Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater

Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements facilitate horizontal gene transfer. However, the prevalence and extent of these phenomena in different taxonomic groups that inhabit wastewater are still not fully understood. Here, we determined the presence of ARGs in metagenome-assembled genomes (MAGs) and evaluated the risks of MAG-carrying ARGs in potential human pathogens. The potential of these ARGs to be transmitted horizontally or vertically was also determined. A total of 5,916 MAGs (completeness >50%, contamination <10%) were recovered, covering 68 phyla and 279 genera. MAGs were dereplicated into 1,204 genome operational taxonomic units (gOTUs) as a proxy for species ( average nucleotide identity >0.95). The dominant ARG classes detected were bacitracin, multi-drug, macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside, and 10.26% of them were located on plasmids. The main hosts of ARGs belonged to Escherichia, Klebsiella, Acinetobacter, Gresbergeria, Mycobacterium, and Thauera. Our data showed that 253 MAGs carried virulence factor genes (VFGs) divided into 44 gOTUs, of which 45 MAGs were carriers of ARGs, indicating that potential human pathogens carried ARGs. Alarmingly, the MAG assigned as Escherichia coli contained 159 VFGs, of which 95 were located on chromosomes and 10 on plasmids. In addition to shedding light on the prevalence of ARGs in individual genomes recovered from activated sludge and wastewater, our study demonstrates a workflow that can identify antimicrobial-resistant pathogens in complex microbial communities.

IMPORTANCE

Antimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including Klebsiella, Escherichia, Acinetobacter, Nitrospira, Ottowia, Pseudomonas, and Thauera, which could have significant implications for AMR transmission. The abundance of bacA, mexL, and aph(3")-I in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.

Identification of Huge Phages from Wastewater Metagenomes

Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual curation by excluding viral contigs that did not contain viral protein-coding genes or consisted of concatemers of several small phage genomes. This dataset showed seven fully annotated huge phage genomes. The phages grouped into distinct phylogenetic clades, likely forming new genera and families. A phylogenomic analysis between our huge phages and phages with smaller genomes, i.e., less than 200 kb, supported the hypothesis that huge phages have undergone convergent evolution. The genomes contained typical phage protein-coding genes, sequential gene cassettes for metabolic pathways, and complete inventories of tRNA genes covering all standard and rare amino acids. Our study showed a pipeline for huge phage analyses that may lead to new enzymes for therapeutic or biotechnological applications.

Optimization of heat treatment and pH of red and white pear cactus [Opuntia ficus-indica (l.) mill.] fruit juice using response surface methodology

The objectives of the study were to determine the effect of heating time and temperature and pH level on the quality of cactus pear juice and to optimize the thermal treatment conditions and the pH for best results using two (red and white) varieties. Response surface methodology was used to optimize the heat treatment conditions and the pH. The heating time and temperature and pH significantly (p<0.05) affected the ascorbic acid content, sensory attributes and microbial load. Using graphical optimization, the best combinations for the red prickly juice were 5.5 to 14 mins and 62°C to 82°C with pH of 5.2 or pH 3.3 to 5.0 and temperature of 62°C to 92°C for 15 mins. For white prickly juice, the optimal ranges were 18.7 to 22.6 mins and 83.9°C to 93.4°C with pH of 5.2 or pH of 3.2 to 5.0 and temperature 93.5°C to 108°C for 15 mins. Using numerical optimization, the optimal conditions were 19.2 mins, 100°C and pH of 4 with a desirability value of 0.774 and 22 mins, 100°C and pH of 3.6 with the desirability value of 0.865 for red and white prickly pear juice, respectively.

Cultural meanings of tuberculosis in Aceh Province, Sumatra

This paper shows how disease transmission and particularly what biomedicine calls tuberculosis are interpreted in the non-Western context of Aceh Province, Sumatra, Indonesia. It tries also to focus on factors influencing perceptions and health-seeking behaviors. Results show that what biomedicine calls TB is represented by a semantic network of illnesses. Parts of this network are clearly identified as transmissible while others are related to specific phenomena affecting the individual, such as terbuk (poisoning) or trouk (fatigue produced by hard work), and are not considered contagious. Forms of transmission are interpreted mostly through empirical and analogic categories. TB is attributed to four different aspects: (a) biomedical categories such as germ theory; (b) socio-economic conditions; (c) transgression of social rules; and (d) poisoning and the influences of supernatural powers. Health-seeking behaviors are related to the perceived causes of the disease, economic factors, and the accessibility of health services.