence of some PFGE profiles and CCs throughout the year in the lagoon and soil shows the ability of L. monocytogenes to survive in this type of environment.

Influence of operating conditions on the persistence of E. coli, enterococci, Clostridium perfringens and Clostridioides difficile in semi-continuous mesophilic anaerobic reactors

This study examined the combined effect of hydraulic retention time (HRT), organic loading rate (OLR) and heat pretreatment of manure (70 °C, 1 h) on the fate of E. coli, enterococci, C. perfringens, C. difficile, and on chemical parameters (volatile fatty acids and ammonia) that may inactivate pathogens. Semi-continuous mesophilic anaerobic reactors were fed with pig manure and horse feed. The operating conditions were 2, 3, 4 COD.L^-1.d^-1 (OLR), 24, 35, 46 days (HRT) and use or not of a thermal pretreatment. The levels of the chemical parameters did not reach concentrations capable of inactivating the four bacteria. Anaerobic digestion led to a Log₁₀ removal > 3 (E. coli), 0.9-2.1 (enterococci), 0.1-0.6 (C. perfringens) and 0-1 (C. difficile). Increasing HRT only reduced the concentration of E. coli in the digestate. Increasing OLR reduced the Log₁₀ removal of enterococci and C. difficile. The heat pretreatment led to non-detection of E. coli in the digestate, reduced the concentration of C. perfringens by 0.8-1.3 Log₁₀ and increased the concentration of C. difficile by 0.04-0.7 Log₁₀. Enterococci, not detected in the heated manure, were present in the digestate. The distribution of genes encoding virulence factors of C. difficile (tcdA and tcdB) and C. perfringens (cpa, cpb2 and cpb) was not impacted by anaerobic digestion or by the heat pretreatment. Enterococci, C. perfringens, C. difficile were present in the digestate at relatively stable concentrations regardless of the operating conditions, indicating that even with heat pretreatment, the biosafety of digestate cannot be guaranteed in mesophilic conditions.

Thermal hydrolyzed food waste liquor as liquid organic fertilizer

Thermal hydrolysis (TH) is an efficient technology for food waste (FW) management. This study investigated the nutrients released from FW under various TH temperature (140, 160, 180, 200 and 220 °C) and evaluated the feasibility of the hydrolyzed liquor (HL) as liquid organic fertilizer. The phytotoxicity and biotoxicity of HL was analyzed using wheat seed and Pseudomonas putida. Results revealed that TH could effectively solubilize FW and release nutrients (N, P and K) and organic substances. The highest content of total nitrogen (TN, 1685 mgN/L) and phosphorus (TP, 235 mgP/L) in the HL was obtained under 180 °C. The K⁺ was 278-293 mg/L regardless of treatment temperature. Secondary nutrients (Ca and Mg) and micro metals (Fe, Cu, Zn, Al, Co and Mn) were all detected at relatively high level, while heavy metals (As and Cd) were generally lower than 0.5 mg/L. Twenty types of free amino acid were identified and the maximum total concentration was 4965.13 mg/L. 2% HL displayed higher germination index (>80%) and enhanced root and shoot lengths. No biotoxicity was observed as confirmed by the bioassay. This study proposes a feasible method to solubilize food waste and produce liquid organic fertilizer.

Conventional and Innovative Hygienization of Feedstock for Biogas Production: Resistance of Indicator Bacteria to Thermal Pasteurization, Pulsed Electric Field Treatment, and Anaerobic Digestion

Animal by-products (ABP) can be valorized via anaerobic digestion (AD) for biogas energy generation. The digestate issued from AD process is usually used to fertilize farming land for agricultural activities, which may cause potential sanitary risk to the environment. The European Union (EU) requires that certain ABP be thermally pasteurized in order to minimize this sanitary risk. This process is called hygienization, which can be replaced by alternative nonthermal technologies like pulsed electric field (PEF). In the present study, Enterococcus faecalis ATCC 19433 and Escherichia coli ATCC 25922 were used as indicator bacteria. Their resistance to thermal pasteurization and PEF treatment were characterized. Results show that Ent. faecalis and E. coli are reduced by 5 log10 in less than 1 min during thermal pasteurization at 70 °C. The critical electric field strength was estimated at 18 kV∙cm−1 for Ent. faecalis and 1 kV∙cm−1 for E. coli. “G+” bacteria Ent. faecalis are generally more resistant than “G−” bacteria E. coli. AD process also plays an important role in pathogens inactivation, whose performance depends on the microorganisms considered, digestion temperature, residence time, and type of feedstock. Thermophilic digestion is usually more efficient in pathogens removal than mesophilic digestion.

Does Mycobacterium tuberculosis var. bovis Survival in the Environment Confound Bovine Tuberculosis Control and Eradication? A Literature Review

Bovine tuberculosis (bTB) is one of the globe's most common, multihost zoonoses and results in substantial socioeconomic costs for governments, farming industries, and tax payers. Despite decades of surveillance and research, surprisingly, little is known about the exact mechanisms of transmission. In particular, as a facultative intracellular pathogen, to what extent does survival of the causative agent, Mycobacterium tuberculosis var. bovis (M. bovis), in the environment constitute an epidemiological risk for livestock and wildlife? Due largely to the classical pathology of cattle cases, the received wisdom was that bTB was spread by direct inhalation and exchange of bioaerosols containing droplets laden with bacteria. Other members of the Mycobacterium tuberculosis complex (MTBC) exhibit differing host ranges, an apparent capacity to persist in environmental fomites, and they favour a range of different transmission routes. It is possible, therefore, that infection from environmental sources of M. bovis could be a disease transmission risk. Recent evidence from GPS-collared cattle and badgers in Britain and Ireland suggests that direct transmission by infectious droplets or aerosols may not be the main mechanism for interspecies transmission, raising the possibility of indirect transmission involving a contaminated, shared environment. The possibility that classical pulmonary TB can be simulated and recapitulated in laboratory animal models by ingestion of contaminated feed is a further intriguing indication of potential environmental risk. Livestock and wildlife are known to shed M. bovis onto pasture, soil, feedstuffs, water, and other fomites; field and laboratory studies have indicated that persistence is possible, but variable, under differing environmental conditions. Given the potential infection risk, it is timely to review the available evidence, experimental approaches, and methodologies that could be deployed to address this potential blind spot and control point. Although we focus on evidence from Western Europe, the concepts are widely applicable to other multihost bTB episystems.

Quantitative microbial risk assessment of occupational and public risks associated with bioaerosols generated during the application of dairy cattle wastewater as biofertilizer

The reuse or recycling of wastewater provides environmental and economic benefits, representing a sustainable and circular alternative for the management of liquid waste. However, the application of effluents to agricultural crops via spraying creates a potentially dangerous situation for individuals exposed to airborne pathogens. This study used Quantitative Microbial Risk Assessment (QMRA) tools to quantitatively assess the microbial risks of occupational and public exposures to bioaerosols in fertigation scenarios by spraying untreated and treated dairy cattle wastewater. Analyses of Escherichia coli (EC) and spores of Clostridium perfringens (CpSP) in raw and treated effluents as well as pathogen / indicator ratios from the literature were used to estimate the concentrations of Escherichia coli O157:H7 (EC O157:H7) and Cryptospodirium spp. (Crypto) in the air, and the results were applied to an atmospheric microbiological dispersion model. From the concentrations of pathogens in the air, infectious risks for downwind receptors were calculated. The risks of infection by EC O157:H7 to workers at 10 m and 50 m away from the emission source ranged between 3.81 × 10 1 and 2.68 × 10 3 pppy (per person per year), whereas to residents at 100 m and 500 m ranged from 4.59 × 10 1 to 1.51 × 10 4 pppy. Peak values (95th percentile) of occupational and public risks associated with the exposure to Crypto were 3.41 × 10 3 and 6.84 × 10 4 pppy at 10 m and 50 m from the source, respectively, and were lower than 1.48 × 10 6 pppy regarding exposures to CpSP. Anaerobic digestion reduced risks by approximately one order of magnitude. The distance from the source was inversely proportional to the risk of exposure. It is recommended that wastewater is treated prior to its reuse and the adoption of application methods with low aerosolization potential. In addition, the need for workers to use personal protective equipment (PPE) is highlighted.

Characterization of Clostridium Perfringens Isolates Collected from Three Agricultural Biogas Plants over a One-Year Period

Digestate produced by agricultural biogas plants (BGPs) may contain pathogenic bacteria. Among them, Clostridium perfringens deserves particular attention due to its ability to grow under anaerobic conditions and persist in amended soil. The aim of this study was to examine the potential pathogenicity and the antimicrobial resistance of C. perfringens in manure and digestate collected from three agricultural biogas plants (BGPs). A total of 157 isolates (92 from manure, 65 from digestate) were screened for genes encoding seven toxins (cpa, cpb, etx, iapcpe, netB, and cpb2). The 138 cpa positive isolates were then screened for tetA(P), tetB(P), tet(M), and erm(Q) genes and tested for antimicrobial susceptibility. The toxinotypes identified in both manure and digestate were type A (78.3% of the isolates), type G (16.7%), type C (3.6%), and type D (1.4%), whereas none of the isolates were type F. Moreover, half of the isolates carried the cpb2 gene. The overall prevalence of tetA(P) gene alone, tetA(P)-tetB(P) genes, and erm(Q) gene was 31.9, 34.8, and 6.5%, respectively. None of the isolates harbored the tet(M) gene. Multiple antimicrobial resistant isolates were found in samples that were collected from all the manure and digestates. Among them, 12.3% were highly resistant to some of the antibiotics tested, especially to clindamycin (MIC ≥ 16 µg/mL) and tilmicosin (MIC > 64 µg/mL). Some isolates were highly resistant to antibiotics used in human medicine, including vancomycin (MIC > 8 µg/mL) and imipenem (MIC > 64 µg/mL). These results suggest that digestate may be a carrier of the virulent and multidrug resistant C. perfringens.

Evaluation of the occurrence of sporulating and nonsporulating pathogenic bacteria in manure and in digestate of five agricultural biogas plants

The number of agricultural biogas plants has been increasing in the past decades in some European countries. Digestates obtained after anaerobic digestion (AD) of manure are usually spread on agricultural land; however, their hygiene status regarding pathogens posing public health and/or animal health challenges has been poorly characterized up to now in France. In this study, three replicates of manure and digestate were collected from five farm biogas plants receiving animal manure in order to assess the occurrence and concentrations of sporulating (Clostridium botulinum, Clostridioides difficile, Clostridium perfringens) and nonsporulating (Listeria monocytogenes, thermotolerant Campylobacter spp., Salmonella, Escherichia coli, enterococci) bacteria. Concentrations of E. coli, enterococci, and C. perfringens in digestates ranged from 10² to 10⁴, 10⁴ to 10⁵, and <10³ to 7 × 10⁵ CFU/g, respectively. Salmonella and C. difficile were detected in manure and digestate from the five biogas plants at concentrations ranging from <1.3 to >7 × 10² MPN/g and from 1.3 to 3 × 10² MPN/g, respectively. Thermotolerant Campylobacter, detected in all the manures, was only found in two digestates at a concentration of cells ranging from <10 to 2.6 × 10² CFU/g. Listeria monocytogenes and C. botulinum were detected in three manures and four digestates. The bacterial counts of L. monocytogenes and C. botulinum did not exceed 3 × 10² and 14 MPN/g, respectively. C. botulinum type B was detected at very low level in both the manure and digestate of farm biogas plants with no botulism history. The levels of pathogenic bacteria in both manure and digestate suggested that some bacteria can persist throughout AD.