Metagenome assembly outskirts of Prague

Pandemics have always threatened human populations throughout history. We recently suffered one that not only claimed a considerable number of lives but also changed our society for more than two years since its appearance. While viral pandemics have a very strong media spread and importance, we are currently suffering a silent pandemic. The ever-growing issue of antibiotic resistance is threatening our health systems worldwide, caused by the continuous appearance of antibiotic resistance genes (ARGs) that confer resistance to all known antibiotics in medical use to several bacteria. The biggest issue is that once fixed in clinical practice, these ARGs will not disappear. Environmental monitoring of ARGs can help us to evaluate risks and potentially aid in suggesting interventions. One of the hot spots for spreading and uptake of novel ARGs are the rivers in the catchment area of cities. Thus, I have carried out a metagenomic sequencing survey of local communities on the outskirts of the city of Prague, a major Central Europe capital in the watershed of the Vltava and Elbe rivers. I found different metagenomic profiles between the soil locations and the sediments from the river shore, related to the differential soil ecological conditions, but also reflecting the different uses of the soil (garden, agriculture, and waste material deposition). Among the pathways enriched for each of the locations, some reflected an increased pollution pressure affecting the sediment microbial communities due to presence of industrial organic compounds. The soil locations seemed to contain a higher percentage of annotated ARGs, although without a very high depth of sequencing. The use of bit-score rather than identity for gene annotation, potentially uncovered an overlooked population of ARGs.