ARRRGH! ARGs in Biosolids?

Reducing my personal carbon footprint, I take a healthy walk to a nearby grocery store, cutting through a nursing home parking lot. A stream of vented air from the home prompts an unavoidable thought: “I wonder if Candida spores are wafting over me.” You may have read the recent New York Times article Nursing Homes Are a Breeding Ground for a Fatal Fungus, and learned that “Candida auris, [is] a highly contagious, drug-resistant fungus that has infected nearly 800 people since it arrived in the United States four years ago, with half of patients dying within 90 days.” A fungus exhibiting drug resistance. I have been hearing a lot about bacteria, but this fungus information is new. Shockingly, nursing homes are characterized as “caldrons that are constantly seeding and reseeding hospitals with increasingly dangerous bacteria.”

Since I know how to have real fun, I visited the website of the Centers for Disease Control, found its “tracking update,” and learned that this fungus had been listed as “nationally notifiable” only last year. Happily, no cases are yet reported from Pennsylvania. I suspect this is just a matter of time. 

While visiting the CDC website, I also stumbled upon another meaningful report: ANTIBIOTIC RESISTANCE THREATS in the United States, 2013.  The report opens with the assertion: “Antibiotic resistance is one of the biggest public health challenges of our time.” Its report was for me a “rathole” I easily fell into, as it lays out the big picture strategies for mitigating the evolution of three organisms of “urgent concern,” a dozen (including Candida) “serious threats,” and another three “concerning threats.” The CDC report sets forth in this report its “four core actions” for reducing the spread of resistant organisms. As part of the first core action is “preventing the spread of resistance.” This is where wastewater treatment infrastructure comes in to play.

Increasing numbers of science journal articles are published annually framing the scale and risk of the sewage pathway for antibiotic resistance genes, or ARGs, and biosolids is part of that pathway. One article, Sources, behaviour and health risks of antimicrobial resistance genes in wastewaters: A hotspot reservoir, asserts “ARGs can be considered as a ‘super-wicked’ problem,” which means (thanks to Wikipedia) it is “difficult or impossible to solve because of incomplete, contradictory, and changing requirements that are often difficult to recognize.” In this review, antibiotic resistance genes (ARGs) are carried into the environment via wastewater, with dermal contact, aerosol inhalation, food contamination, and insect vectors among the intermediate connections, but the review concludes “evidence directly linking ARGs in wastewater to resistance remains weak.” A second review article, Antibiotic Resistance Genes in the Human-Impacted Environment: A One Health Perspective, argues “human health, animal agriculture, and the environment are the core and interrelated components,” and “advanced deployable detection methods [would] provide the surveillance information to identify risks and define barriers that can reduce risks.” It proposes deployment of such detectors along the wastewater treatment pathway.

Are ARGs in biosolids a significant issue? This is the kind of question that causes me to contact Dr. Ian Pepper at University of Arizona, and he pointed me to his 2018 survey in which he asks that same question, but gives his answer: Antibiotic Resistant Bacteria in Municipal Wastes: Is There Reason for Concern? The bottom line is that ARGs are a concern, but biosolids is not a leading pathway.

First and fundamentally, human beings and livestock are the breeders of antibiotic resistance, not biosolids. A 2016 article, Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances, asserts:  “excessive antibiotic use fosters bacterial resistance, and the overly exposed human microbiome has become a significant reservoir of resistance genes, contributing to the increasing difficulty in controlling bacterial infections.” Yes, human waste is carried by sewers, but contacts between people are far more immediate.  This is where, too, the hospital and nursing home settings will always be the critical hotspot for control of antibiotic resistance.

Sewers carry ARGs to our sewage treatment plants. Interestingly, one study even suggested the monitoring of sewage influent as a way to characterize pathogens in the community (Profile and Fate of Bacterial Pathogens in Sewage Treatment Plants Revealed by High-Throughput Metagenomic Approach). Conventional wastewater treatment seems to substantially reduce ARGs, and treatment options could likely be deployed to maximize the barrier to ARG release to the environment. Two articles Strategies to Combat Antibiotic Resistance in the Wastewater Treatment Plants and Critical review of ARGs reduction behavior in various sludge and sewage treatment processes in wastewater treatment plants point to the variety of in-plant processes, particularly anaerobic/anoxic and high temperature processes, that are most effective against hardy pathogens. But much additional research is needed.  

Second, the excessive use of antibiotics in livestock and the comparatively direct pathways of manure to environmental and human exposures constitute a much larger problem than biosolids. An article from South Africa, Systematic review in South Africa reveals antibiotic resistance genes shared between clinical and environmental settings, reported “Data extracted from this review revealed farm settings to be one of the main contributors of antibiotic resistance in healthcare settings. ARB, ARGs, and ARGDs [antimicrobial-resistant gene determinants] were found to be ubiquitous in all settings examined.”

Yet, soils standout as a special pathway for ARGs in the environment. Dr. Pepper reminds us that, first and foremost, soil is the microbiome for production of antibiotics. This aspect has been called the “soil antibiotic resistome.” The article The soil resistome: The anthropogenic, the native, and the unknown conjectures that “many pathogen-associated antibiotic resistance genes originated in antibiotic-producing soil bacteria and reached pathogens via horizontal gene transfer.” What is more, cultivated soils reveal even higher antibiotic resistance than native soils. This was confirmed in a study of urban soils, none associated with biosolids, but affected by urban activities: Case study on the soil antibiotic resistome in an urban community garden concluded “The data demonstrated a diverse population of antibiotic resistance in urban agricultural soils.” You don’t need biosolids amendment to create highly ARG-impacted soils.

What happens when you apply an ARG-rich manure or biosolids to farm soils? For one, bacteria diversity increases (Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil) and in the direction of bacteria that harbored antibiotic resistance for relevant pathogens. But while diversity and numbers increase, the soil microbiome exerts its own effects on biosolids-borne organisms. Research supported by Charlotte Water (Soil microbiome response to land application of wastewater treatment biosolids): ”the data suggests that biosolid application can alter the microbiome of the soil temporarily; however it does not appear to be a result of direct transfer of species between the two mediums.” A research study (Application of biosolids drives the diversity of antibiotic resistance genes in soil and lettuce at harvest) discovered transfer of antibiotic resistance genes to lettuce grown with biosolids. But what kind of biosolids manager applies biosolids to lettuce? And whereas most horticultural applications of biosolids involve a composted product, we learn that spread of antibiotic resistance is likely mitigated by composting (Effect of antibiotic use and composting on antibiotic resistance gene abundance and resistome risks of soils receiving manure-derived amendments). And, just as we are concerned with risks of nutrient runoff from land application activities, a similar concern may be raised for the environmental runoff of ARGs, as was speculated in  Occurrence and ecological determinants of the contamination of floodplain wetlands with Klebsiella pneumoniae and pathogenic or antibiotic-resistant Escherichia coli.

Mostly, scientists can’t be sure what we will learn about the fate of biosolids-borne ARGs in soil. First off, soils are powerful bioreactors, as the flurry of news reports of the “underwear soil microbial activity test” reminds us, which means we can expect soil microbes to heavily influence ARGs. Importantly, as Dr. Pepper opines, the risks of ARGs in biosolids-amended soil likely will prove low when arrayed against myriad other pathways of ARG exposure to humans and others. The kind of studies that might show whether this is true is offered in Human Health Risk Assessment (HHRA) for Environmental Development and Transfer of Antibiotic Resistance, in which the “environmental aspects of antibiotic-resistance development [may] be included in the processes of any HHRA addressing ARB, [in order to fill] research gaps that need to be addressed.” And we need to refine our wastewater treatment processes, as proposed in Toward a Comprehensive Strategy to Mitigate Dissemination of Environmental Sources of Antibiotic Resistance for wastewater treatment and other environmental pathways. Among the potential paybacks from such study is that we may identify beneficial products and methods (antimicrobial biosynthesis), which addresses the CDC’s number four core action for developing new antibiotics (Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes). After all, soil played a role in the earliest development of antibiotics; soil bacteria led to the discovery of early antibiotics of streptomycin. There is opportunity ahead, as shown by the 2018 report that a wholly new method of searching for beneficial soil microbes had led to a new class of antibiotics, malacidins (Powerful Antibiotics Found in Dirt).

So, let me throw out there a wholly fanciful notion I have. Could it be that biosolids is a media that is the “secret sauce” for discovering and developing new antibiotics in biosolids-amended soils? Why do I ask? For over twenty years at Philadelphia’s biosolids center, compost blowers exhausted into my face, manure spreaders slung cake in my direction, rotary screens showered me with biosolids compost dust, centrifuges whipped up aerosolized biosolids. Yet, I took not a single day of sick leave in all those years. Now, I wonder whether the biosolids-borne microbes that surrounded my workplace had conferred to me a special antimicrobial resistance. I wonder, might the biosolids microbiome someday prove to be a source of health-giving microbes and natural antibiotics? ARGHHH! Who Knows About those ARGs?