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Antimicrobial resistance is a major threat to public health. Antimicrobial use in animal husbandry is a major concern since it can favor an increase in antimicrobial resistance among farms. Herein, we aim to better understand and characterize the main resistome profiles in microbial communities found in pig farms. Sampling of swine manure was performed in two different timepoints (October 2019 and January 2020) in each of the 14 different swine farms, located in the mesoregion of Western Santa Catarina state in Brazil, a pole of swine product production of worldwide importance. Samples were divided into three groups: farms with the opened regimen and no usage of antimicrobials (F1; n = 10), farms with the closed regimen and usage of antimicrobials (F2; n = 16), and farms with the closed regimen and no usage of antimicrobials (F3; n = 2). The metagenomic evaluation was performed to obtain and identify genetic elements related to antimicrobial resistance using nanopore sequencing. We used ResistoXplorer software to perform composition, alpha and beta diversity, and clustering analysis. In addition, PCR reactions were performed to confirm the presence or absence of seven different beta-lactamase family genes and five phosphoethanolamine transferase gene variants clinically relevant. Our findings based on the identification of resistance genes at the mechanism level showed a prevalence of alteration of the drug target (72.3%) profile, followed by drug inactivation (17.5%) and drug efflux (10.1%). We identified predominantly aminoglycosides (45.3%), tetracyclines (15.9%), and multiclass (11,2%) resistance genes. PCoA analysis indicates differences between F1 and F2 profiles. F2 samples showed increased diversity when compared to the F1 group. In addition, herein we first report the identification of mcr-4 in a slurry sample (C1F1.1) in Santa Catarina State. In general, our findings reinforce that many factors on the practices of animal husbandry are involved in the resistome profile at the mechanism and class levels. Further studies to better understand microbiome and mobilome aspects of these elements are necessary to elucidate transmission pathways between different bacteria and environments.

Phycoremediation of swine wastewater is a promising treatment since it efficiently removes nutrients and contaminants and, simultaneously, its biomass can be harvested and used to obtain a wide range of valuable compounds and metabolites. In this context, biomass microalgae were investigated for the phycoremediation of swine wastewater, and biomass extracts for its virucidal effect against enveloped and non-enveloped viruses. Microalgae were cultivated in a pilot scale bioreactor fed with swine wastewater as the growth substrate. Hexane, dichloromethane, and methanol were used to obtain the microalgae extracts. Extracts were tested for virucidal potential against HSV-1 and HAdV-5. Virucidal assays were conducted at temperatures that emulate environmental conditions (21 °C) and body temperature (37 °C). The maximum production of microalgae biomass reached a concentration of 318.5 ± 23.6 mgDW L−1. The results showed that phycoremediation removed 100% of ammonia-N and phosphate-P, with rates (k1) of 0.218 ± 0.013 and 0.501 ± 0.038 (day−1), respectively. All microalgae extract reduced 100% of the infectious capacity of HSV-1. The microalgae extracts with dichloromethane and methanol showed inhibition activities at the lowest concentration (3.125 µg mL−1). Virucidal assays against HAdV-5 using microalgae extract of hexane and methanol inhibited the infectious capacity of the virus by 70% at all concentrations tested at 37 °C. At a concentration of 12.5 µg mL−1, the dichloromethane microalgae extract reduced 50?80% of the infectious capacity of HAdV-5, also at 37 °C. Overall, the results suggest that the microalgae can be an attractive source of feedstock biomass for the exploration of alternative virucidal compounds. Resumo: A ficorremediação de águas residuais de suinocultura é um tratamento promissor, pois remove eficientemente nutrientes e contaminantes e, simultaneamente, sua biomassa pode ser colhida e utilizada para obter uma ampla gama de compostos e metabólitos valiosos. Neste contexto, microalgas de biomassa foram investigadas para a fitomediação de águas residuais de suínos, e extratos de biomassa por seu efeito virucida contra vírus envelopados e não envelopados. As microalgas foram cultivadas em um biorreator de escala piloto alimentado com água residuária de suínos como substrato de crescimento. Hexano, diclorometano e metanol foram usados ​​para obter os extratos de microalgas. Os extratos foram testados quanto ao potencial virucida contra HSV-1 e HAdV-5. Os ensaios virucidas foram conduzidos em temperaturas que simulam as condições ambientais (21°C) e a temperatura corporal (37°C).DW L −1 . Os resultados mostraram que a ficorremediação removeu 100% de amônia-N e fosfato-P, com taxas ( k 1 ) de 0,218 ± 0,013 e 0,501 ± 0,038 (dia −1 ), respectivamente. Todos os extratos de microalgas reduziram em 100% a capacidade infecciosa do HSV-1. Os extratos de microalgas com diclorometano e metanol apresentaram atividades de inibição na concentração mais baixa (3,125 µg mL −1 ). Ensaios virucidas contra HAdV-5 usando extrato de microalgas de hexano e metanol inibiram a capacidade infecciosa do vírus em 70% em todas as concentrações testadas a 37 °C. Em uma concentração de 12,5 µg mL -1, o extrato de microalgas diclorometano reduziu 50-80% da capacidade infecciosa do HAdV-5, também a 37 °C. No geral, os resultados sugerem que as microalgas podem ser uma fonte atrativa de biomassa de matéria-prima para a exploração de compostos viricidas alternativos. Made available in DSpace on 2022-04-11T14:01:08Z (GMT). No. of bitstreams: 1 final9878.pdf: 4339051 bytes, checksum: 95cbce0603f5f7c9f945420adecc1925 (MD5) Previous issue date: 2022