Aquaculture is a crucial sector for Egyptian food production, providing a cheap source of animal protein while securing income and employment for a substantial part Egypt's population. Nile tilapia (Oreochromis niloticus) is the most commonly produced fish, usually farmed in earthen ponds around the Northern Delta Lakes. A common practice among farms is to fertilize ponds with chicken manure (CM) in order to increase nutrient levels and promote phytoplankton, consumed by the fish. However, with reports of use of antibiotics in Egypt's poultry sector, and that CM contains residues of antibiotics, antibiotic resistant pathogens and antibiotic resistance genes (ARGs) are production benefits large enough to compensate a potential health hazard?

Using production data from 501 aquaculture farms and fish pond sediment from 28 ponds we evaluated potential benefits in yields and profitability for farms using CM for fertilization, and used qPCRs to screen sediments for three antibiotic resistance genes coding for resistance to the most commonly used antibiotics in the poultry sector. The analysis showed no significant benefits to fish yields or profitability in farms where CM was applied, but a risk of significantly increased nutrient loads. Meanwhile, we detected increased abundances of tetA and tetW resistance genes in fish pond sediment where CM was applied. With the risk of disseminating ARGs and causing eutrophication of local waterways, we recommend that Egyptian tilapia pond farmers refrain from using CM and adopt best management practices for increasing farm profitability in order to to reduce environmental and health hazards.

Notably, 56 worldwide experts gathered for the Antimicrobial Assessment on Global Aquaculture Production (AGAP) series of workshops to (1) evaluate the current state of knowledge on antimicrobial use and identify existing gaps; (2) formulate strategies to identify ecologically relevant impact indicators and establish thresholds for assessment; (3) identify pivotal socioeconomic factors and effective governance mechanisms essential for implementing monitoring practices in aquaculture and extending them across sectors and countries for aquaculture sustainability; (4) develop pathways to enhance our comprehension between antibiotic use in aquaculture and antimicrobial resistance; and (5) explore potential antibiotic monitoring tools that can be universally adapted and implemented across region and sectors. The main outcomes were a roadmap for establishing investigation priorities on the relevant topics regarding antibiotic use in aquaculture, socioeconomic drivers for using antibiotics and behaviors that need more robust and transparent regulatory frameworks to guide farmers, training on antimicrobial use, and access to veterinarians and extension services agents for education. Overall, the workshop evidenced the power of collaboration in addressing complex global challenges to achieve sustainable aquaculture. Despite diligent efforts, some constraints may have inadvertently narrowed the possibility of having more experts and left some pertinent topics unaddressed, but they are needed in the discussion.

Chemicals are being emitted into the environment through human activities, such as agriculture or animal husbandry. Emissions can either occur intentionally, as pesticide application of crops, or inadvertently, such as pharmaceutical residues in wastewater effluents. Chicken manure (CM) is occasionally used as a cheap fertilizer in aquaculture pond farms to increase the productivity and the profitability. Depending on local regulation and production strategy, animal manures can contain substantial amounts of antibiotics (AB) and other pharmaceuticals used for raising animals. The benefits of this practice, however, have not been clearly established in relation to the potential adverse consequences. 

By analysing production data from Egyptian fish farms in Study I, I show that CM fertilization promotes eutrophication, without corresponding to increased fish yields or clear benefits for the producers. Study I support arguments to cease CM fertilization in Egyptian aquaculture if the goal is to increase fish yields or profitability. Additionally, I employ a qPCR assay to show that CM fertilization correlates with increased abundance of antibiotic resistance genes (ARGs) in pond sediment. 

AB emitted to the environment can induce resistance development in bacteria and promote selection of resistant genotypes. Study II aim to capture the effects of AB emitted throughout the value chain of agri-food products, and life cycle assessment (LCA) is investigated for this purpose. LCA is a framework developed to assess environmental impacts throughout the value chain of products. In Study II, I present an approach to quantify potential AB resistance enrichment in the environment within LCA. I also discuss a mass-balance approach to capture the relationship between regional AB use and regional human health impacts, in order to capture the full range of potential impacts caused by emissions of AB. 

Characterizations of potential toxic effects of chemicals in LCA are generally drawn from species sensitivity distribution models that aim to describe an ecosystem-wide response to chemical emission. While this provides insights into the toxicity of a chemical, predictions of the “true” ecosystem wide effects will always be shrouded by uncertainty, depending on the availability and quality of data. Detailed knowledge on adverse effects and potential hazard chemicals impose are required for stakeholders at both global and local scales to make informed decisions on how to regulate the use and emissions of chemicals. 

Study IV identify LCA studies where toxicological impacts are evaluated and chemicals in the inventory are classified towards ecotoxicological impact, but ecotoxicological characterizations are missing, which leads to underestimating the ecotoxicological impact. To enhance the precision of ecotoxicological effect assessments for chemicals, Study III gathers an extensive toxicological dataset and present a method to assess the uncertainty associated with ecotoxicological effect calculations. The proposed method opens up for exploring uncertainty in ecotoxicological effect calculations, but data availability is limiting the number of chemicals that can be assessed for ecotoxicological effect and uncertainty. To gap-fill information on toxic effect of chemicals, Study IV explores quantitative structure-activity relationship (QSAR) models to predict ecotoxicological effect of chemicals. However, mechanistic understanding of toxic mode of action is not provided by these models. Thus, the accuracy and validity of predicted toxicological effect data are not yet established. Since current LCA software lacks functionality to aggregate uncertainties throughout assessments, the use of predicted toxicological data is discouraged.

This thesis presents some of the many challenges we face when assessing toxicological impacts from chemicals emitted to the environment, and provides methods and recommendations how to better evaluate impacts and uncertainties in toxicological characterization of chemicals. 

Kemikalier släpps ut i miljön till följd av mänskliga aktiviteter, såsom jordbruk och djurhållning. Utsläpp kan ske avsiktligt, såsom användande av bekämpningsmedel på grödor, eller oavsiktligt, såsom läkemedelsrester i renat avloppsvatten. Hönsgödsel kan ibland användas som billigt tillskott av näringsämnen till fiskodlingar, i syfte att gynna produktiviteten, tillika lönsamheten. Beroende på lokala regelverk och produktionsmetoder kan gödsel komma att innehålla betydande halter av antibiotika (AB), eller andra läkemedel som används inom djuruppfödningen. Det är dock inte klarlagt hur fördelarna med denna praxis står sig i förhållande till potentiella negativa effekter. 

Genom att analysera produktionsdata från egyptiska fiskodlingar, visar jag i Studie I, att hönsgödselanvändning i fiskodlingar bidrar till övergödning utan att gynna varken produktion eller lönsamhet. Således underbygger resultaten från Studie I argument för att upphöra med hönsgödselanvändning inom egyptisk fiskodling om målet är att öka fiskproduktionen eller lönsamheten. Dessutom visar jag, med hjälp av qPCR-metodik, att hönsgödselanvändning korrelerar med ökad förekomst av antibiotikaresistensgener i fiskdammars sediment.

AB som släpps ut i miljön kan skapa förutsättningar för bakterier att utveckla antibiotikaresistens och främja resistenta genotyper. Studie II undersöker tillämpbarheten av verktyget livscykelanalys (LCA) för utvärdering av effekterna av AB som släpps ut i miljön. LCA är ett ramverk utvecklat för att kunna möjliggöra bedömning av miljöpåverkan genom hela värdekedjan av en produkt. I Studie II presenterar jag ett nytt tillvägagångssätt för att kvantifiera potentiell anrikning av antibiotikaresistens i miljön anpassat för användning inom LCA. Dessutom diskuteras ett massbalansförhållande mellan regional AB-användning och regionala hälsoeffekter på människor, i syfte att fånga upp samtliga effekter som AB kan orsaka till följd av utsläpp i miljön.

För att karaktärisera kemikaliers eventuella toxicitet inom LCA, så används vanligtvis modeller som beskriver arters sinsemellan relativa respons (species sensitivity distribution models) till toxikanter. Dessa modeller syftar till att beskriva en ekosystemomfattande respons till följd av kemikalieutsläpp. Även om dessa tester och modeller kan ge insikter om kemikaliers toxiska egenskaper, kommer de 'sanna' ekosystemomfattande effekterna att förbli dolda av ett visst mått av osäkerhet, vilket beror på mängden, och kvaliteten, av data.

Studie IV undersöker LCA-studier där toxikologisk skada av kemikalieutsläpp utvärderas, men där toxikologiska karaktäriseringar saknas för vissa kemikalier, vilket underskattar miljöskada. För att öka precisionen av beräknad miljöskada från kemikalieutsläpp så har Studie III samlat in en omfattande mängd toxicitetsdata och presenterar ett tillvägagångssätt för att uppskatta osäkerheter i dessa beräkningar. Brist på data begränsar dock antalet kemikalier som miljöskada och tillhörande osäkerheter kan beräknas för. 

För att komplettera den begränsade mängden data så undersöker Studie IV kvantitativ struktur-aktivitet-relation (QSAR) beräkningsmodeller för att förutse toxikologisk effekt av kemikalier. Dock förser oss dessa modeller inte med mekanistisk förståelse kring toxiska verkningsmekanismer vilket gör att noggrannheten och validiteten för QSAR-modellerna inte kan fastställas. Eftersom det saknas funktionalitet inom LCA-mjukvaruprogram för att sammanställa och spåra osäkerheter så avråds användningen av toxikologiska data genererad via QSAR-beräkningsmodeller. 

Den här avhandlingen syftar till att presentera några av de utmaningar som vi står inför vid bedömning av skadeverkan från kemikalier som släpps ut i miljön. Avhandlingen tillhandahåller även metoder och rekommendationer för att med högre noggrannhet kunna utvärdera osäkerheter i sådana bedömningar.

Purpose: With antibiotic resistance (ABR) portrayed as an increasing burden to human health, this study reviews how and to what extent toxicological impacts from antibiotic use are included in LCAs and supplement this with two novel approaches to include ABR, a consequence of antibiotic use, into the LCA framework.

Methods: We review available LCA studies that deal with toxicological aspects of antibiotics to evaluate how these impacts from antibiotics have been characterized. Then, we present two novel approaches for including ABR-related impacts in life cycle impact assessments (LCIAs). The first approach characterizes the potential for ABR enrichment in the environmental compartment as a mid-point indicator, based on minimum selective concentrations for pathogenic bacteria. The second approach attributes human health impacts as an endpoint indictor, using quantitative relationships between the use of antibiotics and human well-being.

Results and discussion: Our findings show that no LCA study to date have accounted for impacts related to ABR. In response, we show that our novel mid-point indicator approach could address this by allowing ABR impacts to be characterized for environmental compartments. We also establish cause-effect pathways between antibiotic use, ABR, and human well-being that generate results which are comparable with USEtox and most endpoint impact assessment approaches for human toxicology.

Conclusions: Our proposed methods show that currently overlooked impacts from ABR enrichment in the environment could be captured within the LCA framework as a robust characterization methodology built around the established impact model USEtox. Substantial amounts of currently unavailable data are, however, needed to calculate emissions of antibiotics into the environment, to develop minimum selective concentrations for non-pathogenic bacteria, and to quantify potential human health impacts from AB use.