The survival of cefazolin-resistant bacteria in mesophilic co-digestion of dairy manure and waste milk

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

The Antibiotics Degradation and Its Mechanisms during the Livestock Manure Anaerobic Digestion

Antibiotics are administered to livestock at subtherapeutic levels to promote growth, and their degradation in manure is slow. High antibiotic concentrations can inhibit bacterial activity. Livestock excretes antibiotics via feces and urine, leading to their accumulation in manure. This can result in the propagation of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Anaerobic digestion (AD) manure treatment technologies are gaining popularity due to their ability to mitigate organic matter pollution and pathogens, and produce methane-rich biogas as renewable energy. AD is influenced by multiple factors, including temperature, pH, total solids (TS), substrate type, organic loading rate (OLR), hydraulic retention time (HRT), intermediate substrates, and pre-treatments. Temperature plays a critical role, and thermophilic AD has been found to be more effective in reducing ARGs in manure compared to mesophilic AD, as evidenced by numerous studies. This review paper investigates the fundamental principles of process parameters affecting the degradation of ARGs in anaerobic digestion. The management of waste to mitigate antibiotic resistance in microorganisms presents a significant challenge, highlighting the need for effective waste management technologies. As the prevalence of antibiotic resistance continues to rise, urgent implementation of effective treatment strategies is necessary.

Aerobic Composting and Anaerobic Digestion Decrease the Copy Numbers of Antibiotic-Resistant Genes and the Levels of Lactose-Degrading Enterobacteriaceae in Dairy Farms in Hokkaido, Japan

Efficient methods for decreasing the spread of antimicrobial resistance genes (ARGs) and transfer of antimicrobial-resistant bacteria (ARB) from livestock manure to humans are urgently needed. Aerobic composting (AC) or anaerobic digestion (AD) are widely used for manure treatment in Japanese dairy farms. To clarify the effects of AC and AD on antimicrobial resistance, the abundances of antimicrobial (tetracycline and cefazolin)-resistant lactose-degrading Enterobacteriaceae as indicator bacteria, copy numbers of ARGs (tetracycline resistance genes and β-lactamase coding genes), and concentrations of residual antimicrobials in dairy cow manure were determined before and after treatment. The concentration of tetracycline/cefazolin-resistant lactose-degrading Enterobacteriaceae was decreased over 1,000-fold by both AC and AD. ARGs such as tetA, tetB, and bla TEM were frequently detected and their copy numbers were significantly reduced by ∼1,000-fold by AD but not by AC. However, several ARG copies remained even after AD treatment. Although concentrations of the majority of residual antimicrobials were decreased by both AC and AD, oxytetracycline level was not decreased after treatment in most cases. In addition, 16S rRNA gene amplicon-based metagenomic analysis revealed that both treatments changed the bacterial community structure. These results suggest that both AC and AD could suppress the transmission of ARB, and AD could reduce ARG copy numbers in dairy cow manure.

Increased (Antibiotic-Resistant) Pathogen Indicator Organism Removal during (Hyper-)Thermophilic Anaerobic Digestion of Concentrated Black Water for Safe Nutrient Recovery

Source separated toilet water is a valuable resource for energy and fertilizers as it has a high concentration of organics and nutrients, which can be reused in agriculture. Recovery of nutrients such as nitrogen, phosphorous, and potassium (NPK) decreases the dependency on energy-intensive processes or processes that rely on depleting natural resources. In new sanitation systems, concentrated black water (BW) is obtained by source-separated collection of toilet water. BW-derived products are often associated with safety issues, amongst which pathogens and antibiotic-resistant pathogens. This study presents results showing that thermophilic (55–60 °C) and hyperthermophilic (70 °C) anaerobic treatments had higher (antibiotic-resistant) culturable pathogen indicators removal than mesophilic anaerobic treatment. Hyperthermophilic and thermophilic anaerobic treatment successfully removed Escherichia coli and extended-spectrum β-lactamases producing E. coli from source-separated vacuum collected BW at retention times of 6–11 days and reached significantly higher removal rates than mesophilic (35 °C) anaerobic treatment (p < 0.05). The difference between thermophilic and hyperthermophilic treatment was insignificant, which justifies operation at 55 °C rather than 70 °C. This study is the first to quantify (antibiotic-resistant) E. coli in concentrated BW (10–40 gCOD/L) and to show that both thermophilic and hyperthermophilic anaerobic treatment can adequately remove these pathogen indicators.

Is anaerobic digestion a reliable barrier for deactivation of pathogens in biosludge?

As World Health Organization advocates, the global burden of sanitation related disease and access to safely managed sanitation and safely treated wastewater should be monitored strictly. However, the spread of pathogens through various agricultural applications or direct discharge of sewage sludge generated in municipal wastewater treatment plants poses a serious challenge on the environment and public health. Anaerobic digestion (AD), the principal method of stabilizing biosolids, can efficiently and largely deactivate viable pathogens, including parasite, virus, and the pathogens harboring antibiotic resistance genes. This review aims to provide a critical overview regarding the deactivation of sludge-associated pathogens by AD, through which a serious concern on the effectiveness and rationality of AD towards sludge pathogens control was raised. Meanwhile, the underlying deactivation mechanisms and affecting factors were all discussed, with the focus on pathogen-associated modeling, engineering design and technological aspects of AD. Lastly, a matric method incorporating the operating strategy of AD with the risk assessment was proposed for evaluating the reliability of AD-based pathogen deactivation, while the research agenda forward was also outlined.

Association of colistin residues and manure treatment with the abundance of mcr-1 gene in swine feedlots

BACKGROUND

The extensive use of colistin in swine production may have contributed to the recent emergence of corresponding mobile resistance gene mcr-1. The use of colistin as a feed additive was banned in China in April 2017.

OBJECTIVES

To examine the occurrence of colistin and dissemination of mcr-1 in swine feedlots before and after the colistin ban and effects of different manure treatments.

METHODS

Environmental samples were collected from swine feedlots before (December 2016) and after (December 2017) the colistin ban. Colistin concentrations were determined by ultra-high performance liquid chromatography coupled to tandem mass spectrometry. The prevalence of mcr-1 were determined by quantitative PCR analysis, while bacterial community composition was investigated by 16S rRNA sequencing.

RESULTS

In 2016, colistin was detected in feed and fresh manure samples at 67 mg/kg and 17 mg/kg, respectively, but was absent from all samples in 2017. In 2016, the relative abundance of mcr-1 in fresh manure was lower than that in solid samples after natural drying, while a higher relative abundance was detected in fresh manure samples compared with biogas slurry samples. A strong correlation between colistin concentration and relative abundance of mcr-1 was observed in fresh manure. The samples collected in 2017 showed a lower relative abundance of mcr-1 compared with those collected in 2016. Bacterial community analysis showed that the abundance of Enterobacteriaceae, which act as a vehicle and reservoir of mcr-1, increased with natural dying but decreased with anaerobic digestion.

CONCLUSIONS

The presence of colistin exerts direct selection pressure for the accumulation of mcr-1 in manure, while the ban on colistin likely halted the dissemination of mcr-1 on pig farms. Anaerobic digestion is an effective waste treatment process for removing mcr-1, which might be mainly driven by the shift in bacterial community structure.

Recent Updates on the Use of Agro-Food Waste for Biogas Production

The production of biogas from anaerobic digestion (AD) of residual agro-food biomasses represents an opportunity for alternative production of energy from renewable sources, according to the European Union legislation on renewable energy. This review provides an overview of the various aspects involved in this process with a focus on the best process conditions to be used for AD-based biogas production from residual agro-food biomasses. After a schematic description of the AD phases, the biogas plants with advanced technologies were described, pointing out the strengths and the weaknesses of the different digester technologies and indicating the main parameters and operating conditions to be monitored. Subsequently, a brief analysis of the factors affecting methane yield from manure AD was conducted and the AD of fruit and vegetables waste was examined. Particular attention was given to studies on co-digestion and pre-treatments as strategies to improve biogas yield. Finally, the selection of specific microorganisms and the genetic manipulation of anaerobic bacteria to speed up the AD process was illustrated. The open challenges concern the achievement of the highest renewable energy yields reusing agro-food waste with the lowest environmental impact and an increment of competitiveness of the agricultural sector in the perspective of a circular economy.

Risk for the development of Antimicrobial Resistance (AMR) due to feeding of calves with milk containing residues of antibiotics

EFSA was requested to: 1) assess the risk for the development of antimicrobial resistance (AMR) due to feeding on farm of calves with colostrum potentially containing residues of antibiotics; 2) assess the risk for the development of AMR due to feeding on farm of calves with milk of cows treated during lactation with an antibiotic and milked during the withdrawal period, and 3) propose possible options to mitigate the risk for the development of AMR derived from such practices. Treatment of dairy cows during the dry period and during lactation is common in the EU Member States. Penicillins, alone or in combination with aminoglycosides, and cephalosporins are most commonly used. Residue levels of antimicrobials decrease with the length of the dry period. When the interval from the start of the drying-off treatment until calving is as long as or longer than the minimum specified in the Summary of Product Characteristics of the antimicrobial, faecal shedding of antimicrobial-resistant bacteria will not increase when calves are fed colostrum from treated cows. Milk from cows receiving antimicrobial treatment during lactation contains substantial residues during the treatment and withdrawal period. Consumption of such milk will lead to increased faecal shedding of antimicrobial-resistant bacteria by calves. A range of possible options exist for restricting the feeding of such milk to calves, which could be targeting the highest priority critically important antimicrobials. β-Lactamases can reduce the concentration of β-lactams which are the most frequently used antimicrobials in milking cows. Options to mitigate the presence of resistant bacteria in raw milk or colostrum are mainly based on thermal inactivation.

Mechanism and Effect of Temperature on Variations in Antibiotic Resistance Genes during Anaerobic Digestion of Dairy Manure

Animal manure comprises an important reservoir for antibiotic resistance genes (ARGs), but the variation in ARGs during anaerobic digestion at various temperatures and its underlying mechanism remain unclear. Thus, we performed anaerobic digestion using dairy manure at three temperature levels (moderate: 20 °C, mesophilic: 35 °C, and thermophilic: 55 °C), to analyze the dynamics of ARGs and bacterial communities by quantitative PCR and 16S rRNA gene sequencing. We found that 8/10 detected ARGs declined and 5/10 decreased more than 1.0 log during thermophilic digestion, whereas only four and five ARGs decreased during moderate and mesophilic digestion, respectively. The changes in ARGs and bacterial communities were similar under the moderate and mesophilic treatments, but distinct from those in the thermophilic system. Potential pathogens such as Bacteroidetes, Proteobacteria, and Corynebacterium were removed by thermophilic digestion but not by moderate and mesophilic digestion. The bacterial community succession was the dominant mechanism that influenced the variation in ARGs and integrons during anaerobic digestion. Thermophilic digestion decreased the amount of mesophilic bacteria (Bacteroidetes and Proteobacteria) carrying ARGs. Anaerobic digestion generally decreased the abundance of integrons by eliminating the aerobic hosts of integrons (Actinomycetales and Bacilli). Thermophilic anaerobic digestion is recommended for the treatment and reuse of animal manure.