It is estimated that by 2050, 40% of microbial infections in Canadians will be resistant to first-line antimicrobials, meaning that 1 in 26 deaths in Canada will be attributable to antimicrobial resistance (CCA, 2019). Clinical settings are often implicated as reservoirs for the accumulation and spread of both the suite of antibiotic resistance genes (ARGs) and the resistant pathogens that express them, which is termed the resistome. However, there is growing evidence that environments impacted by anthropogenic activities, such as wastewater treatment plants and animal husbandry facilities, foster abundant and diverse resistomes (Berendonk et al., 2015). Included in this category is the organic fraction of municipal solid waste (MSW) which constitutes up to 53% of the two billion tonnes of total MSW produced globally each year (Braguglia et al., 2018). To avoid landfill disposal of the organic MSW fraction, a promising technology called anaerobic digestion (AD) allows microbes to break down and stabilize the waste, producing renewable energy (Vasco-Correa et al., 2018). Further, studies have shown that AD can alter the resistome of MSW (Zhang et al., 2016; 2018) but its efficacy in limiting the spread of antimicrobial resistance remains unclear. To fill in this gap, Kanger et al. asked whether AD of food waste, paper and cardboard can reduce ARG abundance and diversity.

            To investigate this, the research group employed a lab-scale AD system consisting of a solid-state leach bed reactor with leachate recycling via a UASB reactor (Guilford et al., 2019). Each week for 88 weeks, the system was filled with digester feed consisting of lignocellulosic fibres (e.g. shredded cardboard, newsprint) and food waste collected from residential green bins. Samples of this feed were taken before digestion and then again after 6 weeks inside the system. Total community DNA was then extracted and subjected to various genetic analyses in order to quantify the impact of AD on the diversity and abundance of microbes and ARGs.  

            First, the authors used small subunit rRNA gene-fragment sequencing to determine how microbial community composition changed due to AD. This analysis was critical, as specific microbes are known drivers of ARGs in these systems (Luo et al., 2017). Sequencing revealed that the digester feed mainly consisted of bacterial and eukaryotic taxa, including several genera of lactic acid bacteria such as Lactobacillus, but also human pathogens such as Staphylococcus aureus. None of these pathogens were detected in the community after digestion. Instead, it was dominated by diverse methane-producing archaea. These results confirmed previous reports that AD significantly alters the microbial community and further found that it can successfully remove certain pathogens from the community.   

            Next, the authors performed total community metagenome sequencing to determine how AD impacts ARG diversity and abundance. Both metrics were higher in the digester feed and comparable to the levels observed in wastewater from livestock farms (Li et al., 2015). Certain ARGs, such as those conferring resistance to fosfomycin, were completely removed by AD whereas the levels of others, such as those conferring resistance to vancomycin, actually increased. These changes tracked with community makeup, as AD removed ARGs from the food waste bacteria and amplified ARGs from the digester bacteria. To explore this further, the authors used metagenomic assembly and binning, to taxonomically annotate the ARGs (Figure 1). This implicated numerous human pathogens in the digester feed as potential hosts to a high number of multidrug-resistance genes. Though ARG abundance was much lower in the digestion products, those that were detected also had connections to pathogenic taxa. An additional concern was the 32% of ARGs located on plasmids, indicating high potential for horizontal gene transfer which can lead to their rapid dissemination in microbial communities. Overall, these findings illustrate that AD can successfully diminish ARG diversity and abundance, however it also highlights that there is still room for development.

            The ten million tonnes of organic waste sent to landfills each year in Canada (Guilford et al., 2019) is not only unsustainable for our planet, but also threatens the future effectiveness of antimicrobials. The risks and benefits of AD elucidated by this study will be extremely helpful in improving this technology to move us towards a greener future, while simultaneously reducing the spread of antimicrobial resistance.

Primary Research Article:

Kanger, K., Guilford, N.G., Lee, H., Nesbø, C.L., Truu, J. and Edwards, E.A., 2020. Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard. FEMS Microbiology Ecology, 96(2), p.fiaa006.

Other References:

Berendonk, T.U., Manaia, C.M., Merlin, C., Fatta-Kassinos, D., Cytryn, E., Walsh, F., Bürgmann, H., Sørum, H., Norström, M., Pons, M.N. and Kreuzinger, N., 2015. Tackling antibiotic resistance: the environmental framework. Nature Reviews Microbiology, 13(5), pp.310-317.

Braguglia, C.M., Gallipoli, A., Gianico, A. and Pagliaccia, P., 2018. Anaerobic bioconversion of food waste into energy: A critical review. Bioresource technology, 248(Pt A), p.37.

Council of Canadian Academies (CCA), 2019. When Antibiotics Fail. Ottawa (ON): The Expert Panel on the Potential Socio-Economic Impacts of Antimicrobial Resistance in Canada, Council of Canadian Academies.

Guilford, N.G., Lee, H.P., Kanger, K., Meyer, T. and Edwards, E.A., 2019. Solid-State Anaerobic Digestion of Mixed Organic Waste: The Synergistic Effect of Food Waste Addition on the Destruction of Paper and Cardboard. Environmental science & technology, 53(21), pp.12677-12687.

Li, B., Yang, Y., Ma, L., Ju, F., Guo, F., Tiedje, J.M. and Zhang, T., 2015. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. The ISME journal, 9(11), pp.2490-2502.

Luo, G., Li, B., Li, L.G., Zhang, T. and Angelidaki, I., 2017. Antibiotic resistance genes and correlations with microbial community and metal resistance genes in full-scale biogas reactors as revealed by metagenomic analysis. Environmental science & technology, 51(7), pp.4069-4080.

Vasco-Correa, J., Khanal, S., Manandhar, A. and Shah, A., 2018. Anaerobic digestion for bioenergy production: Global status, environmental and techno-economic implications, and government policies. Bioresource technology, 247, pp.1015-1026.

Zhang, J., Chen, M., Sui, Q., Wang, R., Tong, J. and Wei, Y., 2016. Fate of antibiotic resistance genes and its drivers during anaerobic co-digestion of food waste and sewage sludge based on microwave pretreatment. Bioresource technology, 217, pp.28-36.

Zhang, J., Mao, F., Loh, K.C., Gin, K.Y.H., Dai, Y. and Tong, Y.W., 2018. Evaluating the effects of activated carbon on methane generation and the fate of antibiotic resistant genes and class I integrons during anaerobic digestion of solid organic wastes. Bioresource technology, 249, pp.729-736.